From 6f34f6a3b460405df0bd7a6f80647eecda772649 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Fri, 27 Apr 2018 17:21:09 +0200 Subject: [PATCH] Update readme.html --- doc/readme.html | 1285 ++++++++++++++++++++--------------------------- 1 file changed, 538 insertions(+), 747 deletions(-) diff --git a/doc/readme.html b/doc/readme.html index 93d0841a5e..521b76b73a 100644 --- a/doc/readme.html +++ b/doc/readme.html @@ -2,169 +2,136 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> - + + The deal.II Readme - - - - - - - - - - -

Installation instructions and further information - on deal.II

- -

System requirements -
1. Supported platforms
2. Additional software requirements
-
Installation -
1. Unpacking
2. Configuring and building the library
3. Configuring and building the documentation
4. Configuration options -
  1. Selecting optional compilation features
  2. Selecting optional library features
  3. Optional interfaces to + + + + + + + + + + +
    Installation instructions and further information on deal.II
    + +
    +
    -
    - - -
    System requirements
    - - -
    Supported platforms
    - -
    - deal.II is mostly developed on Linux using the - GCC compiler. However, it is not - platform specific and we strive to keep the source code compliant - with the C++ 2011 - Standard (see - also here - for a copy of the C++11 standard). -
    - -
    - deal.II supports at least the following - platforms: -
    -
    - GNU/Linux: GCC version 4.8 or later; Clang version 3.3 or later; - ICC versions 15 or later
    - Mac OS X: GCC version 4.8 or later; Clang version 3.3 or later. - Please see the deal.II Wiki for installation instructions.
    - Windows: experimental support for Visual Studio 2017. - Please have a look at the - - FAQ and at the deal.II Wiki for more information and alternative solutions.
    - -
    - Most other combinations of POSIX-style operating systems and C++ - Standard compliant compilers should also work. If they don't, +
  +
+

+
License
+

+ + +
System requirements
+ + +
Supported platforms
+ +
+ deal.II is mostly developed on Linux using the + GCC compiler. However, it is not platform specific and we strive to keep the source code compliant with the C++ 2011 + Standard (see also here for a copy of the C++11 standard). +
+ +
+ deal.II supports at least the following platforms: +
+
+
GNU/Linux: GCC version 4.8 or later; Clang version 3.3 or later; ICC versions 15 or later
+
Mac OS X: GCC version 4.8 or later; Clang version 3.3 or later. Please see the deal.II Wiki for installation instructions.
+
Windows: experimental support for Visual Studio 2017. Please have a look at the + + FAQ and at the deal.II Wiki for more information and alternative solutions.
+ +
+ +
+ Most other combinations of POSIX-style operating systems and C++ Standard compliant compilers should also work. If they don't, please report it as a bug. -
+
- -
Additional software requirements
+ +
Additional software requirements

- In order to compile and use deal.II - you need to have the following programs installed: + In order to compile and use deal.II you need to have the following programs installed:

-
- CMake version 2.8.12 or later -
- -
- GNU make, version - 3.78 or later (or any other generator supported by CMake) -
- -
- For generating the documentation: - Perl 5.x, - doxygen - and dot, which is part of the - GraphViz - package -
- -
- For debugging programs, we have found that the - GNU - debugger GDB is an invaluable tool. GDB is a text-based tool - not always easy to use; kdbg, is one of many graphical user interfaces - for it. Most integrated development environments - like kdevelop - or Eclipse have built - in debuggers as well. deal.II has some support for - pretty printing its own classes through GDB; - see the GDB configuration guide for - setup information. -
- -

- The library generates output in formats readable by - GNUPLOT, - GMV - (general mesh viewer), - Tecplot (ASCII and binary), - Visualization Toolkit (Vtk), - AVS Explorer, - Open DX, - Povray, - and directly to Encapsulated Postscript. -
+
+ CMake version 2.8.12 or later +
-
- gnuplot - and a postscript viewer (for eps) should be - available almost everywhere. In the last few years, most - new visualization programs have moved to support - vtk/vtu format. There are a number - of excellent programs that can read vtk and - vtu, such as - Visit, - ParaView, - as well as others. Povray is freely available for almost all - platforms. AVS is a commercial program available for most Unix - flavors. Tecplot is a commercial program available for Windows - and most Unix platforms. -
-
- In case you didn't find your favorite graphics format above, - adding a new writer to deal.II is not too - difficult, as only a simple intermediate format needs to be - converted into output (without references to cells, nodes, - types of finite elements, and the like). -
- +
+ GNU make, version 3.78 or later (or any other generator supported by CMake) +
+ +
+ For generating the documentation: + Perl 5.x, + doxygen and dot, which is part of the + GraphViz package +
+ +
+ For debugging programs, we have found that the + GNU + debugger GDB is an invaluable tool. GDB is a text-based tool not always easy to use; kdbg, is one of many graphical user interfaces for it. Most integrated development environments + like kdevelop or Eclipse have built in debuggers as well. deal.II has some support for pretty printing its own classes + through GDB; see the GDB configuration guide for setup information. +
+ +
+
+ The library generates output in formats readable by + GNUPLOT, + GMV + (general mesh viewer), + Tecplot (ASCII and binary), + Visualization Toolkit (Vtk), + AVS Explorer, + Open DX, + Povray, and directly to Encapsulated Postscript. +
+ +
+ gnuplot and a postscript viewer (for eps) should be available almost everywhere. In the last few years, most new visualization programs have moved to support + vtk/vtu format. There are a number of excellent programs that can read vtk and + vtu, such as + Visit, + ParaView, as well as others. Povray is freely available for almost all platforms. AVS is a commercial program available for most Unix flavors. Tecplot is a commercial program available + for Windows and most Unix platforms. +
+
+ In case you didn't find your favorite graphics format above, adding a new writer to deal.II is not too difficult, as only a simple intermediate format needs to be converted into output (without references to cells, nodes, + types of finite elements, and the like). +
+

