]> https://gitweb.dealii.org/ - candi.git/commitdiff
Initial CANDI release on GitHub (v0.2) 0.2
authorUwe Köcher <koecher@hsu-hamburg.de>
Wed, 21 May 2014 11:09:40 +0000 (13:09 +0200)
committerUwe Köcher <koecher@hsu-hamburg.de>
Wed, 21 May 2014 11:09:40 +0000 (13:09 +0200)
173 files changed:
AUTHORS [new file with mode: 0644]
COPYING.dorsal [new file with mode: 0644]
COPYING.lesser.dorsal [new file with mode: 0644]
ChangeLog [new file with mode: 0644]
DTM++.toolbox/packages/DTM++.toolbox.package [new file with mode: 0644]
DTM++.toolbox/packages/dealii-snapshot.package [new file with mode: 0644]
DTM++.toolbox/packages/dealii-stable.package [new file with mode: 0644]
DTM++.toolbox/packages/dealii.package [new file with mode: 0644]
DTM++.toolbox/packages/hdf5.package [new file with mode: 0644]
DTM++.toolbox/packages/hwloc.package [new file with mode: 0644]
DTM++.toolbox/packages/p4est.package [new file with mode: 0644]
DTM++.toolbox/packages/trilinos.package [new file with mode: 0644]
DTM++.toolbox/platforms/.single [new file with mode: 0644]
DTM++.toolbox/platforms/contributed/fedora19.platform [new file with mode: 0644]
DTM++.toolbox/platforms/supported/fedora20.platform [new file with mode: 0644]
DTM++.toolbox/platforms/supported/rhel6.platform [new file with mode: 0644]
DTM++.toolbox/platforms/supported/saucy.platform [new file with mode: 0644]
FEniCS/packages/FEniCS-prepare.package [new file with mode: 0644]
FEniCS/packages/FEniCS.package [new file with mode: 0644]
FEniCS/packages/armadillo.package [new file with mode: 0644]
FEniCS/packages/atlas.package [new file with mode: 0644]
FEniCS/packages/automake.package [new file with mode: 0644]
FEniCS/packages/bazaar.package [new file with mode: 0644]
FEniCS/packages/blas.package [new file with mode: 0644]
FEniCS/packages/boost.package [new file with mode: 0644]
FEniCS/packages/bzip2.package [new file with mode: 0644]
FEniCS/packages/cgal.package [new file with mode: 0644]
FEniCS/packages/cln.package [new file with mode: 0644]
FEniCS/packages/cmake.package [new file with mode: 0644]
FEniCS/packages/cppunit.package [new file with mode: 0644]
FEniCS/packages/cusp.package [new file with mode: 0644]
FEniCS/packages/cython.package [new file with mode: 0644]
FEniCS/packages/dolfin-adjoint.package [new file with mode: 0644]
FEniCS/packages/dolfin-snapshot.package [new file with mode: 0644]
FEniCS/packages/dolfin-stable.package [new file with mode: 0644]
FEniCS/packages/dolfin.package [new file with mode: 0644]
FEniCS/packages/dolfin_intel.package [new file with mode: 0644]
FEniCS/packages/dri2proto.package [new file with mode: 0644]
FEniCS/packages/eigen.package [new file with mode: 0644]
FEniCS/packages/ferari-snapshot.package [new file with mode: 0644]
FEniCS/packages/ferari-stable.package [new file with mode: 0644]
FEniCS/packages/ferari.package [new file with mode: 0644]
FEniCS/packages/ffc-snapshot.package [new file with mode: 0644]
FEniCS/packages/ffc-stable.package [new file with mode: 0644]
FEniCS/packages/ffc.package [new file with mode: 0644]
FEniCS/packages/ffc_stable.package [new file with mode: 0644]
FEniCS/packages/fiat-snapshot.package [new file with mode: 0644]
FEniCS/packages/fiat-stable.package [new file with mode: 0644]
FEniCS/packages/fiat.package [new file with mode: 0644]
FEniCS/packages/gccxml.package [new file with mode: 0644]
FEniCS/packages/ginac.package [new file with mode: 0644]
FEniCS/packages/git.package [new file with mode: 0644]
FEniCS/packages/glib2.package [new file with mode: 0644]
FEniCS/packages/glproto.package [new file with mode: 0644]
FEniCS/packages/gmp.package [new file with mode: 0644]
FEniCS/packages/gtest.package [new file with mode: 0644]
FEniCS/packages/h5py.package [new file with mode: 0644]
FEniCS/packages/hdf5.package [new file with mode: 0644]
FEniCS/packages/instant-snapshot.package [new file with mode: 0644]
FEniCS/packages/instant-stable.package [new file with mode: 0644]
FEniCS/packages/instant.package [new file with mode: 0644]
FEniCS/packages/ipython.package [new file with mode: 0644]
FEniCS/packages/lapack.package [new file with mode: 0644]
FEniCS/packages/libadjoint.package [new file with mode: 0644]
FEniCS/packages/libdrm.package [new file with mode: 0644]
FEniCS/packages/libffi.package [new file with mode: 0644]
FEniCS/packages/libxml2.package [new file with mode: 0644]
FEniCS/packages/madlib.package [new file with mode: 0644]
FEniCS/packages/matplotlib.package [new file with mode: 0644]
FEniCS/packages/mesa.package [new file with mode: 0644]
FEniCS/packages/mpfr.package [new file with mode: 0644]
FEniCS/packages/mpi4py.package [new file with mode: 0644]
FEniCS/packages/mtl.package [new file with mode: 0644]
FEniCS/packages/numpy.package [new file with mode: 0644]
FEniCS/packages/numpy_intel.package [new file with mode: 0644]
FEniCS/packages/openmpi.package [new file with mode: 0644]
FEniCS/packages/parmetis.package [new file with mode: 0644]
FEniCS/packages/pastix.package [new file with mode: 0644]
FEniCS/packages/pcre.package [new file with mode: 0644]
FEniCS/packages/petsc.package [new file with mode: 0644]
FEniCS/packages/pkg-config.package [new file with mode: 0644]
FEniCS/packages/ply.package [new file with mode: 0644]
FEniCS/packages/python.package [new file with mode: 0644]
FEniCS/packages/scientificpython.package [new file with mode: 0644]
FEniCS/packages/scipy.package [new file with mode: 0644]
FEniCS/packages/scons.package [new file with mode: 0644]
FEniCS/packages/scotch.package [new file with mode: 0644]
FEniCS/packages/setuptools.package [new file with mode: 0644]
FEniCS/packages/slepc.package [new file with mode: 0644]
FEniCS/packages/sqlite.package [new file with mode: 0644]
FEniCS/packages/suitesparse.package [new file with mode: 0644]
FEniCS/packages/suitesparsewithmetis.package [new file with mode: 0644]
FEniCS/packages/suitesparsewithmetis_OpenMPI.package [new file with mode: 0644]
FEniCS/packages/swig.package [new file with mode: 0644]
FEniCS/packages/swiginac.package [new file with mode: 0644]
FEniCS/packages/syfi-snapshot.package [new file with mode: 0644]
FEniCS/packages/syfi-stable.package [new file with mode: 0644]
FEniCS/packages/syfi.package [new file with mode: 0644]
FEniCS/packages/sympy.package [new file with mode: 0644]
FEniCS/packages/template.package [new file with mode: 0644]
FEniCS/packages/trilinos.package [new file with mode: 0644]
FEniCS/packages/trilinos_intel.package [new file with mode: 0644]
FEniCS/packages/ufc-snapshot.package [new file with mode: 0644]
FEniCS/packages/ufc-stable.package [new file with mode: 0644]
FEniCS/packages/ufc.package [new file with mode: 0644]
FEniCS/packages/ufl-snapshot.package [new file with mode: 0644]
FEniCS/packages/ufl-stable.package [new file with mode: 0644]
FEniCS/packages/ufl.package [new file with mode: 0644]
FEniCS/packages/uflacs.package [new file with mode: 0644]
FEniCS/packages/viper-stable.package [new file with mode: 0644]
FEniCS/packages/viper.package [new file with mode: 0644]
FEniCS/packages/vtk.package [new file with mode: 0644]
FEniCS/packages/vtkdata.package [new file with mode: 0644]
FEniCS/packages/vtkwithqt.package [new file with mode: 0644]
FEniCS/packages/zlib.package [new file with mode: 0644]
FEniCS/patches/armadillo_no_mkl.patch [new file with mode: 0644]
FEniCS/patches/cgal.patch [new file with mode: 0644]
FEniCS/patches/dolfin-armadillo-test.patch [new file with mode: 0644]
FEniCS/patches/madlib.patch [new file with mode: 0644]
FEniCS/patches/petsc.patch [new file with mode: 0644]
FEniCS/patches/python.patch [new file with mode: 0644]
FEniCS/patches/scientificpython.patch [new file with mode: 0644]
FEniCS/patches/slepc.patch [new file with mode: 0644]
FEniCS/patches/trilinos.patch [new file with mode: 0644]
FEniCS/platforms/.single [new file with mode: 0644]
FEniCS/platforms/supported/fedora19.platform [new file with mode: 0644]
FEniCS/platforms/supported/fedora20.platform [new file with mode: 0644]
FEniCS/platforms/supported/rhel6.platform [new file with mode: 0644]
FEniCS/platforms/supported/ubuntu13.platform [new file with mode: 0644]
README.md.dorsal [new file with mode: 0644]
TODO [new file with mode: 0644]
USAGE [new file with mode: 0644]
candi.cfg [new file with mode: 0644]
candi.sh [new file with mode: 0755]
deal.II/packages/boost.package [new file with mode: 0644]
deal.II/packages/dealii-snapshot.package [new file with mode: 0644]
deal.II/packages/dealii-stable.package [new file with mode: 0644]
deal.II/packages/dealii.package [new file with mode: 0644]
deal.II/packages/hdf5.package [new file with mode: 0644]
deal.II/packages/hwloc.package [new file with mode: 0644]
deal.II/packages/p4est.package [new file with mode: 0644]
deal.II/packages/petsc.package [new file with mode: 0644]
deal.II/packages/slepc.package [new file with mode: 0644]
deal.II/packages/trilinos.package [new file with mode: 0644]
deal.II/platforms/.single [new file with mode: 0644]
deal.II/platforms/supported/cygwin.platform [new file with mode: 0644]
deal.II/platforms/supported/fedora19.platform [new file with mode: 0644]
deal.II/platforms/supported/fedora20.platform [new file with mode: 0644]
deal.II/platforms/supported/opensuse12.platform [new file with mode: 0644]
deal.II/platforms/supported/opensuse13.platform [new file with mode: 0644]
deal.II/platforms/supported/rhel6.platform [new file with mode: 0644]
deal.II/platforms/supported/ubuntu13.platform [new file with mode: 0644]
gcc/packages/gcc.package [new file with mode: 0644]
gcc/platforms/.single [new file with mode: 0644]
gcc/platforms/supported/rhel6.platform [new file with mode: 0644]
local-DTM++.toolbox.cfg [new file with mode: 0644]
local-FEniCS.cfg [new file with mode: 0644]
local-deal.II.cfg [new file with mode: 0644]
local-gcc.cfg [new file with mode: 0644]
local-mpi.cfg [new file with mode: 0644]
local.cfg [new symlink]
mpi/packages/mpich.package [new file with mode: 0644]
mpi/packages/mpich2.package [new file with mode: 0644]
mpi/packages/openmpi.package [new file with mode: 0644]
mpi/platforms/.single [new file with mode: 0644]
mpi/platforms/deprecated/fedora19.platform [new file with mode: 0644]
mpi/platforms/supported/fedora19.platform [new file with mode: 0644]
mpi/platforms/supported/fedora20.platform [new file with mode: 0644]
mpi/platforms/supported/rhel6.platform [new file with mode: 0644]
utilities/clean.sh [new file with mode: 0755]
utilities/generate-author-list.sh [new file with mode: 0755]
utilities/install-fenics.sh [new file with mode: 0755]
utilities/test-package-usage.sh [new file with mode: 0755]

diff --git a/AUTHORS b/AUTHORS
new file mode 100644 (file)
index 0000000..9736b68
--- /dev/null
+++ b/AUTHORS
@@ -0,0 +1,44 @@
+NVRI.software/candi is a majorily tweaked DORSAL and maintained by:
+  Uwe Koecher           <uwe.koecher@hsu-hamburg.de>
+
+The origin is Dorsal (licensed under the LGPL):
+  https://bitbucket.org/fenics-project/dorsal/src
+  master c667be2 2013-11-27
+
+Please find the list of the authors of Dorsal below:
+
+Dorsal is written and maintained by:
+
+  Harish Narayanan <hnarayanan@gmail.com>
+  http://home.simula.no/~harish/
+
+Major contributors ordered by number of commits include:
+
+  Garth N. Wells        <gnw20@cam.ac.uk>
+  Anders Logg           <logg@simula.no>
+  Johannes Ring         <johannr@simula.no>
+  Joachim B. Haga       <jobh@simula.no>
+  Roman Putanowicz      <putanowr@l5.pk.edu.pl>
+  Ilmar Wilbers         <ilmarw@simula.no>
+
+Minor contributors in chronological order include:
+
+  Luk ShunTim           <shuntim.luk@polyu.edu.hk>
+  Kristoffer Selim      <selim@simula.no>
+  Peter-Jan Randewijk   <pjrandew@sun.ac.za>
+  Aron Wahlberg         <aron.wahlberg@gmail.com>
+  Douglas N. Arnold     <arnold@umn.edu>
+  Andre Massing         <massing@simula.no>
+  Dimitris Tsarouchas   <dt335@cam.ac.uk>
+  Krishna S. Rudraraju  <rudraa@umich.edu>
+  Alexander Jarosch     <alex@alexj.at>
+  Marie E. Rognes       <meg@simula.no>
+  Patrick Riesen        <priesen@student.ethz.ch>
+  Gerd Wachsmuth        <gerd.wachsmuth@mathematik.tu-chemnitz.de>
+  Johan Hake            <hake@simula.no>
+  Benjamin Kehlet       <benjamik@simula.no>
+  Richard Katz          <richard.katz@earth.ox.ac.uk>
+  Fredrik Valdmanis     <fredva@ifi.uio.no>
+  Michele Marcionelli   <michele.marcionelli@math.ethz.ch>
+
+Missing or incorrect credits? Tell us and we will fix it!
diff --git a/COPYING.dorsal b/COPYING.dorsal
new file mode 100644 (file)
index 0000000..94a9ed0
--- /dev/null
@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
+
+  The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works.  By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users.  We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors.  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+  To protect your rights, we need to prevent others from denying you
+these rights or asking you to surrender the rights.  Therefore, you have
+certain responsibilities if you distribute copies of the software, or if
+you modify it: responsibilities to respect the freedom of others.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must pass on to the recipients the same
+freedoms that you received.  You must make sure that they, too, receive
+or can get the source code.  And you must show them these terms so they
+know their rights.
+
+  Developers that use the GNU GPL protect your rights with two steps:
+(1) assert copyright on the software, and (2) offer you this License
+giving you legal permission to copy, distribute and/or modify it.
+
+  For the developers' and authors' protection, the GPL clearly explains
+that there is no warranty for this free software.  For both users' and
+authors' sake, the GPL requires that modified versions be marked as
+changed, so that their problems will not be attributed erroneously to
+authors of previous versions.
+
+  Some devices are designed to deny users access to install or run
+modified versions of the software inside them, although the manufacturer
+can do so.  This is fundamentally incompatible with the aim of
+protecting users' freedom to change the software.  The systematic
+pattern of such abuse occurs in the area of products for individuals to
+use, which is precisely where it is most unacceptable.  Therefore, we
+have designed this version of the GPL to prohibit the practice for those
+products.  If such problems arise substantially in other domains, we
+stand ready to extend this provision to those domains in future versions
+of the GPL, as needed to protect the freedom of users.
+
+  Finally, every program is threatened constantly by software patents.
+States should not allow patents to restrict development and use of
+software on general-purpose computers, but in those that do, we wish to
+avoid the special danger that patents applied to a free program could
+make it effectively proprietary.  To prevent this, the GPL assures that
+patents cannot be used to render the program non-free.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+                       TERMS AND CONDITIONS
+
+  0. Definitions.
+
+  "This License" refers to version 3 of the GNU General Public License.
+
+  "Copyright" also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
+
+  "The Program" refers to any copyrightable work licensed under this
+License.  Each licensee is addressed as "you".  "Licensees" and
+"recipients" may be individuals or organizations.
+
+  To "modify" a work means to copy from or adapt all or part of the work
+in a fashion requiring copyright permission, other than the making of an
+exact copy.  The resulting work is called a "modified version" of the
+earlier work or a work "based on" the earlier work.
+
+  A "covered work" means either the unmodified Program or a work based
+on the Program.
+
+  To "propagate" a work means to do anything with it that, without
+permission, would make you directly or secondarily liable for
+infringement under applicable copyright law, except executing it on a
+computer or modifying a private copy.  Propagation includes copying,
+distribution (with or without modification), making available to the
+public, and in some countries other activities as well.
+
+  To "convey" a work means any kind of propagation that enables other
+parties to make or receive copies.  Mere interaction with a user through
+a computer network, with no transfer of a copy, is not conveying.
+
+  An interactive user interface displays "Appropriate Legal Notices"
+to the extent that it includes a convenient and prominently visible
+feature that (1) displays an appropriate copyright notice, and (2)
+tells the user that there is no warranty for the work (except to the
+extent that warranties are provided), that licensees may convey the
+work under this License, and how to view a copy of this License.  If
+the interface presents a list of user commands or options, such as a
+menu, a prominent item in the list meets this criterion.
+
+  1. Source Code.
+
+  The "source code" for a work means the preferred form of the work
+for making modifications to it.  "Object code" means any non-source
+form of a work.
+
+  A "Standard Interface" means an interface that either is an official
+standard defined by a recognized standards body, or, in the case of
+interfaces specified for a particular programming language, one that
+is widely used among developers working in that language.
+
+  The "System Libraries" of an executable work include anything, other
+than the work as a whole, that (a) is included in the normal form of
+packaging a Major Component, but which is not part of that Major
+Component, and (b) serves only to enable use of the work with that
+Major Component, or to implement a Standard Interface for which an
+implementation is available to the public in source code form.  A
+"Major Component", in this context, means a major essential component
+(kernel, window system, and so on) of the specific operating system
+(if any) on which the executable work runs, or a compiler used to
+produce the work, or an object code interpreter used to run it.
+
+  The "Corresponding Source" for a work in object code form means all
+the source code needed to generate, install, and (for an executable
+work) run the object code and to modify the work, including scripts to
+control those activities.  However, it does not include the work's
+System Libraries, or general-purpose tools or generally available free
+programs which are used unmodified in performing those activities but
+which are not part of the work.  For example, Corresponding Source
+includes interface definition files associated with source files for
+the work, and the source code for shared libraries and dynamically
+linked subprograms that the work is specifically designed to require,
+such as by intimate data communication or control flow between those
+subprograms and other parts of the work.
+
+  The Corresponding Source need not include anything that users
+can regenerate automatically from other parts of the Corresponding
+Source.
+
+  The Corresponding Source for a work in source code form is that
+same work.
+
+  2. Basic Permissions.
+
+  All rights granted under this License are granted for the term of
+copyright on the Program, and are irrevocable provided the stated
+conditions are met.  This License explicitly affirms your unlimited
+permission to run the unmodified Program.  The output from running a
+covered work is covered by this License only if the output, given its
+content, constitutes a covered work.  This License acknowledges your
+rights of fair use or other equivalent, as provided by copyright law.
+
+  You may make, run and propagate covered works that you do not
+convey, without conditions so long as your license otherwise remains
+in force.  You may convey covered works to others for the sole purpose
+of having them make modifications exclusively for you, or provide you
+with facilities for running those works, provided that you comply with
+the terms of this License in conveying all material for which you do
+not control copyright.  Those thus making or running the covered works
+for you must do so exclusively on your behalf, under your direction
+and control, on terms that prohibit them from making any copies of
+your copyrighted material outside their relationship with you.
+
+  Conveying under any other circumstances is permitted solely under
+the conditions stated below.  Sublicensing is not allowed; section 10
+makes it unnecessary.
+
+  3. Protecting Users' Legal Rights From Anti-Circumvention Law.
+
+  No covered work shall be deemed part of an effective technological
+measure under any applicable law fulfilling obligations under article
+11 of the WIPO copyright treaty adopted on 20 December 1996, or
+similar laws prohibiting or restricting circumvention of such
+measures.
+
+  When you convey a covered work, you waive any legal power to forbid
+circumvention of technological measures to the extent such circumvention
+is effected by exercising rights under this License with respect to
+the covered work, and you disclaim any intention to limit operation or
+modification of the work as a means of enforcing, against the work's
+users, your or third parties' legal rights to forbid circumvention of
+technological measures.
+
+  4. Conveying Verbatim Copies.
+
+  You may convey verbatim copies of the Program's source code as you
+receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice;
+keep intact all notices stating that this License and any
+non-permissive terms added in accord with section 7 apply to the code;
+keep intact all notices of the absence of any warranty; and give all
+recipients a copy of this License along with the Program.
+
+  You may charge any price or no price for each copy that you convey,
+and you may offer support or warranty protection for a fee.
+
+  5. Conveying Modified Source Versions.
+
+  You may convey a work based on the Program, or the modifications to
+produce it from the Program, in the form of source code under the
+terms of section 4, provided that you also meet all of these conditions:
+
+    a) The work must carry prominent notices stating that you modified
+    it, and giving a relevant date.
+
+    b) The work must carry prominent notices stating that it is
+    released under this License and any conditions added under section
+    7.  This requirement modifies the requirement in section 4 to
+    "keep intact all notices".
+
+    c) You must license the entire work, as a whole, under this
+    License to anyone who comes into possession of a copy.  This
+    License will therefore apply, along with any applicable section 7
+    additional terms, to the whole of the work, and all its parts,
+    regardless of how they are packaged.  This License gives no
+    permission to license the work in any other way, but it does not
+    invalidate such permission if you have separately received it.
+
+    d) If the work has interactive user interfaces, each must display
+    Appropriate Legal Notices; however, if the Program has interactive
+    interfaces that do not display Appropriate Legal Notices, your
+    work need not make them do so.
+
+  A compilation of a covered work with other separate and independent
+works, which are not by their nature extensions of the covered work,
+and which are not combined with it such as to form a larger program,
+in or on a volume of a storage or distribution medium, is called an
+"aggregate" if the compilation and its resulting copyright are not
+used to limit the access or legal rights of the compilation's users
+beyond what the individual works permit.  Inclusion of a covered work
+in an aggregate does not cause this License to apply to the other
+parts of the aggregate.
+
+  6. Conveying Non-Source Forms.
+
+  You may convey a covered work in object code form under the terms
+of sections 4 and 5, provided that you also convey the
+machine-readable Corresponding Source under the terms of this License,
+in one of these ways:
+
+    a) Convey the object code in, or embodied in, a physical product
+    (including a physical distribution medium), accompanied by the
+    Corresponding Source fixed on a durable physical medium
+    customarily used for software interchange.
+
+    b) Convey the object code in, or embodied in, a physical product
+    (including a physical distribution medium), accompanied by a
+    written offer, valid for at least three years and valid for as
+    long as you offer spare parts or customer support for that product
+    model, to give anyone who possesses the object code either (1) a
+    copy of the Corresponding Source for all the software in the
+    product that is covered by this License, on a durable physical
+    medium customarily used for software interchange, for a price no
+    more than your reasonable cost of physically performing this
+    conveying of source, or (2) access to copy the
+    Corresponding Source from a network server at no charge.
+
+    c) Convey individual copies of the object code with a copy of the
+    written offer to provide the Corresponding Source.  This
+    alternative is allowed only occasionally and noncommercially, and
+    only if you received the object code with such an offer, in accord
+    with subsection 6b.
+
+    d) Convey the object code by offering access from a designated
+    place (gratis or for a charge), and offer equivalent access to the
+    Corresponding Source in the same way through the same place at no
+    further charge.  You need not require recipients to copy the
+    Corresponding Source along with the object code.  If the place to
+    copy the object code is a network server, the Corresponding Source
+    may be on a different server (operated by you or a third party)
+    that supports equivalent copying facilities, provided you maintain
+    clear directions next to the object code saying where to find the
+    Corresponding Source.  Regardless of what server hosts the
+    Corresponding Source, you remain obligated to ensure that it is
+    available for as long as needed to satisfy these requirements.
+
+    e) Convey the object code using peer-to-peer transmission, provided
+    you inform other peers where the object code and Corresponding
+    Source of the work are being offered to the general public at no
+    charge under subsection 6d.
+
+  A separable portion of the object code, whose source code is excluded
+from the Corresponding Source as a System Library, need not be
+included in conveying the object code work.
+
+  A "User Product" is either (1) a "consumer product", which means any
+tangible personal property which is normally used for personal, family,
+or household purposes, or (2) anything designed or sold for incorporation
+into a dwelling.  In determining whether a product is a consumer product,
+doubtful cases shall be resolved in favor of coverage.  For a particular
+product received by a particular user, "normally used" refers to a
+typical or common use of that class of product, regardless of the status
+of the particular user or of the way in which the particular user
+actually uses, or expects or is expected to use, the product.  A product
+is a consumer product regardless of whether the product has substantial
+commercial, industrial or non-consumer uses, unless such uses represent
+the only significant mode of use of the product.
+
+  "Installation Information" for a User Product means any methods,
+procedures, authorization keys, or other information required to install
+and execute modified versions of a covered work in that User Product from
+a modified version of its Corresponding Source.  The information must
+suffice to ensure that the continued functioning of the modified object
+code is in no case prevented or interfered with solely because
+modification has been made.
+
+  If you convey an object code work under this section in, or with, or
+specifically for use in, a User Product, and the conveying occurs as
+part of a transaction in which the right of possession and use of the
+User Product is transferred to the recipient in perpetuity or for a
+fixed term (regardless of how the transaction is characterized), the
+Corresponding Source conveyed under this section must be accompanied
+by the Installation Information.  But this requirement does not apply
+if neither you nor any third party retains the ability to install
+modified object code on the User Product (for example, the work has
+been installed in ROM).
+
+  The requirement to provide Installation Information does not include a
+requirement to continue to provide support service, warranty, or updates
+for a work that has been modified or installed by the recipient, or for
+the User Product in which it has been modified or installed.  Access to a
+network may be denied when the modification itself materially and
+adversely affects the operation of the network or violates the rules and
+protocols for communication across the network.
+
+  Corresponding Source conveyed, and Installation Information provided,
+in accord with this section must be in a format that is publicly
+documented (and with an implementation available to the public in
+source code form), and must require no special password or key for
+unpacking, reading or copying.
+
+  7. Additional Terms.
+
+  "Additional permissions" are terms that supplement the terms of this
+License by making exceptions from one or more of its conditions.
+Additional permissions that are applicable to the entire Program shall
+be treated as though they were included in this License, to the extent
+that they are valid under applicable law.  If additional permissions
+apply only to part of the Program, that part may be used separately
+under those permissions, but the entire Program remains governed by
+this License without regard to the additional permissions.
+
+  When you convey a copy of a covered work, you may at your option
+remove any additional permissions from that copy, or from any part of
+it.  (Additional permissions may be written to require their own
+removal in certain cases when you modify the work.)  You may place
+additional permissions on material, added by you to a covered work,
+for which you have or can give appropriate copyright permission.
+
+  Notwithstanding any other provision of this License, for material you
+add to a covered work, you may (if authorized by the copyright holders of
+that material) supplement the terms of this License with terms:
+
+    a) Disclaiming warranty or limiting liability differently from the
+    terms of sections 15 and 16 of this License; or
+
+    b) Requiring preservation of specified reasonable legal notices or
+    author attributions in that material or in the Appropriate Legal
+    Notices displayed by works containing it; or
+
+    c) Prohibiting misrepresentation of the origin of that material, or
+    requiring that modified versions of such material be marked in
+    reasonable ways as different from the original version; or
+
+    d) Limiting the use for publicity purposes of names of licensors or
+    authors of the material; or
+
+    e) Declining to grant rights under trademark law for use of some
+    trade names, trademarks, or service marks; or
+
+    f) Requiring indemnification of licensors and authors of that
+    material by anyone who conveys the material (or modified versions of
+    it) with contractual assumptions of liability to the recipient, for
+    any liability that these contractual assumptions directly impose on
+    those licensors and authors.
+
+  All other non-permissive additional terms are considered "further
+restrictions" within the meaning of section 10.  If the Program as you
+received it, or any part of it, contains a notice stating that it is
+governed by this License along with a term that is a further
+restriction, you may remove that term.  If a license document contains
+a further restriction but permits relicensing or conveying under this
+License, you may add to a covered work material governed by the terms
+of that license document, provided that the further restriction does
+not survive such relicensing or conveying.
+
+  If you add terms to a covered work in accord with this section, you
+must place, in the relevant source files, a statement of the
+additional terms that apply to those files, or a notice indicating
+where to find the applicable terms.
+
+  Additional terms, permissive or non-permissive, may be stated in the
+form of a separately written license, or stated as exceptions;
+the above requirements apply either way.
+
+  8. Termination.
+
+  You may not propagate or modify a covered work except as expressly
+provided under this License.  Any attempt otherwise to propagate or
+modify it is void, and will automatically terminate your rights under
+this License (including any patent licenses granted under the third
+paragraph of section 11).
+
+  However, if you cease all violation of this License, then your
+license from a particular copyright holder is reinstated (a)
+provisionally, unless and until the copyright holder explicitly and
+finally terminates your license, and (b) permanently, if the copyright
+holder fails to notify you of the violation by some reasonable means
+prior to 60 days after the cessation.
+
+  Moreover, your license from a particular copyright holder is
+reinstated permanently if the copyright holder notifies you of the
+violation by some reasonable means, this is the first time you have
+received notice of violation of this License (for any work) from that
+copyright holder, and you cure the violation prior to 30 days after
+your receipt of the notice.
+
+  Termination of your rights under this section does not terminate the
+licenses of parties who have received copies or rights from you under
+this License.  If your rights have been terminated and not permanently
+reinstated, you do not qualify to receive new licenses for the same
+material under section 10.
+
+  9. Acceptance Not Required for Having Copies.
+
+  You are not required to accept this License in order to receive or
+run a copy of the Program.  Ancillary propagation of a covered work
+occurring solely as a consequence of using peer-to-peer transmission
+to receive a copy likewise does not require acceptance.  However,
+nothing other than this License grants you permission to propagate or
+modify any covered work.  These actions infringe copyright if you do
+not accept this License.  Therefore, by modifying or propagating a
+covered work, you indicate your acceptance of this License to do so.
+
+  10. Automatic Licensing of Downstream Recipients.
+
+  Each time you convey a covered work, the recipient automatically
+receives a license from the original licensors, to run, modify and
+propagate that work, subject to this License.  You are not responsible
+for enforcing compliance by third parties with this License.
+
+  An "entity transaction" is a transaction transferring control of an
+organization, or substantially all assets of one, or subdividing an
+organization, or merging organizations.  If propagation of a covered
+work results from an entity transaction, each party to that
+transaction who receives a copy of the work also receives whatever
+licenses to the work the party's predecessor in interest had or could
+give under the previous paragraph, plus a right to possession of the
+Corresponding Source of the work from the predecessor in interest, if
+the predecessor has it or can get it with reasonable efforts.
+
+  You may not impose any further restrictions on the exercise of the
+rights granted or affirmed under this License.  For example, you may
+not impose a license fee, royalty, or other charge for exercise of
+rights granted under this License, and you may not initiate litigation
+(including a cross-claim or counterclaim in a lawsuit) alleging that
+any patent claim is infringed by making, using, selling, offering for
+sale, or importing the Program or any portion of it.
+
+  11. Patents.
+
+  A "contributor" is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based.  The
+work thus licensed is called the contributor's "contributor version".
+
+  A contributor's "essential patent claims" are all patent claims
+owned or controlled by the contributor, whether already acquired or
+hereafter acquired, that would be infringed by some manner, permitted
+by this License, of making, using, or selling its contributor version,
+but do not include claims that would be infringed only as a
+consequence of further modification of the contributor version.  For
+purposes of this definition, "control" includes the right to grant
+patent sublicenses in a manner consistent with the requirements of
+this License.
+
+  Each contributor grants you a non-exclusive, worldwide, royalty-free
+patent license under the contributor's essential patent claims, to
+make, use, sell, offer for sale, import and otherwise run, modify and
+propagate the contents of its contributor version.
+
+  In the following three paragraphs, a "patent license" is any express
+agreement or commitment, however denominated, not to enforce a patent
+(such as an express permission to practice a patent or covenant not to
+sue for patent infringement).  To "grant" such a patent license to a
+party means to make such an agreement or commitment not to enforce a
+patent against the party.
+
+  If you convey a covered work, knowingly relying on a patent license,
+and the Corresponding Source of the work is not available for anyone
+to copy, free of charge and under the terms of this License, through a
+publicly available network server or other readily accessible means,
+then you must either (1) cause the Corresponding Source to be so
+available, or (2) arrange to deprive yourself of the benefit of the
+patent license for this particular work, or (3) arrange, in a manner
+consistent with the requirements of this License, to extend the patent
+license to downstream recipients.  "Knowingly relying" means you have
+actual knowledge that, but for the patent license, your conveying the
+covered work in a country, or your recipient's use of the covered work
+in a country, would infringe one or more identifiable patents in that
+country that you have reason to believe are valid.
+
+  If, pursuant to or in connection with a single transaction or
+arrangement, you convey, or propagate by procuring conveyance of, a
+covered work, and grant a patent license to some of the parties
+receiving the covered work authorizing them to use, propagate, modify
+or convey a specific copy of the covered work, then the patent license
+you grant is automatically extended to all recipients of the covered
+work and works based on it.
+
+  A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License.  You may not convey a covered
+work if you are a party to an arrangement with a third party that is
+in the business of distributing software, under which you make payment
+to the third party based on the extent of your activity of conveying
+the work, and under which the third party grants, to any of the
+parties who would receive the covered work from you, a discriminatory
+patent license (a) in connection with copies of the covered work
+conveyed by you (or copies made from those copies), or (b) primarily
+for and in connection with specific products or compilations that
+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.
+
+  Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+  12. No Surrender of Others' Freedom.
+
+  If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License.  If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all.  For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+  13. Use with the GNU Affero General Public License.
+
+  Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU Affero General Public License into a single
+combined work, and to convey the resulting work.  The terms of this
+License will continue to apply to the part which is the covered work,
+but the special requirements of the GNU Affero General Public License,
+section 13, concerning interaction through a network will apply to the
+combination as such.
+
+  14. Revised Versions of this License.
+
+  The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+  Each version is given a distinguishing version number.  If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation.  If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+  If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+  Later license versions may give you additional or different
+permissions.  However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+  15. Disclaimer of Warranty.
+
+  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
diff --git a/COPYING.lesser.dorsal b/COPYING.lesser.dorsal
new file mode 100644 (file)
index 0000000..65c5ca8
--- /dev/null
@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version.
