From: young Date: Mon, 10 May 2010 06:59:24 +0000 (+0000) Subject: Documentation and change-log that accompany the previous commit. NB. both this and... X-Git-Url: https://gitweb.dealii.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=5dfe8b7f95d803de8778e45781610018a5fc7239;p=dealii-svn.git Documentation and change-log that accompany the previous commit. NB. both this and previous patch were written by Markus Buerg. git-svn-id: https://svn.dealii.org/trunk@21111 0785d39b-7218-0410-832d-ea1e28bc413d --- diff --git a/deal.II/doc/external-libs/mumps.html b/deal.II/doc/external-libs/mumps.html new file mode 100644 index 0000000000..468f2f8674 --- /dev/null +++ b/deal.II/doc/external-libs/mumps.html @@ -0,0 +1,302 @@ + + + + + The deal.II Readme on interfacing to PETSc and Trilinos + + + + + + + + + +

Interfacing deal.II + to MUMPS

+ +

This documentation describes the compilation process + of MUMPS and its dependencies starting with + BLACS and following + with SCALAPACK. The compilation + of MUMPS and its dependencies is not as + straightforward is we would like, however, it is not so + difficult that we can not talk about it. That said, we cannot + discuss every possible choice of parameters, because this is too + involved and we would much rather be doing something productive + with the interface in deal.II. Thus we give + only a short walk-through mentioning the most important + parameters needed for successful compliation and linking. +

+ +

The compilation scheme involves repeating the same three steps + for each piece of software we want installed: (i) Selecting an + appropriate makefile; (ii) Modifying symbols in this makefile to + suit the environment; and (iii) running make to actually compile + the software. +

+ +

Note: If you are using a system, which provides + Intel's MKL, you should only have to compile + MUMPS, since BLACS and + SCALPACK are already included in the + MKL. Therefore you can jump directly to + section 3, where the compilation of MUMPS is + considered. Otherwise start right below with the installation + of BLACS. +

+ +

1. BLACS

+ +

The BLACS library + provides basic linear algebra routines together with a + communication model such that they can be used in parallel. The + compilation of this library is highly dependent on the system + and software used and we can only give a general guide through + the configuration process. +

+ +

The library can be found on the + official BLACS + webpage. We require the three + files mpiblacs.tgz, + mpiblacs-patch03.tgz, and + blacstester.tgz. After extraction of these + three files in the same directory, we find a subfolder + named BMAKES in that directory. Inside this + subfolder there are lots of different Bmake-files for + different architectures. The naming of the files are + conventional: Bmake.XXX-YYY, + where XXX stands for the message passing software + of your system + (eg.. MPI, PVM) + and + YYY for the system architecture (eg. LINUX, + SUN4, SUN4SOL). Pick the corresponding file for your combination + of message passing software and system architecture, copy it to + the root directory of BLACS, and rename it + Bmake.inc. Now that we have the correct makefile, + we have to adapt it to the system we are using. +

+ +

We start by opening Bamke.inc in our favourite text editor and + taking a look at the following three sections: + +

In SECTION 1: PATHS AND LIBRARIES set the + MPI environment correctly by changing the + variable MPIDIR to the directory, where your + MPI installation is located + in. Furthermore you will probably have to adjust the + variables MPILIBdir, + MPIINCdir and MPILIB. +
In the section SECTION 2: BLACS INTERNALS + the most important variables are INTFACE and + TRANSCOMM. If you are using OpenMPI, then set + these as follows: INTFACE = -DAdd + and TRANSCOMM = -DUseMpi2. Otherwise, consult + the + BLACS + webpage for details on how to set these values + correctly. +
The last section is named SECTION 3: + Compilers. Here we set the + variables F77 and CC to + correspond to the MPI Fortran and CC + compiler respectively, eg. + mpif77 and mpicc. An important + issue here are the variables F77FLAGS + and CCFLAGS. It is absolutely vital to add the + flag -fPIC to both of them, otherwise it will + not be possible to link deal.II with the + BLACS library correctly when shared + libraries are enabled. +

+ +

Assuming we have done all of that correctly, we go back to + the BLACS root directory and compile the + library with the command make mpi. +

+ +

2. SCALAPACK

+ +

The SCALAPACK + library provides high-performance linear algebra routines for + distributed-memory message-passing MIMD + computers. The library can be found on the + official SCALAPACK + webpage. We require the + file scalapack.tgz only. +

+ +

After extracting the file and changing to the directory which + was created, we find a file + called SLmake.inc.example and rename it + to SLmake.inc. In this file we have to set a few + parameters as we did before with BLACS' + own Bmake.inc. + +