@@ -174,161 +141,107 @@
Unpacking

- The whole library usually comes as a tar.gz file, - which is a file archive compressed with gzip. After downloading it, - unpack it using either + The whole library usually comes as a tar.gz file, which is a file archive compressed with gzip. After downloading it, unpack it using either
-
+
gunzip deal.II-X.Y.Z.tar.gz tar xf deal.II-X.Y.Z.tar -
-
or, if you have GNU tar with
-
+
+
or, if you have GNU tar with
+
tar -xvf deal.II-X.Y.Z.tar.gz -
+
-
Note: You will want to hang on to the source files - of deal.II after installation as it makes - developing much simpler. Consequently, you should do the steps above - in a permanent directory, not on /tmp as one often does - when installing software. -
+
Note: You will want to hang on to the source files of deal.II after installation as it makes developing much simpler. Consequently, you should do the steps above in a permanent directory, not on /tmp as one often + does when installing software. +

Configuring and building the library

- deal.II uses the - CMake - integrated configuration and build system. Unpacking will create a - subdirectory deal.II/ in the current directory. Then do the - following steps:
+ deal.II uses the + CMake integrated configuration and build system. Unpacking will create a subdirectory deal.II/ in the current directory. Then do the following steps:
-
+
mkdir build cd build cmake -DCMAKE_INSTALL_PREFIX=/path/to/install/dir ../deal.II make install make test -
+
-
- These steps compile, link, install the deal.II library, and run a few - consistency checks. The whole process should take between a few minutes - and an hour, depending on your machine. -
+
+ These steps compile, link, install the deal.II library, and run a few consistency checks. The whole process should take between a few minutes and an hour, depending on your machine. +

- Note:
-
-
/path/to/install/dir is the directory which deal.II - should be installed into. This can be a directory in your home - directory (e.g., ~/bin/deal.II) or a directory - such as /usr/local if you have root privileges. - Another option is to use something like `pwd`/../installed/ (note the - backticks). Make sure the installation directory is not the same - as the location where you unpacked deal.II/. -
- -
If your machine has multiple processors, use make - -jN in the last step, where N is the - number of simultaneous build processes you want make - to use at any given time. Allowing make to use - more simultaneous build processes (assuming you have that many - processor cores) will greatly lower the build time. -
- -
If you do not intend to modify the deal.II - sources and recompile things, then you can remove - the build/ directory after the last step. -
- -
In principle, after installing deal.II, you - can remove the source directory as well (i.e., the directory into - which tar unpacked the file you downloaded) since - projects using deal.II should only need files that have been - installed. However, you will find it convenient to keep the source - files around anyway, for one reason: When - debugging you often end up with assertions for which you'd like to - see the place in the library's source files that triggered it. -
- -
The deal.II CMake system can accept a - significant number of configuration parameters. See the - discussion below. -
- -
If you are changing part of the deal.II - code itself, you can re-compile the library using only the - last two commands above in the previously created build - directory. It is also possible to change the configuration used - in this directory by calling cmake a second time, - possibly with different arguments. - However, this sometimes leads to surprising results and you may - not get exactly what you were hoping for. For more information, - see here. -
-
+ Note:
+
+
/path/to/install/dir is the directory which deal.II should be installed into. This can be a directory in your home directory (e.g., ~/bin/deal.II) or a directory such as /usr/local if you have root privileges. + Another option is to use something like `pwd`/../installed/ (note the backticks). Make sure the installation directory is not the same as the location where you unpacked deal.II/. +
+ +
If your machine has multiple processors, use make + -jN in the last step, where N is the number of simultaneous build processes you want make to use at any given time. Allowing make to use more simultaneous build processes (assuming you have that many processor + cores) will greatly lower the build time. +
+ +
If you do not intend to modify the deal.II sources and recompile things, then you can remove the build/ directory after the last step. +
+ +
In principle, after installing deal.II, you can remove the source directory as well (i.e., the directory into which tar unpacked the file you downloaded) since projects using deal.II should only need files that + have been installed. However, you will find it convenient to keep the source files around anyway, for one reason: When debugging you often end up with assertions for which you'd like to see the place in the library's source files that triggered + it. +
+ +
The deal.II CMake system can accept a significant number of configuration parameters. See the discussion below. +
+ +
If you are changing part of the deal.II code itself, you can re-compile the library using only the last two commands above in the previously created build directory. It is also possible to change the configuration used in this + directory by calling cmake a second time, possibly with different arguments. However, this sometimes leads to surprising results and you may not get exactly what you were hoping for. For more information, see here. +
+