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.
diff --git a/ChangeLog b/ChangeLog
new file mode 100644 (file)
index 0000000..759b88a
--- /dev/null
+++ b/ChangeLog
@@ -0,0 +1,379 @@
+2011-12 Garth N. Wells <gnw20@cam.ac.uk>
+       * Added initial support for opensuse12.1
+2011-12 Johannes Ring <johannr@simula.no>
+       * Updated to 1.0.0 versions all fenics packages
+       * Polished support for squeeze, sid, lucid, maverick and snow
+          leopard
+       * Polished petsc package
+       * Polished support for all fedora platforms
+2011-12 Harish Narayanan <hnarayanan@gmail.com>
+       * Updated to recent versions of peripheral packages
+       * Mirrored cgal and scotch locally because upstream server is
+          flaky
+       * Polished support for lion
+       * Polished support for all fedora platforms
+       * Build full petsc on lion
+       * Updated trilinos package
+2011-12 Joachim B Haga <jobh@simula.no>
+       * Added ability to install dependencies 'once:'
+2011-11 Harish Narayanan <hnarayanan@gmail.com>
+       * Polished support for snow leopard and lion
+       * Polished support for oneiric
+       * Removed troublesome pastix from petsc package
+       * Stopped supporting gentoo
+2011-11 Johan Hake <hake@simula.no>
+       * Refined trilinos package
+2011-11 Johannes Ring <johannr@simula.no>
+       * Added bison packages for debian-based platforms
+       * Updated to recent versions of all fenics packages
+       * Added libboost-math-dev to some platforms
+       * Fixed trilinos and scipy packages not finding umfpack on some
+          platforms
+2011-10 Fredrik Valdmanis <fredva@ifi.uio.no>
+       * Added patch for petsc/slepc 3.2
+2011-10 Douglas N. Arnold <arnold@umn.edu>
+       * Polished support for rhel6
+2011-10 Johannes Ring <johannr@simula.no>
+       * Added libboost-mpi-dev to newer ubuntu and debian platforms
+2011-10 Andre Massing <massing@simula.no>
+       * Updated cgal package
+2011-10 Joachim B Haga <jobh@simula.no>
+       * Polish logging of individual package configure
+       * Updated syfi package
+2011-10 Harish Narayanan <hnarayanan@gmail.com>
+       * Added logging of individual package configure
+       * Updated to recent versions of all fenics packages
+       * Updated petsc and slepc to 3.2
+       * Updated dolfin download path to reflect new branching policy
+2011-10 Garth N. Wells <gnw20@cam.ac.uk>
+       * Updated trilinos package
+       * Polished support for oneiric
+       * Updated scotch package
+2011-09 Johannes Ring <johannr@simula.no>
+       * Added mpi support to boost package
+       * Fixed boost mpi support on older ubuntu and debian platforms
+       * Updated cgal package to cmake
+2011-09 Michele Marcionelli <michele.marcionelli@math.ethz.ch>
+       * Added initial support for fedora15
+       * Added patch to help trilinos compilation
+2011-09 Andre Massing <massing@simula.no>
+       * Added initial support for opensuse11.4
+2011-09 Harish Narayanan <hnarayanan@gmail.com>
+       * Incorporated Richard Katz's suggested port_select syntax change
+       * Added patch to compile petsc as a shared library on lion
+       * Polished support for lion
+       * Updated vtk package
+       * Added boost mpi to lion add snowleopard
+2011-09 Fredrik Valdmanis <fredva@ifi.uio.no>
+       * Added initial support for lion
+2011-08 Garth N. Wells <gnw20@cam.ac.uk>
+       * Added initial support for oneiric
+2011-08 Harish Narayanan <hnarayanan@gmail.com>
+       * Updated to recent versions of peripheral packages
+       * Cached recent MTL4 source on fenicsproject.org
+2011-08 Benjamin Kehlet <benjamik@simula.no>
+       * Reported bugs in few packages
+2011-08 Johannes Ring <johannr@simula.no>
+       * Updated to recent versions of all fenics packages
+       * Polished support for rhel6
+       * Allowed vtk to build without human interaction
+       * Fixed parmetis download link
+       * Fixed bug in mtl package
+2011-07 Harish Narayanan <hnarayanan@gmail.com>
+       * Fixed bug in numpy package
+       * Added boost iostream to all debian and ubuntu platforms
+       * Fixed parmetis download link
+       * Fixed swig support by building it manually on some platforms
+2011-07 Benjamin Kehlet <benjamik@simula.no>
+       * Added pcre package
+2011-06 Johan Hake <hake@simula.no>
+       * Polished support for rhel5
+2011-06 Johannes Ring <johannr@simula.no>
+       * Fixed bug in suitesparse with metis package
+       * Debugged swig support on different platforms
+       * Updated syfi to build with cmake instead of scons
+2011-05 Harish Narayanan <hnarayanan@gmail.com>
+       * Changed distribution license to GNU Lesser General Public
+         Licence Version 3
+       * Incorporated Johannes' madlib build instructions
+       * Generalised paths to easier allow for different projects
+       * Removed unnecessary additions introduced by femdk support
+       * Polished support for natty
+2011-05 Garth N. Wells <gnw20@cam.ac.uk>
+       * Updated to recent versions of all packages
+       * Fixed scotch package
+2011-05 Anders Logg <logg@simula.no>
+       * Added support for natty
+2011-04 Harish Narayanan <hnarayanan@gmail.com>
+       * Added Andre's suggested fix for Mac OS X gfortran petsc
+       compilation error
+2011-03 Harish Narayanan <hnarayanan@gmail.com>
+       * Removed unused slepc patch
+       * Removed support for femdk
+2011-02 Anders Logg <logg@simula.no>
+       * Polished support for bigblue
+2011-02 Johannes Ring <johannr@simula.no>
+       * Made maverick similar to lucid
+       * Fixed link to stable ufc
+2011-02 Harish Narayanan <hnarayanan@gmail.com>
+       * Updated swig version
+       * Polished support for sid and squeeze
+       * Made fedora13 and fedora14 identical
+       * Updated to recent versions of peripheral packages
+       * Simplified stable fenics packages
+       * Polished support for snowleopard
+       * Updated to recent versions of all fenics packages
+2011-01 Johannes Ring <johannr@simula.no>
+       * Fixed scotch package on debian and snowleopard
+       * Made sid and squeeze identical
+2011-01 Joachim B Haga <jobh@simula.no>
+       * Converted petsc, slepc and trilinos to standard build chains
+       * Added support for separate dorsal_configure and dorsal_build
+         output
+       * Polished ML support in petsc
+       * Added support for running dolfin in valgrind
+2011-01 Harish Narayanan <hnarayanan@gmail.com>
+       * Moved snowleopard to python27
+2011-01 Johan Hake <hake@simula.no>
+       * Added ml support to petsc package
+2011-01 Garth N. Wells <gnw20@cam.ac.uk>
+       * Added support for rhel6 (and scientificlinux6)
+       * Updated petsc, scotch, boost, cmake and cgal packages
+2010-12 Johannes Ring <johannr@simula.no>
+       * Removed run time path information from dolfin build
+2010-12 Harish Narayanan <hnarayanan@gmail.com>
+       * Fixed bugs in  petsc and mtl4 packages
+       * Made wget smarter about downloading files from flaky URLs
+       * Added generic cmake build option
+2010-12 Gerd Wachsmuth <gerd.wachsmuth@mathematik.tu-chemnitz.de>
+       * Install actual files instead of making symlinks
+2010-12 Garth N. Wells <gnw20@cam.ac.uk>
+       * Added support for fedora14
+       * Enabled trilinos for all supported platforms
+       * Updated petsc and trilinos versions
+2010-11 Garth N. Wells <gnw20@cam.ac.uk>
+       * Added pastix (multi-threaded LU) support to petsc
+       * Updated petsc and trilinos versions
+2010-10 Harish Narayanan <hnarayanan@gmail.com>
+       * Updated fenics.org to fenicsproject.org to reflect move
+       * Updated slepc version
+2010-09 Anders Logg <logg@simula.no>
+       * Polished support for snowleopard
+       * Updated to recent versions of all fenics packages
+2010-09 Garth N. Wells <gnw20@cam.ac.uk>
+       * Updated to slepc 3.1-p2
+2010-09 Harish Narayanan <hnarayanan@gmail.com>
+       * Updated documentation to reflect new directory structure
+       * Updated the "one-click" installer
+       * Polished support for snowleopard
+       * Updated cmake builds to respect CONFOPTS
+2010-08 Garth N. Wells <gnw20@cam.ac.uk>
+       * Moved lenny to deprecated
+       * Moved sid to supported
+2010-08 Marie E. Rognes <meg@simula.no>
+       * Polished support for gentoo
+2010-08 Harish Narayanan <hnarayanan@gmail.com>
+       * Polished support for snowleopard
+       * Added support for fedora machines without redhat-lsb
+       * Added scripts for auto-generating author lists and listing
+         unused packages and patches
+       * Removed several unused packages
+       * Fixed bugs related to new platform file placements
+       * Added support for 32/64-bit architecture-independent builds
+       * Fixed python crashing bug introduced by cmake on darwin
+       * Fixed breakages introduced in snowleopard
+       * Removed (nonexistent) support for xp
+       * Updated documentation to reflect new directory structure
+       * Updated the "one-click" installer
+2010-08 Johannes Ring <johannr@simula.no>
+       * Added patch for scientificpython to help it detect numpy
+       * Modified trilinos package to account for the new cmake-based
+         install of its 10.x branch
+2010-08 Anders Logg <logg@simula.no>
+       * Fixed bugs introduced by move to petsc/slepc 3.1x
+       * Broke many things through several hasty changes
+       * Fixed breakages introduced in snowleopard
+       * Fixed missing malloc.h bug in parmetis
+       * Modified dolfin package to account for new cmake-based install
+       * Split platform files into supported, contributed and deprecated
+       * Fixed breakages introduced in ubuntu platforms
+       * Resumed mirroring files hosted on unstable servers
+       * Polished support for maverick
+       * Tested and corrected breakages in different platforms
+       * Updated to recent versions of all fenics packages
+2010-08 Garth N. Wells <gnw20@cam.ac.uk>
+       * Updated to petsc/slepc 3.1x
+       * Broke many things through several hasty changes
+       * Added initial support for maverick
+       * Added initial support for opensuse11.3
+       * Added lib64 to library search path on 64bit machines
+       * Added out-of-source build support to cmake
+       * Fixed breakages introduced in fedora13
+       * Fixed architecture-sniffing in scotch platform
+       * Polished support for opensuse11.3
+       * Removed scons requirement from supported platform files
+       * Added initial support for squeeze
+       * Tested and corrected breakages in different platforms
+2010-07 Douglas N. Arnold <arnold@umn.edu>
+       * Added initial support for fedora13
+2010-07 Patrick Riesen <priesen@student.ethz.ch>
+       * Fixed armadillo package on 64-bit machines
+2010-06 Harish Narayanan <harish@simula.no>
+       * Updated to recent versions of all packages
+        * Updated documentation
+2010-06 Alexander Jarosch <alex@alexj.at>
+       * Polished support for gentoo/sabayon
+        * Added initial support for gentoo/sabayon
+2010-05 Harish Narayanan <harish@simula.no>
+       * Added package for armadillo
+       * Removed ssl certificate checking
+2010-05 Anders Logg <logg@simula.no>
+       * Fixed bugs introduced by new directory structure
+2010-04 Roman Putanowicz <putanowr@l5.pk.edu.pl>
+       * Generalised dorsal to handle projects other than FEniCS
+       * Added support for separate build directories
+2010-04 Harish Narayanan <harish@simula.no>
+       * Added initial support for fedora12
+       * Polished support for fedora11
+2010-04 Joachim B Haga <jobh@simula.no>
+       * Added initial support for lucid
+       * Polished platform sniffing
+2010-03 Harish Narayanan <harish@simula.no>
+       * Updated to recent versions of all packages
+2010-03 Krishna S. Rudraraju <rudraa@umich.edu>
+       * Fixed numpy link
+2010-03 Dimitris Tsarouchas <dt335@cam.ac.uk>
+       * Polished parallel support on karmic
+2010-03 Douglas N. Arnold <arnold@umn.edu>
+       * Polished support for fedora11
+       * Fixed gforge links
+2010-03 Aron Wahlberg <aron@simula.no>
+       * Fixed vtk on snowleopard
+2010-02 Harish Narayanan <harish@simula.no>
+       * Removed support for gts
+       * Modified the default installation location to be more elegant
+       * Added the ability to install single packages
+       * Enabled a parallel version of scotch
+       * Polished support for snowleopard
+       * Added package for MAdLib
+       * Updated to recent versions of all packages
+       * Added scientific python support to all platforms
+2010-01 Harish Narayanan <harish@simula.no>
+       * Fixed cgal error on leopard
+2009-12 Anders Logg <logg@simula.no>
+       * Added zenity support to the "one-click" installer
+2009-12 Harish Narayanan <harish@simula.no>
+       * Vastly improved documentation with the introduction of a small
+         usage manual
+       * Added initial version of the "one-click" installer
+       * Polished cgal package and added it to all platforms
+       * Added initial support for opensuse11.2
+       * Added skip-based platform example
+       * Updated to recent versions of all packages
+2009-11 Andre Massing <massing@simula.no>
+       * Added initial support for cgal
+2009-11 Harish Narayanan <harish@simula.no>
+       * Polished support for fedora11
+       * Added support for bzr repositories
+       * Reflected recent move of fenics projects to launchpad
+       * Removed default building of syfi and its dependencies
+2009-11 Douglas N. Arnold <arnold@umn.edu>
+       * Added initial support for fedora11
+2009-10 Harish Narayanan <harish@simula.no>
+       * Polished support for bigblue
+       * Streamlined the main build script
+       * Improved support for snowleopard (and moved to MacPorts)
+       * Improved support for rhel5
+       * Added ability to skip building of specific packages
+2009-10 Garth N. Wells <gnw20@cam.ac.uk>
+       * Improved support for rhel5
+2009-09 Joachim B Haga <jobh@simula.no>
+       * Prettified display of home directory in output
+2009-09 Harish Narayanan <harish@simula.no>
+       * Started experimenting with mumps support (in petsc)
+       * Added initial support for snowleopard
+       * Updated to recent versions of all packages
+2009-09 Harish Narayanan <harish@simula.no>
+       * Started mirroring files hosted on unstable servers
+       * Removed support for gutsy
+2009-08 Anders Logg <logg@simula.no>
+       * Added initial support for karmic
+2009-07 Harish Narayanan <harish@simula.no>
+       * Updated to recent versions of all packages
+       * Matched FEniCS package versions to Automatic Augustin
+2009-06 Harish Narayanan <harish@simula.no>
+       * Moved to the new DOLFIN build sequence
+2009-05 Joachim B Haga <jobh@simula.no>
+       * Fixed patching sequence to ensure patches don't fail after the
+         first application
+2009-05 Harish Narayanan <harish@simula.no>
+       * Introduced a simple patching schema
+2009-04 Anders Logg <logg@simula.no>
+       * Added support for jaunty
+2009-04 Harish Narayanan <harish@simula.no>
+       * Updated to recent versions of all packages
+       * Worked around Trilinos bug with repeated installs
+       * Added support for git repositories
+       * Added package for swiginac
+2009-03 Aron Wahlberg <aron.wahlberg@gmail.com>
+       * Improved support for tiger
+2009-03 Peter-Jan Randewijk <pjrandew@sun.ac.za>
+       * Added initial support for opensuse11.1
+2009-02 Harish Narayanan <harish@simula.no>
+       * Added support for lenny
+       * Modified ufc package to account for new scons-based install
+       * Generalised petsc/slepc packages to handle slight differences in
+         2x and 3x versions of the software
+       * Updated to recent versions of all packages
+2009-01 Harish Narayanan <harish@simula.no>
+       * Added support for fedora10
+       * Added preliminary support for tiger
+       * Added support for etch
+       * Improved functionality of rhel4/rhel5
+       * Introduced a mechanism for installing stable
+         versions of FEniCS packages
+       * Updated to recent versions of all packages
+2008-11 Joachim B Haga <jobh@simula.no>
+       * Introduced the function 'default' instead of
+         'export' to prevent clobbering existing variables
+2008-11 Harish Narayanan <harish@simula.no>
+       * Modularised DOLFIN package file and added remaining
+         dependencies
+       * Updated to recent versions of all packages
+2008-10 Joachim B Haga <jobh@simula.no>
+       * Automatically guess the platform
+       * Create build log and rebuild script for individual
+         packages
+       * Support for parallel make/scons
+       * Improved slepc/petsc packages to avoid the need
+         for manually setting LD_LIBRARY_PATH
+       * Display platfom-specific instructions as part of
+         the build process
+2008-10 Harish Narayanan <harish@simula.no>
+       * Automatically probe for system python version
+       * Added preliminary support for xp
+2008-09 Luk ShunTim <shuntim.luk@polyu.edu.hk>
+       * Added support for sid
+2008-09 Harish Narayanan <harish@simula.no>
+       * Added support for leopard
+       * Removed the need for gfortran (in mpi, petsc,
+         suitesparse)
+       * Added support for custom configuration options
+       * Added colour progress/error reporting
+       * Updated to recent versions of all packages
+2008-09 Ilmar Wilbers <ilmarw@simula.no>
+       * Added support for intrepid
+       * Added support for gutsy
+2008-08 Harish Narayanan <harish@simula.no>
+       * Changed distribution license to GPL version 3
+       * Complete rewrite; modularised the scripts
+       * Created a framework for easy addition of additional
+         platforms
+       * Added support for rhel5
+2008-07 Ilmar Wilbers <ilmarw@simula.no>
+       * Added basic error reporting
+       * Replaced autotools-based builds (for dolfin, syfi)
+         with scons
+       * Added support for hardy
+2007-06 Harish Narayanan <hnarayan@umich.edu>
+       * Initial release for rhel4
diff --git a/DTM++.toolbox/packages/DTM++.toolbox.package b/DTM++.toolbox/packages/DTM++.toolbox.package
new file mode 100644 (file)
index 0000000..5cfe10a
--- /dev/null
@@ -0,0 +1,37 @@
+NAME=DTM++.toolbox
+VERSION=deal.II-8.1.0
+BUILDCHAIN=ignore
+
+MODULEFILE_PATH=${INSTALL_PATH}/conf/modulefiles/candi/toolbox/${NAME}/${COMPILER}
+CONFIG_FILE=${MODULEFILE_PATH}/${VERSION}
+CURRENT_MODULES=$(echo ${LOADEDMODULES} | sed 's/:/\ /')
+
+# **********************************************************************************
+package_specific_conf() {
+    # Generate modulefile
+    
+    mkdir -p ${MODULEFILE_PATH}
+    rm -f $CONFIG_FILE
+    echo "#%Module 1.0
+#
+#  DTM++.TOOLBOX module for use with 'environment-modules' package:
+#
+module-whatis          "Provides the DTM++.TOOLBOX."
+conflict               candi/toolbox
+module load ${CURRENT_MODULES}
+
+setenv                  TOOLBOX         ${INSTALL_PATH}
+setenv                  DEAL_II_DIR     ${INSTALL_PATH}
+" >> $CONFIG_FILE
+    
+    echo
+    echo "${NAME} has now been installed in"
+    echo
+    cecho ${GOOD} "    ${INSTALL_PATH}"
+    echo
+    echo "To update your environment variables, use the created modulefile:"
+    echo
+    cecho ${GOOD} "    $CONFIG_FILE"
+    echo
+}
+
diff --git a/DTM++.toolbox/packages/dealii-snapshot.package b/DTM++.toolbox/packages/dealii-snapshot.package
new file mode 100644 (file)
index 0000000..1ef1236
--- /dev/null
@@ -0,0 +1,47 @@
+NAME=deal.II-svn
+SOURCE=https://svn.dealii.org/trunk/deal.II
+PACKING=svn
+BUILDCHAIN=custom
+
+CONFOPTS=" \
+${DEAL_CONFOPTS} \
+"
+
+CONFOPTS="${CONFOPTS} \
+-D HDF5_DIR=${HDF5_DIR} \
+"
+
+CONFOPTS="${CONFOPTS} \
+-D TRILINOS_DIR=${TRILINOS_DIR} \
+"
+
+CONFOPTS="${CONFOPTS} \
+-D PETSC_DIR=${PETSC_DIR} \
+"
+
+CONFOPTS="${CONFOPTS} \
+-D SLEPC_DIR=${SLEPC_DIR} \
+"
+
+CONFOPTS="${CONFOPTS} \
+-D CMAKE_INSTALL_PREFIX:PATH="${INSTALL_PATH}" \
+"
+
+package_specific_setup () {
+    echo "Build ${NAME} in ${BUILD_PATH}/${NAME}"
+    mkdir -p "${BUILD_PATH}/${NAME}"
+    cd "${BUILD_PATH}/${NAME}"
+
+    DEALII_SOURCE="${DOWNLOAD_PATH}/${EXTRACTSTO}"
+
+    # configure
+    cmake ${CONFOPTS} ${DEALII_SOURCE}
+
+    # make
+    make -j${PROCS}
+    make install
+}
+
+package_specific_register () {
+    export DEALII_DIR=${INSTALL_PATH}
+}
diff --git a/DTM++.toolbox/packages/dealii-stable.package b/DTM++.toolbox/packages/dealii-stable.package
new file mode 100644 (file)
index 0000000..281d946
--- /dev/null
@@ -0,0 +1,8 @@
+VERSION=8.1.0
+NAME=deal.II-${VERSION}
+SOURCE=https://dealii.googlecode.com/files/
+PACKING=.tar.gz
+CHECKSUM=aa8fadc2ce5eb674f44f997461bf668d
+BUILDCHAIN=cmake
+EXTRACTSTO=deal.II
+
diff --git a/DTM++.toolbox/packages/dealii.package b/DTM++.toolbox/packages/dealii.package
new file mode 100644 (file)
index 0000000..d587556
--- /dev/null
@@ -0,0 +1,49 @@
+NAME=deal.II-svn
+SOURCE=https://svn.dealii.org/trunk/deal.II
+PACKING=svn
+BUILDCHAIN=cmake
+
+DEAL_CONFOPTS=" \
+-D CMAKE_BUILD_TYPE=DebugRelease \
+-D DEAL_II_COMPONENT_DOCUMENTATION:BOOL=OFF \
+-D DEAL_II_WITH_ARPACK:BOOL=OFF \
+-D DEAL_II_WITH_BOOST:BOOL=ON \
+-D DEAL_II_WITH_FUNCTIONPARSER:BOOL=ON \
+-D DEAL_II_WITH_LAPACK:BOOL=ON \
+-D DEAL_II_WITH_METIS:BOOL=OFF \
+-D DEAL_II_WITH_MUMPS:BOOL=OFF \
+-D DEAL_II_WITH_MPI:BOOL=ON \
+-D DEAL_II_WITH_NETCDF:BOOL=OFF \
+-D DEAL_II_WITH_P4EST:BOOL=ON \
+-D DEAL_II_WITH_PETSC:BOOL=OFF \
+-D DEAL_II_WITH_SLEPC:BOOL=OFF \
+-D DEAL_II_WITH_THREADS:BOOL=OFF \
+-D DEAL_II_WITH_TRILINOS:BOOL=ON \
+-D DEAL_II_WITH_UMFPACK:BOOL=ON \
+-D DEAL_II_WITH_ZLIB:BOOL=ON \
+-D DEAL_II_WITH_HDF5:BOOL=ON \
+"
+
+CONFOPTS=" \
+${DEAL_CONFOPTS} \
+"
+
+CONFOPTS="${CONFOPTS} \
+-D HDF5_DIR=${HDF5_DIR} \
+"
+
+CONFOPTS="${CONFOPTS} \
+-D TRILINOS_DIR=${TRILINOS_DIR} \
+"
+
+CONFOPTS="${CONFOPTS} \
+-D PETSC_DIR=${PETSC_DIR} \
+"
+
+CONFOPTS="${CONFOPTS} \
+-D SLEPC_DIR=${SLEPC_DIR} \
+"
+
+package_specific_register () {
+    export DEAL_II_DIR=${INSTALL_PATH}
+}
diff --git a/DTM++.toolbox/packages/hdf5.package b/DTM++.toolbox/packages/hdf5.package
new file mode 100644 (file)
index 0000000..5ec2792
--- /dev/null
@@ -0,0 +1,13 @@
+VERSION=1.8.12
+NAME=hdf5-${VERSION}
+SOURCE=http://www.hdfgroup.org/ftp/HDF5/releases/${NAME}/src/
+PACKING=.tar.gz
+CHECKSUM=d804802feb99b87fc668a90e6fa34411
+BUILDCHAIN=autotools
+
+CONFOPTS="--enable-shared --enable-parallel"
+
+package_specific_register () {
+    export HDF5_DIR=${INSTALL_PATH}
+}
+
diff --git a/DTM++.toolbox/packages/hwloc.package b/DTM++.toolbox/packages/hwloc.package
new file mode 100644 (file)
index 0000000..e0bbdc0
--- /dev/null
@@ -0,0 +1,7 @@
+VERSION=1.9
+NAME=hwloc-${VERSION}
+SOURCE=http://www.open-mpi.org/software/hwloc/v${VERSION}/downloads/
+PACKING=.tar.gz
+CHECKSUM=1f9f9155682fe8946a97c08896109508
+BUILDCHAIN=autotools
+
diff --git a/DTM++.toolbox/packages/p4est.package b/DTM++.toolbox/packages/p4est.package
new file mode 100644 (file)
index 0000000..bc1555b
--- /dev/null
@@ -0,0 +1,89 @@
+NAME=p4est-0.3.4.2
+SOURCE=http://www.p4est.org/tarball/
+PACKING=.tar.gz
+CHECKSUM=ef38ea3be84628b1548188106a5b01e7
+BUILDCHAIN=custom
+
+package_specific_setup () {
+    function bdie () {
+        echo "Error: $@"
+        exit 1
+    }
+
+    if test -z "$CFLAGS" -a -z "$P4EST_CFLAGS_FAST" ; then
+        export CFLAGS_FAST="-O2"
+    else
+        export CFLAGS_FAST="$CFLAGS $P4EST_CFLAGS_FAST"
+    fi
+    echo "CFLAGS_FAST: $CFLAGS_FAST"
+    
+    if test -z "$CFLAGS" -a -z "$P4EST_CFLAGS_DEBUG" ; then
+        export CFLAGS_DEBUG="-O0 -g"
+    else
+        export CFLAGS_DEBUG="$CFLAGS $P4EST_CFLAGS_DEBUG"
+    fi
+    echo "CFLAGS_DEBUG: $CFLAGS_DEBUG"
+
+    # choose names for fast and debug build directories
+    BUILD_FAST="${BUILD_PATH}/${NAME}/FAST"
+    BUILD_DEBUG="${BUILD_PATH}/${NAME}/DEBUG"
+
+    # choose names for fast and debug installation directories
+    INSTALL_FAST="${INSTALL_PATH}/${NAME}/FAST"
+    INSTALL_DEBUG="${INSTALL_PATH}/${NAME}/DEBUG"
+    
+    echo
+    echo "This script tries configure and build the p4est library."
+    echo "Build FAST: $BUILD_FAST"
+    echo "Build DEBUG: $BUILD_DEBUG"
+    echo "Install FAST: $INSTALL_FAST"
+    echo "Install DEBUG: $INSTALL_DEBUG"
+    echo "Checking environment: CFLAGS P4EST_CFLAGS_FAST P4EST_CFLAGS_DEBUG"
+
+    test -f "${UNPACK_PATH}/${EXTRACTSTO}/src/p4est.h" || bdie "Main header file missing"
+    test -f "${UNPACK_PATH}/${EXTRACTSTO}/configure" || bdie "Configure script missing"
+    
+    echo "See output in files .../config.output and .../make.output"
+    echo
+    
+    # remove old versions
+    if test -d "${BUILD_PATH}/${NAME}"; then
+        rm -rf "${BUILD_PATH}/${NAME}"
+    fi
+
+    echo "Build FAST version in $BUILD_FAST"
+    mkdir -p "$BUILD_FAST"
+    cd "$BUILD_FAST"
+    "${UNPACK_PATH}/${EXTRACTSTO}/configure" --enable-mpi --enable-shared \
+        --disable-vtk-binary --without-blas \
+        --prefix="$INSTALL_FAST" CFLAGS="$CFLAGS_FAST" \
+        CPPFLAGS="-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL" \
+        "$@" > config.output || bdie "Error in configure"
+    make -C sc -j${PROCS} > make.output || bdie "Error in make sc"
+    make -j${PROCS} >> make.output || bdie "Error in make p4est"
+    make install >> make.output || bdie "Error in make install"
+    echo "FAST version installed in $INSTALL_FAST"
+    
+    echo
+    echo "Build DEBUG version in $BUILD_DEBUG"
+    mkdir -p "$BUILD_DEBUG"
+    cd "$BUILD_DEBUG"
+    "${UNPACK_PATH}/${EXTRACTSTO}/configure" --enable-debug --enable-mpi --enable-shared \
+        --disable-vtk-binary --without-blas \
+        --prefix="$INSTALL_DEBUG" CFLAGS="$CFLAGS_DEBUG" \
+        CPPFLAGS="-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL" \
+        "$@" > config.output || bdie "Error in configure"
+    make -C sc -j${PROCS} > make.output || bdie "Error in make sc"
+    make -j${PROCS} >> make.output || bdie "Error in make p4est"
+    make install >> make.output || bdie "Error in make install"
+    echo "DEBUG version installed in $INSTALL_DEBUG"
+    echo
+    
+    cd "${BUILD_PATH}/${NAME}"
+    touch dorsal_successful_build
+}
+
+
+package_specific_register () {
+    export P4EST_DIR=${INSTALL_PATH}/${NAME}
+}
diff --git a/DTM++.toolbox/packages/trilinos.package b/DTM++.toolbox/packages/trilinos.package
new file mode 100644 (file)
index 0000000..4b7e3e2
--- /dev/null
@@ -0,0 +1,27 @@
+VERSION=11.8.1
+NAME=trilinos-${VERSION}-Source
+SOURCE=http://trilinos.sandia.gov/download/files/
+PACKING=.tar.gz
+CHECKSUM=3c9465b6d63d824e9dc0365ca73c3370
+BUILDCHAIN=cmake
+
+CONFOPTS="-D Trilinos_ENABLE_OpenMP:BOOL=OFF \
+          -D TPL_ENABLE_TBB:BOOL=OFF \
+          -D Trilinos_ENABLE_OPTIONAL_PACKAGES:BOOL=ON \
+          -D Trilinos_ENABLE_Didasko:BOOL=ON \
+          -D Trilinos_ENABLE_Sacado:BOOL=ON \
+          -D Trilinos_ENABLE_Stratimikos:BOOL=ON \
+          -D CMAKE_BUILD_TYPE:STRING=RELEASE \
+          -D CMAKE_CXX_FLAGS:STRING=-fPIC -g -O3 \
+          -D CMAKE_C_FLAGS:STRING=-fPIC -g -O3 \
+          -D CMAKE_FORTRAN_FLAGS:STRING=-g -O5 \
+          -D Trilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran \
+          -D CMAKE_VERBOSE_MAKEFILE:BOOL=FALSE \
+          -D Trilinos_VERBOSE_CONFIGURE:BOOL=FALSE \
+          -D TPL_ENABLE_MPI:BOOL=ON \
+          -D BUILD_SHARED_LIBS:BOOL=ON"
+
+package_specific_register () {
+    export TRILINOS_DIR=${INSTALL_PATH}
+}
+
diff --git a/DTM++.toolbox/platforms/.single b/DTM++.toolbox/platforms/.single
new file mode 100644 (file)
index 0000000..e69de29
diff --git a/DTM++.toolbox/platforms/contributed/fedora19.platform b/DTM++.toolbox/platforms/contributed/fedora19.platform
new file mode 100644 (file)
index 0000000..acd426b
--- /dev/null
@@ -0,0 +1,34 @@
+# Fedora 19
+
+# This build script assumes that you have several packages already
+# installed via Fedora's yum using the following command:
+#
+# su -c 'yum install -y svn \
+# @development-tools gcc-c++ openmpi-devel cmake \
+# blas blas-devel lapack lapack-devel \
+# boost boost-devel boost-python boost-openmpi boost-openmpi-devel boost-openmpi-python \
+# doxygen graphviz graphviz-devel splint qt-devel'
+#
+# If you have multiple MPI libraries installed, make sure the
+# appropriate version is selected.
+# 
+# Check available and loaded modules:
+# 
+# module avial
+# module list
+# 
+# and load an appropriate module, e.g.:
+#
+# module load openmpi-x86_64
+##
+
+# Platform specific variables
+default UMFPACK_INCLUDE_DIR=/usr/include/suitesparse
+
+# Define the packages this platform needs
+PACKAGES=(
+p4est
+hdf5
+trilinos
+dealii
+)
diff --git a/DTM++.toolbox/platforms/supported/fedora20.platform b/DTM++.toolbox/platforms/supported/fedora20.platform
new file mode 100644 (file)
index 0000000..db6fe3a
--- /dev/null
@@ -0,0 +1,37 @@
+# Fedora 20
+
+# This build script assumes that you have several packages already
+# installed via Fedora's yum using the following command:
+#
+# su -c 'yum install -y svn \
+# @development-tools gcc-c++ openmpi-devel cmake \
+# blas blas-devel lapack lapack-devel \
+# boost boost-devel boost-python boost-openmpi boost-openmpi-devel boost-openmpi-python \
+# doxygen graphviz graphviz-devel splint qt-devel'
+#
+# If you have multiple MPI libraries installed, make sure the
+# appropriate version is selected.
+# 
+# Check available and loaded modules:
+# 
+# module avial
+# module list
+# 
+# and load an appropriate module, e.g.:
+#
+# module load openmpi-x86_64
+##
+
+# Platform specific variables
+default UMFPACK_INCLUDE_DIR=/usr/include/suitesparse
+
+# Define the packages this platform needs
+PACKAGES=(
+once:hwloc
+once:hdf5
+once:p4est
+once:trilinos
+dealii
+skip:DTM++.toolbox
+)
+
diff --git a/DTM++.toolbox/platforms/supported/rhel6.platform b/DTM++.toolbox/platforms/supported/rhel6.platform
new file mode 100644 (file)
index 0000000..1e85b57
--- /dev/null
@@ -0,0 +1,35 @@
+# RHEL 6
+
+# This build script assumes that you have several packages already
+# installed via Fedora's yum using the following command:
+#
+# su -c 'yum install -y svn \
+# @development-tools gcc-c++ openmpi-devel cmake \
+# blas blas-devel lapack lapack-devel \
+# boost boost-devel boost-python boost-openmpi boost-openmpi-devel boost-openmpi-python \
+# doxygen graphviz graphviz-devel splint qt-devel'
+#
+# If you have multiple MPI libraries installed, make sure the
+# appropriate version is selected.
+# 
+# Check available and loaded modules:
+# 
+# module avial
+# module list
+# 
+# and load an appropriate module, e.g.:
+#
+# module load openmpi-x86_64
+##
+
+# Platform specific variables
+default UMFPACK_INCLUDE_DIR=/usr/include/suitesparse
+
+# Define the packages this platform needs
+PACKAGES=(
+once:hdf5
+once:p4est
+once:trilinos
+dealii
+skip:DTM++.toolbox
+)
diff --git a/DTM++.toolbox/platforms/supported/saucy.platform b/DTM++.toolbox/platforms/supported/saucy.platform
new file mode 100644 (file)
index 0000000..6a94355
--- /dev/null
@@ -0,0 +1,22 @@
+# Fedora 20
+
+# This build script assumes that you have several packages already
+# installed via Fedora's yum using the following command:
+#
+# su -c 'apt-get install build-essential automake autoconf gfortran \
+# libblas-dev liblapack-dev splint openmpi1.6 cmake git subversion'
+#
+# If you have multiple MPI libraries installed, make sure the
+# appropriate version is selected.
+##
+
+# Platform specific variables
+
+# Define the packages this platform needs
+PACKAGES=(
+once:hdf5
+once:p4est
+once:trilinos
+dealii
+skip:DTM++.toolbox
+)
diff --git a/FEniCS/packages/FEniCS-prepare.package b/FEniCS/packages/FEniCS-prepare.package
new file mode 100644 (file)
index 0000000..e057278
--- /dev/null
@@ -0,0 +1,25 @@
+NAME=FEniCS_prepare
+BUILDCHAIN=ignore
+
+package_specific_conf() {
+    # Generate FEniCS folders
+    mkdir -p ${INSTALL_PATH}/conf
+    mkdir -p ${INSTALL_PATH}/bin
+    mkdir -p ${INSTALL_PATH}/include
+    mkdir -p ${INSTALL_PATH}/lib
+    mkdir -p ${INSTALL_PATH}/lib/python${PYTHONVER}/site-packages
+    mkdir -p ${INSTALL_PATH}/share
+    export PATH=${INSTALL_PATH}/bin:${PATH}
+    export LD_LIBRARY_PATH=${INSTALL_PATH}/lib:${LD_LIBRARY_PATH}
+    export DYLD_LIBRARY_PATH=${INSTALL_PATH}/lib:${DYLD_LIBRARY_PATH}
+    export PYTHONPATH=${INSTALL_PATH}/lib/python${PYTHONVER}/site-packages:${PYTHONPATH}
+    export PKG_CONFIG_PATH=${INSTALL_PATH}/lib/pkgconfig:${PKG_CONFIG_PATH}
+
+    # Add some extra library paths for 64 bit machines
+    if [ "$ARCH" == "x86_64" ]; then
+        export LD_LIBRARY_PATH=${INSTALL_PATH}/lib64:${LD_LIBRARY_PATH}
+        export DYLD_LIBRARY_PATH=${INSTALL_PATH}/lib64:${DYLD_LIBRARY_PATH}
+        export PYTHONPATH=${INSTALL_PATH}/lib64/python${PYTHONVER}/site-packages:${PYTHONPATH}
+    fi
+}
+
diff --git a/FEniCS/packages/FEniCS.package b/FEniCS/packages/FEniCS.package
new file mode 100644 (file)
index 0000000..6d65396
--- /dev/null
@@ -0,0 +1,90 @@
+NAME=FEniCS
+VERSION=1.3.0
+BUILDCHAIN=ignore
+
+MODULEFILE_PATH=${INSTALL_PATH}/conf/modulefiles/NVRI.software/toolbox/${NAME}
+CONFIG_FILE=${MODULEFILE_PATH}/${VERSION}
+CURRENT_MODULES=$(echo ${LOADEDMODULES} | sed 's/:/\ /')
+
+# **********************************************************************************
+package_specific_conf() {
+    # Generate modulefile
+    
+    mkdir -p ${MODULEFILE_PATH}
+    rm -f $CONFIG_FILE
+    echo "#%Module 1.0
+#
+#  FEniCS module for use with 'environment-modules' package:
+#
+
+conflict NVRI.software/toolbox
+
+module load ${CURRENT_MODULES}
+
+# Define prefix so PATH and MANPATH can be updated.