The first important variable is the + variable home. Here you have to take care, that + this points to the SCALAPACK directory + (ie. where you are right now). Next, the variable + BLACSdir points to the directory, where your + BLACS libraries are located. Then set the + variable SMPLIB to the MPI + library. +
Now we have to get SCALAPACK to know + about the location of the BLACS library, + which we installed first. This is done by editing the + following bunch of variables BLACSFINIT, + BLACSCINIT, and + BLACSLIB. + +
- BLACSFINIT has to point to your + F77init-library of BLACS. Check the + name of the BLACS library file + containing F77init in its name and put in + this name here; +
- BLACSCINIT has to point to + the BLACS library file + containing Cinit in its name; +
- Finally, BLACSLIB points to the remaining + BLACS library file. +
+
Next we set the compilers correctly + again. F77 and CC should point to + your MPI Fortran and CC compiler + respectively. Also at this place we have to add the + flag -fPIC to the F77FLAGS and to + the CCFLAGS. To the variable CDEFS + you have to add the value of the + variable INTFACE in the configuration + file Bmake.inc in BLACS. +
Finally, we should check that the variables + named BLAS and + LAPACK point to your BLAS + and LAPACK libraries compiled on your + system. +

+ +

If all variables are set correctly we can go ahead and compile + the SCALAPACK library with the + command make. +

+ +

3. MUMPS

+ +

Now we come to the main program for which we are doing all + this. We want to install the parallel sparse direct + solver MUMPS. +

+ +

After downloading the solver from its + official webpage, + extracting it, and changing to the directory which was created, we + find a subfolder named + Make.inc where there are bunch of different + Makefiles for different machine architecture. Here it is + important to realize that for each architecture there are two + different files — one with the ending .SEQ + and one without. The makefiles with the extension + .SEQ are the ones required for the sequential + version of MUMPS. Since we want to use MUMPS + in parallel, we take the file + without this extension which looks suitable for the + architecture we are building on and copy this into + the MUMPS root directory and rename it + as Makefile.inc. +

+ +

As before, we open the makefile Makefile.inc in + our favourite text editor and start modifying variables: + +

The first variables we have to edit are the compilers + again. As usual the variable CC should point to + your MPI CC + compiler, eg. mpicc. The + variables FC and FL should both + point to your MPI Fortran90 compiler, + eg. mpif90. +
Now let us consider the + variable SCALAP. This one should point to your + SCALAPACK0 and BLACS + installations as follows: + -L/XXX -lscalapack -L/YYY -lblacs -lblacsCinit + -lblacsF77init -lblacs -lblacsCinit; + where XXX stands for the directory containing + the SCALAPACK library + and YYY for the directory containing the + BLACS library. The + variable INCPAR should point to + the MPI include directory. +
Now we turn to the variable LIBPAR which + should contain the same value as the + variable SCALAP plus a pointer to + the MPI library. Therefore we propose to + set it to the following value: $(SCALAP) -L/XXX + -lmpi, where XXX stands for the + directory containing your MPI + libraries. Please check, if the + variable LIBBLAS points to your BLAS + installation. The variable + CDEFS has to contain the same value as the variable + INTFACE of + BLACS' own Bmake.inc. If you + are using OpenMPI this should be the + value -DAdd_. Further we have to add to all + three compiler flag variables OPTF, + OPTC, and OPTL the flag + -fPIC. Without adding this last flag it will + not be possible to link deal.II with MUMPS as a shared + library. +

+ +

Now we are done with configuration and can + compile MUMPS with the + command make. +

+ +

4. Linking with deal.II

+ +

To be able to use the interface of deal.II + for the MUMPS solver we then + configure deal.II with the following + additional options: +

+	--with-mumps=path/to/mumps
+	  --with-blacs=path/to/blacs
+	  --with-scalapack=path/to/scalpack
+	
+

+ + + diff --git a/deal.II/doc/news/changes.h b/deal.II/doc/news/changes.h index 9afaefa2ca..607fa3ac4a 100644 --- a/deal.II/doc/news/changes.h +++ b/deal.II/doc/news/changes.h @@ -427,6 +427,15 @@ inconvenience this causes.

lac

+
+ New: A class SparseDirectMumps that provides an interface to + the MUltifrontal Massively Parallel sparse direct Solver (MUMPS). +
+
+ (Markus Buerg 2010/05/10) +
Fixed: BlockSparsityPattern::copy_from accidentally only copied diff --git a/deal.II/doc/readme.html b/deal.II/doc/readme.html index ba75003a21..92f4952307 100644 --- a/deal.II/doc/readme.html +++ b/deal.II/doc/readme.html @@ -723,6 +723,17 @@ this page. + +
MUltifrontal Massively Parallel sparse direct Solver (MUMPS)
+
+ It is possible to make use some subroutines that make use of the + MUltifrontal Massively Parallel sparse direct Solver + (MUMPS). For a detailed description of how to compile MUMPS (and + some dependencies) and linking with deal.II, see + this page. +
+
FunctionParser