- The commands above build and install the deal.II - libraries in two variants: + The commands above build and install the deal.II libraries in two variants:

-
-
Debug mode: This version of the - library is compiled with compiler flags so - that the library contains information that can be used by debuggers. -
- -
- In addition, this library contains a great number of safety - checks on most arguments of all functions you could possibly call. - These assertions have proven to be an - invaluable means to finding programming bugs since they will - almost always abort your program if something goes wrong. In our - experience, more than ninety per cent of all errors are invalid - parameters (such as vectors having the wrong size, etc.) and they - are usually found almost instantaneously, displaying the file - name and line number of where the problem occurred. -
-
- With GCC Debug mode, by default, uses the -Og flag. It promises most of the - debugging experience of -O0 but at a better performance. - This is a reasonable choice for unit tests and enables numerous asserts - within the library. Sometimes, however, one needs Debug mode to use - -O0, where all compiler optimizations are avoided and code and variables - are exactly as indicated in the C++ program (e.g. with -Og GCC 6.2.0 - optimizes out local variables). - This can be achieved by configuring deal.II with - -DDEAL_II_HAVE_FLAG_Og=false. -
-
- -
Optimized mode: You will want to link with this version of - the library once you know that your program is working as - expected. It does not contain the safety checks any more - and is compiled with aggressive compiler optimizations. The - resulting executables are smaller and will run between 2 and 10 - times faster than the debug executables. -
-
+
+
Debug mode: This version of the library is compiled with compiler flags so that the library contains information that can be used by debuggers. +
+ +
+ In addition, this library contains a great number of safety checks on most arguments of all functions you could possibly call. These assertions have proven to be an invaluable means to finding programming bugs since they will almost always abort your + program if something goes wrong. In our experience, more than ninety per cent of all errors are invalid parameters (such as vectors having the wrong size, etc.) and they are usually found almost instantaneously, displaying the file name + and line number of where the problem occurred. +
+
+ With GCC Debug mode, by default, uses the -Og flag. It promises most of the debugging experience of -O0 but at a better performance. This is a reasonable choice for unit tests and enables numerous asserts within + the library. Sometimes, however, one needs Debug mode to use + -O0, where all compiler optimizations are avoided and code and variables are exactly as indicated in the C++ program (e.g. with -Og GCC 6.2.0 optimizes out local variables). This can be achieved by configuring + deal.II with + -DDEAL_II_HAVE_FLAG_Og=false. +
+
+ +
Optimized mode: You will want to link with this version of the library once you know that your program is working as expected. It does not contain the safety checks any more and is compiled with aggressive compiler optimizations. The resulting + executables are smaller and will run between 2 and 10 times faster than the debug executables. +
+
- At this point, you have generated everything necessary to write - programs based on deal.II. If you are new to - deal.II, you may want to continue with the - tutorial. + At this point, you have generated everything necessary to write programs based on deal.II. If you are new to + deal.II, you may want to continue with the + tutorial.

Configuring and building the documentation

- All the documentation about the version that you downloaded and that can - be found at the - http://www.dealii.org/ domain can also be generated locally. To do - so, invoke cmake in the build instructions above as follows: + All the documentation about the version that you downloaded and that can be found at the + http://www.dealii.org/ domain can also be generated locally. To do so, invoke cmake in the build instructions above as follows:

@@ -336,48 +249,28 @@

- For this to succeed, you will need Perl 5.x, - doxygen - and dot (which is part of - the GraphViz - package) to be installed. + For this to succeed, you will need Perl 5.x, + doxygen and dot (which is part of the GraphViz package) to be installed.