+setenv        INSTALL_PATH      ${INSTALL_PATH}
+prepend-path  PATH               ${INSTALL_PATH}/bin
+prepend-path  PYTHONPATH         ${INSTALL_PATH}/lib/python${PYTHONVER}/site-packages
+prepend-path  PYTHONPATH         ${INSTALL_PATH}/lib64/python${PYTHONVER}/site-packages
+prepend-path  LD_LIBRARY_PATH    ${INSTALL_PATH}/lib
+prepend-path  DYLD_LIBRARY_PATH  ${INSTALL_PATH}/lib
+prepend-path  PKG_CONFIG_PATH    ${INSTALL_PATH}/lib/pkgconfig
+prepend-path  MANPATH            ${INSTALL_PATH}/share/man
+prepend-path  CPLUS_INCLUDE_PATH ${INSTALL_PATH}/include
+prepend-path  CMAKE_PREFIX_PATH  ${INSTALL_PATH}
+
+setenv        BOOST_DIR          ${INSTALL_PATH}
+" >> $CONFIG_FILE
+    
+    echo
+    echo "${NAME} has now been installed in"
+    echo
+    cecho ${GOOD} "    ${INSTALL_PATH}"
+    echo
+    echo "To update your environment variables, use the created modulefile:"
+    echo
+    cecho ${GOOD} "    $CONFIG_FILE"
+    echo
+
+    # Generate configuration file for building against FEniCS installation
+
+    mkdir -p $INSTALL_PATH/share/fenics
+    CONFIG_FILE=$INSTALL_PATH/share/fenics/fenics.conf
+    rm -f $CONFIG_FILE
+    echo "
+# Source this file to set up your environment for building against FEniCS
+
+# Standard paths
+export INSTALL_PATH=${INSTALL_PATH}
+export PATH=\$INSTALL_PATH/bin:\$PATH
+export PYTHONPATH=\$INSTALL_PATH/lib/python${PYTHONVER}/site-packages:\$PYTHONPATH
+export LD_LIBRARY_PATH=\$INSTALL_PATH/lib:\$LD_LIBRARY_PATH
+export DYLD_LIBRARY_PATH=\$INSTALL_PATH/lib:\$DYLD_LIBRARY_PATH
+export PKG_CONFIG_PATH=\$INSTALL_PATH/lib/pkgconfig:\$PKG_CONFIG_PATH
+export MANPATH=\$INSTALL_PATH/share/man:\$MANPATH
+export CPLUS_INCLUDE_PATH=\$INSTALL_PATH/include:\$CPLUS_INCLUDE_PATH
+export CMAKE_PREFIX_PATH=\$INSTALL_PATH:\$CMAKE_PREFIX_PATH
+" >> $CONFIG_FILE
+
+    for PACKAGE in ${PACKAGES[@]}
+    do
+       case ${PACKAGE} in
+            *boost) echo "
+export BOOST_DIR=\$INSTALL_PATH
+" >> $CONFIG_FILE;;
+           *vtk | *vtkwithqt) echo "
+# FIXME: This needs to be updated when the VTK version is changed
+export LD_LIBRARY_PATH=\$INSTALL_PATH/lib/vtk-5.8:\$LD_LIBRARY_PATH
+export DYLD_LIBRARY_PATH=\$INSTALL_PATH/lib/vtk-5.8:\$DYLD_LIBRARY_PATH
+" >> $CONFIG_FILE;;
+       esac
+    done
+    
+    echo "To update your environment variables, run the following command:"
+    echo
+    cecho ${GOOD} "    source $CONFIG_FILE"
+    echo
+    echo "For future reference, we recommend that you add this command to your"
+    echo "configuration (.bashrc, .profile or similar)."
+    echo
+}
diff --git a/FEniCS/packages/armadillo.package b/FEniCS/packages/armadillo.package
new file mode 100644 (file)
index 0000000..4bb8419
--- /dev/null
@@ -0,0 +1,26 @@
+NAME=armadillo-3.6.1
+SOURCE=http://downloads.sourceforge.net/arma/
+PACKING=.tar.gz
+CHECKSUM=cf0e72fbd2ed07d9fbde01ec8feee953
+BUILDCHAIN=cmake
+
+CONFOPTS="-D CMAKE_INSTALL_PREFIX:PATH=${INSTALL_PATH}
+         -D INSTALL_LIB_DIR:STRING=lib"
+
+if [ ! -z "${ATLAS_LIB_DIR}" ]; then
+    CONFOPTS="${CONFOPTS}
+              -D LAPACK_LIBRARY:FILEPATH=${ATLAS_LIB_DIR}/liblapack.a
+              -D BLAS_LIBRARY:FILEPATH=${ATLAS_LIB_DIR}/libatlas.a"
+fi
+
+package_specific_setup() {
+    # Apply patch to prevent Armadillo from picking up MKL
+    # when ATLAS_LIB_DIR is defined
+    if [ ! -z "${ATLAS_LIB_DIR}" ]; then
+       patch -p1 --forward < ${ORIG_DIR}/FEniCS/patches/armadillo_no_mkl.patch || true
+    fi
+}
+
+package_specific_register () {
+    export ARMADILLO_DIR=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/atlas.package b/FEniCS/packages/atlas.package
new file mode 100644 (file)
index 0000000..552301e
--- /dev/null
@@ -0,0 +1,70 @@
+# ATLAS package. This package also provides LAPACK.
+
+NAME=atlas3.10.0-with-lapack-3.4.2
+SOURCE=http://fenicsproject.org/pub/software/contrib/
+PACKING=.tar.bz2
+BUILDCHAIN=custom
+EXTRACTSTO=ATLAS
+
+package_specific_build () {
+
+    # Try to change CPU frequency
+    if [ x$CPU_SCALING == "xyes" ]; then
+
+        read -p "SCALING CPU"
+
+        # Determine number of cores and frequency
+        CORES=`grep processor /proc/cpuinfo | sort | awk '{print $3}'`
+        NUM_CORES=`grep processor /proc/cpuinfo | sort | tail -1 | awk '{print $3}'`
+        MAX_FREQ=`cpufreq-info | grep limits | awk '{print $6$7}' | tail -1`
+
+        echo
+        echo "It looks like your machine has $NUM_CORES cores and that the maximum"
+        echo "CPU frequency is $MAX_FREQ."
+        echo
+
+        echo
+        echo "Adjusting CPU frequency and governor. Be patient, this may take some time."
+        for i in $CORES; do
+            echo "Adjusting frequency for core $i"
+            sudo cpufreq-set -c $i -u $MAX_FREQ
+            sudo cpufreq-selector -g performance -c $i
+        done
+
+    fi
+
+    # Create and enter build directory
+    mkdir -p build
+    cd build
+
+    # Determine CPU frequency
+    CPU_MHZ=`cat /proc/cpuinfo | grep "cpu MHz" | awk '{print $4}' | cut -d'.' -f1 | tail -1`
+
+    # Configure ATLAS
+    ../configure -b 64 -D c -DPentiumCPS=$CPU_MHZ --shared \
+      --prefix=$INSTALL_PATH \
+      --with-netlib-lapack-tarfile=../lapack-3.4.2.tgz
+
+    # Build
+    make build
+
+    # Check
+    make check
+    make ptcheck
+    make time
+
+    # Install
+    make install
+}
+
+package_specific_install () {
+    echo "Nothing to do here, install handled by ATLAS."
+}
+
+package_specific_register () {
+    export ATLAS_DIR=${INSTALL_PATH}
+    export ATLAS_LIB_DIR=${INSTALL_PATH}/lib
+
+    # This is important for building Trilinos
+    export BLAS_LIBRARY_NAMES="cblas f77blas atlas"
+}
diff --git a/FEniCS/packages/automake.package b/FEniCS/packages/automake.package
new file mode 100644 (file)
index 0000000..ef8ea0d
--- /dev/null
@@ -0,0 +1,6 @@
+VERSION=1.14
+NAME=automake-${VERSION}
+SOURCE=http://ftp.gnu.org/gnu/automake/
+PACKING=.tar.gz
+BUILDCHAIN=autotools
+#EXTRACTSTO=Mesa-${VERSION}
\ No newline at end of file
diff --git a/FEniCS/packages/bazaar.package b/FEniCS/packages/bazaar.package
new file mode 100644 (file)
index 0000000..eb89de9
--- /dev/null
@@ -0,0 +1,5 @@
+NAME=bzr-2.5.1
+SOURCE=http://launchpad.net/bzr/2.5/2.5.1/+download/
+PACKING=.tar.gz
+CHECKSUM=ac5079858364a046071000d5cdccb67b
+BUILDCHAIN=python
diff --git a/FEniCS/packages/blas.package b/FEniCS/packages/blas.package
new file mode 100644 (file)
index 0000000..9c22ba1
--- /dev/null
@@ -0,0 +1,21 @@
+NAME=blas
+SOURCE=http://netlib.org/blas/
+PACKING=.tgz
+BUILDCHAIN=custom
+EXTRACTSTO=BLAS
+
+package_specific_build () {
+    sed -i 's/gfortran/mpif90/g' make.inc
+    sed -i 's/-O3/-O3 -fPIC/g' make.inc
+    sed -i 's/blas$(PLAT).a/libblas.a/g' make.inc
+    make -j ${PROCS}
+}
+
+package_specific_install () {
+    cp *.a ${INSTALL_PATH}/lib/
+}
+
+package_specific_register () {
+    export BLAS_DIR=${INSTALL_PATH}
+    export LAPACKANDBLAS_DIR=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/boost.package b/FEniCS/packages/boost.package
new file mode 100644 (file)
index 0000000..025f136
--- /dev/null
@@ -0,0 +1,27 @@
+NAME=boost_1_55_0
+SOURCE=http://downloads.sourceforge.net/boost/
+PACKING=.tar.bz2
+CHECKSUM=d6eef4b4cacb2183f2bf265a5a03a354
+BUILDCHAIN=custom
+
+if [ ! -z "${BZIP2_DIR}" ]; then
+    CONFOPTS="${CONFOPTS}
+              -sNO_BZIP2=0
+              -sBZIP2_BINARY=bz2
+              -sBZIP2_INCLUDE=${BZIP2_DIR}/include
+              -sBZIP2_LIBPATH=${BZIP2_DIR}/lib"
+fi
+
+package_specific_build () {
+    cp -rf ${UNPACK_PATH}/${NAME}/* .
+    ./bootstrap.sh --prefix=${INSTALL_PATH}
+    echo "using mpi ;" > user-config.jam
+    ./b2 -j ${PROCS} --user-config=user-config.jam --build-dir=candi_build_dir link=shared install ${CONFOPTS}
+}
+
+package_specific_register () {
+    export BOOST_ROOT=${INSTALL_PATH}
+    export BOOST_INCLUDEDIR=${INSTALL_PATH}/include
+    export BOOST_LIBRARYDIR=${INSTALL_PATH}/lib
+    export BOOST_USE_MULTITHREADED=OFF
+}
diff --git a/FEniCS/packages/bzip2.package b/FEniCS/packages/bzip2.package
new file mode 100644 (file)
index 0000000..d939e16
--- /dev/null
@@ -0,0 +1,14 @@
+NAME=bzip2-1.0.6
+SOURCE=http://bzip.org/1.0.6/
+PACKING=.tar.gz
+BUILDCHAIN=custom
+
+package_specific_build () {
+    sed -i 's/^CFLAGS=-Wall/CFLAGS=-fPIC -Wall/g' Makefile
+    make
+    make install PREFIX=${INSTALL_PATH}
+}
+
+package_specific_register () {
+    export BZIP2_DIR=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/cgal.package b/FEniCS/packages/cgal.package
new file mode 100644 (file)
index 0000000..7a534f4
--- /dev/null
@@ -0,0 +1,20 @@
+NAME=CGAL-4.3
+SOURCE=http://fenicsproject.org/pub/software/contrib/
+PACKING=.tar.gz
+CHECKSUM=3fa2d43adbf5c05d76c5ec01f5033cc9
+BUILDCHAIN=cmake
+
+CONFOPTS="-D CMAKE_BUILD_TYPE:STRING=Release
+          -D BUILD_SHARED_LIBS:BOOL=ON
+          -D WITH_CGAL_Core:BOOL=OFF
+          -D WITH_CGAL_ImageIO:BOOL=OFF
+          -D WITH_CGAL_Qt3:BOOL=OFF
+          -D WITH_CGAL_Qt4:BOOL=OFF"
+
+if [ ! -z "${BOOST_USE_MULTITHREADED}" ]; then
+    CONFOPTS="${CONFOPTS} -D Boost_USE_MULTITHREADED:BOOL=${BOOST_USE_MULTITHREADED}"
+fi
+
+package_specific_register () {
+    export CGAL_DIR=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/cln.package b/FEniCS/packages/cln.package
new file mode 100644 (file)
index 0000000..11341ae
--- /dev/null
@@ -0,0 +1,4 @@
+NAME=cln-1.3.2
+SOURCE=ftp://ftpthep.physik.uni-mainz.de/pub/gnu/
+PACKING=.tar.bz2
+BUILDCHAIN=autotools
diff --git a/FEniCS/packages/cmake.package b/FEniCS/packages/cmake.package
new file mode 100644 (file)
index 0000000..b2817ed
--- /dev/null
@@ -0,0 +1,9 @@
+NAME=cmake-2.8.12.1
+SOURCE=http://www.cmake.org/files/v2.8/
+PACKING=.tar.gz
+BUILDCHAIN=autotools
+
+package_specific_setup () {
+    ./bootstrap --prefix=${INSTALL_PATH}
+    export CMAKE_LIBRARY_PATH=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/cppunit.package b/FEniCS/packages/cppunit.package
new file mode 100644 (file)
index 0000000..909240c
--- /dev/null
@@ -0,0 +1,8 @@
+NAME=cppunit-1.12.1
+SOURCE=http://downloads.sourceforge.net/cppunit/
+PACKING=.tar.gz
+BUILDCHAIN=autotools
+
+package_specific_register () {
+    export CPPUNIT_DIR=${INSTALL_PATH}
+}
\ No newline at end of file
diff --git a/FEniCS/packages/cusp.package b/FEniCS/packages/cusp.package
new file mode 100644 (file)
index 0000000..bb34b88
--- /dev/null
@@ -0,0 +1,9 @@
+NAME=cusp-v0.3.1
+SOURCE=http://cusp-library.googlecode.com/files/
+PACKING=.zip
+BUILDCHAIN=custom
+EXTRACTSTO=cusp
+
+package_specific_register () {
+    export CUSP_DIR=${DOWNLOAD_PATH}
+}
diff --git a/FEniCS/packages/cython.package b/FEniCS/packages/cython.package
new file mode 100644 (file)
index 0000000..b3ade83
--- /dev/null
@@ -0,0 +1,5 @@
+VERSION=0.19.2
+NAME=Cython-${VERSION}
+SOURCE=http://cython.org/release/
+PACKING=.tar.gz
+BUILDCHAIN=python
diff --git a/FEniCS/packages/dolfin-adjoint.package b/FEniCS/packages/dolfin-adjoint.package
new file mode 100644 (file)
index 0000000..1704c0f
--- /dev/null
@@ -0,0 +1,4 @@
+NAME=dolfin-adjoint
+SOURCE=lp:
+PACKING=bzr
+BUILDCHAIN=python
diff --git a/FEniCS/packages/dolfin-snapshot.package b/FEniCS/packages/dolfin-snapshot.package
new file mode 100644 (file)
index 0000000..9215599
--- /dev/null
@@ -0,0 +1,4 @@
+VERSION=snapshot
+NAME=dolfin-${VERSION}
+SOURCE=http://fenicsproject.org/pub/software/dolfin/
+PACKING=.tar.gz
diff --git a/FEniCS/packages/dolfin-stable.package b/FEniCS/packages/dolfin-stable.package
new file mode 100644 (file)
index 0000000..2571e31
--- /dev/null
@@ -0,0 +1,14 @@
+VERSION=1.3.0
+NAME=dolfin-${VERSION}
+SOURCE=https://bitbucket.org/fenics-project/dolfin/downloads/
+PACKING=.tar.gz
+CHECKSUM=bc5b9f18ee7738b2e9e6768c7aa57c58
+
+package_specific_setup () {
+    # Let CMake picks correct VTK, follow-up of issue151
+    # https://bitbucket.org/fenics-project/dolfin/issue/151
+    # Applies to DOLFIN 1.3.0, not applicable to 1.3.0+.
+    if [ "$VERSION" == "1.3.0" ]; then
+      patch -p1 --forward < ${ORIG_DIR}/FEniCS/patches/dolfin-1.3.0-vtk.patch || true
+    fi
+}
diff --git a/FEniCS/packages/dolfin.package b/FEniCS/packages/dolfin.package
new file mode 100644 (file)
index 0000000..1fd4c39
--- /dev/null
@@ -0,0 +1,42 @@
+NAME=dolfin
+SOURCE=https://bitbucket.org/fenics-project/
+PACKING=git
+BUILDCHAIN=cmake
+
+CONFOPTS="-DCGAL_DISABLE_ROUNDING_MATH_CHECK:BOOL=ON"
+
+if [ -x "${SWIG_EXECUTABLE}" ]; then
+    CONFOPTS="${CONFOPTS} -D SWIG_EXECUTABLE:FILEPATH=${SWIG_EXECUTABLE}"
+fi
+
+if [ ! -z "${PYTHON_EXECUTABLE}" ]; then
+    CONFOPTS="${CONFOPTS} -D PYTHON_EXECUTABLE:FILEPATH=${PYTHON_EXECUTABLE}"
+fi
+
+if [ ! -z "${PYTHON_INCLUDE_DIR}" ]; then
+    CONFOPTS="${CONFOPTS} -D PYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_DIR}"
+fi
+
+if [ ! -z "${PYTHON_LIBRARY}" ]; then
+    CONFOPTS="${CONFOPTS} -D PYTHON_LIBRARY:PATH=${PYTHON_LIBRARY}"
+fi
+
+if [ ! -z "${BOOST_USE_MULTITHREADED}" ]; then
+    CONFOPTS="${CONFOPTS} -D Boost_USE_MULTITHREADED:BOOL=${BOOST_USE_MULTITHREADED}"
+fi
+
+if [ ! -z "${BLAS_LIBRARIES}" ]; then
+    CONFOPTS="${CONFOPTS} -D BLAS_LIBRARIES:FILEPATH=\"${BLAS_LIBRARIES}\""
+fi
+
+if [ ! -z "${ATLAS_LIB_DIR}" ]; then
+    CONFOPTS="${CONFOPTS}
+              -D LAPACK_LIBRARIES=${ATLAS_LIB_DIR}/liblapack.a
+              -D BLAS_LIBRARIES=\"${ATLAS_LIB_DIR}/libcblas.a;${ATLAS_LIB_DIR}/libf77blas.a;${ATLAS_LIB_DIR}/libatlas.a\""
+fi
+
+if [ ! -z "${HDF5_DIR}" ]; then
+    CONFOPTS="${CONFOPTS}
+              -D HDF5_INCLUDE_DIRS=${HDF5_DIR}/include"
+fi
+
diff --git a/FEniCS/packages/dolfin_intel.package b/FEniCS/packages/dolfin_intel.package
new file mode 100644 (file)
index 0000000..3869035
--- /dev/null
@@ -0,0 +1,30 @@
+VERSION=1.0-beta
+NAME=dolfin-${VERSION}
+SOURCE=http://launchpad.net/dolfin/trunk/${VERSION}/+download/
+PACKING=.tar.gz
+BUILDCHAIN=cmake
+
+# Dolfin is compiled with GNU compiler because the Intel compiler used does not support 
+#  the "tuple" template and it cannot read the boost headers properly.
+
+# Compiler flags are added to ensure proper linking to Intel MKL
+COMPILERFLAGS="'-fPIC -DMPICH_IGNORE_CXX_SEEK -m64 -DMKL_ILP64 -lpthread -lmkl_rt -lifcore -lsvml'"
+
+CONFOPTS="-DCMAKE_SKIP_RPATH:BOOL=ON
+         -DCGAL_DISABLE_ROUNDING_MATH_CHECK:BOOL=ON
+         -D CMAKE_CXX_FLAGS:STRING=${COMPILERFLAGS}
+         -D CMAKE_C_FLAGS:STRING=${COMPILERFLAGS}"
+
+package_specific_setup () {
+# The CMake Armadillo does not pass because it does not pass the correct linking options.
+#  The patch basically make the test pass all the time. 
+    patch -p1 --forward < ${ORIG_DIR}/FEniCS/patches/dolfin-armadillo-test.patch || true
+# Intel compiler cannot find iostream. Maybe because it is not in the intel mpi.h. 
+    find . -name "*.cpp" | xargs sed -i -e 's,#include <mpi.h>,#include <mpi.h>\n#include <iostream>,g'
+# Link to intel MKL BLAS
+    export BLAS_DIR=/soft/intel/mkl/10.3.6.233/composer_xe_2011_sp1.6.233/mkl/lib/intel64
+}
+
+if [ -x "${SWIG_EXECUTABLE}" ]; then
+    CONFOPTS="${CONFOPTS} -D SWIG_EXECUTABLE:FILEPATH=${SWIG_EXECUTABLE}"
+fi
diff --git a/FEniCS/packages/dri2proto.package b/FEniCS/packages/dri2proto.package
new file mode 100644 (file)
index 0000000..25c1a78
--- /dev/null
@@ -0,0 +1,5 @@
+VERSION=2.8
+NAME=dri2proto-${VERSION}
+SOURCE=http://ftp.x.org/pub/individual/proto/
+PACKING=.tar.gz
+BUILDCHAIN=autotools
\ No newline at end of file
diff --git a/FEniCS/packages/eigen.package b/FEniCS/packages/eigen.package
new file mode 100644 (file)
index 0000000..5dfa917
--- /dev/null
@@ -0,0 +1,9 @@
+NAME=eigen3_3.2.0
+SOURCE=http://fenicsproject.org/pub/software/contrib/
+PACKING=.tar.bz2
+BUILDCHAIN=cmake
+EXTRACTSTO=eigen-eigen-ffa86ffb5570
+
+package_specific_register () {
+    export EIGEN_DIR=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/ferari-snapshot.package b/FEniCS/packages/ferari-snapshot.package
new file mode 100644 (file)
index 0000000..279e8a0
--- /dev/null
@@ -0,0 +1,4 @@
+VERSION=snapshot
+NAME=ferari-${VERSION}
+SOURCE=http://fenicsproject.org/pub/software/ferari/
+PACKING=.tar.gz
diff --git a/FEniCS/packages/ferari-stable.package b/FEniCS/packages/ferari-stable.package
new file mode 100644 (file)
index 0000000..fca36d5
--- /dev/null
@@ -0,0 +1,5 @@
+VERSION=1.0.0
+NAME=ferari-${VERSION}
+SOURCE=http://launchpad.net/ferari/trunk/${VERSION}/+download/
+PACKING=.tar.gz
+CHECKSUM=e41ed02517f0e8832f27d24e7755c0e2
diff --git a/FEniCS/packages/ferari.package b/FEniCS/packages/ferari.package
new file mode 100644 (file)
index 0000000..7df52f1
--- /dev/null
@@ -0,0 +1,4 @@
+NAME=ferari
+SOURCE=https://bitbucket.org/fenics-project/
+PACKING=git
+BUILDCHAIN=python
diff --git a/FEniCS/packages/ffc-snapshot.package b/FEniCS/packages/ffc-snapshot.package
new file mode 100644 (file)
index 0000000..f24f5d9
--- /dev/null
@@ -0,0 +1,4 @@
+VERSION=snapshot
+NAME=ffc-${VERSION}
+SOURCE=http://fenicsproject.org/pub/software/ffc/
+PACKING=.tar.gz
diff --git a/FEniCS/packages/ffc-stable.package b/FEniCS/packages/ffc-stable.package
new file mode 100644 (file)
index 0000000..3ebbacc
--- /dev/null
@@ -0,0 +1,5 @@
+VERSION=1.3.0
+NAME=ffc-${VERSION}
+SOURCE=https://bitbucket.org/fenics-project/ffc/downloads/
+PACKING=.tar.gz
+CHECKSUM=d57f736ff0b756935a5ffd7c8b30247b
diff --git a/FEniCS/packages/ffc.package b/FEniCS/packages/ffc.package
new file mode 100644 (file)
index 0000000..9d4fd69
--- /dev/null
@@ -0,0 +1,4 @@
+NAME=ffc
+SOURCE=https://bitbucket.org/fenics-project/
+PACKING=git
+BUILDCHAIN=python
diff --git a/FEniCS/packages/ffc_stable.package b/FEniCS/packages/ffc_stable.package
new file mode 100644 (file)
index 0000000..8f7ff6d
--- /dev/null
@@ -0,0 +1,5 @@
+VERSION=1.3.0
+NAME=ffc-${VERSION}
+SOURCE=http://launchpad.net/ffc/1.3.x/${VERSION}/+download/
+PACKING=.tar.gz
+BUILDCHAIN=python
diff --git a/FEniCS/packages/fiat-snapshot.package b/FEniCS/packages/fiat-snapshot.package
new file mode 100644 (file)
index 0000000..7bc5383
--- /dev/null
@@ -0,0 +1,4 @@
+VERSION=snapshot
+NAME=fiat-${VERSION}
+SOURCE=http://fenicsproject.org/pub/software/fiat/
+PACKING=.tar.gz
diff --git a/FEniCS/packages/fiat-stable.package b/FEniCS/packages/fiat-stable.package
new file mode 100644 (file)
index 0000000..0de3b06
--- /dev/null
@@ -0,0 +1,6 @@
+VERSION=1.3.0
+NAME=fiat-${VERSION}
+SOURCE=https://bitbucket.org/fenics-project/fiat/downloads/
+PACKING=.tar.gz
+CHECKSUM=e12267262b97a40fea97c0dad9804dd7
+
diff --git a/FEniCS/packages/fiat.package b/FEniCS/packages/fiat.package
new file mode 100644 (file)
index 0000000..e279ab4
--- /dev/null
@@ -0,0 +1,4 @@
+NAME=fiat
+SOURCE=https://bitbucket.org/fenics-project/
+PACKING=git
+BUILDCHAIN=python
diff --git a/FEniCS/packages/gccxml.package b/FEniCS/packages/gccxml.package
new file mode 100644 (file)
index 0000000..aebbeff
--- /dev/null
@@ -0,0 +1,4 @@
+NAME=gccxml
+SOURCE=https://github.com/gccxml/
+PACKING=git
+BUILDCHAIN=cmake
diff --git a/FEniCS/packages/ginac.package b/FEniCS/packages/ginac.package
new file mode 100644 (file)
index 0000000..854035f
--- /dev/null
@@ -0,0 +1,4 @@
+NAME=ginac-1.6.1
+SOURCE=ftp://ftpthep.physik.uni-mainz.de/pub/GiNaC/
+PACKING=.tar.bz2
+BUILDCHAIN=autotools
diff --git a/FEniCS/packages/git.package b/FEniCS/packages/git.package
new file mode 100644 (file)
index 0000000..bf0ae39
--- /dev/null
@@ -0,0 +1,6 @@
+VERSION=1.8.0.2
+NAME=git-${VERSION}
+SOURCE=http://git-core.googlecode.com/files/
+PACKING=.tar.gz
+BUILDCHAIN=autotools
+TARGETS=('' 'install prefix=${INSTALL_PATH}')
diff --git a/FEniCS/packages/glib2.package b/FEniCS/packages/glib2.package
new file mode 100644 (file)
index 0000000..e051b33
--- /dev/null
@@ -0,0 +1,4 @@
+NAME=glib-2.32.3
+SOURCE=http://ftp.gnome.org/pub/GNOME/sources/glib/2.32/
+PACKING=.tar.xz
+BUILDCHAIN=autotools
diff --git a/FEniCS/packages/glproto.package b/FEniCS/packages/glproto.package
new file mode 100644 (file)
index 0000000..e45669c
--- /dev/null
@@ -0,0 +1,5 @@
+VERSION=1.4.17
+NAME=glproto-${VERSION}
+SOURCE=http://ftp.x.org/pub/individual/proto/
+PACKING=.tar.gz
+BUILDCHAIN=autotools
\ No newline at end of file
diff --git a/FEniCS/packages/gmp.package b/FEniCS/packages/gmp.package
new file mode 100644 (file)
index 0000000..56914a8
--- /dev/null
@@ -0,0 +1,9 @@
+NAME=gmp-5.0.5
+SOURCE=ftp://ftp.gnu.org/gnu/gmp/
+PACKING=.tar.bz2
+BUILDCHAIN=autotools
+CONFOPTS="--enable-cxx"
+
+package_specific_register () {
+    export GMP_DIR=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/gtest.package b/FEniCS/packages/gtest.package
new file mode 100644 (file)
index 0000000..b48c392
--- /dev/null
@@ -0,0 +1,20 @@
+NAME=gtest-1.6.0
+SOURCE=http://googletest.googlecode.com/files/
+PACKING=.zip
+BUILDCHAIN=custom
+
+package_specific_build () {
+    mkdir -p build
+    cd build
+    cmake -DBUILD_SHARED_LIBS:BOOL=ON ..
+    make
+}
+
+package_specific_install () {
+    cp -rf include/gtest ${INSTALL_PATH}/include/
+    cp -f build/libgtest*.* ${INSTALL_PATH}/lib/
+}
+
+package_specific_register () {
+    export GTEST_DIR=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/h5py.package b/FEniCS/packages/h5py.package
new file mode 100644 (file)
index 0000000..601826c
--- /dev/null
@@ -0,0 +1,13 @@
+VERSION=2.2.0
+NAME=h5py-${VERSION}
+SOURCE=http://h5py.googlecode.com/files/
+PACKING=.tar.gz
+BUILDCHAIN=custom
+
+package_specific_build () {
+    if [ ! -z "${HDF5_DIR}" ]; then
+       python setup.py build --hdf5=${HDF5_DIR} --mpi=yes
+    fi
+
+    python setup.py install --prefix=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/hdf5.package b/FEniCS/packages/hdf5.package
new file mode 100644 (file)
index 0000000..e72daa5
--- /dev/null
@@ -0,0 +1,21 @@
+VERSION=1.8.12
+NAME=hdf5-${VERSION}
+SOURCE=http://www.hdfgroup.org/ftp/HDF5/releases/${NAME}/src/
+PACKING=.tar.gz
+CHECKSUM=d804802feb99b87fc668a90e6fa34411
+BUILDCHAIN=autotools
+
+CONFOPTS="--with-pthread
+          --enable-unsupported
+          --enable-shared
+          --enable-production=yes
+          --enable-parallel=yes
+          --enable-largefile=yes
+          --with-default-api-version=v18"
+
+#          --disable-sharedlib-rpath
+
+package_specific_register () {
+    export HDF5_DIR=${INSTALL_PATH}
+}
+
diff --git a/FEniCS/packages/instant-snapshot.package b/FEniCS/packages/instant-snapshot.package
new file mode 100644 (file)
index 0000000..f0fa964
--- /dev/null
@@ -0,0 +1,4 @@
+VERSION=snapshot
+NAME=instant-${VERSION}
+SOURCE=http://fenicsproject.org/pub/software/instant/
+PACKING=.tar.gz
diff --git a/FEniCS/packages/instant-stable.package b/FEniCS/packages/instant-stable.package
new file mode 100644 (file)
index 0000000..5cd2c8b
--- /dev/null
@@ -0,0 +1,5 @@
+VERSION=1.3.0
+NAME=instant-${VERSION}
+SOURCE=https://bitbucket.org/fenics-project/instant/downloads/
+PACKING=.tar.gz
+CHECKSUM=5c25d2ce48ee761a7113f7a80b25327e
diff --git a/FEniCS/packages/instant.package b/FEniCS/packages/instant.package
new file mode 100644 (file)
index 0000000..4596048
--- /dev/null
@@ -0,0 +1,4 @@
+NAME=instant
+SOURCE=https://bitbucket.org/fenics-project/
+PACKING=git
+BUILDCHAIN=python
diff --git a/FEniCS/packages/ipython.package b/FEniCS/packages/ipython.package
new file mode 100644 (file)
index 0000000..b351ee6
--- /dev/null
@@ -0,0 +1,6 @@
+VERSION=0.11
+NAME=ipython-${VERSION}
+SOURCE=http://archive.ipython.org/release/${VERSION}/
+PACKING=.tar.gz
+BUILDCHAIN=python
+
diff --git a/FEniCS/packages/lapack.package b/FEniCS/packages/lapack.package
new file mode 100644 (file)
index 0000000..304740c
--- /dev/null
@@ -0,0 +1,23 @@
+VERSION=3.3.1
+NAME=lapack-${VERSION}
+SOURCE=http://www.netlib.org/lapack/
+PACKING=.tgz
+BUILDCHAIN=custom
+
+package_specific_build () {
+    cp make.inc.example make.inc
+    sed -i 's/gfortran/mpif90 -O3 -fPIC/g' make.inc
+    sed -i 's/lapack$(PLAT).a/liblapack.a/g' make.inc
+    sed -i 's/tmglib$(PLAT).a/libtmglib.a/g' make.inc
+    sed -i 's,../../blas$(PLAT).a,${INSTALL_PATH}/lib/libblas.a,g' make.inc
+    make lapack_install lib -j ${PROCS}
+}
+
+package_specific_install () {
+    cp *.a ${INSTALL_PATH}/lib/
+}
+
+package_specific_register () {
+    export LAPACK_DIR=${INSTALL_PATH}
+    export LAPACKANDBLAS_DIR=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/libadjoint.package b/FEniCS/packages/libadjoint.package
new file mode 100644 (file)
index 0000000..a16fa26
--- /dev/null
@@ -0,0 +1,8 @@
+NAME=libadjoint
+SOURCE=lp:
+PACKING=bzr
+BUILDCHAIN=custom
+
+package_specific_build () {
+    make install prefix=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/libdrm.package b/FEniCS/packages/libdrm.package
new file mode 100644 (file)
index 0000000..6db68b2
--- /dev/null
@@ -0,0 +1,5 @@
+VERSION=2.4.46
+NAME=libdrm-${VERSION}
+SOURCE=http://dri.freedesktop.org/libdrm/
+PACKING=.tar.gz
+BUILDCHAIN=autotools
\ No newline at end of file
diff --git a/FEniCS/packages/libffi.package b/FEniCS/packages/libffi.package
new file mode 100644 (file)
index 0000000..f8ed8cb
--- /dev/null
@@ -0,0 +1,4 @@
+NAME=libffi-3.0.11
+SOURCE=ftp://sourceware.org/pub/libffi/
+PACKING=.tar.gz
+BUILDCHAIN=autotools
diff --git a/FEniCS/packages/libxml2.package b/FEniCS/packages/libxml2.package
new file mode 100644 (file)
index 0000000..42c71ec
--- /dev/null
@@ -0,0 +1,11 @@
+VERSION=2.6.2
+NAME=libxml2-${VERSION}
+SOURCE=ftp://xmlsoft.org/libxml2/old/
+PACKING=.tar.gz
+BUILDCHAIN=custom
+
+package_specific_build () {
+    ./configure --prefix=${INSTALL_PATH}
+    make -j ${PROCS}
+    make install
+}
diff --git a/FEniCS/packages/madlib.package b/FEniCS/packages/madlib.package
new file mode 100644 (file)
index 0000000..ce9e5f9
--- /dev/null
@@ -0,0 +1,9 @@
+NAME=madlib-1.3.0
+SOURCE=http://sites.uclouvain.be/madlib/sources/
+PACKING=.tar.gz
+BUILDCHAIN=autotools
+CONFOPTS="--enable-ann --enable-gmsh --enable-petsc --enable-extendedAPI"
+
+package_specific_setup () {
+    patch -p1 --forward < ${ORIG_DIR}/FEniCS/patches/madlib.patch || true
+}
diff --git a/FEniCS/packages/matplotlib.package b/FEniCS/packages/matplotlib.package
new file mode 100644 (file)
index 0000000..35519cf
--- /dev/null
@@ -0,0 +1,4 @@
+NAME=matplotlib-1.0.1
+SOURCE=http://sourceforge.net/projects/matplotlib/files/matplotlib/$NAME/
+PACKING=.tar.gz
+BUILDCHAIN=python
diff --git a/FEniCS/packages/mesa.package b/FEniCS/packages/mesa.package
new file mode 100644 (file)
index 0000000..e36a0f9
--- /dev/null
@@ -0,0 +1,6 @@
+VERSION=9.2.1
+NAME=MesaLib-${VERSION}
+SOURCE=ftp://ftp.freedesktop.org/pub/mesa/${VERSION}/
+PACKING=.tar.gz
+BUILDCHAIN=autotools
+EXTRACTSTO=Mesa-${VERSION}
\ No newline at end of file
diff --git a/FEniCS/packages/mpfr.package b/FEniCS/packages/mpfr.package
new file mode 100644 (file)
index 0000000..6e20f8a
--- /dev/null
@@ -0,0 +1,15 @@
+VERSION=3.1.2
+NAME=mpfr-${VERSION}
+SOURCE=http://www.mpfr.org/mpfr-3.1.2/
+PACKING=.tar.bz2
+BUILDCHAIN=custom
+
+package_specific_build () {
+    ./configure --prefix=${INSTALL_PATH} --enable-shared=yes --with-gmp=${GMP_DIR}
+    make -j ${PROCS}
+    make install
+}
+
+package_specific_register () {
+    export MPFR_DIR=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/mpi4py.package b/FEniCS/packages/mpi4py.package
new file mode 100644 (file)
index 0000000..9d6c1fa
--- /dev/null
@@ -0,0 +1,5 @@
+VERSION=1.3.1
+NAME=mpi4py-${VERSION}
+SOURCE=https://mpi4py.googlecode.com/files/
+PACKING=.tar.gz
+BUILDCHAIN=python
diff --git a/FEniCS/packages/mtl.package b/FEniCS/packages/mtl.package
new file mode 100644 (file)
index 0000000..80414cf
--- /dev/null
@@ -0,0 +1,13 @@
+NAME=MTL-4.0.8447-Linux
+SOURCE=http://fenicsproject.org/pub/software/contrib/
+PACKING=.tar.bz2
+CHECKSUM=ff08fecd44e6e9bccc41bdd6f147952e
+BUILDCHAIN=custom
+
+package_specific_build () {
+    cp -r ${UNPACK_PATH}/${EXTRACTSTO}/usr/* ${INSTALL_PATH}
+}
+
+package_specific_register () {
+    export MTL4_DIR=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/numpy.package b/FEniCS/packages/numpy.package
new file mode 100644 (file)
index 0000000..04cf657
--- /dev/null
@@ -0,0 +1,33 @@
+NAME=numpy-1.6.2
+SOURCE=http://downloads.sourceforge.net/numpy/
+PACKING=.tar.gz
+BUILDCHAIN=python
+
+package_specific_setup () {
+    if [ ! -z "${ATLAS_LIB_DIR}" ]; then
+       echo "
+[DEFAULT]
+library_dirs = ${ATLAS_LIB_DIR}
+include_dirs = ${ATLAS_DIR}/include
+
+[blas_opt]
+libraries = f77blas, cblas, atlas
+
+[lapack_opt]
+libraries = lapack, f77blas, cblas, atlas
+" > site.cfg
+
+    elif [ ! -z "${LAPACKANDBLAS_DIR}" ]; then
+       echo "
+[atlas]
+library_dirs = ${LAPACKANDBLAS_DIR}
+atlas_libs = lapack, blas
+" > site.cfg
+    fi
+
+    python setup.py build --fcompiler=gnu95
+}
+
+package_specific_register () {
+    ln -sf ${INSTALL_PATH}/lib/python${PYTHONVER}/site-packages/numpy/core/include/numpy ${INSTALL_PATH}/include/python${PYTHONVER}
+}
diff --git a/FEniCS/packages/numpy_intel.package b/FEniCS/packages/numpy_intel.package
new file mode 100644 (file)
index 0000000..965daf7
--- /dev/null
@@ -0,0 +1,20 @@
+NAME=numpy-1.6.1
+SOURCE=http://downloads.sourceforge.net/numpy/
+PACKING=.tar.gz
+BUILDCHAIN=custom
+
+MKLLIB=/soft/intel/mkl/10.3.6.233/composer_xe_2011_sp1.6.233/mkl/lib/intel64
+MKLINCLUDE=/soft/intel/mkl/10.3.6.233/composer_xe_2011_sp1.6.233/mkl/include
+
+package_specific_build () {
+    echo "[mkl]" > site.cfg
+    echo "library_dirs = ${MKLLIB}" >> site.cfg
+    echo "include_dirs = ${MKLINCLUDE}" >> site.cfg
+    echo "mkl_libs = mkl_intel,mkl_intel_thread,mkl_core,mkl_rt" >> site.cfg
+    python setup.py config --compiler=intelem build_clib --compiler=intelem build_ext --compiler=intelem install --prefix=${INSTALL_PATH}
+}
+
+package_specific_register () {
+    ln -sf ${INSTALL_PATH}/lib/python${PYTHONVER}/site-packages/numpy/core/include/numpy ${INSTALL_PATH}/include/python${PYTHONVER}
+}
+
diff --git a/FEniCS/packages/openmpi.package b/FEniCS/packages/openmpi.package
new file mode 100644 (file)
index 0000000..829ee26
--- /dev/null
@@ -0,0 +1,12 @@
+NAME=openmpi-1.6.2
+SOURCE=http://www.open-mpi.org/software/ompi/v1.6/downloads/
+PACKING=.tar.bz2
+BUILDCHAIN=autotools
+
+CONFOPTS="--enable-mpi-thread-multiple
+          --enable-opal-multi-threads
+          --with-threads=posix
+          --disable-mpi-profile"
+
+# FIXME: This must be used on OS X:
+#CONFOPTS="${CONFOPTS} --disable-mpi-f90"
diff --git a/FEniCS/packages/parmetis.package b/FEniCS/packages/parmetis.package
new file mode 100644 (file)
index 0000000..498f141
--- /dev/null
@@ -0,0 +1,21 @@
+NAME=parmetis-4.0.2
+SOURCE=http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/
+PACKING=.tar.gz
+CHECKSUM=0912a953da5bb9b5e5e10542298ffdce
+BUILDCHAIN=custom
+
+package_specific_build() {
+    cp -rf ${UNPACK_PATH}/${EXTRACTSTO}/* .
+    cd metis
+    make config prefix=${INSTALL_PATH} shared=1
+    make -j ${PROCS}
+    make install
+    cd ..
+    make config prefix=${INSTALL_PATH} shared=1
+    make -j ${PROCS}
+    make install
+}
+
+package_specific_register () {
+    export PARMETIS_DIR=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/pastix.package b/FEniCS/packages/pastix.package
new file mode 100644 (file)
index 0000000..8596d27
--- /dev/null
@@ -0,0 +1,275 @@
+NAME=pastix_release_4030
+SOURCE=https://gforge.inria.fr/frs/download.php/32044/
+PACKING=.tar.bz2
+BUILDCHAIN=custom
+
+package_specific_build () {
+    if [ -z ${PASTIX_ARCH} ]; then
+       PASTIX_ARCH="i686_pc_linux"
+    fi
+    VERSIONBIT="_64bit"
+    VERSIONINT="_int64"
+    CCTYPES="-DFORCE_INT64 -DINTSSIZE64"
+
+    # FIXME: Use the following on 32-bit architectures:
+    #VERSIONBIT="_32bit"
+    #VERSIONINT="_int32"
+    #CCTYPES="-DFORCE_INT32 -DINTSSIZE32"
+
+    if [ "${ATLAS_LIB_DIR}" ]; then
+        BLAS_HOME="${ATLAS_LIB_DIR}"
+        BLASLIB="-L${ATLAS_LIB_DIR} -lcblas -lf77blas -latlas"
+    elif [ "${BLAS_DIR}" ]; then
+       BLAS_HOME="${BLAS_DIR}"
+        BLASLIB="-L${BLAS_DIR} -lblas"
+    else
+        BLAS_HOME="/path/to/blas"
+        BLASLIB="-lblas"
+    fi
+
+    # Create config file
+    cd src
+    cat > config.in << EOF
+HOSTARCH    = ${PASTIX_ARCH}
+VERSIONBIT  = ${VERSIONBIT}
+EXEEXT      =
+OBJEXT      = .o
+LIBEXT      = .a
+CCPROG      = gcc -Wall
+CFPROG      = gfortran
+CF90PROG    = gfortran -ffree-form
+MCFPROG     = mpif90
+CF90CCPOPT  = -ffree-form -x f95-cpp-input
+# Compilation options for optimization (make expor)
+CCFOPT      = -O3
+# Compilation options for debug (make | make debug)
+CCFDEB      = -g3
+
+LKFOPT      =
+MKPROG      = make
+MPCCPROG    = mpicc -Wall
+CPP         = cpp
+ARFLAGS     = ruv
+ARPROG      = ar
+EXTRALIB    = -lgfortran -lm -lrt
+
+VERSIONMPI  = _mpi
+VERSIONSMP  = _smp
+VERSIONSCH  = _static
+VERSIONINT  = _int
+VERSIONPRC  = _simple
+VERSIONFLT  = _real
+VERSIONORD  = _scotch
+
+###################################################################
+#                  SETTING INSTALL DIRECTORIES                    #
+###################################################################
+ROOT       = ${INSTALL_PATH}
+INCLUDEDIR = \${ROOT}/include
+LIBDIR     = \${ROOT}/lib
+BINDIR     = \${ROOT}/bin
+
+###################################################################
+#                  SHARED LIBRARY GENERATION                      #
+###################################################################
+SHARED=1
+SHARED_FLAGS =  -shared -Wl,-soname,__SO_NAME__
+CCFDEB       := \${CCFDEB} -fPIC
+CCFOPT       := \${CCFOPT} -fPIC
+CFPROG       := \${CFPROG} -fPIC
+
+###################################################################
+#                          INTEGER TYPE                           #
+###################################################################
+# Uncomment the following lines for integer type support (Only 1)
+
+#VERSIONINT  = _long
+#CCTYPES     = -DFORCE_LONG -DLONG
+#---------------------------
+#VERSIONINT  = _int32
+#CCTYPES     = -DFORCE_INT32 -DINTSIZE32
+#---------------------------
+#VERSIONINT  = _int64
+#CCTYPES     = -DFORCE_INT64 -DINTSSIZE64
+#---------------------------
+VERSIONINT  = ${VERSIONINT}
+CCTYPES     = ${CCTYPES}
+
+###################################################################
+#                           FLOAT TYPE                            #
+###################################################################
+CCTYPESFLT  =
+# Uncomment the following lines for double precision support
+VERSIONPRC  = _double
+CCTYPESFLT := \$(CCTYPESFLT) -DFORCE_DOUBLE -DPREC_DOUBLE
+
+# Uncomment the following lines for float=complex support
+#VERSIONFLT  = _complex
+#CCTYPESFLT := \$(CCTYPESFLT) -DFORCE_COMPLEX -DTYPE_COMPLEX
+
+
+###################################################################
+#                          MPI/THREADS                            #
+###################################################################
+
+# Uncomment the following lines for sequential (NOMPI) version
+#VERSIONMPI  = _nompi
+#CCTYPES    := \$(CCTYPES) -DFORCE_NOMPI
+#MPCCPROG    = \$(CCPROG)
+#MCFPROG     = \$(CFPROG)
+
+# Uncomment the following lines for non-threaded (NOSMP) version
+#VERSIONSMP  = _nosmp
+#CCTYPES    := \$(CCTYPES) -DFORCE_NOSMP
+
+# Uncomment the following line to enable a progression thread
+#CCPASTIX   := \$(CCPASTIX) -DTHREAD_COMM
+
+# Uncomment the following line if your MPI doesn't support MPI_THREAD_MULTIPLE level
+#CCPASTIX   := \$(CCPASTIX) -DPASTIX_FUNNELED
+
+# Uncomment the following line if your MPI doesn't support MPI_Datatype correctly
+#CCPASTIX   := \$(CCPASTIX) -DNO_MPI_TYPE
+
+# Uncomment the following line if you want to use semaphore barrier
+# instead of MPI barrier (with IPARM_AUTOSPLIT_COMM)
+#CCPASTIX    := \$(CCPASTIX) -DWITH_SEM_BARRIER
+
+# Uncomment the following lines to enable StarPU.
+#CCPASTIX   := \${CCPASTIX} \`pkg-config libstarpu --cflags\` -DWITH_STARPU
+#EXTRALIB   := \$(EXTRALIB) \`pkg-config libstarpu --libs\`
+
+# Uncomment the following line to enable StarPU profiling
+# ( IPARM_VERBOSE > API_VERBOSE_NO ).
+#CCPASTIX   := \${CCPASTIX} -DSTARPU_PROFILING
+
+# Uncomment the following line to disable CUDA (StarPU)
+#CCPASTIX   := \${CCPASTIX} -DFORCE_NO_CUDA
+
+###################################################################
+#                          Options                                #
+###################################################################
+
+# Show memory usage statistics
+#CCPASTIX   := \$(CCPASTIX) -DMEMORY_USAGE
+
+# Show memory usage statistics in solver
+#CCPASTIX   := \$(CCPASTIX) -DSTATS_SOPALIN
+
+# Uncomment following line for dynamic thread scheduling support
+#CCPASTIX   := \$(CCPASTIX) -DPASTIX_DYNSCHED
+
+# Uncomment the following lines for Out-of-core
+#CCPASTIX   := \$(CCPASTIX) -DOOC -DOOC_NOCOEFINIT -DOOC_DETECT_DEADLOCKS
+
+###################################################################
+#                      GRAPH PARTITIONING                         #
+###################################################################
+
+# Uncomment the following lines for using metis ordering
+#VERSIONORD  = _metis
+#METIS_HOME  = \${HOME}/metis-4.0
+#CCPASTIX   := \$(CCPASTIX) -DMETIS -I\$(METIS_HOME)/Lib
+#EXTRALIB   := \$(EXTRALIB) -L\$(METIS_HOME) -lmetis
+
+# Scotch always needed to compile
+SCOTCH_HOME ?= ${SCOTCH_DIR}
+SCOTCH_INC ?= \$(SCOTCH_HOME)/include
+SCOTCH_LIB ?= \$(SCOTCH_HOME)/lib
+# Uncomment on of this blocks
+#scotch
+#CCPASTIX   := \$(CCPASTIX) -I\$(SCOTCH_INC) -DWITH_SCOTCH
+#EXTRALIB   := \$(EXTRALIB) -L\$(SCOTCH_LIB) -lscotch -lscotcherrexit
+#ptscotch
+CCPASTIX   := \$(CCPASTIX) -I\$(SCOTCH_INC) -DDISTRIBUTED -DWITH_SCOTCH
+EXTRALIB   := \$(EXTRALIB) -L\$(SCOTCH_LIB) -lptscotch -lscotcherrexit
+
+###################################################################
+#                Portable Hardware Locality                       #
+###################################################################
+# If HwLoc library is available, Uncomment the following lines to bind correctly threads on cpus
+#HWLOC_HOME ?= /opt/hwloc/
+#HWLOC_INC  ?= \$(HWLOC_HOME)/include
+#HWLOC_LIB  ?= \$(HWLOC_HOME)/lib
+#CCPASTIX   := \$(CCPASTIX) -I\$(HWLOC_INC) -DWITH_HWLOC
+#EXTRALIB   := \$(EXTRALIB) -L\$(HWLOC_LIB) -lhwloc
+
+###################################################################
+#                             MARCEL                              #
+###################################################################
+
+# Uncomment following lines for marcel thread support
+#VERSIONSMP := \$(VERSIONSMP)_marcel
+#CCPASTIX   := \$(CCPASTIX) \`pm2-config --cflags\` -I\${PM2_ROOT}/marcel/include/pthread
+#EXTRALIB   := \$(EXTRALIB) \`pm2-config --libs\`
+# ---- Thread Posix ------
+EXTRALIB   := \$(EXTRALIB) -lpthread
+
+# Uncomment following line for bubblesched framework support (need marcel support)
+#VERSIONSCH  = _dyn
+#CCPASTIX   := \$(CCPASTIX) -DPASTIX_BUBBLESCHED
+
+###################################################################
+#                              BLAS                               #
+###################################################################
+
+# Choose Blas library (Only 1)
+# Do not forget to set BLAS_HOME if it is not in your environnement
+BLAS_HOME = ${BLAS_HOME}
+BLASLIB   = ${BLASLIB}
+#----  Blas    ----
+#BLASLIB  = -lblas
+#---- Gotoblas ----
+#BLASLIB  = -L\${BLAS_HOME} -lgoto
+#----  MKL     ----
+#Uncomment the correct line
+#BLASLIB  = -L\$(BLAS_HOME) -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
+#BLASLIB  = -L\$(BLAS_HOME) -lmkl_intel -lmkl_sequential -lmkl_core
+#----  Acml    ----
+#BLASLIB  = -L\$(BLAS_HOME) -lacml
+
+###################################################################
+#                         PYTHON WRAPPER                          #
+###################################################################
+#MPI4PY_DIR    = /path/to//mpi4py
+#MPI4PY_INC    = \$(MPI4PY_DIR)/src/include/
+#MPI4PY_LIBDIR = \$(MPI4PY_DIR)/build/lib.linux-x86_64-2.7/
+#PYTHON_INC    = /usr/include/python2.7/
+#CCTYPES      := \$(CCTYPES) -fPIC
+
+###################################################################
+#                          DO NOT TOUCH                           #
+###################################################################
+
+FOPT      := \$(CCFOPT)
+FDEB      := \$(CCFDEB)
+CCHEAD    := \$(CCPROG) \$(CCTYPES) \$(CCFOPT)
+CCFOPT    := \$(CCFOPT) \$(CCTYPES) \$(CCPASTIX)
+CCFDEB    := \$(CCFDEB) \$(CCTYPES) \$(CCPASTIX)
+
+
+###################################################################
+#                        MURGE COMPATIBILITY                      #
+###################################################################
+# Uncomment if you need MURGE interface to be thread safe
+# CCPASTIX   := \$(CCPASTIX) -DMURGE_THREADSAFE
+
+MAKE     = \$(MKPROG)
+CC       = \$(MPCCPROG)
+CFLAGS   = \$(CCFOPT) \$(CCTYPESFLT)
+FC       = \$(MCFPROG)
+FFLAGS   = \$(CCFOPT)
+LDFLAGS  = \$(EXTRALIB) \$(BLASLIB)
+EOF
+
+    # Build and install
+    make -j ${PROCS}
+    make install
+
+    # Workaround for bug in 4030 release
+    sed -i 's/u_int64_t/uint64_t/g' ${INSTALL_PATH}/include/pastix.h
+}
+
+package_specific_register () {
+    export PASTIX_DIR=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/pcre.package b/FEniCS/packages/pcre.package
new file mode 100644 (file)
index 0000000..ad7dac4
--- /dev/null
@@ -0,0 +1,6 @@
+NAME=pcre-8.21
+SOURCE=http://downloads.sourceforge.net/pcre/
+PACKING=.tar.gz
+CHECKSUM=b8c9469717262a1e486cffc288b28283
+BUILDCHAIN=autotools
+
diff --git a/FEniCS/packages/petsc.package b/FEniCS/packages/petsc.package
new file mode 100644 (file)
index 0000000..b44c4c9
--- /dev/null
@@ -0,0 +1,37 @@
+NAME=petsc-3.4.2
+SOURCE=http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/
+PACKING=.tar.gz
+CHECKSUM=449e27f3c9a37d0bd9d7941cc79a09a9
+BUILDCHAIN=custom
+
+CONFOPTS="COPTFLAGS=-O2
+          --with-debugging=0 --with-shared-libraries=1
+          --with-clanguage=cxx --with-c-support=1"
+
+for external_pkg in umfpack hypre mumps scalapack blacs ptscotch scotch metis parmetis ${PETSC_EXTRA_PACKAGES}; do
+    CONFOPTS="${CONFOPTS} --download-${external_pkg}=1"
+done
+
+if [ "${TRILINOS_DIR}" ]; then
+    CONFOPTS="${CONFOPTS} --with-ml=1
+              --with-ml-lib=${TRILINOS_DIR}/lib/libml.so
+              --with-ml-include=${TRILINOS_DIR}/include"
+fi
+
+if [ "${CUDA_DIR}" ] && [ "${CUSP_DIR}" ]; then
+    CONFOPTS="${CONFOPTS} --with-cuda=1 --with-cuda-dir=${CUDA_DIR}
+    --with-cusp=1 --with-cusp-dir=${CUSP_DIR}
+    --with-thrust=1 --with-thrust-dir=${CUDA_DIR}/include"
+fi
+
+package_specific_build () {
+    cp -rf ${UNPACK_PATH}/${EXTRACTSTO}/* .
+    ./configure --prefix=${INSTALL_PATH} ${CONFOPTS}
+    make PETSC_DIR=${PWD} PETSC_ARCH=${PETSC_ARCH} all
+    make PETSC_DIR=${PWD} PETSC_ARCH=${PETSC_ARCH} install
+}
+
+package_specific_register () {
+    export PETSC_DIR=${INSTALL_PATH}
+    unset PETSC_ARCH
+}
diff --git a/FEniCS/packages/pkg-config.package b/FEniCS/packages/pkg-config.package
new file mode 100644 (file)
index 0000000..b61b6b0
--- /dev/null
@@ -0,0 +1,4 @@
+NAME=pkg-config-0.28
+SOURCE=http://pkgconfig.freedesktop.org/releases/
+PACKING=.tar.gz
+BUILDCHAIN=autotools
diff --git a/FEniCS/packages/ply.package b/FEniCS/packages/ply.package
new file mode 100644 (file)
index 0000000..f19f156
--- /dev/null
@@ -0,0 +1,5 @@
+VERSION=3.4
+NAME=ply-${VERSION}
+SOURCE=http://www.dabeaz.com/ply/
+PACKING=.tar.gz
+BUILDCHAIN=python
diff --git a/FEniCS/packages/python.package b/FEniCS/packages/python.package
new file mode 100644 (file)
index 0000000..fb4f254
--- /dev/null
@@ -0,0 +1,18 @@
+VERSION=2.7.2
+NAME=Python-${VERSION}
+SOURCE=http://www.python.org/ftp/python/${VERSION}/
+PACKING=.tar.bz2
+BUILDCHAIN=autotools
+CONFOPTS="--enable-shared"
+
+package_specific_setup() {
+    patch -p1 --forward < ${ORIG_DIR}/FEniCS/patches/python.patch || true
+}
+
+package_specific_register() {
+    export PYTHON_DIR=${INSTALL_PATH}
+    export PYTHON_EXECUTABLE=${PYTHON_DIR}/bin/python
+    export PYTHON_INCLUDE_DIR=${PYTHON_DIR}/include/python2.7
+    # FIXME: should be .dylib on OS X
+    export PYTHON_LIBRARY=${PYTHON_DIR}/lib/libpython2.7.so
+}
diff --git a/FEniCS/packages/scientificpython.package b/FEniCS/packages/scientificpython.package
new file mode 100644 (file)
index 0000000..f9eb004
--- /dev/null
@@ -0,0 +1,9 @@
+NAME=ScientificPython-2.8
+SOURCE=http://sourcesup.cru.fr/frs/download.php/2309/
+PACKING=.tar.gz
+CHECKSUM=82d8592635d6ae8608b3073dacf9e694
+BUILDCHAIN=python
+
+package_specific_setup () {
+    patch -p --forward < ${ORIG_DIR}/FEniCS/patches/scientificpython.patch || true
+}
diff --git a/FEniCS/packages/scipy.package b/FEniCS/packages/scipy.package
new file mode 100644 (file)
index 0000000..f837bd9
--- /dev/null
@@ -0,0 +1,34 @@
+NAME=scipy-0.12.0
+SOURCE=http://downloads.sourceforge.net/scipy/
+PACKING=.tar.gz
+BUILDCHAIN=python
+
+package_specific_setup () {
+    if [ ! -z "${ATLAS_LIB_DIR}" ]; then
+       echo "
+[blas_opt]
+library_dirs = ${ATLAS_LIB_DIR}
+include_dirs = ${ATLAS_DIR}/include
+libraries = f77blas, cblas, atlas
+
+[lapack_opt]
+library_dirs = ${ATLAS_LIB_DIR}
+include_dirs = ${ATLAS_DIR}/include
+libraries = lapack, f77blas, cblas, atlas
+" >> site.cfg
+    fi
+
+    if [ ! -z "${UMFPACK_DIR}" ]; then
+       echo "
+[amd]
+library_dirs = ${UMFPACK_DIR}/lib
+include_dirs = ${UMFPACK_DIR}/include/suitesparse
+amd_libs = amd
+
+[umfpack]
+library_dirs = ${UMFPACK_DIR}/lib
+include_dirs = ${UMFPACK_DIR}/include/suitesparse
+umfpack_libs = umfpack
+" >> site.cfg
+    fi
+}
diff --git a/FEniCS/packages/scons.package b/FEniCS/packages/scons.package
new file mode 100644 (file)
index 0000000..2e2a2eb
--- /dev/null
@@ -0,0 +1,6 @@
+NAME=scons-2.0.1
+SOURCE=http://downloads.sourceforge.net/scons/
+PACKING=.tar.gz
+CHECKSUM=beca648b894cdbf85383fffc79516d18
+BUILDCHAIN=python
+
diff --git a/FEniCS/packages/scotch.package b/FEniCS/packages/scotch.package
new file mode 100644 (file)
index 0000000..0f0dbeb
--- /dev/null
@@ -0,0 +1,37 @@
+NAME=scotch_6.0.0_esmumps
+SOURCE=http://fenicsproject.org/pub/software/contrib/
+PACKING=.tar.gz
+CHECKSUM=c50d6187462ba801f9a82133ee666e8e
+BUILDCHAIN=autotools
+EXTRACTSTO=scotch_6.0.0_esmumps/src
+PROCS=1
+TARGETS=('' 'ptscotch' 'ptesmumps')
+
+package_specific_setup () {
+    cd ${UNPACK_PATH}/${EXTRACTSTO}
+    if [ ${SCOTCH_ARCH} == "pc_linux2" ]
+    then
+        SCOTCH_ARCH=$(echo $ARCH|sed 's/_/-/g')_${SCOTCH_ARCH}
+    fi
+    perl -pi -e 's/^CFLAGS\t\t=/CFLAGS  = -fPIC/g' Make.inc/Makefile.inc.${SCOTCH_ARCH}
+    perl -pi -e 's/^CCS.*= gcc/CCS  = mpicc/g' Make.inc/Makefile.inc.${SCOTCH_ARCH}
+    perl -pi -e 's/^CCD.*= gcc/CCD  = mpicc/g' Make.inc/Makefile.inc.${SCOTCH_ARCH}
+    if [ ${SCOTCH_ARCH} == "i686_mac_darwin8" ]
+    then
+       # Darwin does not have a pthread_barrier_t implementation
+       perl -pi -e 's/-DSCOTCH_PTHREAD/-DCOMMON_PTHREAD_BARRIER/g' Make.inc/Makefile.inc.${SCOTCH_ARCH}
+    else
+       perl -pi -e 's/-DSCOTCH_PTHREAD//g' Make.inc/Makefile.inc.${SCOTCH_ARCH}
+    fi
+    ln -sf Make.inc/Makefile.inc.${SCOTCH_ARCH} Makefile.inc
+}
+
+package_specific_install () {
+    make ptesmumps install -j ${PROCS} prefix=${INSTALL_PATH}
+    cp -f ../lib/*scotc*[^m].a ${INSTALL_PATH}/lib
+    cp -f ../lib/*esmumps.a ${INSTALL_PATH}/lib
+}
+
+package_specific_register () {
+    export SCOTCH_DIR=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/setuptools.package b/FEniCS/packages/setuptools.package
new file mode 100644 (file)
index 0000000..9e3df47
--- /dev/null
@@ -0,0 +1,5 @@
+VERSION=1.4.1
+NAME=setuptools-${VERSION}
+SOURCE=https://pypi.python.org/packages/source/s/setuptools/
+PACKING=.tar.gz
+BUILDCHAIN=python
diff --git a/FEniCS/packages/slepc.package b/FEniCS/packages/slepc.package
new file mode 100644 (file)
index 0000000..1bb716a
--- /dev/null
@@ -0,0 +1,21 @@
+NAME=slepc-3.4.2
+SOURCE=http://www.fenicsproject.org/pub/software/contrib/
+PACKING=.tar.gz
+CHECKSUM=78ff6a709f50ccd765fa61589400d5f3
+BUILDCHAIN=custom
+
+package_specific_setup () {
+    cp -rf ${UNPACK_PATH}/${EXTRACTSTO}/* .
+    patch -p1 --forward < ${ORIG_DIR}/FEniCS/patches/slepc.patch || true
+    export SLEPC_DIR=${PWD}
+}
+
+package_specific_build () {
+    SLEPC_DIR=${PWD} ./configure --prefix=${INSTALL_PATH}
+    make PETSC_ARCH=arch-installed-petsc all
+    make PETSC_ARCH=arch-installed-petsc install
+}
+
+package_specific_register () {
+    export SLEPC_DIR=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/sqlite.package b/FEniCS/packages/sqlite.package
new file mode 100644 (file)
index 0000000..7e321ab
--- /dev/null
@@ -0,0 +1,11 @@
+VERSION=3070800
+NAME=sqlite-autoconf-${VERSION}
+SOURCE=http://www.sqlite.org/
+PACKING=.tar.gz
+BUILDCHAIN=custom
+
+package_specific_build () {
+    ./configure --prefix=${INSTALL_PATH}
+    make -j ${PROCS}
+    make install
+}
diff --git a/FEniCS/packages/suitesparse.package b/FEniCS/packages/suitesparse.package
new file mode 100644 (file)
index 0000000..bbf3315
--- /dev/null
@@ -0,0 +1,54 @@
+NAME=SuiteSparse-4.0.2
+SOURCE=http://www.cise.ufl.edu/research/sparse/SuiteSparse/
+PACKING=.tar.gz
+BUILDCHAIN=custom
+EXTRACTSTO=SuiteSparse
+
+package_specific_build () {
+    mkdir -p ${INSTALL_PATH}/include/suitesparse
+    cat > SuiteSparse_config/SuiteSparse_config.mk << EOF
+#CF = \$(CFLAGS) \$(CPPFLAGS) \$(TARGET_ARCH) -O3 -fexceptions -fPIC
+CF = \$(CFLAGS) \$(CPPFLAGS) \$(TARGET_ARCH) -O3 -fexceptions -fPIC -DNTIMER
+RANLIB = ranlib
+ARCHIVE = \$(AR) \$(ARFLAGS)
+CP = cp -f
+MV = mv -f
+F77 = gfortran
+F77FLAGS = \$(FFLAGS) -O
+F77LIB =
+#LIB = -lm -lrt
+LIB = -lm
+INSTALL_LIB = ${INSTALL_PATH}/lib
+INSTALL_INCLUDE = ${INSTALL_PATH}/include/suitesparse
+XERBLA =
+GPU_BLAS_PATH =
+GPU_CONFIG =
+UMFPACK_CONFIG =
+CHOLMOD_CONFIG = \$(GPU_CONFIG) -DNPARTITION
+SPQR_CONFIG =
+TBB =
+CLEAN = *.o *.obj *.ln *.bb *.bbg *.da *.tcov *.gcov gmon.out *.bak *.d *.gcda *.gcno
+EOF
+
+    if [ ! -z "${ATLAS_LIB_DIR}" ]; then
+        cat >> SuiteSparse_config/SuiteSparse_config.mk << EOF
+BLAS = -L${ATLAS_LIB_DIR} -lcblas -lf77blas -latlas
+LAPACK = -L${ATLAS_LIB_DIR} -llapack
+EOF
+    else
+        cat >> SuiteSparse_config/SuiteSparse_config.mk << EOF
+BLAS = -lblas -lgfortran
+LAPACK = -llapack
+EOF
+    fi
+
+    make
+}
+
+package_specific_install () {
+    make install
+}
+
+package_specific_register () {
+    export UMFPACK_DIR=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/suitesparsewithmetis.package b/FEniCS/packages/suitesparsewithmetis.package
new file mode 100644 (file)
index 0000000..48aa4b1
--- /dev/null
@@ -0,0 +1,31 @@
+NAME=SuiteSparse
+SOURCE=http://www.cise.ufl.edu/research/sparse/SuiteSparse/current/
+PACKING=.tar.gz
+BUILDCHAIN=custom
+
+package_specific_build () {
+    perl -pi -e 's/^CFLAGS = -O/CFLAGS = -fPIC -O/g' UFconfig/UFconfig.mk
+    perl -pi -e 's/-lgfortran.*n//g' UFconfig/UFconfig.mk
+    perl -pi -e 's/-lg2c//g' UFconfig/UFconfig.mk
+    if [ ! -e metis-4.0.3.tar.gz ]
+    then
+       wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-4.0.3.tar.gz
+    fi
+    tar -xzf metis-4.0.3.tar.gz
+    ln -sf metis-4.0.3 metis-4.0
+    cd metis-4.0
+    perl -pi -e 's/COPTIONS =/COPTIONS = -fPIC/g' Makefile.in
+    make
+    cd ..
+    make
+}
+
+package_specific_install () {
+    mkdir -p ${INSTALL_PATH}/include/suitesparse
+    ln -sf `find ${PWD} -name '*.h' | grep -vi demo | xargs` ${INSTALL_PATH}/include/suitesparse
+    ln -sf `find ${PWD} -name 'lib*.a' | xargs` ${INSTALL_PATH}/lib
+}
+
+package_specific_register () {
+    export UMFPACK_DIR=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/suitesparsewithmetis_OpenMPI.package b/FEniCS/packages/suitesparsewithmetis_OpenMPI.package
new file mode 100644 (file)
index 0000000..b60dbaa
--- /dev/null
@@ -0,0 +1,45 @@
+VERSION=3.4.0
+NAME=SuiteSparse-${VERSION}
+SOURCE=http://www.cise.ufl.edu/research/sparse/SuiteSparse/
+PACKING=.tar.gz
+BUILDCHAIN=custom
+EXTRACTSTO=SuiteSparse
+
+package_specific_build () {
+    sed -i 's/CFLAGS = -O/CFLAGS = -fPIC -O/g' UFconfig/UFconfig.mk
+    sed -i 's/CC = cc/CC = mpicc/g' UFconfig/UFconfig.mk
+    sed -i 's/CPLUSPLUS = g++/CPLUSPLUS = mpiCC/g' UFconfig/UFconfig.mk
+    sed -i 's/F77 = f77/F77 = mpif90/g' UFconfig/UFconfig.mk
+    sed -i 's/-lg2c//g' UFconfig/UFconfig.mk
+    sed -i 's,-lblas,-L${INSTALL_PATH}/lib/ -lblas,g' UFconfig/UFconfig.mk
+    sed -i 's,begin,,g' UFconfig/UFconfig.mk
+    sed -i 's,-llapack,-L${INSTALL_PATH}/lib/ -llapack,g' UFconfig/UFconfig.mk
+    sed -i 's,XERBLA =,# XERBLA =,g' UFconfig/UFconfig.mk
+    sed -i 's,# # XERBLA = ../../UFconfig/xerbla/libxerbla.a, XERBLA = ../../UFconfig/xerbla/libxerbla.a,' UFconfig/UFconfig.mk
+    sed -i 's,-fexceptions, -fexceptions,g' UFconfig/UFconfig.mk
+
+    if [ ! -e metis-4.0.3.tar.gz ]
+    then
+       wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-4.0.3.tar.gz
+    fi
+    tar -xzf metis-4.0.3.tar.gz
+    ln -sf metis-4.0.3 metis-4.0
+    cd metis-4.0
+    perl -pi -e 's/COPTIONS =/COPTIONS = -fPIC/g' Makefile
+    make -j
+    cd ..