- The documentation contains links to pictures (e.g., for the - tutorial programs) that are by default stored online at the - dealii.org domain. If you want to use the documentation - completely offline, you can run - the contrib/utilities/makeofflinedoc.sh script in - an installed documentation directory to download all images. + The documentation contains links to pictures (e.g., for the tutorial programs) that are by default stored online at the dealii.org domain. If you want to use the documentation completely offline, you can run the contrib/utilities/makeofflinedoc.sh script in an installed documentation directory to download all images.
-
Finally, the default for locally installed documentation is to - render formulas as images. You can force formulas to be - displayed via the MathJax system by - adding -DDEAL_II_DOXYGEN_USE_MATHJAX=ON to the - CMake call above. These formulas are then rendered natively by the - browser. With -DDEAL_II_DOXYGEN_USE_ONLINE_MATHJAX=OFF - CMake will try to find a local installation of MathJax scripts, - otherwise the online version of the scripts will be used in the - documentation. +
Finally, the default for locally installed documentation is to render formulas as images. You can force formulas to be displayed via the MathJax system by adding -DDEAL_II_DOXYGEN_USE_MATHJAX=ON to the CMake call above. These formulas + are then rendered natively by the browser. With -DDEAL_II_DOXYGEN_USE_ONLINE_MATHJAX=OFF CMake will try to find a local installation of MathJax scripts, otherwise the online version of the scripts will be used in the documentation.

- Upon calling make and make install, this will - install both this readme, other installation instructions, as well as the - manual that documents - all functions and classes as well as - the tutorial + Upon calling make and make install, this will install both this readme, other installation instructions, as well as the + manual that documents + all functions and classes as well as the tutorial of well-documented example programs (the "steps").

- Note: Generating this documentation can take a really long - time — running doxygen through our hundreds of thousands of - lines of code can take 15-20 minutes even on a fast machine during which - you will not get any output from make. + Note: Generating this documentation can take a really long + time — running doxygen through our hundreds of thousands of lines of code can take 15-20 minutes even on a fast machine during which you will not get any output from make.
@@ -385,455 +278,370 @@
Configuration options

- deal.II has a large number of optional interfaces to - other libraries. By default, cmake will automatically + deal.II has a large number of optional interfaces to other libraries. By default, cmake will automatically enable support for all external libraries it can find in default - paths. - However, this behavior can be changed using command line switches to - the initial call to cmake. A detailed description - can be found here: Detailed build system description. + paths. However, this behavior can be changed using command line switches to the initial call to cmake. A detailed description can be found here: Detailed build system description.

- In the following, let us summarize the most common configuration - options. + In the following, let us summarize the most common configuration options.
- -
Selecting optional compilation features
-
+ +
Selecting optional compilation features
+

-
Unity build: deal.II may be compiled with a unity build; - that is, one may configure the build process so that the library is - compiled as a few large files instead of many small ones. The unity - build feature may be enabled by passing - the -DDEAL_II_UNITY_BUILD=ON argument - to cmake. This feature is disabled by default. -
-
- - -
Selecting optional library features
+
Unity build: deal.II may be compiled with a unity build; that is, one may configure the build process so that the library is compiled as a few large files instead of many small ones. The unity build feature may be enabled by passing + the -DDEAL_II_UNITY_BUILD=ON argument to cmake. This feature is disabled by default. +
+
+ + +
Selecting optional library features

-
-
- Threading: By default, deal.II supports parallelism between - multiple cores on the same machine using threads and a - task-based model built on the - Threading Building Blocks. You can switch - threading off by passing the -DDEAL_II_WITH_THREADS=OFF - argument to cmake. -
-
- -
-
- MPI: To enable parallel computations beyond a single node - using the Message +
+
+ Threading: By default, deal.II supports parallelism between multiple cores on the same machine using threads and a task-based model built on the + Threading Building Blocks. You can switch threading off by passing the -DDEAL_II_WITH_THREADS=OFF argument to cmake. +
+
+ +
+
+ MPI: To enable parallel computations beyond a single node using the Message Passing Interface (MPI), pass the - -DDEAL_II_WITH_MPI=ON argument - to cmake. If cmake found MPI but you - specifically do not want to use it, then - pass -DDEAL_II_WITH_MPI=OFF. -
-
- -
-
- 64bit indices: By default, deal.II use unsigned int (32bit) - indices for degrees of freedom, using - the types::global_dof_index type. This limits the number of - unknowns to approximately four - billions. If larger problem must be solved, pass the - -DDEAL_II_WITH_64BIT_INDICES=ON argument to - cmake. You will not be able to solve problems of this size on - a single machine, but only when using clusters of computers and linear - algebra packages PETSc or Trilinos. - To use this option with PETSc, PETSc must be compiled - with the option --with-64-bit-indices. -
-
+ -DDEAL_II_WITH_MPI=ON argument to cmake. If cmake found MPI but you specifically do not want to use it, then pass -DDEAL_II_WITH_MPI=OFF. +
+ + +
+
+ 64bit indices: By default, deal.II use unsigned int (32bit) indices for degrees of freedom, using the types::global_dof_index type. This limits the number of unknowns to approximately four billions. If larger problem + must be solved, pass the + -DDEAL_II_WITH_64BIT_INDICES=ON argument to + cmake. You will not be able to solve problems of this size on a single machine, but only when using clusters of computers and linear algebra packages PETSc or Trilinos. To use this option with PETSc, PETSc must be compiled + with the option --with-64-bit-indices. +
+