+    cd UFconfig/xerbla/
+    make all
+    cd ../../
+    make 
+}
+
+package_specific_install () {
+    mkdir -p ${INSTALL_PATH}/include/suitesparse
+    ln -sf `find ${PWD} -name '*.h' | grep -vi demo | xargs` ${INSTALL_PATH}/include/suitesparse
+    ln -sf `find ${PWD} -name 'lib*.a' | xargs` ${INSTALL_PATH}/lib
+}
+
+package_specific_register () {
+    export UMFPACK_DIR=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/swig.package b/FEniCS/packages/swig.package
new file mode 100644 (file)
index 0000000..395e48a
--- /dev/null
@@ -0,0 +1,26 @@
+NAME=swig-2.0.3
+SOURCE=http://downloads.sourceforge.net/swig/
+PACKING=.tar.gz
+CHECKSUM=e548ea3882b994c4907d6be86bef90f2
+BUILDCHAIN=autotools
+
+package_specific_setup () {
+    if [ ! -z ${SWIG_CC} ]; then
+       export TMP_SWIG_CC=${CC}
+       export CC=${SWIG_CC}
+    fi
+    if [ ! -z ${SWIG_CXX} ]; then
+       export TMP_SWIG_CXX=${CXX}
+       export CXX=${SWIG_CXX}
+    fi
+}
+
+package_specific_register () {
+    if [ ! -z ${TMP_SWIG_CC} ]; then
+       export CC=${TMP_SWIG_CC}
+    fi
+    if [ ! -z ${TMP_SWIG_CXX} ]; then
+       export CXX=${TMP_SWIG_CXX}
+    fi
+    export SWIG_EXECUTABLE=${INSTALL_PATH}/bin/swig
+}
diff --git a/FEniCS/packages/swiginac.package b/FEniCS/packages/swiginac.package
new file mode 100644 (file)
index 0000000..542eb06
--- /dev/null
@@ -0,0 +1,8 @@
+NAME=swiginac-1.5.1.1
+SOURCE=http://download.berlios.de/swiginac/
+PACKING=.tgz
+BUILDCHAIN=python
+
+package_specific_setup () {
+python setup.py build
+}
diff --git a/FEniCS/packages/syfi-snapshot.package b/FEniCS/packages/syfi-snapshot.package
new file mode 100644 (file)
index 0000000..cdbb81e
--- /dev/null
@@ -0,0 +1,4 @@
+VERSION=snapshot
+NAME=syfi-${VERSION}
+SOURCE=http://fenicsproject.org/pub/software/syfi/
+PACKING=.tar.gz
diff --git a/FEniCS/packages/syfi-stable.package b/FEniCS/packages/syfi-stable.package
new file mode 100644 (file)
index 0000000..7ad8409
--- /dev/null
@@ -0,0 +1,4 @@
+VERSION=1.0.0
+NAME=syfi-${VERSION}
+SOURCE=http://launchpad.net/fenics-syfi/1.0.x/${VERSION}/+download/
+PACKING=.tar.gz
diff --git a/FEniCS/packages/syfi.package b/FEniCS/packages/syfi.package
new file mode 100644 (file)
index 0000000..2d683eb
--- /dev/null
@@ -0,0 +1,8 @@
+NAME=fenics-syfi
+SOURCE=lp:
+PACKING=bzr
+BUILDCHAIN=cmake
+
+if [ -x "${SWIG_EXECUTABLE}" ]; then
+    CONFOPTS="-D SWIG_EXECUTABLE:FILEPATH=${SWIG_EXECUTABLE}"
+fi
diff --git a/FEniCS/packages/sympy.package b/FEniCS/packages/sympy.package
new file mode 100644 (file)
index 0000000..6f69395
--- /dev/null
@@ -0,0 +1,4 @@
+NAME=sympy-0.7.1
+SOURCE=http://pypi.python.org/packages/source/s/sympy/
+PACKING=.tar.gz
+BUILDCHAIN=python
diff --git a/FEniCS/packages/template.package b/FEniCS/packages/template.package
new file mode 100644 (file)
index 0000000..61a4ae9
--- /dev/null
@@ -0,0 +1,28 @@
+NAME=foo-x.y.z
+SOURCE=http://foo.org/downloads/foo/
+PACKING=[.tar.gz|.tar.bz2|.tbz2|.tgz|.zip|hg|svn|git|bzr]
+BUILDCHAIN=[autotools|python|scons|cmake|custom]
+EXTRACTSTO=barnotfoo
+CONFOPTS=""
+SCONSOPTS=""
+TARGETS=('' install)
+
+package_specific_setup () {
+    # Any non-standard configuration and pre-build instructions go
+    # here.
+}
+
+package_specific_build () {
+    # Any custom build instructions go here. This function is only
+    # used if the 'custom' buildchain is defined.
+}
+
+package_specific_install () {
+    # Any non-standard installation and post-build instructions go
+    # here.
+}
+
+package_specific_register () {
+    # Any environment variables defined by this package that are
+    # required by other packages go here.
+}
diff --git a/FEniCS/packages/trilinos.package b/FEniCS/packages/trilinos.package
new file mode 100644 (file)
index 0000000..43bab49
--- /dev/null
@@ -0,0 +1,80 @@
+VERSION=11.8.1
+NAME=trilinos-${VERSION}-Source
+SOURCE=http://trilinos.sandia.gov/download/files/
+PACKING=.tar.gz
+CHECKSUM=3c9465b6d63d824e9dc0365ca73c3370
+BUILDCHAIN=custom
+
+package_specific_setup () {
+echo "Build ${NAME}"
+
+CONFOPTS="-D Trilinos_ENABLE_OpenMP:BOOL=OFF \
+          -D TPL_ENABLE_TBB:BOOL=OFF \
+          -D Trilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON \
+          -D Trilinos_ENABLE_Epetra:BOOL=ON \
+          -D Trilinos_ENABLE_ML:BOOL=ON \
+          -D Trilinos_ENABLE_PyTrilinos:BOOL=ON \
+          -D Trilinos_ENABLE_TESTS:BOOL=OFF \
+          -D Trilinos_ENABLE_EXAMPLES:BOOL=OFF \ 
+          -D Trilinos_ENABLE_Didasko:BOOL=ON \
+          -D Trilinos_ENABLE_Sacado:BOOL=ON \
+          -D Trilinos_ENABLE_Stratimikos:BOOL=ON \
+          -D CMAKE_BUILD_TYPE:STRING=RELEASE \
+          -D CMAKE_VERBOSE_MAKEFILE:BOOL=FALSE \
+          -D Trilinos_VERBOSE_CONFIGURE:BOOL=FALSE \
+          -D TPL_ENABLE_MPI:BOOL=ON \
+          -D TPL_ENABLE_UMFPACK:BOOL=ON \
+          -D CMAKE_INSTALL_PREFIX:PATH=${INSTALL_PATH} \
+          -D BUILD_SHARED_LIBS:BOOL=ON"
+
+GFORTRAN_EXECUTABLE=$(which gfortran)
+if [ ! -z "${GFORTRAN_EXECUTABLE}" ]; then
+    CONFOPTS="${CONFOPTS}
+              -D Trilinos_ENABLE_Fortran:BOOL=ON
+              -D CMAKE_Fortran_COMPILER:FILEPATH=mpif90"
+else
+    CONFOPTS="${CONFOPTS} -D Trilinos_ENABLE_Fortran:BOOL=OFF"
+fi
+
+if [ ! -z "${ATLAS_LIB_DIR}" ]; then
+    CONFOPTS="${CONFOPTS}
+              -D BLAS_LIBRARY_NAMES=\"cblas;f77blas;atlas\"
+              -D BLAS_LIBRARY_DIRS=${ATLAS_LIB_DIR}
+              -D LAPACK_LIBRARY_DIRS=${ATLAS_LIB_DIR}"
+fi
+
+if [ ! -z "${UMFPACK_DIR}" ]; then
+    CONFOPTS="${CONFOPTS}
+              -D UMFPACK_INCLUDE_DIRS=${UMFPACK_DIR}/include/suitesparse
+              -D UMFPACK_LIBRARY_DIRS=${UMFPACK_DIR}/lib
+              -D UMFPACK_LIBRARY_NAMES=\"umfpack;cholmod;camd;ccolamd;colamd;amd;suitesparseconfig\""
+elif [ ! -z "${UMFPACK_INCLUDE_DIR}" ]; then
+    CONFOPTS="${CONFOPTS} -D UMFPACK_INCLUDE_DIRS=${UMFPACK_INCLUDE_DIR}"
+fi
+
+if [ -x "${SWIG_EXECUTABLE}" ]; then
+    CONFOPTS="${CONFOPTS} -D SWIG_EXECUTABLE:FILEPATH=${SWIG_EXECUTABLE}"
+fi
+
+if [ ! -z "${PYTHON_INCLUDE_DIR}" ]; then
+    CONFOPTS="${CONFOPTS} -D PYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_DIR}"
+fi
+
+if [ ! -z "${PYTHON_LIBRARY}" ]; then
+    CONFOPTS="${CONFOPTS} -D PYTHON_LIBRARY:PATH=${PYTHON_LIBRARY}"
+fi
+
+
+TRILINOS_SOURCE="${UNPACK_PATH}/${EXTRACTSTO}"
+
+# configure
+cmake ${CONFOPTS} ${TRILINOS_SOURCE}
+
+# make
+make -j${PROCS}
+make install
+}
+
+package_specific_register () {
+    export TRILINOS_DIR=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/trilinos_intel.package b/FEniCS/packages/trilinos_intel.package
new file mode 100644 (file)
index 0000000..22aae22
--- /dev/null
@@ -0,0 +1,36 @@
+NAME=trilinos-10.10.2-Source
+SOURCE=http://trilinos.sandia.gov/download/files/
+PACKING=.tar.gz
+BUILDCHAIN=cmake
+
+MKLINCLUDE="/soft/intel/mkl/10.3.6.233/composer_xe_2011_sp1.6.233/mkl/include"
+COMPILERFLAGS="'-fPIC -DMPICH_IGNORE_CXX_SEEK -m64 -DMKL_ILP64 -lpthread'"
+MKLLIBS="\"-lmkl_rt\""
+
+CONFOPTS="-D CMAKE_CXX_COMPILER:FILEPATH='mpicxx'
+          -D CMAKE_C_COMPILER:FILEPATH='mpicc'
+          -D Trilinos_INSTALL_INCLUDE_DIR:PATH=include/trilinos
+          -D Trilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON
+          -D Trilinos_ENABLE_PyTrilinos:BOOL=ON
+          -D Trilinos_ENABLE_Fortran:BOOL=OFF
+          -D Trilinos_ENABLE_TESTS:BOOL=ON
+          -D Trilinos_ENABLE_EXAMPLES:BOOL=OFF
+          -D CMAKE_BUILD_TYPE:STRING=Release
+          -D BUILD_SHARED_LIBS:BOOL=ON
+          -D TPL_ENABLE_MPI:BOOL=ON
+         -D CMAKE_CXX_FLAGS:STRING=${COMPILERFLAGS}
+         -D CMAKE_C_FLAGS:STRING=${COMPILERFLAGS}
+         -D CMAKE_SKIP_BUILD_RPATH:BOOL=ON
+          -D CMAKE_BUILD_WITH_INSTALL_RPATH:BOOL=OFF
+         -D BLAS_INCLUDE_DIRS:PATH=${MKLINCLUDE}
+         -D LAPCK_INCLUDE_DIRS:PATH=${MKLINCLUDE}
+         -D TPL_BLAS_LIBRARIES:STRING=${MKLLIBS}
+         -D TPL_LAPACK_LIBRARIES:STRING=${MKLLIBS}"
+
+if [ -x "${SWIG_EXECUTABLE}" ]; then
+    CONFOPTS="${CONFOPTS} -D SWIG_EXECUTABLE:FILEPATH=${SWIG_EXECUTABLE}"
+fi
+
+package_specific_register () {
+    export TRILINOS_DIR=${INSTALL_PATH}
+}
diff --git a/FEniCS/packages/ufc-snapshot.package b/FEniCS/packages/ufc-snapshot.package
new file mode 100644 (file)
index 0000000..676efe4
--- /dev/null
@@ -0,0 +1,4 @@
+VERSION=snapshot
+NAME=ufc-${VERSION}
+SOURCE=http://fenicsproject.org/pub/software/ufc/
+PACKING=.tar.gz
diff --git a/FEniCS/packages/ufc-stable.package b/FEniCS/packages/ufc-stable.package
new file mode 100644 (file)
index 0000000..a8ae9c0
--- /dev/null
@@ -0,0 +1,6 @@
+VERSION=2.3.0
+NAME=ufc-${VERSION}
+SOURCE=https://bitbucket.org/fenics-project/ufc-deprecated/downloads/
+PACKING=.tar.gz
+CHECKSUM=11ee6ff8b7b44705932c6ebc6ae265d3
+BUILDCHAIN=cmake
diff --git a/FEniCS/packages/ufc.package b/FEniCS/packages/ufc.package
new file mode 100644 (file)
index 0000000..8a04e2f
--- /dev/null
@@ -0,0 +1,20 @@
+NAME=ufc-deprecated
+SOURCE=https://bitbucket.org/fenics-project/
+PACKING=git
+BUILDCHAIN=nothing
+
+if [ -x "${SWIG_EXECUTABLE}" ]; then
+    CONFOPTS="${CONFOPTS} -D SWIG_EXECUTABLE:FILEPATH=${SWIG_EXECUTABLE}"
+fi
+
+if [ ! -z "${PYTHON_EXECUTABLE}" ]; then
+    CONFOPTS="${CONFOPTS} -D PYTHON_EXECUTABLE:FILEPATH=${PYTHON_EXECUTABLE}"
+fi
+
+if [ ! -z "${PYTHON_INCLUDE_DIR}" ]; then
+    CONFOPTS="${CONFOPTS} -D PYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_DIR}"
+fi
+
+if [ ! -z "${PYTHON_LIBRARY}" ]; then
+    CONFOPTS="${CONFOPTS} -D PYTHON_LIBRARY:PATH=${PYTHON_LIBRARY}"
+fi
diff --git a/FEniCS/packages/ufl-snapshot.package b/FEniCS/packages/ufl-snapshot.package
new file mode 100644 (file)
index 0000000..9778e0c
--- /dev/null
@@ -0,0 +1,4 @@
+VERSION=snapshot
+NAME=ufl-${VERSION}
+SOURCE=http://fenicsproject.org/pub/software/ufl/
+PACKING=.tar.gz
diff --git a/FEniCS/packages/ufl-stable.package b/FEniCS/packages/ufl-stable.package
new file mode 100644 (file)
index 0000000..7ba629e
--- /dev/null
@@ -0,0 +1,5 @@
+VERSION=1.3.0
+NAME=ufl-${VERSION}
+SOURCE=https://bitbucket.org/fenics-project/ufl/downloads/
+PACKING=.tar.gz
+CHECKSUM=c57de98161c10bbbc0339ef2d1a4749d
diff --git a/FEniCS/packages/ufl.package b/FEniCS/packages/ufl.package
new file mode 100644 (file)
index 0000000..d75bb9a
--- /dev/null
@@ -0,0 +1,4 @@
+NAME=ufl
+SOURCE=https://bitbucket.org/fenics-project/
+PACKING=git
+BUILDCHAIN=python
diff --git a/FEniCS/packages/uflacs.package b/FEniCS/packages/uflacs.package
new file mode 100644 (file)
index 0000000..6792e6a
--- /dev/null
@@ -0,0 +1,4 @@
+NAME=uflacs
+SOURCE=https://bitbucket.org/fenics-project/
+PACKING=git
+BUILDCHAIN=python
diff --git a/FEniCS/packages/viper-stable.package b/FEniCS/packages/viper-stable.package
new file mode 100644 (file)
index 0000000..4631ba1
--- /dev/null
@@ -0,0 +1,5 @@
+VERSION=1.0.0
+NAME=viper-${VERSION}
+SOURCE=http://launchpad.net/fenics-viper/1.0.x/${VERSION}/+download/
+PACKING=.tar.gz
+CHECKSUM=4aa7d37934c98e637b45eb9cc7d03cdd
diff --git a/FEniCS/packages/viper.package b/FEniCS/packages/viper.package
new file mode 100644 (file)
index 0000000..beceebf
--- /dev/null
@@ -0,0 +1,4 @@
+NAME=fenics-viper
+SOURCE=lp:
+PACKING=bzr
+BUILDCHAIN=python
diff --git a/FEniCS/packages/vtk.package b/FEniCS/packages/vtk.package
new file mode 100644 (file)
index 0000000..c4c16da
--- /dev/null
@@ -0,0 +1,26 @@
+NAME=vtk-5.10.1
+SOURCE=http://www.vtk.org/files/release/5.10/
+PACKING=.tar.gz
+BUILDCHAIN=cmake
+EXTRACTSTO=VTK5.10.1
+
+CONFOPTS="-D CMAKE_BUILD_TYPE:STRING=Release
+          -D BUILD_TESTING:BOOL=OFF
+          -D BUILD_SHARED_LIBS:BOOL=ON
+          -D VTK_WRAP_PYTHON:BOOL=ON
+          -D VTK_USE_TK:BOOL=ON
+          -D VTK_USE_GL2PS:BOOL=ON
+          -D VTK_USE_QT:BOOL=ON"
+
+if [ -d "${VTK_DATA_ROOT}" ]; then
+    CONFOPTS="${CONFOPTS} -D VTK_DATA_ROOT:PATH=${VTK_DATA_ROOT}"
+fi
+
+package_specific_setup () {
+#    chmod 600 Utilities/vtktiff/tif_fax3sm.c
+}
+
+package_specific_register () {
+    export LD_LIBRARY_PATH=${INSTALL_PATH}/lib/vtk-5.8:${LD_LIBRARY_PATH}
+    export DYLD_LIBRARY_PATH=${INSTALL_PATH}/lib/vtk-5.8:${DYLD_LIBRARY_PATH}
+}
diff --git a/FEniCS/packages/vtkdata.package b/FEniCS/packages/vtkdata.package
new file mode 100644 (file)
index 0000000..80e74a4
--- /dev/null
@@ -0,0 +1,9 @@
+NAME=vtkdata-5.10.1
+SOURCE=http://www.vtk.org/files/release/5.10/
+PACKING=.tar.gz
+BUILDCHAIN=custom
+EXTRACTSTO=VTKData5.10.1
+
+package_specific_register () {
+    export VTK_DATA_ROOT=${PWD}
+}
diff --git a/FEniCS/packages/vtkwithqt.package b/FEniCS/packages/vtkwithqt.package
new file mode 100644 (file)
index 0000000..7bcf02b
--- /dev/null
@@ -0,0 +1,26 @@
+NAME=vtk-5.10.1
+SOURCE=http://www.vtk.org/files/release/5.10/
+PACKING=.tar.gz
+BUILDCHAIN=cmake
+EXTRACTSTO=VTK5.10.1
+
+CONFOPTS="-D CMAKE_BUILD_TYPE:STRING=Release
+          -D BUILD_TESTING:BOOL=OFF
+          -D BUILD_SHARED_LIBS:BOOL=ON
+          -D VTK_WRAP_PYTHON:BOOL=ON
+          -D VTK_USE_TK:BOOL=ON
+          -D VTK_USE_GL2PS:BOOL=ON
+          -D VTK_USE_QT=ON"
+
+if [ -d "${VTK_DATA_ROOT}" ]; then
+    CONFOPTS="${CONFOPTS} -D VTK_DATA_ROOT:PATH=${VTK_DATA_ROOT}"
+fi
+
+package_specific_setup () {
+#    chmod 600 Utilities/vtktiff/tif_fax3sm.c
+}
+
+package_specific_register () {
+    export LD_LIBRARY_PATH=${INSTALL_PATH}/lib/vtk-5.8:${LD_LIBRARY_PATH}
+    export DYLD_LIBRARY_PATH=${INSTALL_PATH}/lib/vtk-5.8:${DYLD_LIBRARY_PATH}
+}
diff --git a/FEniCS/packages/zlib.package b/FEniCS/packages/zlib.package
new file mode 100644 (file)
index 0000000..1c7207a
--- /dev/null
@@ -0,0 +1,4 @@
+NAME=zlib-1.2.7
+SOURCE=http://zlib.net/
+PACKING=.tar.gz
+BUILDCHAIN=autotools
diff --git a/FEniCS/patches/armadillo_no_mkl.patch b/FEniCS/patches/armadillo_no_mkl.patch
new file mode 100644 (file)
index 0000000..d243c82
--- /dev/null
@@ -0,0 +1,16 @@
+Hack to prevent Armadillo from picking up MKL when we want to build with ATLAS.
+--- armadillo-3.2.3.orig/CMakeLists.txt        2012-12-13 11:18:32.399393689 +0100
++++ armadillo-3.2.3/CMakeLists.txt     2012-12-13 11:18:43.595393294 +0100
+@@ -72,9 +72,9 @@
+ else()
+   set(ARMA_OS unix)
+   
+-  include(ARMA_FindMKL)
+-  include(ARMA_FindACMLMP)
+-  include(ARMA_FindACML)
++  #include(ARMA_FindMKL)
++  #include(ARMA_FindACMLMP)
++  #include(ARMA_FindACML)
+   
+   message(STATUS "MKL_FOUND     = ${MKL_FOUND}")
+   message(STATUS "ACMLMP_FOUND  = ${ACMLMP_FOUND}")
diff --git a/FEniCS/patches/cgal.patch b/FEniCS/patches/cgal.patch
new file mode 100644 (file)
index 0000000..15b41ed
--- /dev/null
@@ -0,0 +1,11 @@
+--- src/CGAL/KDS_Log.cpp~      2009-07-24 13:41:31.000000000 +0100
++++ src/CGAL/KDS_Log.cpp       2010-01-20 17:38:15.000000000 +0000
+@@ -23,7 +23,7 @@
+ #include <CGAL/Kinetic/internal/debug_counters.h>
+ #include <iostream>
+ CGAL_BEGIN_NAMESPACE
+-Log::State Log::state_;
++// Log::State Log::state_;
+ CGAL_END_NAMESPACE
+ CGAL_KINETIC_BEGIN_INTERNAL_NAMESPACE
diff --git a/FEniCS/patches/dolfin-armadillo-test.patch b/FEniCS/patches/dolfin-armadillo-test.patch
new file mode 100644 (file)
index 0000000..a3993e8
--- /dev/null
@@ -0,0 +1,17 @@
+diff -Nru dolfin-1.0-beta.orig/cmake/modules/FindArmadillo.cmake dolfin-1.0-beta/cmake/modules/FindArmadillo.cmake
+--- dolfin-1.0-beta.orig/cmake/modules/FindArmadillo.cmake      2011-09-23 11:17:38.459186000 -0500
++++ dolfin-1.0-beta/cmake/modules/FindArmadillo.cmake   2011-09-23 11:20:56.447560000 -0500
+@@ -173,6 +173,13 @@
+  endif()
+ endif()
+
++# Armadillo test is not working, but this does not seem to be a problem,
++# so ignore a failed test
++if (NOT ARMADILLO_TEST_RUNS)
++  MESSAGE( "Warning: Armadillo test run failed.  Ignoring." )
++  set(ARMADILLO_TEST_RUNS TRUE)
++endif()
++
+ # Standard package handling
+ include(FindPackageHandleStandardArgs)
+ find_package_handle_standard_args(Armadillo
\ No newline at end of file
diff --git a/FEniCS/patches/madlib.patch b/FEniCS/patches/madlib.patch
new file mode 100644 (file)
index 0000000..c512a2e
--- /dev/null
@@ -0,0 +1,46 @@
+diff -Nru madlib-1.3.0.orig/Benchmarks/moveIt/Parameters.h madlib-1.3.0/Benchmarks/moveIt/Parameters.h
+--- madlib-1.3.0.orig/Benchmarks/moveIt/Parameters.h   2010-11-12 15:00:57.000000000 +0100
++++ madlib-1.3.0/Benchmarks/moveIt/Parameters.h        2010-11-12 15:00:57.000000000 +0100
+@@ -18,6 +18,7 @@
+ #include "SizeFieldBase.h"
+ #include "LocalSizeField.h"
++#include <math.h>
+ #include <string.h>
+ using std::string;
+ #include <list>
+diff -Nru madlib-1.3.0.orig/configure madlib-1.3.0/configure
+--- madlib-1.3.0.orig/configure        2010-11-12 15:00:57.000000000 +0100
++++ madlib-1.3.0/configure     2010-11-17 15:58:05.000000000 +0100
+@@ -18697,7 +18697,7 @@
+ includedir="${prefix}/include/MAdLib"
+-allincludedir="${prefix}/include_all/MAdLib"
++allincludedir="${prefix}/include/MAdLib"
+diff -Nru madlib-1.3.0.orig/configure.ac madlib-1.3.0/configure.ac
+--- madlib-1.3.0.orig/configure.ac     2010-11-12 15:00:57.000000000 +0100
++++ madlib-1.3.0/configure.ac  2010-11-17 15:58:14.000000000 +0100
+@@ -724,7 +724,7 @@
+ AC_CONFIG_MACRO_DIR([m4])
+ includedir="${prefix}/include/MAdLib"
+-allincludedir="${prefix}/include_all/MAdLib"
++allincludedir="${prefix}/include/MAdLib"
+ dnl Write output
+ AC_SUBST(UNAME)
+diff -Nru madlib-1.3.0.orig/Mesh/MshTags.h madlib-1.3.0/Mesh/MshTags.h
+--- madlib-1.3.0.orig/Mesh/MshTags.h   2010-11-12 15:00:57.000000000 +0100
++++ madlib-1.3.0/Mesh/MshTags.h        2010-11-12 15:00:57.000000000 +0100
+@@ -14,6 +14,7 @@
+ #ifndef MSHTAGS__H
+ #define MSHTAGS__H
++#include <cstdio>
+ #include <string>
+ #include <sstream>
diff --git a/FEniCS/patches/petsc.patch b/FEniCS/patches/petsc.patch
new file mode 100644 (file)
index 0000000..2f403eb
--- /dev/null
@@ -0,0 +1,56 @@
+diff -Nru petsc-3.2-p6.orig/src/mat/impls/aij//mpi/mpicusp/mpiaijAssemble.cu petsc-3.2-p6/src/mat/impls/aij//mpi/mpicusp/mpiaijAssemble.cu
+--- petsc-3.2-p6.orig/src/mat/impls/aij//mpi/mpicusp/mpiaijAssemble.cu 2012-02-09 14:29:16.530465405 +0100
++++ petsc-3.2-p6/src/mat/impls/aij//mpi/mpicusp/mpiaijAssemble.cu      2012-02-09 14:51:53.720465807 +0100
+@@ -15,7 +15,7 @@
+ #include <cusp/array1d.h>
+ #include <cusp/print.h>
+ #include <cusp/coo_matrix.h>
+-#include <cusp/detail/device/reduce_by_key.h>
++//#include <cusp/detail/device/reduce_by_key.h>
+ #include <cusp/io/matrix_market.h>
+@@ -430,7 +430,8 @@
+   //     the Cusp one is 2x faster, but still not optimal
+   // This could possibly be done in-place
+   ierr = PetscInfo(J, "Compressing matrices\n");CHKERRQ(ierr);
+-  cusp::detail::device::reduce_by_key
++  //cusp::detail::device::reduce_by_key
++  thrust::reduce_by_key
+     (thrust::make_zip_iterator(thrust::make_tuple(diagCOO.row_indices.begin(), diagCOO.column_indices.begin())) + diagonalOffset,
+      thrust::make_zip_iterator(thrust::make_tuple(diagCOO.row_indices.end(),   diagCOO.column_indices.end())),
+      diagCOO.values.begin() + diagonalOffset,
+@@ -438,7 +439,8 @@
+      A.values.begin(),
+      thrust::equal_to< thrust::tuple<IndexType,IndexType> >(),
+      thrust::plus<ValueType>());
+-  cusp::detail::device::reduce_by_key
++  //cusp::detail::device::reduce_by_key
++  thrust::reduce_by_key
+     (thrust::make_zip_iterator(thrust::make_tuple(offdiagCOO.row_indices.begin(), offdiagCOO.column_indices.begin())) + offdiagonalOffset,
+      thrust::make_zip_iterator(thrust::make_tuple(offdiagCOO.row_indices.end(),   offdiagCOO.column_indices.end())),
+      offdiagCOO.values.begin() + offdiagonalOffset,
+diff -Nru petsc-3.2-p6.orig/src/mat/impls/aij//seq/seqcusp/aijAssemble.cu petsc-3.2-p6/src/mat/impls/aij//seq/seqcusp/aijAssemble.cu
+--- petsc-3.2-p6.orig/src/mat/impls/aij//seq/seqcusp/aijAssemble.cu    2012-02-09 14:30:01.830465419 +0100
++++ petsc-3.2-p6/src/mat/impls/aij//seq/seqcusp/aijAssemble.cu 2012-02-09 14:51:55.470465809 +0100
+@@ -14,7 +14,7 @@
+ #include <cusp/array1d.h>
+ #include <cusp/print.h>
+ #include <cusp/coo_matrix.h>
+-#include <cusp/detail/device/reduce_by_key.h>
++//#include <cusp/detail/device/reduce_by_key.h>
+ #include <cusp/io/matrix_market.h>
+@@ -258,9 +258,10 @@
+   // sum values with the same (i,j) index
+   // XXX thrust::reduce_by_key is unoptimized right now, so we provide a SpMV-based one in cusp::detail
+   //     the Cusp one is 2x faster, but still not optimal
++  // FEniCS patch: reduce_by_key is removed in Cusp 0.3, so we use the Thrust version to ensure compatiblity
+   // This could possibly be done in-place
+   ierr = PetscInfo(J, "Compressing matrix\n");CHKERRQ(ierr);
+-#if 1
++#if 0
+   cusp::detail::device::reduce_by_key
+     (thrust::make_zip_iterator(thrust::make_tuple(COO.row_indices.begin(), COO.column_indices.begin())),
+      thrust::make_zip_iterator(thrust::make_tuple(COO.row_indices.end(),   COO.column_indices.end())),
diff --git a/FEniCS/patches/python.patch b/FEniCS/patches/python.patch
new file mode 100644 (file)
index 0000000..42c5195
--- /dev/null
@@ -0,0 +1,21 @@
+diff -Nru Python-2.7.2.orig/Makefile.pre.in Python-2.7.2/Makefile.pre.in
+--- Python-2.7.2.orig/Makefile.pre.in  2013-04-08 12:39:28.000000000 +0200
++++ Python-2.7.2/Makefile.pre.in       2013-04-08 12:40:25.000000000 +0200
+@@ -426,7 +426,7 @@
+ libpython$(VERSION).so: $(LIBRARY_OBJS)
+       if test $(INSTSONAME) != $(LDLIBRARY); then \
+               $(BLDSHARED) -Wl,-h$(INSTSONAME) -o $(INSTSONAME) $(LIBRARY_OBJS) $(MODLIBS) $(SHLIBS) $(LIBC) $(LIBM) $(LDLAST); \
+-              $(LN) -f $(INSTSONAME) $@; \
++              $(LN) -fs $(INSTSONAME) $@; \
+       else \
+               $(BLDSHARED) -o $@ $(LIBRARY_OBJS) $(MODLIBS) $(SHLIBS) $(LIBC) $(LIBM) $(LDLAST); \
+       fi
+@@ -792,7 +792,7 @@
+       then rm -f $(DESTDIR)$(BINDIR)/$(PYTHON); \
+       else true; \
+       fi
+-      (cd $(DESTDIR)$(BINDIR); $(LN) python$(VERSION)$(EXE) $(PYTHON))
++      (cd $(DESTDIR)$(BINDIR); $(LN) -s python$(VERSION)$(EXE) $(PYTHON))
+       -rm -f $(DESTDIR)$(BINDIR)/python-config
+       (cd $(DESTDIR)$(BINDIR); $(LN) -s python$(VERSION)-config python-config)
+       -test -d $(DESTDIR)$(LIBPC) || $(INSTALL) -d -m $(DIRMODE) $(DESTDIR)$(LIBPC)
diff --git a/FEniCS/patches/scientificpython.patch b/FEniCS/patches/scientificpython.patch
new file mode 100644 (file)
index 0000000..b3ad83d
--- /dev/null
@@ -0,0 +1,28 @@
+diff -Nru ScientificPython-2.8.orig/setup.py ScientificPython-2.8/setup.py
+--- ScientificPython-2.8.orig/setup.py 2008-10-28 14:31:44.000000000 +0100
++++ ScientificPython-2.8/setup.py      2010-08-20 09:29:16.000000000 +0200
+@@ -40,13 +40,17 @@
+     extra_compile_args.append("-DNUMARRAY=1")
+ else :
+     extra_compile_args.append("-DNUMPY=1")
+-    if sys.platform == 'win32':
+-        arrayobject_h_include = [os.path.join(sys.prefix,
+-                                 "Lib/site-packages/numpy/core/include")]
+-    else:
+-        arrayobject_h_include = [os.path.join(sys.prefix,
+-                                "lib/python%s.%s/site-packages/numpy/core/include"
+-                                % sys.version_info [:2])]
++    try:
++        import numpy
++        arrayobject_h_include = [numpy.get_include()]
++    except ImportError:
++        if sys.platform == 'win32':
++            arrayobject_h_include = [os.path.join(sys.prefix,
++                                     "Lib/site-packages/numpy/core/include")]
++        else:
++            arrayobject_h_include = [os.path.join(sys.prefix,
++                                     "lib/python%s.%s/site-packages/numpy/core/include"
++                                     % sys.version_info [:2])]
+ math_libraries = []
+ if sys.platform != 'win32':
diff --git a/FEniCS/patches/slepc.patch b/FEniCS/patches/slepc.patch
new file mode 100644 (file)
index 0000000..963209f
--- /dev/null
@@ -0,0 +1,14 @@
+diff -Nru slepc-3.4.1.orig/config/configure.py slepc-3.4.1/config/configure.py
+--- slepc-3.4.1.orig/config/configure.py       2013-08-14 10:14:04.157596562 +0200
++++ slepc-3.4.1/config/configure.py    2013-08-14 10:14:37.341561962 +0200
+@@ -297,8 +297,8 @@
+   pkgconfig = open(os.sep.join([pkgconfigdir,'SLEPc.pc']),'w')
+ except:
+   sys.exit('ERROR: cannot create pkgconfig file in ' + pkgconfigdir)
+-if prefixinstall and os.path.isfile(os.sep.join([prefixdir,'include','slepc.h'])):
+-  sys.exit('ERROR: prefix directory ' + prefixdir + ' contains files from a previous installation')
++#if prefixinstall and os.path.isfile(os.sep.join([prefixdir,'include','slepc.h'])):
++#  sys.exit('ERROR: prefix directory ' + prefixdir + ' contains files from a previous installation')
+ # Create temporary directory and makefile for running tests
+ try:
diff --git a/FEniCS/patches/trilinos.patch b/FEniCS/patches/trilinos.patch
new file mode 100644 (file)
index 0000000..1c4b827
--- /dev/null
@@ -0,0 +1,36 @@
+diff -Nru trilinos-11.0.3-Source.orig/cmake/TPLs/FindTPLUMFPACK.cmake trilinos-11.0.3-Source/cmake/TPLs/FindTPLUMFPACK.cmake
+--- trilinos-11.0.3-Source.orig/cmake/TPLs/FindTPLUMFPACK.cmake        2012-11-21 10:00:57.966984315 +0100
++++ trilinos-11.0.3-Source/cmake/TPLs/FindTPLUMFPACK.cmake     2012-11-21 10:08:21.946968616 +0100
+@@ -55,7 +55,14 @@
+ INCLUDE(TribitsTplDeclareLibraries)
+-TRIBITS_TPL_DECLARE_LIBRARIES( UMFPACK
+-  REQUIRED_HEADERS umfpack.h amd.h UFconfig.h
+-  REQUIRED_LIBS_NAMES umfpack amd
+-  )
++IF (APPLE)
++  TRIBITS_TPL_DECLARE_LIBRARIES( UMFPACK
++    REQUIRED_HEADERS umfpack.h amd.h UFconfig.h
++    REQUIRED_LIBS_NAMES umfpack amd SuiteSparse
++    )
++ELSE()
++  TRIBITS_TPL_DECLARE_LIBRARIES( UMFPACK
++    REQUIRED_HEADERS umfpack.h amd.h UFconfig.h
++    REQUIRED_LIBS_NAMES umfpack amd
++    )
++ENDIF()
+diff -Nru trilinos-11.0.3-Source.orig/packages/PyTrilinos/src/CMakeLists.txt trilinos-11.0.3-Source/packages/PyTrilinos/src/CMakeLists.txt
+--- trilinos-11.0.3-Source.orig/packages/PyTrilinos/src/CMakeLists.txt 2012-11-21 10:00:58.226984311 +0100
++++ trilinos-11.0.3-Source/packages/PyTrilinos/src/CMakeLists.txt      2012-11-21 10:09:24.498966402 +0100
+@@ -195,6 +195,10 @@
+   PROPERTIES LINK_FLAGS "${EXTRA_LINK_ARGS}"
+   )
++if (APPLE)
++  TARGET_LINK_LIBRARIES(pytrilinos ${PYTHON_LIBRARIES})
++endif()
++
+ #
+ # Define the PyTrilinos swig setup
+ SET(CMAKE_SWIG_FLAGS "")
diff --git a/FEniCS/platforms/.single b/FEniCS/platforms/.single
new file mode 100644 (file)
index 0000000..e69de29
diff --git a/FEniCS/platforms/supported/fedora19.platform b/FEniCS/platforms/supported/fedora19.platform
new file mode 100644 (file)
index 0000000..18fe032
--- /dev/null
@@ -0,0 +1,62 @@
+# Fedora 19
+
+# This build script assumes that you have several packages already
+# installed via Fedora's yum using the following command:
+#
+# su -c 'yum install -y redhat-lsb bzr bzrtools subversion \
+# libxml2-devel gcc gcc-c++ openmpi-devel openmpi numpy swig wget \
+# atlas-devel suitesparse-devel blas-devel \
+# lapack-devel cln-devel ginac-devel python-devel cmake \
+# ScientificPython mpfr-devel armadillo-devel gmp-devel CGAL-devel \
+# cppunit-devel flex bison bzip2-devel python-ply eigen3 scotch scotch-devel \
+# vtk vtkdata vtk-devel vtk-python tk tk-devel tcl tcl-devel \
+# sphinx python-sphinx python-numpydoc'
+#
+# If you have multiple MPI libraries installed, make sure the
+# appropriate version is selected. For this, on a 32-bit operating
+# system, run:
+#
+# module load openmpi-i386
+#
+# or on a 64-bit operating system, run:
+#
+# module load openmpi-x86_64
+#
+# After Dorsal has completed, please make sure the following
+# environment variable is set before running any Python DOLFIN
+# programs:
+#
+# export BOOST_DIR=${INSTALL_PATH}
+#
+# Also, if you are using SELinux, you may need to disable it to run
+# DOLFIN programs.
+##
+
+# Platform specific variables
+default PETSC_ARCH=linux-gnu-cxx-opt
+default SCOTCH_ARCH=pc_linux2
+default UMFPACK_INCLUDE_DIR=/usr/include/suitesparse
+
+# Define the packages this platform needs
+PACKAGES=(
+skip:FEniCS-prepare
+once:hdf5
+once:boost
+once:parmetis
+once:trilinos
+once:petsc
+once:slepc
+once:vtkwithqt
+# swiginac
+# once:scotch
+fiat
+ferari
+ufc
+ufl
+ffc
+# syfi
+viper
+instant
+dolfin
+skip:FEniCS
+)
diff --git a/FEniCS/platforms/supported/fedora20.platform b/FEniCS/platforms/supported/fedora20.platform
new file mode 100644 (file)
index 0000000..89562c4
--- /dev/null
@@ -0,0 +1,62 @@
+# Fedora 20
+
+# This build script assumes that you have several packages already
+# installed via Fedora's yum using the following command:
+#
+# su -c 'yum install -y redhat-lsb bzr bzrtools subversion \
+# libxml2-devel gcc gcc-c++ openmpi-devel openmpi numpy swig wget \
+# atlas-devel suitesparse-devel blas-devel \
+# lapack-devel cln-devel ginac-devel python-devel cmake \
+# ScientificPython mpfr-devel armadillo-devel gmp-devel CGAL-devel \
+# cppunit-devel flex bison bzip2-devel python-ply eigen3 scotch scotch-devel \
+# vtk vtkdata vtk-devel vtk-python tk tk-devel tcl tcl-devel \
+# sphinx python-sphinx python-numpydoc'
+#
+# If you have multiple MPI libraries installed, make sure the
+# appropriate version is selected. For this, on a 32-bit operating
+# system, run:
+#
+# module load openmpi-i386
+#
+# or on a 64-bit operating system, run:
+#
+# module load openmpi-x86_64
+#
+# After Dorsal has completed, please make sure the following
+# environment variable is set before running any Python DOLFIN
+# programs:
+#
+# export BOOST_DIR=${INSTALL_PATH}
+#
+# Also, if you are using SELinux, you may need to disable it to run
+# DOLFIN programs.
+##
+
+# Platform specific variables
+default PETSC_ARCH=linux-gnu-cxx-opt
+default SCOTCH_ARCH=pc_linux2
+default UMFPACK_INCLUDE_DIR=/usr/include/suitesparse
+
+# Define the packages this platform needs
+PACKAGES=(
+skip:FEniCS-prepare
+#once:hdf5
+once:boost
+once:parmetis
+once:trilinos
+once:petsc
+once:slepc
+#once:sphinx
+# swiginac
+# once:scotch
+fiat
+ferari
+ufc
+ufl
+ffc
+# syfi
+viper
+instant
+dolfin
+skip:FEniCS
+)
diff --git a/FEniCS/platforms/supported/rhel6.platform b/FEniCS/platforms/supported/rhel6.platform
new file mode 100644 (file)
index 0000000..5ae711e
--- /dev/null
@@ -0,0 +1,66 @@
+# RHEL 6
+
+# This build script assumes that you have several packages already
+# installed via RHEL's yum using the following command:
+#
+# su -c 'yum install -y redhat-lsb bzr bzrtools subversion \
+# libxml2-devel gcc gcc-c++ openmpi-devel openmpi numpy swig wget \
+# vtk-python atlas-devel suitesparse-devel blas-devel \
+# lapack-devel cln-devel ginac-devel python-devel cmake \
+# ScientificPython mpfr-devel armadillo-devel gmp-devel CGAL-devel \
+# cppunit-devel flex bison bzip2-devel python-ply eigen3 scotch scotch-devel'
+#
+# If you have multiple MPI libraries installed, make sure the
+# appropriate version is selected. For this, on a 32-bit operating
+# system, run:
+#
+# module load openmpi-i386
+#
+# or on a 64-bit operating system, run:
+#
+# module load openmpi-x86_64
+#
+# After Dorsal has completed, please make sure the following
+# environment variable is set before running any Python DOLFIN
+# programs:
+#
+# export BOOST_DIR=${INSTALL_PATH}
+#
+# Also, if you are using SELinux, you may need to disable it to run
+# DOLFIN programs.
+##
+
+# Platform specific variables
+default PETSC_ARCH=linux-gnu-cxx-opt
+default SCOTCH_ARCH=pc_linux2
+default UMFPACK_INCLUDE_DIR=/usr/include/suitesparse
+
+# Define the packages this platform needs
+PACKAGES=(
+skip:FEniCS-prepare
+once:boost
+once:pcre
+once:scientificpython
+once:cgal
+once:bazaar
+once:scons
+once:mtl
+once:hdf5
+once:parmetis
+once:swig
+once:trilinos
+once:petsc
+once:slepc
+once:armadillo
+once:scotch
+fiat
+ferari
+ufc
+ufl
+ffc
+# syfi
+viper
+instant
+dolfin
+skip:FEniCS
+)
diff --git a/FEniCS/platforms/supported/ubuntu13.platform b/FEniCS/platforms/supported/ubuntu13.platform
new file mode 100644 (file)
index 0000000..ad24035
--- /dev/null
@@ -0,0 +1,40 @@
+# Ubuntu 13.10 (Saucy Salamander)
+
+# This build script assumes that you have several packages already
+# installed via Ubuntu's apt-get using the following commands:
+#
+# sudo apt-get install bzr bzrtools cmake flex g++ gfortran \
+# libarmadillo-dev libatlas-base-dev libboost-dev \
+# libboost-{filesystem,iostreams,mpi,program-options,thread,math,timer,chrono}-dev \
+# libcln-dev libcppunit-dev libginac-dev \
+# liblapack-dev libmpfr-dev libopenmpi-dev libptscotch-dev \
+# libsuitesparse-dev libxml2-dev openmpi-bin pkg-config \
+# python-dev python-numpy python-scientific python-vtk subversion swig \
+# wget bison libhwloc-dev python-ply libvtk5-dev python-netcdf \
+# libhdf5-openmpi-dev libeigen3-dev
+#
+# Also, if you have multiple MPI libraries installed, make sure
+# "sudo update-alternatives --config mpi" is set to openmpi.
+##
+
+# Platform specific variables
+default PETSC_ARCH=linux-gnu-cxx-opt
+default UMFPACK_INCLUDE_DIR=/usr/include/suitesparse
+
+# Define the packages this platform needs
+PACKAGES=(
+skip:FEniCS-prepare
+cgal
+parmetis
+trilinos
+petsc
+slepc
+fiat
+#ferari
+ufc
+ufl
+ffc
+instant
+dolfin
+skip:FEniCS
+)
diff --git a/README.md.dorsal b/README.md.dorsal
new file mode 100644 (file)
index 0000000..79ff7dc
--- /dev/null
@@ -0,0 +1,56 @@
+Copyright (C) 2007 -- 2013
+Harish Narayanan (<hnarayanan@gmail.com>)
+
+Licensing information follows a little later in this file.
+
+# Dorsal
+
+This directory tree holds Dorsal, a set of simple scripts to build
+components of the FEniCS Project (as well as their dependencies) for
+various platforms. Currently, Dorsal supports the following
+environments:
+
+* Fedora 13, 14, 15
+* Ubuntu 12.04 LTS, 12.10, 13.04
+* openSUSE 11.3, 11.4, 12.1
+* Red Hat Enterprise Linux 6
+* Debian GNU/Linux 6.0, Unstable
+* Mac OS X 10.6, 10.7 (with MacPorts)
+
+If your favourite platform is not on the list above, let us know about
+it, and we can work together toward adding it.
+
+Please refer to the file USAGE for details on compiling and installing
+the FEniCS Project with the help of Dorsal. USAGE demonstrates how
+Dorsal comes in handy under common usage scenarios. The file also
+provides a brief overview of the underlying structure of Dorsal, so
+you may want to go through it if you are interested in extending
+Dorsal to suit your needs.
+
+If you run into any problems, ensure that you've installed all the
+preliminary dependencies for your platform (usually from the system
+package manager) that Dorsal assumes you already have. An incomplete
+list of this is provided in the .platform file for each platform,
+along with platform-specific tips. In most cases, these should solve
+your problem. If you're having further difficulty, please go through
+the file USAGE for detailed usage and troubleshooting instructions, or
+see http://fenicsproject.org/support for contact information.
+
+Dorsal is collaboratively developed free software. The file AUTHORS
+contains a complete list of authors and contributors to the project,
+and its evolution is catalogued in the file ChangeLog. You are free to
+redistribute Dorsal and/or modify it under the terms of the GNU Lesser
+General Public License as published by the Free Software Foundation;
+either version 3, or (at your option) any later version. If you are
+interested in contributing to the project, please take a look at the
+file TODO for some ideas.
+
+This software is distributed in the hope that it will be useful, but
+WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this software; see the file COPYING.lesser. If not,
+write to the Free Software Foundation, 59 Temple Place - Suite 330,
+Boston, MA 02111-1307, USA.
diff --git a/TODO b/TODO
new file mode 100644 (file)
index 0000000..e2e752d
--- /dev/null
+++ b/TODO
@@ -0,0 +1,26 @@
+* Introduce automatic dependency resolution.
+  Difficulty: High      Urgency: Low
+
+* Test Dorsal on supported platforms and correct the package lists if
+  necessary. Feel free to contribute information for other platforms
+  as well.
+  Difficulty: Low       Urgency: High
+
+* Add (MD5/SHA1) check summing mechanism to the downloading routine
+  (and corresponding hashes to the package files) to verify if
+  downloaded files are sane.
+  Difficulty: Moderate  Urgency: Moderate
+
+* Sniff out 32/64 bit-ness of machines automatically to suitably set
+  GMP_ARCH, SCOTCH_ARCH etc.
+  Difficulty: Moderate Urgency: High
+
+* Insert download links somewhere in the documentation.
+  Difficulty: Trivial   Urgency: Moderate
+
+* Introduce mechanism to update package lists.
+  Difficulty: Moderate Urgency: Low
+
+* Add the ability to "clean" a build. This could be as simple as
+  cleaning the dorsal_build folder, or something more complex.
+  Difficulty: Moderate Urgency: Low
diff --git a/USAGE b/USAGE
new file mode 100644 (file)
index 0000000..0d5f9df
--- /dev/null
+++ b/USAGE
@@ -0,0 +1,309 @@
+Using, troubleshooting and extending Dorsal
+
+ This document contains instructions for compiling and installing the
+ FEniCS Project with the help of Dorsal. It contains the following
+ sections, which catalogue common use cases, provide information on
+ troubleshooting common problems, and present a brief look at the
+ design of Dorsal, should you want to extend it.
+
+  Basic usage
+  Repeated builds
+  Coexisting stable and development builds
+  Mixed stable and development builds
+  Troubleshooting and getting help
+  Elements of Dorsal's design
+
+
+ Basic usage
+
+  The simplest scenario is setting up everything for the first time on
+  a supported platform. In order to do this, you:
+
+   1. First tweak dorsal.cfg to your liking. This file lets you
+      specify some key information to Dorsal, including where you'd
+      like to download and install the FEniCS Project components, and
+      whether you'd like to install stable releases or (potentially
+      unstable) development versions of projects.
+
+   2. Invoke the build script by running:
+
+      ./dorsal.sh
+
+   3. At this point, Dorsal attempts to guess your operating
+      environment (platform) and provides a list of instructions to
+      ensure your system is ready for installing FEniCS. Go through
+      these carefully, and copy and paste appropriate commands into
+      another terminal window to prepare your system.
+
+      If Dorsal fails to recognise your platform, or you want to
+      specify a known platform you are interested in (myplatform),
+      invoke Dorsal via:
+
+      ./dorsal.sh FEniCS/platforms/supported/myplatform.platform
+
+   4. Once you've completed these steps, hit enter to begin the
+      installation!
+
+  If all goes according to plan, you should see a lot of
+  compilation-related text scroll past your screen and eventually end
+  up with a complete, up-to-date installation of various FEniCS
+  projects and their corresponding dependencies.
+
+  Don't forget to follow any post-build instructions before rushing
+  off to try the demos!
+
+
+ Repeated builds
+
+  The FEniCS Project is under active development. If you are
+  interested in keeping up with the development versions of its
+  components, you will want to frequently rerun dorsal.sh (with
+  STABLE_BUILD set to false in dorsal.cfg).
+
+  Unfortunately, Dorsal is not currently smart enough to automatically
+  figure out what it has previously installed. It will insist on
+  rebuilding all projects and their dependencies, even though you are
+  probably only interested in tracking a few fast-changing FEniCS
+  Project components.
+
+  In order to get around this limitation, Dorsal has a package
+  skipping mechanism which you can use to manually specify packages
+  you would like it to skip on subsequent rebuilds. The following
+  steps describe how you use this mechanism to rebuild just the
+  projects you want to track.
+
+   1. Ensure that STABLE_BUILD set to false in dorsal.cfg. This makes
+      sure Dorsal knows to fetch and build development versions of
+      projects.
+
+   2. Create a new copy of your system's platform file
+      (system.platform) in the platforms folder. Call it, say,
+      myplatform.platform.
+
+      cd FEniCS/platforms/supported
+      cp system.platform myplatform.platform
+
+   3. Open myplatform.platform in your favourite text editor, and
+      prepend the string `skip:' (without the quotes) before every
+      package on the list PACKAGES you would like Dorsal to skip on
+      subsequent builds. So now, your list might look something like
+      the following:
+
+      PACKAGES=(
+      skip:parmetis
+      skip:petsc
+      skip:slepc
+      skip:gmp
+      skip:mtl
+      skip:trilinos
+      skip:scotch
+      fiat
+      ferari
+      ufc
+      ufl
+      ffc
+      viper
+      instant
+      dolfin
+      )
+
+      See the file fenics.platform for an example of what I use on my
+      (Mac OS X Snow Leopard) machine. Notice that this file is
+      identical to snowleopard.platform, with a few packages 'skip:'ped.
+
+   4. Now, every time you wish to rebuild just the few packages you
+      want to track, invoke Dorsal via:
+
+      ./dorsal.sh FEniCS/platforms/supported/myplatform.platform
+
+  Using Dorsal in this manner should save you a lot of time if you
+  need to rebuild FEniCS often.
+
+
+ Coexisting stable and development builds
+
+  Another common requirement is tracking both stable releases (to get
+  actual work done!) and development versions (to check out and
+  contribute to new functionality) of FEniCS Project components.
+
+  In order to achieve this, you:
+
+   1. Modify the variables in dorsal.cfg to build stable releases of
+      FEniCS Project components and install them in some convenient
+      location. e.g.,
+
+      DOWNLOAD_PATH=${HOME}/Work/FEniCS/stable/src
+      INSTALL_PATH=${HOME}/Work/FEniCS/stable
+      STABLE_BUILD=true
+
+   2. Invoke the build script by running:
+
+      ./dorsal.sh
+
+   3. Modify the variables in dorsal.cfg to build development versions
+      of FEniCS Project components and install them in another
+      location. e.g.,
+
+      DOWNLOAD_PATH=${HOME}/Work/FEniCS/unstable/src
+      INSTALL_PATH=${HOME}/Work/FEniCS/unstable
+      STABLE_BUILD=false
+
+   4. Invoke the build script once more by running:
+
+      ./dorsal.sh
+
+
+ Mixed stable and development builds
+
+  A final use case is tracking an arbitrary mix of stable releases and
+  development versions of FEniCS Project components. It is sometimes
+  necessary to do this when you want to follow bleeding edge versions
+  of some FEniCS projects, but some others are simultaneously broken.
+
+  In order to achieve this, you:
+
+   1. Ensure STABLE_BUILD=false in dorsal.cfg to make sure Dorsal
+      knows to go and fetch development versions of packages by
+      default.
+
+   2. Create a new copy of your system's platform file
+      (system.platform) in the platforms folder. Call it, say,
+      myplatform.platform.
+
+      cd platforms
+      cp system.platform myplatform.platform
+
+   3. Open myplatform.platform in your favourite text editor, and
+      append the string `-stable' to all the packages you want stable
+      versions of. So now, your list might look something like the
+      following:
+
+      PACKAGES=(
+      ...
+      fiat
+      ferari
+      ufc-stable
+      ufl
+      ffc-stable
+      viper
+      instant
+      dolfin
+      )
+
+   4. Now, invoke Dorsal via:
+
+      ./dorsal.sh FEniCS/platforms/supported/myplatform.platform
+
+ Installing FEniCS with CUDA support
+
+  Dorsal can build PETSc with support for CUDA, using the Cusp and Thrust
+  libraries. This enables DOLFIN to use PETSc's interfacing to Cusp for GPU
+  acceleration of the solution of linear systems. Before builing with Dorsal, 
+  you must manually install CUDA and verify the installation. Instructions
+  are provided at NVIDIA's webpages: www.nvidia.com.
+  
+  After instaling CUDA, do the following to have Dorsal build PETSc
+  with CUDA support:
+
+   1. Set the variable CUDA_DIR, either in your environment:
+
+       export CUDA_DIR=<path to cuda install> (default /usr/local/cuda)
+
+      or in the .platform file corresponding to your system:
+     
+       default CUDA_DIR=<path to cuda install>
+
+   2. Add "cusp" to the list of packages to install in your the .platform-file
+      corresponding to your system. It's important to add "cusp" before "petsc",
+      like this:
+
+      PACKAGES=(
+      cusp
+      ...
+      petsc
+      ...
+      dolfin
+      )
+
+   3. Invoke dorsal.sh as usual.
+
+
+ Troubleshooting and getting help
+
+  If you run into any problems, ensure that you've installed all the
+  preliminary dependencies for your platform (usually from the system
+  package manager) that Dorsal assumes you already have. An incomplete
+  list of this is provided in the .platform file for each platform,
+  along with platform-specific tips. In most cases, these should solve
+  your problem.
+
+  If you know Dorsal supports your platform but it fails to
+  automatically recognise it, try invoking Dorsal by specifying your
+  platform manually:
+
+  ./dorsal.sh FEniCS/platforms/supported/myplatform.platform
+
+  If you're having further difficulty, please see
+  http://fenicsproject.org/support for contact information. We will
+  try to help.
+
+
+ Elements of Dorsal's design
+
+  Dorsal is written in bash and its design is based on a simplified
+  version of the FreeBSD Ports system. The main Dorsal script
+  (dorsal.sh) can be a bit magic in a few places (mostly thanks to ace
+  bash hacker Joachim Berdal Haga), but at the level a user interacts
+  with it, Dorsal is pretty uncomplicated.
+
+  Here is the entire story.
+
+  Platform files are files specific to a given platform. These files
+  live in the `platforms' folder and have the suffix
+  `.platform'. These files contain any system specific variables,
+  build instructions, and contains a list of packages that Dorsal
+  needs to build. Usually, the more packages that your system package
+  manager can handle, the smaller this list will be.
+
+  If you are interested in adding support for a new platform, you
+  should look for an existing platform that is similar to yours, make
+  a copy of it, and try to modify it to suit your needs.
+
+  In order to inform Dorsal how to build each package, we introduce
+  package files. Not surprisingly, package files have the suffix
+  `.package' and live in the `packages' folder. These files specify
+  several package details, including where the package should be
+  downloaded from, how it is packed, what buildchain it uses, any
+  package-specific build instructions if needed, etc. A superset of
+  these attributes are documented in packages/template.package.
+
+  If you are interested in adding support for a new package, take a
+  look at packages/template.package, as well as other related packages
+  for ideas.
+
+  A majority of the package files are only 3--4 lines long, but some
+  highly-specialised ones (e.g. dolfin.package) are significantly
+  bigger. Through needing to support a large number of varied
+  packages, Dorsal has evolved a fairly flexible package definition
+  structure. In my opinion, this is what gives Dorsal its
+  versatility.
+
+  When you invoke Dorsal via:
+
+  ./dorsal.sh FEniCS/platforms/supported/myplatform.platform
+
+  the build script sets any platform specific variables defined in
+  myplatform.platform, and attempts to build and install each package
+  in the list PACKAGES. For each package in the list, it looks at the
+  corresponding package file for hints on how to treat the package.
+
+  Furthermore, when Dorsal is invoked without any arguments:
+
+  ./dorsal.sh
+
+  it tries to do an additional step. Dorsal first tries to guess an
+  appropriate platform file for your system (by probing your operating
+  system for something specific to it), and then proceeds to work on
+  that platform file.
+
+  That completes the story.
diff --git a/candi.cfg b/candi.cfg
new file mode 100644 (file)
index 0000000..96be80e
--- /dev/null
+++ b/candi.cfg
@@ -0,0 +1,75 @@
+# Global configuration variables go here. You will want to tweak this
+# file to suit your needs. If you want to keep local changes that are
+# not overwritten by repository updates, those can be written
+# to local.cfg instead (entries there will override those in this file).
+
+# Meta-project to build
+PROJECT=deal.II
+CLEAN_BUILD=false
+
+#########################################################################
+#Choose components of deal.II
+DEAL_CONFOPTS=" \
+-D CMAKE_BUILD_TYPE=DebugRelease \
+-D DEAL_II_COMPONENT_DOCUMENTATION:BOOL=OFF \
+-D DEAL_II_WITH_ARPACK:BOOL=OFF \
+-D DEAL_II_WITH_BOOST:BOOL=ON \
+-D DEAL_II_WITH_FUNCTIONPARSER:BOOL=ON \
+-D DEAL_II_WITH_LAPACK:BOOL=ON \
+-D DEAL_II_WITH_METIS:BOOL=OFF \
+-D DEAL_II_WITH_MUMPS:BOOL=OFF \
+-D DEAL_II_WITH_MPI:BOOL=ON \
+-D DEAL_II_WITH_NETCDF:BOOL=OFF \
+-D DEAL_II_WITH_P4EST:BOOL=ON \
+-D DEAL_II_WITH_PETSC:BOOL=ON \
+-D DEAL_II_WITH_SLEPC:BOOL=ON \
+-D DEAL_II_WITH_THREADS:BOOL=OFF \
+-D DEAL_II_WITH_TRILINOS:BOOL=ON \
+-D DEAL_II_WITH_UMFPACK:BOOL=ON \
+-D DEAL_II_WITH_ZLIB:BOOL=ON \
+-D DEAL_II_WITH_HDF5:BOOL=ON \
+"
+
+# Please add the following path(es) to DEAL_CONFOPTS ahead,
+# if you wish to use (self-compiled) versions of them together
+# with deal.II.
+# Make sure, that the coinciding option is setted to "ON".
+# If you want to use the packages from your system, you
+# may not set the variables (usually deal.II is smart enough
+# to recognise them automatically).
+# If you want to install the packages using CANDI,
+# simply set the option to ON and do NOT specify the path,
+# this will be done automatically elsewhere.
+#
+#-D ARPACK_DIR= \
+#-D METIS_DIR= \
+#-D MUMPS_DIR= \
+#-D P4EST_DIR= \
+#-D TRILINOS_DIR= \
+#-D HDF5_DIR= \
+
+#########################################################################
+# Prefix directory
+PREFIX_PATH=${HOME}/apps/candi
+COMPILER=native-openmpi
+
+# Where do you want the downloaded source files to go?
+DOWNLOAD_PATH=${PREFIX_PATH}/src
+
+# Where do you want to unpack source files to go?
+UNPACK_PATH=${PREFIX_PATH}/unpack
+
+# Where do you want the build files to go?
+BUILD_PATH=${PREFIX_PATH}/${PROJECT}/${COMPILER}-build
+
+# Where do you want the compiled software installed?
+INSTALL_PATH=${PREFIX_PATH}/${PROJECT}/${COMPILER}
+
+# How many processes would you like to build using?
+PROCS=1
+
+# Would you like to build stable versions of projects?
+# If STABLE_BUILD=false, then the development version of deal.II will be
+# installed.
+STABLE_BUILD=true
+
diff --git a/candi.sh b/candi.sh
new file mode 100755 (executable)
index 0000000..3ef631e
--- /dev/null
+++ b/candi.sh
@@ -0,0 +1,626 @@
+#!/usr/bin/env bash
+set -a
+
+#  Copyright (C) 2013-2014 by Uwe Koecher                                      #
+#  AND by the DORSAL Authors, cf. the file AUTHORS for details                 #
+#                                                                              #
+#  This file is part of CANDI.                                                 #
+#                                                                              #
+#  CANDI is free software: you can redistribute it and/or modify               #
+#  it under the terms of the GNU Lesser General Public License as              #
+#  published by the Free Software Foundation, either                           #
+#  version 2.1 of the License, or (at your option) any later version.          #
+#                                                                              #
+#  CANDI is distributed in the hope that it will be useful,                    #
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of              #
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               #
+#  GNU Lesser General Public License for more details.                         #
+#                                                                              #
+#  You should have received a copy of the GNU Lesser General Public License    #
+#  along with CANDI.  If not, see <http://www.gnu.org/licenses/>.              #
+
+#  REMARK: CANDI (Compile & Install) is a majorly tweaked and extended         #
+#          software based on DORSAL.                                           #
+#  The origin is DORSAL (also licensed under the LGPL):                        #
+#          https://bitbucket.org/fenics-project/dorsal/src                     #
+#          master c667be2 2013-11-27                                           #
+
+# The Unix date command does not work with nanoseconds, so use
+# the GNU date instead. This is available in the 'coreutils' package
+# from MacPorts.
+if builtin command -v gdate > /dev/null; then
+    DATE_CMD=$(which gdate)
+else
+    DATE_CMD=$(which date)
+fi
+
+# Start global timer
+TIC_GLOBAL="$(${DATE_CMD} +%s%N)"
+
+# Colours for progress and error reporting
+BAD="\033[1;31m"
+GOOD="\033[1;32m"
+WARN="\033[1;34m"
+BOLD="\033[1m"
+
+### Define helper functions ###
+
+prettify_dir() {
+   # Make a directory name more readable by replacing homedir with "~"
+   echo ${1/#$HOME\//~\/}
+}
+
+cecho() {
+    # Display messages in a specified colour
+    COL=$1; shift
+    echo -e "${COL}$@\033[0m"
+}
+
+default () {
+    # Export a variable, if it is not already set
+    VAR="${1%%=*}"
+    VALUE="${1#*=}"
+    eval "[[ \$$VAR ]] || export $VAR='$VALUE'"
+}
+
+quit_if_fail() {
+    # Exit with some useful information if something goes wrong
+    STATUS=$?
+    if [ ${STATUS} -ne 0 ]; then
+        cecho ${BAD} 'Failure with exit status:' ${STATUS}
+        cecho ${BAD} 'Exit message:' $1
+        exit ${STATUS}
+    fi
+}
+
+package_fetch () {
+    # First, make sure we're in the right directory before downloading
+    cd ${DOWNLOAD_PATH}
+
+    cecho ${GOOD} "Fetching ${NAME}"
+
+    # Fetch the package appropriately from its source
+    if [ ${PACKING} = ".tar.bz2" ] || [ ${PACKING} = ".tar.gz" ] || [ ${PACKING} = ".tbz2" ] || [ ${PACKING} = ".tgz" ] || [ ${PACKING} = ".tar.xz" ] || [ ${PACKING} = ".zip" ]; then
+        # Only download archives that do not exist
+        if [ ! -e ${NAME}${PACKING} ]; then
+            if [ ${STABLE_BUILD} = false ] && [ ${USE_SNAPSHOTS} = true ]; then
+                wget --retry-connrefused --no-check-certificate --server-response -c ${SOURCE}${NAME}${PACKING} -O ${NAME}${PACKING}
+            else
+                wget --retry-connrefused --no-check-certificate -c ${SOURCE}${NAME}${PACKING} -O ${NAME}${PACKING}
+            fi
+        fi
+
+        # Download again when using snapshots and unstable packages, but
+        # only when the timestamp has changed
+        if [ ${STABLE_BUILD} = false ] && [ ${USE_SNAPSHOTS} = true ]; then
+            wget --timestamping --retry-connrefused --no-check-certificate ${SOURCE}${NAME}${PACKING}
+        fi
+    elif [ ${PACKING} = "hg" ]; then
+        cd ${UNPACK_PATH}
+        # Suitably clone or update hg repositories
+        if [ ! -d ${NAME} ]; then
+            hg clone ${SOURCE}${NAME}
+        else
+            cd ${NAME}
+            hg pull --update
+            cd ..
+        fi
+    elif [ ${PACKING} = "svn" ]; then
+        cd ${UNPACK_PATH}
+        # Suitably check out or update svn repositories
+        if [ ! -d ${NAME} ]; then
+            svn co ${SOURCE} ${NAME}
+        else
+            cd ${NAME}
+            svn up
+            cd ..
+        fi
+    elif [ ${PACKING} = "git" ]; then
+        cd ${UNPACK_PATH}
+        # Suitably clone or update git repositories
+        if [ ! -d ${NAME} ]; then
+            git clone ${SOURCE}${NAME}
+        else
+            cd ${NAME}
+            git pull
+            cd ..
+        fi
+    elif [ ${PACKING} = "bzr" ]; then
+        cd ${UNPACK_PATH}
+        # Suitably branch or update bzr repositories
+        if [ ! -d ${NAME} ]; then
+            bzr branch ${SOURCE}${NAME}
+        else
+            cd ${NAME}
+            bzr pull
+            cd ..
+        fi
+    fi
+
+    # Quit with a useful message if something goes wrong
+    quit_if_fail "Error fetching ${NAME}."
+}
+
+package_verify() {
+    # First make sure we're in the right directory before verifying checksum
+    cd ${DOWNLOAD_PATH}
+
+    # Only need to verify archives
+    if [ ${PACKING} = ".tar.bz2" ] || [ ${PACKING} = ".tar.gz" ] ||  [ ${PACKING} = ".tbz2" ] || ${PACKING} = ".tgz" ] || [ ${PACKING} = ".tar.xz" ] || [ ${PACKING} = ".zip" ]; then
+        cecho ${GOOD} "Verifying ${NAME}${PACKING}"
+      
+        # Check checksum has been specified for the package
+        if [ -z "${CHECKSUM}" ]; then
+            cecho ${WARN} "No checksum for ${NAME}${PACKING}"
+            return 1
+        fi
+        
+        # Skip checksum if asked to ignore
+        if [ "${CHECKSUM}" = "ignore" ]; then
+            cecho ${WARN} "Skipped checksum check for ${NAME}${PACKING}"
+            return 1
+        fi
+        
+        # Make sure the archive was downloaded
+        if [ ! -e ${NAME}${PACKING} ]; then
+            cecho ${BAD} "${NAME}${PACKING} does not exist. Please download first."
+            exit 1
+        fi
+        
+        # Verify checksum using md5/md5sum
+        if builtin command -v md5 > /dev/null; then
+            test "${CHECKSUM}" = "$(md5 -q ${NAME}${PACKING})" && echo "${NAME}${PACKING}: OK"
+        elif builtin command -v md5sum > /dev/null; then
+            echo "${CHECKSUM}  ${NAME}${PACKING}" | md5sum --check -
+        else
+            cecho ${BAD} "Neither md5 nor md5sum were found in the PATH"
+            return 1
+        fi
+    fi
+    
+    # Quit with a useful message if something goes wrong
+    quit_if_fail "Error verifying checksum for ${NAME}${PACKING}"
+}
+
+
+package_unpack() {
+    # First make sure we're in the right directory before unpacking
+    cd ${UNPACK_PATH}
+    FILE_TO_UNPACK=${DOWNLOAD_PATH}/${NAME}${PACKING}
+
+    # Only need to unpack archives
+    if [ ${PACKING} = ".tar.bz2" ] || [ ${PACKING} = ".tar.gz" ] || [ ${PACKING} = ".tbz2" ] || [ ${PACKING} = ".tgz" ] || [ ${PACKING} = ".tar.xz" ] || [ ${PACKING} = ".zip" ]; then
+        cecho ${GOOD} "Unpacking ${NAME}"
+        # Make sure the archive was downloaded
+        if [ ! -e ${FILE_TO_UNPACK} ]; then
+            cecho ${BAD} "${FILE_TO_UNPACK} does not exist. Please download first."
+            exit 1
+        fi
+
+        # Unpack the archive only if it isn't already or when using
+        # snapshots and unstable packages
+        if [ ${STABLE_BUILD} = false ] && [ ${USE_SNAPSHOTS} = true ] || [ ! -d "${EXTRACTSTO}" ]; then
+            # Unpack the archive in accordance with its packing
+            if [ ${PACKING} = ".tar.bz2" ] || [ ${PACKING} = ".tbz2" ]; then
+                tar xjf ${FILE_TO_UNPACK}
+            elif [ ${PACKING} = ".tar.gz" ] || [ ${PACKING} = ".tgz" ]; then
+                tar xzf ${FILE_TO_UNPACK}
+            elif [ ${PACKING} = ".tar.xz" ]; then
+                tar xJf ${FILE_TO_UNPACK}
+            elif [ ${PACKING} = ".zip" ]; then
+                unzip ${FILE_TO_UNPACK}
+            fi
+        fi
+    fi
+
+    unset FILE_TO_UNPACK
+
+    # Quit with a useful message if something goes wrong
+    quit_if_fail "Error unpacking ${NAME}."