- +
Optional interfaces to other software packages

- When configuring interfacing to external libraries, the - cmake script by default tries to find all of these - libraries in a number of standard locations on your file system. - For optional interfaces, it gives up if the library is not - found and deal.II will be built without support - for them. - However, there is one interface that we need to have: BOOST 1.59 or newer. - If it is not found externally cmake will resort to the - bundled boost version that is part of the deal.II - tar file. + When configuring interfacing to external libraries, the + cmake script by default tries to find all of these libraries in a number of standard locations on your file system. For optional interfaces, it gives up if the library is not found and deal.II will be built + without support for them. However, there is one interface that we need to have: BOOST 1.59 or newer. If it is not found externally cmake will resort to the bundled boost version + that is part of the deal.II tar file.

- The following paragraphs describe how the interfaces to the - various packages, deal.II interacts with, - can be configured. + The following paragraphs describe how the interfaces to the various packages, deal.II interacts with, can be configured.

Notes:
-
+

- The majority of libraries mentioned below should be readily + The majority of libraries mentioned below should be readily packaged by most Linux distributions. Usually you need to install a development version of a library package, e.g. ending in -dev or -devel. After that cmake will automatically find the library and use it. -
+
- Configuring the interface to a self compiled package, - say foo can usually be done by specifying - -DFOO_DIR=/path/to/foo. Alternatively, you can - set FOO_DIR as an environment variable in your - .bashrc or .cshrc file so that - you do not have to enter this argument again the next time - you invoke cmake in a fresh build directory. - Any value passed on the command line wins over a value that - may be found in an environment variable. -
+ Configuring the interface to a self compiled package, say foo can usually be done by specifying + -DFOO_DIR=/path/to/foo. Alternatively, you can set FOO_DIR as an environment variable in your + .bashrc or .cshrc file so that you do not have to enter this argument again the next time you invoke cmake in a fresh build directory. Any value passed on the command line wins over a value that may be + found in an environment variable. +
- To explicitly enable or disable support for - a library foo use the argument - -DDEAL_II_WITH_FOO=ON resp. - -DDEAL_II_WITH_FOO=OFF for cmake. -
+ To explicitly enable or disable support for a library foo use the argument + -DDEAL_II_WITH_FOO=ON resp. + -DDEAL_II_WITH_FOO=OFF for cmake. +