+}
+
+package_build() {
+    # Get things ready for the compilation process
+    cecho ${GOOD} "Building ${NAME}"
+    if [ ! -d "${EXTRACTSTO}" ]; then
+        cecho ${BAD} "${EXTRACTSTO} does not exist -- please unpack first."
+        exit 1
+    fi
+
+    # Set the BUILDDIR if nothing else was specified
+    default BUILDDIR=${BUILD_PATH}/${NAME}
+
+    # Clean the build directory if specified
+    if [ -d ${BUILDDIR} ] && [ ${CLEAN_BUILD} = "true" ]; then
+        rm -rf ${BUILDDIR}
+    fi
+
+    # Create build directory if it does not exist
+    if [ ! -d ${BUILDDIR} ]; then
+        mkdir -p ${BUILDDIR}
+    fi
+
+    # Move to the build directory
+    cd ${BUILDDIR}
+
+    # Carry out any package-specific setup
+    package_specific_setup
+    quit_if_fail "There was a problem in build setup for ${NAME}."
+
+    # Use the appropriate build system to compile and install the
+    # package
+    for cmd_file in candi_configure candi_build; do
+        echo "#!/usr/bin/env bash" >${cmd_file}
+        chmod a+x ${cmd_file}
+
+        # Write variables to files so that they can be run stand-alone
+        declare -x| grep -v "!::"| grep -v "ProgramFiles(x86)" >>${cmd_file}
+
+        # From this point in candi_*, errors are fatal
+        echo "set -e" >>${cmd_file}
+    done
+
+    if [ ${BUILDCHAIN} = "autotools" ]; then
+        if [ -f ${UNPACK_PATH}/${EXTRACTSTO}/configure ]; then
+            echo ${UNPACK_PATH}/${EXTRACTSTO}/configure ${CONFOPTS} --prefix=${INSTALL_PATH} >>candi_configure
+        fi
+
+        for target in "${TARGETS[@]}"; do
+            echo make ${MAKEOPTS} -j ${PROCS} $target >>candi_build
+        done
+    elif [ ${BUILDCHAIN} = "python" ]; then
+        echo cp -rf ${UNPACK_PATH}/${EXTRACTSTO}/* . >>candi_configure
+        echo python setup.py install --prefix=${INSTALL_PATH} >>candi_build
+    elif [ ${BUILDCHAIN} = "scons" ]; then
+        echo cp -rf ${UNPACK_PATH}/${EXTRACTSTO}/* . >>candi_configure
+        for target in "${TARGETS[@]}"; do
+            echo scons -j ${PROCS} ${SCONSOPTS} prefix=${INSTALL_PATH} $target >>candi_build
+        done
+    elif [ ${BUILDCHAIN} = "cmake" ]; then
+        echo cmake ${CONFOPTS} -DCMAKE_INSTALL_PREFIX=${INSTALL_PATH} ${UNPACK_PATH}/${EXTRACTSTO} >>candi_configure
+        for target in "${TARGETS[@]}"; do
+            echo make ${MAKEOPTS} -j ${PROCS} $target >>candi_build
+        done
+#        for target in "${TARGETS[@]}"; do
+#            echo make -C ${BUILDDIR} ${MAKEOPTS} -j ${PROCS} $target >>candi_build
+#        done
+    elif [ ${BUILDCHAIN} = "custom" ]; then
+        # Write the function definition to file
+        declare -f package_specific_build >>candi_build
+        echo package_specific_build >>candi_build
+    fi
+    echo "touch candi_successful_build" >> candi_build
+
+    # Run the generated build scripts
+    if [ ${BASH_VERSINFO} -ge 3 ]; then
+        set -o pipefail
+        ./candi_configure 2>&1 | tee candi_configure.log
+    else
+        ./candi_configure
+    fi
+    quit_if_fail "There was a problem configuring ${NAME}."
+
+    if [ ${BASH_VERSINFO} -ge 3 ]; then
+        set -o pipefail
+        ./candi_build 2>&1 | tee candi_build.log
+    else
+        ./candi_build
+    fi
+    quit_if_fail "There was a problem building ${NAME}."
+
+    # Carry out any package-specific post-build instructions
+    package_specific_install
+    quit_if_fail "There was a problem in post-build instructions for ${NAME}."
+}
+
+package_register() {
+    # Set any package-specific environment variables
+    package_specific_register
+    quit_if_fail "There was a problem setting environment variables for ${NAME}."
+}
+
+package_conf() {
+    # Write any package-specific environment variables to a config file,
+    # i.e. e.g. a modulefile or source-able *.conf file
+    package_specific_conf
+    quit_if_fail "There was a problem creating the configfiles for ${NAME}."
+}
+
+guess_platform() {
+    # Try to guess the name of the platform we're running on
+    if [ -f /usr/bin/cygwin1.dll ]
+    then
+        echo cygwin
+    elif [ -f /etc/fedora-release ]
+    then
+        local FEDORANAME=`gawk '{if (match($0,/\((.*)\)/,f)) print f[1]}' /etc/fedora-release`
+        case ${FEDORANAME} in
+            "Schrödinger’s Cat"*) echo fedora19;;
+            Heisenbug*)           echo fedora20;;
+        esac
+    elif [ -x /usr/bin/sw_vers ]
+    then
+        local MACOSVER=$(sw_vers -productVersion)
+        case ${MACOSVER} in
+            10.4*)    echo tiger;;
+            10.5*)    echo leopard;;
+            10.6*)    echo snowleopard;;
+            10.7*)    echo lion;;
+            10.8*)    echo mountainlion;;
+    esac
+    elif [ -x /usr/bin/lsb_release ]; then
+        local DISTRO=$(lsb_release -i -s)
+        local CODENAME=$(lsb_release -c -s)
+        local DESCRIPTION=$(lsb_release -d -s)
+        case ${DISTRO}:${CODENAME}:${DESCRIPTION} in
+            *:*:*Ubuntu*\ 13*)     echo ubuntu13;;
+            *:Tikanga*:*)          echo rhel5;;
+            *:Santiago*:*)         echo rhel6;;
+            Scientific:Carbon*:*)  echo rhel6;;
+            *:*:*CentOS*\ 5*)      echo rhel5;;
+            *:*:*CentOS*\ 6*)      echo rhel6;;
+            *:*:*openSUSE\ 12*)    echo opensuse12;;
+            *:*:*openSUSE\ 13*)    echo opensuse13;;
+        esac
+    fi
+}
+
+guess_architecture() {
+    # Try to guess the architecture of the platform we are running on
+    ARCH=unknown
+    if [ -x /usr/bin/uname -o -x /bin/uname ]
+    then
+        ARCH=`uname -m`
+    fi
+}
+
+###############################################################################
+# Start the build process
+
+export ORIG_DIR=`pwd`
+
+# Read configuration variables from candi.cfg
+source candi.cfg
+
+# For changes specific to your local setup or for debugging, use local.cfg
+if [ -f local.cfg ]; then
+    source local.cfg
+fi
+
+# If any variables are missing, revert them to defaults
+default PROJECT=deal.II
+default DOWNLOAD_PATH=${HOME}/apps/candi/${PROJECT}/src
+default UNPACK_PATH=${HOME}/apps/candi/${PROJECT}/unpack
+default BUILD_PATH=${HOME}/apps/candi/${PROJECT}/build
+default CLEAN_BUILD=false
+default INSTALL_PATH=${HOME}/apps/candi/${PROJECT}
+default PROCS=1
+default STABLE_BUILD=true
+default USE_SNAPSHOTS=false
+
+# Check if project was specified correctly
+if [ -d ${PROJECT} ]; then
+    if [ -d ${PROJECT}/platforms -a -d ${PROJECT}/packages ]; then
+        cecho ${GOOD} "Found configuration for project ${PROJECT}."
+    else
+        cecho ${BAD} "No subdirectories 'platforms' and 'packages' in ${PROJECT}."
+        echo "Please make sure there exists proper project configuration directory."
+        exit 1
+    fi
+else
+    cecho ${BAD} "Error: No project configuration directory found for project ${PROJECT}."
+    echo "Please check if you have specified right project name in candi.cfg"
+    echo "Please check if you have directory called ${PROJECT}"
+    echo "with subdirectories ${PROJECT}/platforms and ${PROJECT}/packages"
+    exit 1
+fi
+
+# Check if candi.sh was invoked correctly
+if [ $# -eq 0 ]; then
+    PLATFORM_SUPPORTED=${PROJECT}/platforms/supported/`guess_platform`.platform
+    PLATFORM_CONTRIBUTED=${PROJECT}/platforms/contributed/`guess_platform`.platform
+    PLATFORM_DEPRECATED=${PROJECT}/platforms/deprecated/`guess_platform`.platform
+    if [ -e ${PLATFORM_SUPPORTED} ]; then
+        PLATFORM=${PLATFORM_SUPPORTED}
+        cecho ${GOOD} "Building ${PROJECT} using ${PLATFORM}."
+    elif [ -e ${PLATFORM_CONTRIBUTED} ]; then
+        PLATFORM=${PLATFORM_CONTRIBUTED}
+        cecho ${GOOD} "Building ${PROJECT} using ${PLATFORM}."
+        cecho ${BOLD} "Warning: Platform is not officially supported but may still work!"
+    elif [ -e ${PLATFORM_DEPRECATED} ]; then
+        PLATFORM=${PLATFORM_DEPRECATED}
+        cecho ${GOOD} "Building ${PROJECT} using ${PLATFORM}."
+        cecho ${BAD} "Warning: Platform is deprecated and will be removed shortly but may still work!"
+    else
+       cecho ${BAD} "Error: Platform to build for not specified (and not automatically recognised)."
+       echo "If you know the platform you are interested in (myplatform), please specify it directly, as:"
+       echo "./candi.sh ${PROJECT}/platforms/myplatform.platform"
+       echo "If you'd like to learn more, refer to the file USAGE for detailed usage instructions."
+       exit 1
+    fi
+    echo "-------------------------------------------------------------------------------"
+    # Show the initial comments in the platform file, as it often
+    # contains instructions about packages that should be installed
+    # first, etc. Remove first field '#' so that cut-and-paste of
+    # e.g. apt-get commands is easy.
+    awk '/^##/ {exit} {$1=""; print}' <${PLATFORM}
+    echo
+    echo "Downloading files to:   $(prettify_dir ${DOWNLOAD_PATH})"
+    echo "Unpacking files to:   $(prettify_dir ${UNPACK_PATH})"
+    echo "Building projects in: $(prettify_dir ${BUILD_PATH})"
+    echo "Installing projects in: $(prettify_dir ${INSTALL_PATH})"
+    echo
+    if [ ${STABLE_BUILD} = true ]; then
+        echo "Building stable point-releases of ${PROJECT} projects."
+    else
+        if [ ${USE_SNAPSHOTS} = true ]; then
+           echo "Building development versions of ${PROJECT} projects (using snapshots)."
+        else
+            echo "Building development versions of ${PROJECT} projects."
+        fi
+    fi
+    echo "-------------------------------------------------------------------------------"
+    cecho ${GOOD} "Please make sure you've read the instructions above and your system"
+    cecho ${GOOD} "is ready for installing ${PROJECT}. We find it easiest to copy and paste"
+    cecho ${GOOD} "these instructions in another terminal window."
+
+    if builtin command -v module > /dev/null; then
+        echo ""
+        echo "-------------------------------------------------------------------------------"
+        cecho ${GOOD} "$(module list)"
+        echo "-------------------------------------------------------------------------------"
+    fi
+    
+    echo ""
+    cecho ${GOOD} "Once ready, hit enter to continue!"
+    read
+elif [ $# -eq 1 ]; then
+    PLATFORM=${1}
+elif [ $# -eq 2 ]; then
+    # Check if the user wants to install a single package
+    if [ ${1} == "install-package" ]; then
+        PACKAGE=${2}
+        # Check if the package exists
+        if [ ! -e ${PROJECT}/packages/${PACKAGE}.package ]; then
+            cecho ${BAD} "${PROJECT}/packages/${PACKAGE}.package does not exist yet. Please create it."
+            exit 1
+        fi
+        PACKAGES=(${PACKAGE})
+        PLATFORM="${PROJECT}/platforms/.single"
+    else
+        echo "If you'd like to install a single package, please use the syntax:"
+        echo "./candi.sh install-package foo"
+        exit 1
+    fi
+fi
+
+# Make sure the requested platform exists
+if [ -e "${PLATFORM}" ]; then
+    source ${PLATFORM}
+else
+    cecho ${BAD} "Platform set '${PLATFORM}' not found. Refer to the file README to check if your platform is supported."
+    exit 1
+fi
+
+# If the platform doesn't override the system python by installing its
+# own, figure out the version of the existing python
+default PYTHONVER=`python -c "import sys; print sys.version[:3]"`
+
+# Create necessary directories and set appropriate variables
+mkdir -p ${DOWNLOAD_PATH}
+mkdir -p ${UNPACK_PATH}
+mkdir -p ${BUILD_PATH}
+mkdir -p ${INSTALL_PATH}
+
+ORIG_INSTALL_PATH=${INSTALL_PATH}
+ORIG_PROCS=${PROCS}
+guess_architecture
+
+# Reset timings
+TIMINGS=""
+
+# Fetch and build individual packages
+for PACKAGE in ${PACKAGES[@]}; do
+    # Start timer
+    TIC="$(${DATE_CMD} +%s%N)"
+    
+    # Return to the main CANDI directory
+    cd ${ORIG_DIR}
+    
+    # Skip building this package if the user requests it
+    SKIP=false
+    case ${PACKAGE} in
+        skip:*) SKIP=true;  PACKAGE=${PACKAGE#*:};;
+        once:*) SKIP=maybe; PACKAGE=${PACKAGE#*:};;
+    esac
+    
+    # Check if the package exists
+    if [ ! -e ${PROJECT}/packages/${PACKAGE}.package ]; then
+        cecho ${BAD} "${PROJECT}/packages/${PACKAGE}.package does not exist yet. Please create it."
+        exit 1
+    fi
+    
+    # Reset package-specific variables
+    unset NAME
+    unset VERSION
+    unset SOURCE
+    unset PACKING
+    unset EXTRACTSTO
+    unset CHECKSUM
+    unset BUILDCHAIN
+    unset BUILDDIR
+    unset CONFOPTS
+    unset MAKEOPTS
+    unset SCONSOPTS
+    unset CONFIG_FILE
+    TARGETS=('' install)
+    PROCS=${ORIG_PROCS}
+    INSTALL_PATH=${ORIG_INSTALL_PATH}
+    
+    # Reset package-specific functions
+    package_specific_setup () { true; }
+    package_specific_build () { true; }
+    package_specific_install () { true; }
+    package_specific_register () { true; }
+    package_specific_conf() { true; }
+
+    # Fetch information pertinent to the package
+    source ${PROJECT}/packages/${PACKAGE}.package
+    
+    # Turn to a stable version of the package if that's what the user
+    # wants and it exists
+    if [ ${STABLE_BUILD} = true ] && [ -e ${PROJECT}/packages/${PACKAGE}-stable.package ]; then
+        source ${PROJECT}/packages/${PACKAGE}-stable.package
+    elif [ ${STABLE_BUILD} = false ] && [ ${USE_SNAPSHOTS} = true ] && [ -e ${PROJECT}/packages/${PACKAGE}-snapshot.package ]; then
+        source ${PROJECT}/packages/${PACKAGE}-snapshot.package
+    fi
+    
+    # Ensure that the package file is sanely constructed
+    if [ ! "${BUILDCHAIN}" ]; then
+        cecho ${BAD} "${PACKAGE}.package is not properly formed. Please check that all necessary variables are defined."
+        exit 1
+    fi
+
+    if [ ! "${BUILDCHAIN}" = "ignore" ] ; then
+        if [ ! "${NAME}" ] || [ ! "${SOURCE}" ] || [ ! "${PACKING}" ]; then
+            cecho ${BAD} "${PACKAGE}.package is not properly formed. Please check that all necessary variables are defined."
+            exit 1
+        fi
+    fi
+    
+    # Most packages extract to a directory named after the package
+    default EXTRACTSTO=${NAME}
+
+    if [ ${SKIP} = maybe ] && [ ! -f ${BUILD_PATH}/${NAME}/candi_successful_build ]; then
+        SKIP=false
+    fi
+    
+    # Fetch, unpack and build package
+    if [ ${SKIP} = false ]; then
+        # Fetch, unpack and build the current package
+        package_fetch
+        package_verify
+        package_unpack
+        package_build
+    else
+        # Let the user know we're skipping the current package
+        cecho ${GOOD} "Skipping ${NAME}"
+    fi
+    package_register
+    package_conf
+    
+    # Store timing
+    TOC="$(($(${DATE_CMD} +%s%N)-TIC))"
+    TIMINGS="$TIMINGS"$"\n""$PACKAGE: ""$((TOC/1000000000)) s"
+done
+
+# Stop global timer
+TOC_GLOBAL="$(($(${DATE_CMD} +%s%N)-TIC_GLOBAL))"
+
+# Display a summary
+echo
+cecho ${GOOD} "Build finished in $((TOC_GLOBAL/1000000000)) seconds."
+echo
+echo "Summary of timings:"
+echo -e "$TIMINGS"
+
diff --git a/deal.II/packages/boost.package b/deal.II/packages/boost.package
new file mode 100644 (file)
index 0000000..025f136
--- /dev/null
@@ -0,0 +1,27 @@
+NAME=boost_1_55_0
+SOURCE=http://downloads.sourceforge.net/boost/
+PACKING=.tar.bz2
+CHECKSUM=d6eef4b4cacb2183f2bf265a5a03a354
+BUILDCHAIN=custom
+
+if [ ! -z "${BZIP2_DIR}" ]; then
+    CONFOPTS="${CONFOPTS}
+              -sNO_BZIP2=0
+              -sBZIP2_BINARY=bz2
+              -sBZIP2_INCLUDE=${BZIP2_DIR}/include
+              -sBZIP2_LIBPATH=${BZIP2_DIR}/lib"
+fi
+
+package_specific_build () {
+    cp -rf ${UNPACK_PATH}/${NAME}/* .
+    ./bootstrap.sh --prefix=${INSTALL_PATH}
+    echo "using mpi ;" > user-config.jam
+    ./b2 -j ${PROCS} --user-config=user-config.jam --build-dir=candi_build_dir link=shared install ${CONFOPTS}
+}
+
+package_specific_register () {
+    export BOOST_ROOT=${INSTALL_PATH}
+    export BOOST_INCLUDEDIR=${INSTALL_PATH}/include
+    export BOOST_LIBRARYDIR=${INSTALL_PATH}/lib
+    export BOOST_USE_MULTITHREADED=OFF
+}
diff --git a/deal.II/packages/dealii-snapshot.package b/deal.II/packages/dealii-snapshot.package
new file mode 100644 (file)
index 0000000..1ef1236
--- /dev/null
@@ -0,0 +1,47 @@
+NAME=deal.II-svn
+SOURCE=https://svn.dealii.org/trunk/deal.II
+PACKING=svn
+BUILDCHAIN=custom
+
+CONFOPTS=" \
+${DEAL_CONFOPTS} \
+"
+
+CONFOPTS="${CONFOPTS} \
+-D HDF5_DIR=${HDF5_DIR} \
+"
+
+CONFOPTS="${CONFOPTS} \
+-D TRILINOS_DIR=${TRILINOS_DIR} \
+"
+
+CONFOPTS="${CONFOPTS} \
+-D PETSC_DIR=${PETSC_DIR} \
+"
+
+CONFOPTS="${CONFOPTS} \
+-D SLEPC_DIR=${SLEPC_DIR} \
+"
+
+CONFOPTS="${CONFOPTS} \
+-D CMAKE_INSTALL_PREFIX:PATH="${INSTALL_PATH}" \
+"
+
+package_specific_setup () {
+    echo "Build ${NAME} in ${BUILD_PATH}/${NAME}"
+    mkdir -p "${BUILD_PATH}/${NAME}"
+    cd "${BUILD_PATH}/${NAME}"
+
+    DEALII_SOURCE="${DOWNLOAD_PATH}/${EXTRACTSTO}"
+
+    # configure
+    cmake ${CONFOPTS} ${DEALII_SOURCE}
+
+    # make
+    make -j${PROCS}
+    make install
+}
+
+package_specific_register () {
+    export DEALII_DIR=${INSTALL_PATH}
+}
diff --git a/deal.II/packages/dealii-stable.package b/deal.II/packages/dealii-stable.package
new file mode 100644 (file)
index 0000000..281d946
--- /dev/null
@@ -0,0 +1,8 @@
+VERSION=8.1.0
+NAME=deal.II-${VERSION}
+SOURCE=https://dealii.googlecode.com/files/
+PACKING=.tar.gz
+CHECKSUM=aa8fadc2ce5eb674f44f997461bf668d
+BUILDCHAIN=cmake
+EXTRACTSTO=deal.II
+
diff --git a/deal.II/packages/dealii.package b/deal.II/packages/dealii.package
new file mode 100644 (file)
index 0000000..4a80bda
--- /dev/null
@@ -0,0 +1,60 @@
+VERSION=svn
+NAME=deal.II-${VERSION}
+SOURCE=https://svn.dealii.org/trunk/deal.II
+PACKING=svn
+BUILDCHAIN=cmake
+
+CONFOPTS=" \
+${DEAL_CONFOPTS} \
+"
+
+CONFOPTS="${CONFOPTS} \
+-D HDF5_DIR=${HDF5_DIR} \
+"
+
+CONFOPTS="${CONFOPTS} \
+-D TRILINOS_DIR=${TRILINOS_DIR} \
+"
+
+CONFOPTS="${CONFOPTS} \
+-D PETSC_DIR=${PETSC_DIR} \
+"
+
+CONFOPTS="${CONFOPTS} \
+-D SLEPC_DIR=${SLEPC_DIR} \
+"
+
+# **********************************************************************************
+package_specific_conf() {
+MODULEFILE_PATH=${INSTALL_PATH}/conf/modulefiles/deal.II/${COMPILER}
+CONFIG_FILE=${MODULEFILE_PATH}/${VERSION}
+CURRENT_MODULES=$(echo ${LOADEDMODULES} | sed 's/:/\ /')
+
+    # Generate modulefile
+    
+    mkdir -p ${MODULEFILE_PATH}
+    rm -f $CONFIG_FILE
+    echo "#%Module 1.0
+#
+#  deal.II module for use with 'environment-modules' package:
+#
+module-whatis          "Provides the deal.II toolbox."
+conflict                deal.II
+module load ${CURRENT_MODULES}
+
+setenv                  DEAL_II_DIR         ${INSTALL_PATH}
+" >> $CONFIG_FILE
+    
+    echo
+    echo "${NAME} has now been installed in"
+    echo
+    cecho ${GOOD} "    ${INSTALL_PATH}"
+    echo
+    echo "To update your environment variables, use the created modulefile:"
+    echo
+    cecho ${GOOD} "    $CONFIG_FILE"
+    echo
+
+    export DEAL_II_DIR=${INSTALL_PATH}
+}
+
diff --git a/deal.II/packages/hdf5.package b/deal.II/packages/hdf5.package
new file mode 100644 (file)
index 0000000..5ec2792
--- /dev/null
@@ -0,0 +1,13 @@
+VERSION=1.8.12
+NAME=hdf5-${VERSION}
+SOURCE=http://www.hdfgroup.org/ftp/HDF5/releases/${NAME}/src/
+PACKING=.tar.gz
+CHECKSUM=d804802feb99b87fc668a90e6fa34411
+BUILDCHAIN=autotools
+
+CONFOPTS="--enable-shared --enable-parallel"
+
+package_specific_register () {
+    export HDF5_DIR=${INSTALL_PATH}
+}
+
diff --git a/deal.II/packages/hwloc.package b/deal.II/packages/hwloc.package
new file mode 100644 (file)
index 0000000..e0bbdc0
--- /dev/null
@@ -0,0 +1,7 @@
+VERSION=1.9
+NAME=hwloc-${VERSION}
+SOURCE=http://www.open-mpi.org/software/hwloc/v${VERSION}/downloads/
+PACKING=.tar.gz
+CHECKSUM=1f9f9155682fe8946a97c08896109508
+BUILDCHAIN=autotools
+
diff --git a/deal.II/packages/p4est.package b/deal.II/packages/p4est.package
new file mode 100644 (file)
index 0000000..bc1555b
--- /dev/null
@@ -0,0 +1,89 @@
+NAME=p4est-0.3.4.2
+SOURCE=http://www.p4est.org/tarball/
+PACKING=.tar.gz
+CHECKSUM=ef38ea3be84628b1548188106a5b01e7
+BUILDCHAIN=custom
+
+package_specific_setup () {
+    function bdie () {
+        echo "Error: $@"
+        exit 1
+    }
+
+    if test -z "$CFLAGS" -a -z "$P4EST_CFLAGS_FAST" ; then
+        export CFLAGS_FAST="-O2"
+    else
+        export CFLAGS_FAST="$CFLAGS $P4EST_CFLAGS_FAST"
+    fi
+    echo "CFLAGS_FAST: $CFLAGS_FAST"
+    
+    if test -z "$CFLAGS" -a -z "$P4EST_CFLAGS_DEBUG" ; then
+        export CFLAGS_DEBUG="-O0 -g"
+    else
+        export CFLAGS_DEBUG="$CFLAGS $P4EST_CFLAGS_DEBUG"
+    fi
+    echo "CFLAGS_DEBUG: $CFLAGS_DEBUG"
+
+    # choose names for fast and debug build directories
+    BUILD_FAST="${BUILD_PATH}/${NAME}/FAST"
+    BUILD_DEBUG="${BUILD_PATH}/${NAME}/DEBUG"
+
+    # choose names for fast and debug installation directories
+    INSTALL_FAST="${INSTALL_PATH}/${NAME}/FAST"
+    INSTALL_DEBUG="${INSTALL_PATH}/${NAME}/DEBUG"
+    
+    echo
+    echo "This script tries configure and build the p4est library."
+    echo "Build FAST: $BUILD_FAST"
+    echo "Build DEBUG: $BUILD_DEBUG"
+    echo "Install FAST: $INSTALL_FAST"
+    echo "Install DEBUG: $INSTALL_DEBUG"
+    echo "Checking environment: CFLAGS P4EST_CFLAGS_FAST P4EST_CFLAGS_DEBUG"
+
+    test -f "${UNPACK_PATH}/${EXTRACTSTO}/src/p4est.h" || bdie "Main header file missing"
+    test -f "${UNPACK_PATH}/${EXTRACTSTO}/configure" || bdie "Configure script missing"
+    
+    echo "See output in files .../config.output and .../make.output"
+    echo
+    
+    # remove old versions
+    if test -d "${BUILD_PATH}/${NAME}"; then
+        rm -rf "${BUILD_PATH}/${NAME}"
+    fi
+
+    echo "Build FAST version in $BUILD_FAST"
+    mkdir -p "$BUILD_FAST"
+    cd "$BUILD_FAST"
+    "${UNPACK_PATH}/${EXTRACTSTO}/configure" --enable-mpi --enable-shared \
+        --disable-vtk-binary --without-blas \
+        --prefix="$INSTALL_FAST" CFLAGS="$CFLAGS_FAST" \
+        CPPFLAGS="-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL" \
+        "$@" > config.output || bdie "Error in configure"
+    make -C sc -j${PROCS} > make.output || bdie "Error in make sc"
+    make -j${PROCS} >> make.output || bdie "Error in make p4est"
+    make install >> make.output || bdie "Error in make install"
+    echo "FAST version installed in $INSTALL_FAST"
+    
+    echo
+    echo "Build DEBUG version in $BUILD_DEBUG"
+    mkdir -p "$BUILD_DEBUG"
+    cd "$BUILD_DEBUG"
+    "${UNPACK_PATH}/${EXTRACTSTO}/configure" --enable-debug --enable-mpi --enable-shared \
+        --disable-vtk-binary --without-blas \
+        --prefix="$INSTALL_DEBUG" CFLAGS="$CFLAGS_DEBUG" \
+        CPPFLAGS="-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL" \
+        "$@" > config.output || bdie "Error in configure"
+    make -C sc -j${PROCS} > make.output || bdie "Error in make sc"
+    make -j${PROCS} >> make.output || bdie "Error in make p4est"
+    make install >> make.output || bdie "Error in make install"
+    echo "DEBUG version installed in $INSTALL_DEBUG"
+    echo
+    
+    cd "${BUILD_PATH}/${NAME}"
+    touch dorsal_successful_build
+}
+
+
+package_specific_register () {
+    export P4EST_DIR=${INSTALL_PATH}/${NAME}
+}
diff --git a/deal.II/packages/petsc.package b/deal.II/packages/petsc.package
new file mode 100644 (file)
index 0000000..b95cb27
--- /dev/null
@@ -0,0 +1,63 @@
+VERSION=3.4.4
+NAME=petsc-${VERSION}
+SOURCE=http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/
+PACKING=.tar.gz
+CHECKSUM=7edbc68aa6d8d6a3295dd5f6c2f6979d
+BUILDCHAIN=custom
+
+CONFOPTS="
+  --with-debugging=0
+  --with-shared-libraries=1
+  --with-mpi=1
+  --with-x=0
+"
+
+for external_pkg in hypre; do
+    CONFOPTS="${CONFOPTS} --download-${external_pkg}=1"
+done
+
+if [ "$CC" ]; then
+    CONFOPTS="${CONFOPTS} CC=$CC"
+fi
+
+if [ "$CXX" ]; then
+    CONFOPTS="${CONFOPTS} CXX=$CXX"
+fi
+
+if [ "$FC" ]; then
+    CONFOPTS="${CONFOPTS} FC=$FC"
+fi
+
+if [ "$F77" ]; then
+    CONFOPTS="${CONFOPTS} F77=$F77"
+fi
+
+if [ "$F90" ]; then
+    CONFOPTS="${CONFOPTS} F90=$F90"
+fi
+
+if [ "${TRILINOS_DIR}" ]; then
+    CONFOPTS="${CONFOPTS} --with-ml=1
+              --with-ml-lib=${TRILINOS_DIR}/lib/libml.so
+              --with-ml-include=${TRILINOS_DIR}/include"
+fi
+
+if [ "${CUDA_DIR}" ] && [ "${CUSP_DIR}" ]; then
+    CONFOPTS="${CONFOPTS} --with-cuda=1 --with-cuda-dir=${CUDA_DIR}
+    --with-cusp=1 --with-cusp-dir=${CUSP_DIR}
+    --with-thrust=1 --with-thrust-dir=${CUDA_DIR}/include"
+fi
+
+package_specific_setup () {
+    cd ${BUILDDIR}
+    cp -rf ${UNPACK_PATH}/${EXTRACTSTO}/* .
+    
+    ./configure --prefix=${INSTALL_PATH}/${NAME} ${CONFOPTS}
+    
+    make all test install
+}
+
+package_specific_register () {
+    export PETSC_DIR=${INSTALL_PATH}/${NAME}
+}
+
diff --git a/deal.II/packages/slepc.package b/deal.II/packages/slepc.package
new file mode 100644 (file)
index 0000000..90c31a5
--- /dev/null
@@ -0,0 +1,19 @@
+VERSION=3.4.4
+NAME=slepc-${VERSION}
+SOURCE=http://www.grycap.upv.es/slepc/download/download.php?filename=
+PACKING=.tar.gz
+CHECKSUM=329179c5139027c7b293dd5ab0bc112c
+BUILDCHAIN=custom
+
+package_specific_setup () {
+    cd ${BUILDDIR}
+    cp -rf ${UNPACK_PATH}/${EXTRACTSTO}/* .
+    
+    ./configure --prefix=${INSTALL_PATH}/${NAME} ${CONFOPTS}
+    make SLEPC_DIR=$PWD PETSC_DIR=${PETSC_DIR} PETSC_ARCH=arch-installed-petsc all test install
+}
+
+package_specific_register () {
+    export SLEPC_DIR=${INSTALL_PATH}/${NAME}
+}
+
diff --git a/deal.II/packages/trilinos.package b/deal.II/packages/trilinos.package
new file mode 100644 (file)
index 0000000..4b7e3e2
--- /dev/null
@@ -0,0 +1,27 @@
+VERSION=11.8.1
+NAME=trilinos-${VERSION}-Source
+SOURCE=http://trilinos.sandia.gov/download/files/
+PACKING=.tar.gz
+CHECKSUM=3c9465b6d63d824e9dc0365ca73c3370
+BUILDCHAIN=cmake
+
+CONFOPTS="-D Trilinos_ENABLE_OpenMP:BOOL=OFF \
+          -D TPL_ENABLE_TBB:BOOL=OFF \
+          -D Trilinos_ENABLE_OPTIONAL_PACKAGES:BOOL=ON \
+          -D Trilinos_ENABLE_Didasko:BOOL=ON \
+          -D Trilinos_ENABLE_Sacado:BOOL=ON \
+          -D Trilinos_ENABLE_Stratimikos:BOOL=ON \
+          -D CMAKE_BUILD_TYPE:STRING=RELEASE \
+          -D CMAKE_CXX_FLAGS:STRING=-fPIC -g -O3 \
+          -D CMAKE_C_FLAGS:STRING=-fPIC -g -O3 \
+          -D CMAKE_FORTRAN_FLAGS:STRING=-g -O5 \
+          -D Trilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran \
+          -D CMAKE_VERBOSE_MAKEFILE:BOOL=FALSE \
+          -D Trilinos_VERBOSE_CONFIGURE:BOOL=FALSE \
+          -D TPL_ENABLE_MPI:BOOL=ON \
+          -D BUILD_SHARED_LIBS:BOOL=ON"
+
+package_specific_register () {
+    export TRILINOS_DIR=${INSTALL_PATH}
+}
+
diff --git a/deal.II/platforms/.single b/deal.II/platforms/.single
new file mode 100644 (file)
index 0000000..e69de29
diff --git a/deal.II/platforms/supported/cygwin.platform b/deal.II/platforms/supported/cygwin.platform
new file mode 100644 (file)
index 0000000..e9e31bb
--- /dev/null
@@ -0,0 +1,32 @@
+# cygwin
+# 
+# This build script assumes that you have several packages already
+# installed:
+#
+# subversion, git, development-tools (gcc, g++, autoconf, automake, cmake)
+# openmpi, blas, lapack (development packages also!)
+# Please also make sure, that in your local.cfg only the indended packages
+# are switched ON.
+# 
+# Issues:
+# - p4est will NOT compile without errors
+# - boost 1.55 will NOT compile without errors
+# 
+# Untested:
+# - MPI
+# - Trilinos, PetSC, Slepc
+# 
+##
+
+#
+# Define the packages this platform needs
+PACKAGES=(
+#once:boost
+#once:hdf5
+#once:p4est
+#once:trilinos
+#once:petsc
+#once:slepc
+dealii
+)
+
diff --git a/deal.II/platforms/supported/fedora19.platform b/deal.II/platforms/supported/fedora19.platform
new file mode 100644 (file)
index 0000000..d6f9609
--- /dev/null
@@ -0,0 +1,27 @@
+# Fedora 19
+
+# This build script assumes that you have several packages already
+# installed via Fedora's yum using the following command:
+#
+# su -c 'yum install -y svn \
+# @development-tools gcc-c++ cmake \
+# blas blas-devel lapack lapack-devel \
+# doxygen graphviz graphviz-devel qt-devel '
+# 
+# ARPACK system packages: arpack arpack-devel
+# METIS  system packages: metis metis-devel
+#
+##
+
+#
+# Define the packages this platform needs
+PACKAGES=(
+#once:boost
+#once:hdf5
+once:p4est
+once:trilinos
+once:petsc
+once:slepc
+dealii
+)
+
diff --git a/deal.II/platforms/supported/fedora20.platform b/deal.II/platforms/supported/fedora20.platform
new file mode 100644 (file)
index 0000000..89f7ca5
--- /dev/null
@@ -0,0 +1,27 @@
+# Fedora 20
+
+# This build script assumes that you have several packages already
+# installed via Fedora's yum using the following command:
+#
+# su -c 'yum install -y svn \
+# @development-tools gcc-c++ cmake \
+# blas blas-devel lapack lapack-devel \
+# doxygen graphviz graphviz-devel qt-devel '
+# 
+# ARPACK system packages: arpack arpack-devel
+# METIS  system packages: metis metis-devel
+#
+##
+
+#
+# Define the packages this platform needs
+PACKAGES=(
+#once:boost
+once:hdf5
+once:p4est
+once:trilinos
+once:petsc
+once:slepc
+dealii
+)
+
diff --git a/deal.II/platforms/supported/opensuse12.platform b/deal.II/platforms/supported/opensuse12.platform
new file mode 100644 (file)
index 0000000..5e54364
--- /dev/null
@@ -0,0 +1,33 @@
+# openSUSE 12
+# 
+# This build script assumes that you have several packages already
+# installed via openSUSE's zypper using the following commands:
+#
+# > su -c 'zypper -n in -t pattern devel_basis devel_C_C++ devel_qt4'
+# 
+# > su -c 'zypper -n in Modules gcc-fortran subversion git cmake \
+#   openmpi openmpi-devel splint blas-devel lapack-devel \
+#   doxygen graphviz graphviz-devel'
+# 
+# Then reboot and run candi again.
+# 
+# NOTE: There is a small "bug" in openmpi 1.6, you must set the following
+#       softlink to run mpi-programs:
+#       > su -c 'mkdir /usr/lib64/mpi/gcc/openmpi/etc'
+# 
+#       > su -c 'ln -s /etc/openmpi-default-hostfile \
+#         /usr/lib64/mpi/gcc/openmpi/etc/openmpi-default-hostfile'
+##
+
+#
+# Define the packages this platform needs
+PACKAGES=(
+#once:boost
+once:hdf5
+once:p4est
+once:trilinos
+once:petsc
+once:slepc
+dealii
+)
+
diff --git a/deal.II/platforms/supported/opensuse13.platform b/deal.II/platforms/supported/opensuse13.platform
new file mode 100644 (file)
index 0000000..a0ce565
--- /dev/null
@@ -0,0 +1,28 @@
+# openSUSE 13
+# 
+# This build script assumes that you have several packages already
+# installed via openSUSE's zypper using the following commands:
+#
+# > su -c 'zypper -n in -t pattern devel_basis devel_C_C++ devel_qt4'
+# 
+# and
+# 
+# > su -c 'zypper -n in Modules gcc-fortran subversion git cmake \
+#   openmpi openmpi-devel splint blas-devel lapack-devel \
+#   doxygen graphviz graphviz-devel'
+# 
+# Then reboot and run candi again.
+##
+
+#
+# Define the packages this platform needs
+PACKAGES=(
+#once:boost
+once:hdf5
+once:p4est
+once:trilinos
+once:petsc
+once:slepc
+dealii
+)
+
diff --git a/deal.II/platforms/supported/rhel6.platform b/deal.II/platforms/supported/rhel6.platform
new file mode 100644 (file)
index 0000000..29f38ea
--- /dev/null
@@ -0,0 +1,25 @@
+# RHEL 6
+
+# This build script assumes that you have several packages already
+# installed via RHEL's yum using the following command:
+#
+# su -c 'yum install -y svn git wget \
+# @development-tools gcc-c++ cmake \
+# blas blas-devel lapack lapack-devel \
+# doxygen graphviz graphviz-devel qt-devel '
+# 
+# ARPACK: arpack arpack-devel
+# METIS: metis metis-devel
+#
+##
+
+#
+# Define the packages this platform needs
+PACKAGES=(
+once:hdf5
+once:p4est
+once:trilinos
+once:petsc
+once:slepc
+dealii
+)
diff --git a/deal.II/platforms/supported/ubuntu13.platform b/deal.II/platforms/supported/ubuntu13.platform
new file mode 100644 (file)
index 0000000..616b88c
--- /dev/null
@@ -0,0 +1,25 @@
+# ubuntu 13
+# 
+# This build script assumes that you have several packages already
+# installed via ubuntu's apt-get using the following commands:
+#
+# > su -c 'apt-get install build-essential automake autoconf \
+#   gfortran openmpi1.6 cmake subversion git splint splint-dev \
+#   blas libblas-dev lapack liblapack-dev libblas3gf liblapack3gf \
+#   tcl tcl-dev environment-modules'
+# 
+# Then reboot and run candi again.
+##
+
+#
+# Define the packages this platform needs
+PACKAGES=(
+#once:boost
+once:hdf5
+once:p4est
+once:trilinos
+once:petsc
+once:slepc
+dealii
+)
+
diff --git a/gcc/packages/gcc.package b/gcc/packages/gcc.package
new file mode 100644 (file)
index 0000000..279fe2e
--- /dev/null
@@ -0,0 +1,61 @@
+VERSION=${GCC}
+NAME=gcc-${VERSION}
+SOURCE=ftp://ftp.fu-berlin.de/unix/languages/gcc/releases/${NAME}/
+PACKING=.tar.gz
+CHECKSUM=ignore
+BUILDCHAIN=autotools
+
+if [ ${GCC} = "4.7.3" ]; then
+    CHECKSUM=d518eace24a53aef59c2c69498ea4989
+elif [ ${GCC} = "4.8.2" ]; then
+    CHECKSUM=deca88241c1135e2ff9fa5486ab5957b
+fi
+
+MODULEFILE_PATH=${INSTALL_PATH}/conf/modulefiles/compiler/gcc
+CONFIG_FILE=${MODULEFILE_PATH}/${VERSION}
+
+# **********************************************************************************
+package_specific_conf() {
+    # Generate modulefile
+    
+    mkdir -p ${MODULEFILE_PATH}
+    CONFIG_FILE=${MODULEFILE_PATH}/${NAME}
+    rm -f $CONFIG_FILE
+    echo "#%Module 1.0
+#
+# GNU/GCC ${VERSION} Compiler modulefile
+#
+
+proc ModulesHelp { } {
+   puts stderr "\tThis module adds GNU ${VERSION} Compiler."
+}
+conflict compiler
+  
+module-whatis   "Sets up the GNU ${VERSION} Compiler environment."
+
+prepend-path            PATH           ${INSTALL_PATH}/bin
+prepend-path            MANPATH                ${INSTALL_PATH}/share/man
+prepend-path            INFOPATH       ${INSTALL_PATH}/share/info
+prepend-path            LD_LIBRARY_PATH ${INSTALL_PATH}/lib64
+prepend-path            LD_RUN_PATH     ${INSTALL_PATH}/lib64
+
+setenv                 LIBDIR          ${INSTALL_PATH}/lib64
+setenv                 LDFLAGS         \"-Wl,-rpath -Wl,${INSTALL_PATH}/lib64\"
+
+setenv                 CC              ${INSTALL_PATH}/bin/gcc
+setenv                 CXX             ${INSTALL_PATH}/bin/g++
+setenv                 FC              ${INSTALL_PATH}/bin/gfortran
+setenv                 FF              ${INSTALL_PATH}/bin/gfortran
+" >> $CONFIG_FILE
+    
+    echo
+    echo "${NAME} has now been installed in"
+    echo
+    cecho ${GOOD} "    ${INSTALL_PATH}"
+    echo
+    echo "To update your environment variables, use the created modulefile:"
+    echo
+    cecho ${GOOD} "    $CONFIG_FILE"
+    echo
+}
+
diff --git a/gcc/platforms/.single b/gcc/platforms/.single
new file mode 100644 (file)
index 0000000..e69de29
diff --git a/gcc/platforms/supported/rhel6.platform b/gcc/platforms/supported/rhel6.platform
new file mode 100644 (file)
index 0000000..149eb54
--- /dev/null
@@ -0,0 +1,18 @@
+# RHEL 6
+
+# This build script assumes that you have several packages already
+# installed via Fedora's yum using the following command:
+#
+# su -c 'yum install -y \
+# @development-tools gcc-c++ \
+# glibc glibc-devel glibc.i686 glibc-devel.i686 \
+# libmpc libmpc-devel mpfr mpfr-devel gmp gmp-devel \
+# gzip bzip2 '
+#
+##
+
+# Define the packages this platform needs
+PACKAGES=(
+once:gcc
+)
+
diff --git a/local-DTM++.toolbox.cfg b/local-DTM++.toolbox.cfg
new file mode 100644 (file)
index 0000000..cf5a8bb
--- /dev/null
@@ -0,0 +1,34 @@
+# Global configuration variables go here. You will want to tweak this
+# file to suit your needs. If you want to keep local changes that are
+# not overwritten by repository updates, those can be written
+# to local.cfg instead (entries there will override those in this file).
+
+# Meta-project to build
+PROJECT=DTM++.toolbox
+CLEAN_BUILD=false
+COMPILER=native-openmpi
+
+# How many processes would you like to build using?
+PROCS=1
+
+# Prefix directory
+PREFIX_PATH=~/apps/candi
+
+# Where do you want the downloaded source files to go?
+DOWNLOAD_PATH=${PREFIX_PATH}/src
+
+# Where do you want to unpack source files to go?
+UNPACK_PATH=${PREFIX_PATH}/unpack
+
+# Where do you want the build files to go?
+BUILD_PATH=${PREFIX_PATH}/${PROJECT}/${COMPILER}-build
+
+# Where do you want the compiled software installed?
+INSTALL_PATH=${PREFIX_PATH}/${PROJECT}/${COMPILER}
+
+# Would you like to build stable versions of projects?
+# If STABLE_BUILD=false, then the development version of deal.II will be
+# installed.
+STABLE_BUILD=true
+#STABLE_BUILD=false
+
diff --git a/local-FEniCS.cfg b/local-FEniCS.cfg
new file mode 100644 (file)
index 0000000..42daf31
--- /dev/null
@@ -0,0 +1,31 @@
+# Global configuration variables go here. You will want to tweak this
+# file to suit your needs. If you want to keep local changes that are
+# not overwritten by repository updates, those can be written
+# to local.cfg instead (entries there will override those in this file).
+
+# Meta-project to build
+PROJECT=FEniCS
+CLEAN_BUILD=false
+COMPILER=native-openmpi
+
+PREFIX_PATH=~/apps/candi
+
+# Where do you want the downloaded source files to go?
+DOWNLOAD_PATH=${PREFIX_PATH}/src
+
+# Where do you want to unpack source files to go?
+UNPACK_PATH=${PREFIX_PATH}/unpack/${PROJECT}
+
+# Where do you want the build files to go?
+BUILD_PATH=${PREFIX_PATH}/${PROJECT}/${COMPILER}-build
+
+# Where do you want the compiled software installed?
+INSTALL_PATH=${PREFIX_PATH}/${PROJECT}/${COMPILER}
+
+# How many processes would you like to build using?
+PROCS=1
+
+# Would you like to build stable versions of projects?
+STABLE_BUILD=true
+# Would you like to use snapshots when using STABLE_BUILD=false?
+USE_SNAPSHOTS=false
diff --git a/local-deal.II.cfg b/local-deal.II.cfg
new file mode 100644 (file)
index 0000000..7f3a792
--- /dev/null
@@ -0,0 +1,74 @@
+# Global configuration variables go here. You will want to tweak this
+# file to suit your needs. If you want to keep local changes that are
+# not overwritten by repository updates, those can be written
+# to local.cfg instead (entries there will override those in this file).
+
+# Meta-project to build
+PROJECT=deal.II
+CLEAN_BUILD=false
+
+#########################################################################
+#Choose components of deal.II
+DEAL_CONFOPTS=" \
+-D CMAKE_BUILD_TYPE=DebugRelease \
+-D DEAL_II_COMPONENT_DOCUMENTATION:BOOL=OFF \
+-D DEAL_II_WITH_ARPACK:BOOL=OFF \
+-D DEAL_II_WITH_BOOST:BOOL=ON \
+-D DEAL_II_WITH_FUNCTIONPARSER:BOOL=ON \
+-D DEAL_II_WITH_LAPACK:BOOL=ON \
+-D DEAL_II_WITH_METIS:BOOL=OFF \
+-D DEAL_II_WITH_MUMPS:BOOL=OFF \
+-D DEAL_II_WITH_MPI:BOOL=ON \
+-D DEAL_II_WITH_NETCDF:BOOL=OFF \
+-D DEAL_II_WITH_P4EST:BOOL=ON \
+-D DEAL_II_WITH_PETSC:BOOL=ON \
+-D DEAL_II_WITH_SLEPC:BOOL=ON \
+-D DEAL_II_WITH_THREADS:BOOL=OFF \
+-D DEAL_II_WITH_TRILINOS:BOOL=ON \
+-D DEAL_II_WITH_UMFPACK:BOOL=ON \
+-D DEAL_II_WITH_ZLIB:BOOL=ON \
+-D DEAL_II_WITH_HDF5:BOOL=ON \
+"
+
+# Please add the following path(es) to DEAL_CONFOPTS ahead,
+# if you wish to use (self-compiled) versions of them together
+# with deal.II.
+# Make sure, that the coinciding option is setted to "ON".
+# If you want to use the packages from your system, you
+# may not set the variables (usually deal.II is smart enough
+# to recognise them automatically).
+# If you want to install the packages using CANDI,
+# simply set the option to ON and do NOT specify the path,
+# this will be done automatically elsewhere.
+#
+#-D ARPACK_DIR= \
+#-D METIS_DIR= \
+#-D MUMPS_DIR= \
+#-D P4EST_DIR= \
+#-D TRILINOS_DIR= \
+#-D HDF5_DIR= \
+
+#########################################################################
+# Prefix directory
+PREFIX_PATH=~/apps/candi
+COMPILER=native-openmpi
+
+# Where do you want the downloaded source files to go?
+DOWNLOAD_PATH=${PREFIX_PATH}/src
+
+# Where do you want to unpack source files to go?
+UNPACK_PATH=${PREFIX_PATH}/unpack
+
+# Where do you want the build files to go?
+BUILD_PATH=${PREFIX_PATH}/${PROJECT}/${COMPILER}-build
+
+# Where do you want the compiled software installed?
+INSTALL_PATH=${PREFIX_PATH}/${PROJECT}/${COMPILER}
+
+# How many processes would you like to build using?
+PROCS=1
+
+# Would you like to build stable versions of projects?
+# If STABLE_BUILD=false, then the development version of deal.II will be
+# installed.
+STABLE_BUILD=true
diff --git a/local-gcc.cfg b/local-gcc.cfg
new file mode 100644 (file)
index 0000000..ac39276
--- /dev/null
@@ -0,0 +1,29 @@
+# Global configuration variables go here. You will want to tweak this
+# file to suit your needs. If you want to keep local changes that are
+# not overwritten by repository updates, those can be written
+# to local.cfg instead (entries there will override those in this file).
+
+# Meta-project to build
+PROJECT=gcc
+#VERSION=4.7.3
+VERSION=4.8.2
+
+# How many processes would you like to build using?
+PROCS=1
+
+PREFIX_PATH=~/appl/candi
+
+# Where do you want the downloaded source files to go?
+DOWNLOAD_PATH=${PREFIX_PATH}/src
+
+# Where do you want to unpack source files to go?
+UNPACK_PATH=${PREFIX_PATH}/unpack
+
+# Where do you want the build files to go?
+BUILD_PATH=${PREFIX_PATH}/compiler/${PROJECT}-${VERSION}-build
+
+# Where do you want the compiled software installed?
+INSTALL_PATH=${PREFIX_PATH}/compiler/${PROJECT}/${VERSION}
+
+GCC=${VERSION}
+
diff --git a/local-mpi.cfg b/local-mpi.cfg
new file mode 100644 (file)
index 0000000..4805fe8
--- /dev/null
@@ -0,0 +1,27 @@
+# Global configuration variables go here. You will want to tweak this
+# file to suit your needs. If you want to keep local changes that are
+# not overwritten by repository updates, those can be written
+# to local.cfg instead (entries there will override those in this file).
+
+# Meta-project to build
+PROJECT=mpi
+#COMPILER=llvm
+COMPILER=gcc-4.8.2
+
+# How many processes would you like to build using?
+PROCS=1
+
+PREFIX_PATH=~/apps/candi
+
+# Where do you want the downloaded source files to go?
+DOWNLOAD_PATH=${PREFIX_PATH}/src
+
+# Where do you want the build files to go?
+BUILD_PATH=${PREFIX_PATH}/${PROJECT}/${COMPILER}-build
+
+# Where do you want to unpack source files to go?
+UNPACK_PATH=${PREFIX_PATH}/unpack
+
+# Where do you want the compiled software installed?
+INSTALL_PATH=${PREFIX_PATH}/compiler/${PROJECT}
+
diff --git a/local.cfg b/local.cfg
new file mode 120000 (symlink)
index 0000000..a980d14
--- /dev/null
+++ b/local.cfg
@@ -0,0 +1 @@
+local-DTM++.toolbox.cfg
\ No newline at end of file
diff --git a/mpi/packages/mpich.package b/mpi/packages/mpich.package
new file mode 100644 (file)
index 0000000..2c2a1d6
--- /dev/null
@@ -0,0 +1,68 @@
+VERSION=3.0.4
+NAME=mpich-${VERSION}
+SOURCE=http://www.mpich.org/static/downloads/${VERSION}/
+PACKING=.tar.gz
+CHECKSUM=9c5d5d4fe1e17dd12153f40bc5b6dbc0
+
+BUILDCHAIN=autotools
+PROCS=1
+CONFOPTS="-q CFLAGS=-fPIC CXXFLAGS=-fPIC FFLAGS=-fPIC FCFLAGS=-fPIC"
+INSTALL_PATH=${INSTALL_PATH}/${COMPILER}/${NAME}
+
+MODULEFILE_PATH=${INSTALL_PATH}/conf/modulefiles/compiler/mpi/${COMPILER}
+CONFIG_FILE=${MODULEFILE_PATH}/${NAME}
+
+# **********************************************************************************
+package_specific_conf() {
+    # Generate modulefile
+
+    mkdir -p ${MODULEFILE_PATH}
+    rm -f $CONFIG_FILE
+    echo "#%Module 1.0
+#
+# ${NAME} against ${COMPILER}
+#
+
+conflict compiler
+
+prepend-path           PATH            ${PATH}
+prepend-path           MANPATH         ${MANPATH}
+prepend-path            INFOPATH       ${INFOPATH}
+prepend-path           LD_LIBRARY_PATH ${LD_LIBRARY_PATH}
+prepend-path           LD_RUN_PATH     ${LD_RUN_PATH}
+
+setenv                 LIBDIR          ${LIBDIR}
+setenv                 LDFLAGS         \"${LDFLAGS}\"
+
+prepend-path           PATH            ${INSTALL_PATH}/bin
+prepend-path           LD_LIBRARY_PATH ${INSTALL_PATH}/lib
+prepend-path           MANPATH         ${INSTALL_PATH}/share/man
+
+setenv                 MPI_BIN         ${INSTALL_PATH}/bin
+setenv                 MPI_SYSCONFIG   ${INSTALL_PATH}/etc
+setenv                 MPI_INCLUDE     ${INSTALL_PATH}/include
+setenv                 MPI_LIB         ${INSTALL_PATH}/lib
+setenv                 MPI_MAN         ${INSTALL_PATH}/share/man
+setenv                 MPI_COMPILER    mpich-x86_64
+setenv                 MPI_SUFFIX      _mpich
+setenv                 MPI_HOME        ${INSTALL_PATH}
+
+setenv                 CC              ${INSTALL_PATH}/bin/mpicc
+setenv                 CXX             ${INSTALL_PATH}/bin/mpic++
+setenv                 FC              ${INSTALL_PATH}/bin/mpif90
+setenv                 FF              ${INSTALL_PATH}/bin/mpif77
+setenv                 F90             ${INSTALL_PATH}/mpif90
+setenv                 F77             ${INSTALL_PATH}/bin/mpif77
+" >> $CONFIG_FILE
+
+    echo
+    echo "${NAME} has now been installed in"
+    echo
+    cecho ${GOOD} "    ${INSTALL_PATH}"
+    echo
+    echo "To update your environment variables, use the created modulefile:"
+    echo
+    cecho ${GOOD} "    $CONFIG_FILE"
+    echo
+}
+
diff --git a/mpi/packages/mpich2.package b/mpi/packages/mpich2.package
new file mode 100644 (file)
index 0000000..502cc05
--- /dev/null
@@ -0,0 +1,68 @@
+VERSION=1.4.1p1
+NAME=mpich2-${VERSION}
+SOURCE=http://www.mpich.org/static/downloads/${VERSION}/
+PACKING=.tar.gz
+CHECKSUM=b470666749bcb4a0449a072a18e2c204
+
+BUILDCHAIN=autotools
+PROCS=1
+CONFOPTS="-q CFLAGS=-fPIC CXXFLAGS=-fPIC FFLAGS=-fPIC FCFLAGS=-fPIC"
+INSTALL_PATH=${INSTALL_PATH}/${COMPILER}/${NAME}
+
+MODULEFILE_PATH=${INSTALL_PATH}/conf/modulefiles/compiler/mpi/${COMPILER}
+CONFIG_FILE=${MODULEFILE_PATH}/${NAME}
+
+# **********************************************************************************
+package_specific_conf() {
+    # Generate modulefile
+
+    mkdir -p ${MODULEFILE_PATH}
+    rm -f $CONFIG_FILE
+    echo "#%Module 1.0
+#
+# ${NAME} against ${COMPILER}
+#
+
+conflict compiler
+
+prepend-path           PATH            ${PATH}
+prepend-path           MANPATH         ${MANPATH}
+prepend-path            INFOPATH       ${INFOPATH}
+prepend-path           LD_LIBRARY_PATH ${LD_LIBRARY_PATH}
+prepend-path           LD_RUN_PATH     ${LD_RUN_PATH}
+
+setenv                 LIBDIR          ${LIBDIR}
+setenv                 LDFLAGS         \"${LDFLAGS}\"
+
+prepend-path           PATH            ${INSTALL_PATH}/bin
+prepend-path           LD_LIBRARY_PATH ${INSTALL_PATH}/lib
+prepend-path           MANPATH         ${INSTALL_PATH}/share/man
+
+setenv                 MPI_BIN         ${INSTALL_PATH}/bin
+setenv                 MPI_SYSCONFIG   ${INSTALL_PATH}/etc
+setenv                 MPI_INCLUDE     ${INSTALL_PATH}/include
+setenv                 MPI_LIB         ${INSTALL_PATH}/lib
+setenv                 MPI_MAN         ${INSTALL_PATH}/share/man
+setenv                 MPI_COMPILER    mpich-x86_64
+setenv                 MPI_SUFFIX      _mpich
+setenv                 MPI_HOME        ${INSTALL_PATH}
+
+setenv                 CC              ${INSTALL_PATH}/bin/mpicc
+setenv                 CXX             ${INSTALL_PATH}/bin/mpic++
+setenv                 FC              ${INSTALL_PATH}/bin/mpif90
+setenv                 FF              ${INSTALL_PATH}/bin/mpif77
+setenv                 F90             ${INSTALL_PATH}/mpif90
+setenv                 F77             ${INSTALL_PATH}/bin/mpif77
+" >> $CONFIG_FILE
+
+    echo
+    echo "${NAME} has now been installed in"
+    echo
+    cecho ${GOOD} "    ${INSTALL_PATH}"
+    echo
+    echo "To update your environment variables, use the created modulefile:"
+    echo
+    cecho ${GOOD} "    $CONFIG_FILE"
+    echo
+}
+
diff --git a/mpi/packages/openmpi.package b/mpi/packages/openmpi.package
new file mode 100644 (file)
index 0000000..843c377
--- /dev/null
@@ -0,0 +1,67 @@
+VERSION=1.6.5
+NAME=openmpi-${VERSION}
+SOURCE=http://www.open-mpi.org/software/ompi/v1.6/downloads/
+PACKING=.tar.bz2
+CHECKSUM=03aed2a4aa4d0b27196962a2a65fc475
+
+BUILDCHAIN=autotools
+PROCS=1
+#CONFOPTS="--disable-dlopen"
+TARGETS=('' all install)
+
+MODULEFILE_PATH=${INSTALL_PATH}/conf/modulefiles/compiler/mpi/${COMPILER}
+CONFIG_FILE=${MODULEFILE_PATH}/${NAME}
+
+# **********************************************************************************
+package_specific_conf() {
+    # Generate modulefile
+
+    mkdir -p ${MODULEFILE_PATH}
+    CONFIG_FILE=${MODULEFILE_PATH}/${NAME}
+    rm -f $CONFIG_FILE
+    echo "#%Module 1.0
+#
+# ${NAME} against ${COMPILER}
+#
+
+prepend-path           PATH            ${PATH}
+prepend-path           MANPATH         ${MANPATH}
+prepend-path            INFOPATH       ${INFOPATH}
+prepend-path           LD_LIBRARY_PATH ${LD_LIBRARY_PATH}
+prepend-path           LD_RUN_PATH     ${LD_RUN_PATH}
+
+setenv                 LIBDIR          ${LIBDIR}
+setenv                 LDFLAGS         \"${LDFLAGS}\"
+
+prepend-path           PATH            ${INSTALL_PATH}/${COMPILER}/${NAME}/bin
+prepend-path           LD_LIBRARY_PATH ${INSTALL_PATH}/${COMPILER}/${NAME}/lib
+prepend-path           MANPATH         ${INSTALL_PATH}/${COMPILER}/${NAME}/share/man
+
+setenv                 MPI_BIN         ${INSTALL_PATH}/${COMPILER}/${NAME}/bin
+setenv                 MPI_SYSCONFIG   ${INSTALL_PATH}/${COMPILER}/${NAME}/etc
+setenv                 MPI_INCLUDE     ${INSTALL_PATH}/${COMPILER}/${NAME}/include
+setenv                 MPI_LIB         ${INSTALL_PATH}/${COMPILER}/${NAME}/lib
+setenv                 MPI_MAN         ${INSTALL_PATH}/${COMPILER}/${NAME}/share/man
+setenv                 MPI_COMPILER    openmpi-x86_64
+setenv                 MPI_SUFFIX      _openmpi
+setenv                 MPI_HOME        ${INSTALL_PATH}/${COMPILER}/${NAME}
+
+setenv                 CC              ${INSTALL_PATH}/${COMPILER}/${NAME}/bin/mpicc
+setenv                 CXX             ${INSTALL_PATH}/${COMPILER}/${NAME}/bin/mpic++
+setenv                 FC              ${INSTALL_PATH}/${COMPILER}/${NAME}/bin/mpif90
+setenv                 FF              ${INSTALL_PATH}/${COMPILER}/${NAME}/bin/mpif77
+setenv                 F90             ${INSTALL_PATH}/${COMPILER}/${NAME}/mpif90
+setenv                 F77             ${INSTALL_PATH}/${COMPILER}/${NAME}/bin/mpif77
+" >> $CONFIG_FILE
+
+    echo
+    echo "${NAME} has now been installed in"
+    echo
+    cecho ${GOOD} "    ${INSTALL_PATH}/${COMPILER}/${NAME}"
+    echo
+    echo "To update your environment variables, use the created modulefile:"
+    echo
+    cecho ${GOOD} "    $CONFIG_FILE"
+    echo
+}
+
diff --git a/mpi/platforms/.single b/mpi/platforms/.single
new file mode 100644 (file)
index 0000000..e69de29
diff --git a/mpi/platforms/deprecated/fedora19.platform b/mpi/platforms/deprecated/fedora19.platform
new file mode 100644 (file)
index 0000000..40d2c52
--- /dev/null
@@ -0,0 +1,16 @@
+# Fedora 19
+
+# This build script assumes that you have several packages already
+# installed via Fedora's yum using the following command:
+#
+# su -c 'yum install -y svn \
+# @development-tools gcc-c++ cmake \
+# blas blas-devel lapack lapack-devel \
+# doxygen graphviz graphviz-devel qt-devel'
+#
+##
+
+# Define the packages this platform needs
+PACKAGES=(
+dealii
+)
diff --git a/mpi/platforms/supported/fedora19.platform b/mpi/platforms/supported/fedora19.platform
new file mode 100644 (file)
index 0000000..8b72349
--- /dev/null
@@ -0,0 +1,13 @@
+# Fedora 20
+
+# This build script assumes that you have installed
+# an appropriate C/C++ and Fortran compiler.
+#
+##
+
+# Define the packages this platform needs
+PACKAGES=(
+#mpich2
+#mpich
+openmpi
+)
diff --git a/mpi/platforms/supported/fedora20.platform b/mpi/platforms/supported/fedora20.platform
new file mode 100644 (file)
index 0000000..b3e3fdb
--- /dev/null
@@ -0,0 +1,13 @@
+# Fedora 20
+
+# This build script assumes that you have installed
+# an appropriate C/C++ and Fortran compiler.
+#
+##
+
+# Define the packages this platform needs
+PACKAGES=(
+once:mpich2
+once:mpich
+once:openmpi
+)
diff --git a/mpi/platforms/supported/rhel6.platform b/mpi/platforms/supported/rhel6.platform
new file mode 100644 (file)
index 0000000..06f8aeb
--- /dev/null
@@ -0,0 +1,14 @@
+# RHEL 6
+
+# This build script assumes that you have installed
+# an appropriate C/C++ and Fortran compiler.
+#
+# su -c 'yum install -y libtool-ltdl libtool-ltdl-devel'
+##
+
+# Define the packages this platform needs
+PACKAGES=(
+once:mpich2
+#once:mpich
+#once:openmpi
+)
diff --git a/utilities/clean.sh b/utilities/clean.sh
new file mode 100755 (executable)
index 0000000..5414277
--- /dev/null
@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+
+# This is a utility script to clean temporary files originating from
+# Emacs and elsewhere
+
+rm `find .. -name '*~' | xargs`
\ No newline at end of file
diff --git a/utilities/generate-author-list.sh b/utilities/generate-author-list.sh
new file mode 100755 (executable)
index 0000000..94de744
--- /dev/null
@@ -0,0 +1,10 @@
+bzr log -n0 | grep 'committer:' | sed -e 's/^.*committer: //g' \
+| sed -e 's/<.*>//g' | sed 's/[ \t]*$//' \
+| sed -e 's/garth.*/Garth N. Wells/g' \
+| sed -e 's/gnw20.*/Garth N. Wells/g' \
+| sed -e 's/harish.*/Harish Narayanan/g' \
+| sed -e 's/hnarayan.*/Harish Narayanan/g' \
+| sed -e 's/ilmar.*/Ilmar Wilbers/g' \
+| sed -e 's/Joachim B Haga/Joachim B. Haga/g' \
+| sed -e 's/logg.*/Anders Logg/g' \
+| sort | uniq -c | sort -k 2,2n -r | gawk '{print $2" "$3" "$4}'
\ No newline at end of file
diff --git a/utilities/install-fenics.sh b/utilities/install-fenics.sh
new file mode 100755 (executable)
index 0000000..a34c704
--- /dev/null
@@ -0,0 +1,141 @@
+#!/usr/bin/env bash
+
+# Set default values of some useful variables
+export VERSION="1.0-beta"       # Latest released Dorsal version
+export PREFIX=${HOME}/local     # Default download/install location
+export ORIG_DIR=`pwd`           # Store original directory, so we can
+                               # return to it when finished
+
+# Colours for progress and error reporting
+BAD="\033[1;31m"
+GOOD="\033[1;32m"
+BOLD="\033[1m"
+
+### Define helper functions ###
+
+cecho() {
+    # Display messages in a specified colour
+    COL=$1; shift
+    echo -e "${COL}$@\033[0m"
+}
+
+default () {
+    # Export a variable, if it is not already set
+    VAR="${1%%=*}"
+    VALUE="${1#*=}"
+    eval "[[ \$$VAR ]] || export $VAR='$VALUE'"
+}
+
+# Make a directory name more readable by replacing homedir with ~
+prettify_dir() {
+   echo ${1/#$HOME\//~\/}
+}
+
+# Make a directory name entered with ~ for the homedir more portable
+unprettify_dir() {
+   echo ${1/#~\//$HOME\/}
+}
+
+# Fetch the latest released version of Dorsal
+fetch_dorsal() {
+    default TMPDIR=/tmp
+    cd ${TMPDIR}
+    cecho ${GOOD} "Fetching the FEniCS installer files"
+    wget -N http://launchpad.net/dorsal/trunk/${VERSION}/+download/dorsal-${VERSION}.tar.bz2
+    if [ -d "dorsal-${VERSION}" ]
+    then
+       rm -fr dorsal-${VERSION}
+    fi
+    tar -xjf dorsal-${VERSION}.tar.bz2
+    cd dorsal-${VERSION}
+}
+
+# Set up the build configuration (using some sensible defaults)
+cfg_dorsal() {
+    echo "PROJECT=FEniCS"               >  dorsal.cfg
+    echo "DOWNLOAD_PATH=${PREFIX}/src"  >> dorsal.cfg
+    echo "INSTALL_PATH=${PREFIX}"       >> dorsal.cfg
+    echo "PROCS=2"                      >> dorsal.cfg
+    echo "STABLE_BUILD=true"            >> dorsal.cfg
+}
+
+# Run the build script
+run_dorsal() {
+    ./dorsal.sh
+    cd ${ORIG_DIR}
+}
+
+
+while :
+do
+
+    SELECTION1="Install FEniCS"
+    SELECTION2="Change installation path [$(prettify_dir ${PREFIX})]"
+    SELECTION3="Exit installer"
+
+    if [ -x /usr/bin/zenity ]; then
+
+        SELECTION=`/usr/bin/zenity \
+                   --width 350 --height 225 \
+                   --title "FEniCS Installer" \
+                   --text "Welcome to the FEniCS Installer" \
+                   --list --radiolist \
+                   --column Select \
+                   --column Action \
+                     True  "${SELECTION1}" \
+                     False "${SELECTION2}" \
+                     False "${SELECTION3}"`
+
+        case ${SELECTION} in
+           "${SELECTION1}")
+                fetch_dorsal
+                cfg_dorsal
+               run_dorsal
+                ;;
+            "${SELECTION2}")
+               PREFIX=`zenity --title 'Select installation path' --file-selection --directory`
+                ;;
+            "${SELECTION3}")
+                cd ${ORIG_DIR}
+                exit 0
+                ;;
+            *)
+                echo "default"
+                ;;
+        esac
+
+    else
+
+        clear
+        echo "-------------------------------------------------------------------------------"
+        echo "                     Welcome to the FEniCS installer"
+        echo "-------------------------------------------------------------------------------"
+        echo ""
+        echo "          [1] ${SELECTION1}"
+        echo "          [2] ${SELECTION2}"
+        echo "          [3] ${SELECTION3}"
+        echo ""
+        echo "-------------------------------------------------------------------------------"
+        echo ""
+        echo -n "What would you like to do? [1-3]: "
+        read OPTION
+
+        case ${OPTION} in
+           1)  fetch_dorsal
+                cfg_dorsal
+               run_dorsal
+               ;;
+           2)  echo "Please enter your preferred installation path: ";
+               read PREFIX
+               PREFIX=$(unprettify_dir ${PREFIX})
+               ;;
+           3)  cd ${ORIG_DIR}
+               exit 0
+               ;;
+           *) ;;
+        esac
+        echo ""
+
+    fi
+
+done
diff --git a/utilities/test-package-usage.sh b/utilities/test-package-usage.sh
new file mode 100755 (executable)
index 0000000..c2b1d21
--- /dev/null
@@ -0,0 +1,26 @@
+#!/usr/bin/env bash
+
+# This is a utility script to check whether the numerous defined
+# packages in Dorsal are used or not. It is used sporadically to cull
+# unused packages.
+
+# Colours for progress and error reporting
+BAD="\033[1;31m"
+GOOD="\033[1;32m"
+
+cecho() {
+    # Display messages in a specified colour
+    COL=$1; shift
+    echo -e "${COL}$@\033[0m"
+}
+
+for packagefull in ../FEniCS/packages/*.package
+do
+    package=`basename ${packagefull} .package`
+    if [[ "${package}" != *stable ]]
+    then
+       grep -q ${package} ../FEniCS/platforms/*/*.platform \
+           && cecho ${GOOD} ${package} "package is used." \
+           || cecho ${BAD} ${package} "package is not used."
+    fi
+done
\ No newline at end of file

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