-
+
+ ADOL-C
+
+
+ ADOL-C is a package that facilitates the evaluation of first and higher derivatives of vector functions. In particular, it can be used for automatic differentiation. For using + ADOL-C with deal.II, version 2.6.4 or newer is required. To use a self compiled version, specify + -DADOLC_DIR=/path/to/adolc on the command line. +
+
+ +
ARPACK
-
-
- ARPACK is a library for computing large - scale eigenvalue problems. - ARPACK - should be readily packaged by most Linux distributions. - (Don't forget to install a development version of the library). - To use a self compiled version, specify - -DARPACK_DIR=/path/to/arpack on the command line. - - For a detailed description on how to compile ARPACK and linking with deal.II, see - this page. -
-
- -
+
+
+ ARPACK is a library for computing large scale eigenvalue problems. + ARPACK should be readily packaged by most Linux distributions. (Don't forget to install a development version of the library). To use a self compiled version, specify + -DARPACK_DIR=/path/to/arpack on the command line. For a detailed description on how to compile ARPACK and linking with deal.II, see + this page. +
+
+ +
+ Assimp
+
+
+ is a portable Open Source library to import various well-known 3D model formats in a uniform manner. A subset of these formats can be read from within deal.II to generate two-dimensional + meshes, possibly embedded in a three-dimensional space. + Assimp should be readily packaged by most Linux distributions. (Don't forget to install a development version of the library). To use a self compiled version, specify + -DASSIMP_DIR=/path/to/assimp on the command line. +
+
+ + +
BLAS, LAPACK
-
-
- BLAS - (the Basic Linear Algebra Subroutines) and - LAPACK - (Linear Algebra Package) are two packages that support - low-level linear algebra operations on vectors and dense - matrices. - Both libraries should be packaged by almost all Linux - distributions and found automatically whenever available. - (You might have to install development versions of the libraries - for deal.II being able to use them). - For details on how to set up deal.II with a - non standard BLAS/LAPACK implementation, see the - advanced +
+
+ BLAS (the Basic Linear Algebra Subroutines) and + LAPACK ( + Linear Algebra Package) are two packages that support low-level linear algebra operations on vectors and dense matrices. Both libraries should be packaged by almost all Linux distributions and found automatically whenever available. + (You might have to install development versions of the libraries for deal.II being able to use them). For details on how to set up deal.II with a non standard BLAS/LAPACK implementation, see the + advanced setup section in the CMake ReadME. -
-
- - -
CUDA
-
-
- CUDA is a parallel - computing platform and API model created by Nvidia. It allows software - developers and software engineers to use CUDA-enabled GPU for general - purpose processing. - - Details about compatibility and configuration can be found here. -
- -
GSL
-
-
- The GNU Scientific Library - provides a wide range of mathematical routines such as random number - generators, special functions and least-squares fitting. - GSL should be - readily packaged by most Linux distributions. (Don't forget - to install a development version of the library). - To use a self compiled version, specify - -DGSL_DIR=/path/to/gsl on the command line. -
-
- -
HDF5
-
-
- The HDF5 library - provides graphical output capabilities in HDF5/XDMF - format. - HDF5 should be - readily packaged by most Linux distributions. (Don't forget - to install a development version of the library). - To use a self compiled version, specify - -DHDF5_DIR=/path/to/hdf5 on the command line. -
-
- - -
+ + + +
CUDA
+
+
+ CUDA is a parallel computing platform and API model created by Nvidia. It allows software developers and software engineers to use CUDA-enabled GPU for general purpose processing. Details + about compatibility and configuration can be found here. +
+ +
+ Gmsh
+
+
+ is a 3D finite element mesh generator. The executable can be used to create meshes from within deal.II by specifying the relevant input data. + Gmsh should be readily packaged by most Linux distributions. (Don't forget to install a development version of the library). To use a self compiled version, specify + -DGMSH_DIR=/path/to/gmsh on the command line. +
+
+ +
GSL
+
+
+ The GNU Scientific Library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. + GSL should be readily packaged by most Linux distributions. (Don't forget to install a development version of the library). To use a self compiled version, specify + -DGSL_DIR=/path/to/gsl on the command line. +
+
+ +
HDF5
+
+
+ The HDF5 library provides graphical output capabilities in HDF5/XDMF format. + HDF5 should be readily packaged by most Linux distributions. (Don't forget to install a development version of the library). To use a self compiled version, specify + -DHDF5_DIR=/path/to/hdf5 on the command line. +
+
+ + +
METIS
-
-
- METIS is a library that - provides various methods to partition - graphs. deal.II uses it in programs like the - step-17 tutorial to partition a mesh for parallel computing. - To use a self compiled version, specify - -DMETIS_DIR=/path/to/metis on the command line. - deal.II supports METIS 5 and later. -
- -
- Note: A more modern way to support parallel computations is - shown in the step-40 tutorial program and is based on - the p4est library instead of METIS. See below on - installing p4est. -
-
- - -
+
+
+ METIS is a library that provides various methods to partition graphs. deal.II uses it in programs like the step-17 tutorial to partition + a mesh for parallel computing. To use a self compiled version, specify + -DMETIS_DIR=/path/to/metis on the command line. + deal.II supports METIS 5 and later. +
+ +
+ Note: A more modern way to support parallel computations is shown in the step-40 tutorial program and is based on the p4est library instead of METIS. See below on installing p4est. +
+
+ + +
muparser
-
-
- muparser - is a library that allows to enter functions in text form and have them - interpreted at run time. This is particularly useful in input - parameter files. cmake will usually find the version of - this library that comes bundled with deal.II, but you - can specify -DMUPARSER_DIR=/path/to/muparser if desired. -
-
- - -
+
+
+ muparser is a library that allows to enter functions in text form and have them interpreted at run time. This is particularly useful in input parameter files. cmake will usually + find the version of this library that comes bundled with deal.II, but you can specify -DMUPARSER_DIR=/path/to/muparser if desired. +
+
+ +
+ nanoflann
+
+
+ nanoflann is a C++11 header-only library for building KD-Trees of datasets with different topologies. In particular, it can be used for operations such as finding the + vertex or cell closest to a given evaluation point that occur frequently in many applications using unstructured meshes. scale eigenvalue problems. + nanoflann should be readily packaged by most Linux distributions. (Don't forget to install a development version of the library). To use a self compiled version, specify + -DNANOFLANN_DIR=/path/to/nanoflann on the command line. +
+
+ +
NetCDF
+
+ NetCDF is a library that provides services for reading and writing mesh data (and many other things). deal.II can use it to read meshes via one + of the functions of the GridIn class. + NetCDF should be readily packaged by most Linux distributions. (Don't forget to install a development version of the library). To use a self compiled version, pass + -DNETCDF_DIR=/path/to/netcdf to cmake. +
+
+ +
OpenCASCADE
-
- Open CASCADE Technology is a software development kit for - applications dealing with 3D CAD data, freely available in - open source. Our internal interface works with the legacy - version of OpenCASCADE, which you can download and install - from the official website, as well as with the OpenCASCADE - Community Edition (OCE, available at - https://github.com/tpaviot/oce), - which offers a cmake - interface for its compilation. Alternatively, you can - install one of the many external applications that ship with - OpenCASCADE internally (for example - SALOME, or - FreeCAD). Further - installation instructions can be - found here. -
- -
NetCDF
-
- NetCDF is a library that provides services for - reading and writing mesh data (and many other - things). deal.II can use it to read meshes via - one of the functions of the GridIn class. - NetCDF should be readily packaged by most - Linux distributions. (Don't forget to install a development - version of the library). To use a self compiled version, pass - -DNETCDF_DIR=/path/to/netcdf to cmake. -
- - -
p4est
-
-
- p4est - is a library that deal.II uses to - distribute very large meshes across multiple processors (think - meshes with a billion cells on 10,000 processors). Using and - installing p4est is discussed here. - To use a self compiled version, pass the argument - -DP4EST_DIR=/path/to/p4est to the - cmake command. -
-
- - -
+ Open CASCADE Technology is a software development kit for applications dealing with 3D CAD data, freely available in open source. Our internal interface works with the legacy version of OpenCASCADE, which you can download and install from the official + website, as well as with the OpenCASCADE Community Edition (OCE, available at + https://github.com/tpaviot/oce), which offers a cmake interface for its compilation. Alternatively, you can install one of the many external applications that ship with OpenCASCADE internally + (for example + SALOME, or + FreeCAD). Further installation instructions can be found here. + + +
p4est
+
+
+ p4est is a library that deal.II uses to distribute very large meshes across multiple processors (think meshes with a billion cells on 10,000 processors). Using and + installing p4est is discussed here. To use a self compiled version, pass the argument + -DP4EST_DIR=/path/to/p4est to the + cmake command. +
+
+ + +
PETSc
-
-
- PETSc is a - library that supports parallel linear algebra and many other things. - - PETSc - is already packaged by some Linux distributions and should be - found automatically if present. (Don't forget to install a - development version of the library). To use a self compiled - version of PETSc, add -DPETSC_DIR=/path/to/petsc +
+ + PETSc is a library that supports parallel linear algebra and many other things. + + PETSc is already packaged by some Linux distributions and should be found automatically if present. (Don't forget to install a development version of the library). To use a + self compiled version of PETSc, add -DPETSC_DIR=/path/to/petsc -DPETSC_ARCH=architecture to the argument list for - cmake. The values for these arguments must be - the same as those specified when building PETSc. - + cmake. The values for these arguments must be the same as those specified when building PETSc. + - - To disable the PETSc interfaces in cases where cmake - automatically finds it, use -DDEAL_II_WITH_PETSC=OFF. - More information on configuring and building PETSc can be - found here. - -
+ + To disable the PETSc interfaces in cases where cmake automatically finds it, use -DDEAL_II_WITH_PETSC=OFF. More information on configuring and building PETSc can be found here. + + - + ScaLAPACK - - - scalapack - is a library of high-performance linear algebra routines for parallel - distributed memory machines. ScaLAPACK solves dense and banded linear - systems, least squares problems, eigenvalue problems, and singular value - problems. In order to enable this feature, add - -DSCALAPACK_DIR=/path/to/scalapack to the argument list for - cmake. If ScaLAPACK does not have embedded BLACS, you might - need to pass -DBLACS_DIR=/path/to/blacs as well. - - - - - SLEPc - - - SLEPc is a library for eigenvalue - computations that builds on PETSc. Its configuration works - just like that for PETSc, except that the variable to set - is SLEPC_DIR. For the interface with SLEPc to - work, deal.II's PETSc interface must also - be configured correctly (see above). - - - - To disable the SLEPc interfaces in cases where cmake - automatically finds it, use -DDEAL_II_WITH_PETSC=OFF. - More information on configuring and building SLEPc can be - found here. - - - - - + + scalapack is a library of high-performance linear algebra routines for parallel distributed memory machines. ScaLAPACK solves dense and banded linear systems, least squares problems, eigenvalue + problems, and singular value problems. In order to enable this feature, add + -DSCALAPACK_DIR=/path/to/scalapack to the argument list for + cmake. If ScaLAPACK does not have embedded BLACS, you might need to pass -DBLACS_DIR=/path/to/blacs as well. + + + + + SLEPc + + + SLEPc is a library for eigenvalue computations that builds on PETSc. Its configuration works just like that for PETSc, except that the variable to set is SLEPC_DIR. + For the interface with SLEPc to work, deal.II's PETSc interface must also be configured correctly (see above). + + + + To disable the SLEPc interfaces in cases where cmake automatically finds it, use -DDEAL_II_WITH_PETSC=OFF. More information on configuring and building SLEPc can be found here. + + + + + SUNDIALS + + + SUNDIALS is a collection of solvers for nonlinear and differential/algebraic equations. + SUNDIALS should be readily packaged by most Linux distributions. (Don't forget to install a development version of the library). To use a self compiled version, + specify + -DSUNDIALS_DIR=/path/to/sundials on the command line. + + + + Threading Building Blocks (TBB) - - - The Threading Building Blocks (TBB) - is a library that provides advanced services for using multiple - processor cores on a single machine and is used - in deal.II to parallelize many operations. If not - found in a system-wide location, cmake will - resort to the version bundled as part of - the deal.II download. It is always enabled unless - threads are explicitly disabled, see above. - - - - - Trilinos - - - Trilinos is a - library for parallel linear algebra and all sorts of other things as - well. - - To interface with a self compiled version of Trilinos - add -DTRILINOS_DIR=/path/to/trilinos to the - argument list for cmake. Alternatively, you can - also set an environment variable TRILINOS_DIR - and cmake will pick up this path. - - - - To disable the Trilinos interfaces in cases where - cmake automatically finds it, use - -DDEAL_II_WITH_TRILINOS=OFF. More details about - compatibility and configuration can be found - here. - - - - - + + The Threading Building Blocks (TBB) is a library that provides advanced services for using multiple processor cores on a single machine and is used in deal.II to parallelize many operations. If not found in a system-wide location, cmake will resort to the version bundled as part of the deal.II download. It is always enabled unless threads are explicitly disabled, + see above. + + + + Trilinos + + + Trilinos is a library for parallel linear algebra and all sorts of other things as well. To interface with a self compiled version of Trilinos add -DTRILINOS_DIR=/path/to/trilinos to the argument list for cmake. Alternatively, you can also set an environment variable TRILINOS_DIR and cmake will pick up this path. + + + + To disable the Trilinos interfaces in cases where + cmake automatically finds it, use + -DDEAL_II_WITH_TRILINOS=OFF. More details about compatibility and configuration can be found + here. + + + + + UMFPACK - - - UMFPACK, - which is part of SuiteSparse, is a sparse direct solver that we often use - in prototype codes where the goal is to simply get a linear system solved - robustly. The interface will be enabled by default, either using a version - installed on your system of using a version that comes bundled with - deal.II. It can be disabled explicitly by using the - -DDEAL_II_WITH_UMFPACK=OFF argument. - To use a self compiled version, pass the argument - -DUMFPACK_DIR=/path/to/umfpack to the - cmake command. - - - - SuiteSparse has its own license. To use it with deal.II, please read it - and make sure that you agree with it. You can find the license of - SuiteSparse inside the SuiteSparse download at the link given above. We - include UMFPACK in the deal.II distributions courtesy of its - author, Timothy + + + UMFPACK, which is part of SuiteSparse, is a sparse direct solver that we often use in prototype codes where the goal is to simply get a linear system solved robustly. + The interface will be enabled by default, either using a version installed on your system of using a version that comes bundled with + deal.II. It can be disabled explicitly by using the + -DDEAL_II_WITH_UMFPACK=OFF argument. To use a self compiled version, pass the argument + -DUMFPACK_DIR=/path/to/umfpack to the + cmake command. + + + + SuiteSparse has its own license. To use it with deal.II, please read it and make sure that you agree with it. You can find the license of SuiteSparse inside the SuiteSparse download at the link given above. We include UMFPACK in the deal.II distributions + courtesy of its author, Timothy A. Davis. - - + +
+ + zlib + + + zlib is a software library used for lossless data-compression. It is used in deal.II whenever compressed data is to be written. + zlib should be readily packaged by most Linux distributions. (Don't forget to install a development version of the library). To use a self compiled version, specify + -DZLIB_DIR=/path/to/zlib on the command line. + + - + More information on configuring and building the library - The deal.II cmake system allows far - greater control over what exactly is configured or built than just the - outline above. If you want to learn more about this, take a look - here. You might also be interested in - CMake for user projects or - build system internals. + The deal.II cmake system allows far greater control over what exactly is configured or built than just the outline above. If you want to learn more about this, take a look + here. You might also be interested in + CMake for user projects or + build system internals. @@ -841,72 +649,55 @@ License - The deal.II library is free software; you can use it, redistribute - it, and/or modify it under the terms of the - GNU Lesser General - Public License (LGPL) as published by the Free Software - Foundation; either version 2.1 of the License, or (at your option) - any later version. + The deal.II library is free software; you can use it, redistribute it, and/or modify it under the terms of the + GNU Lesser General + Public License (LGPL) as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. - This allows you to use the library free of charge for private, - academic, or commercial use (under the terms of the LGPL v2.1 or - later). You are guaranteed full access to the source code and are - encouraged to help in the further development of the library. Follow - this + This allows you to use the library free of charge for private, academic, or commercial use (under the terms of the LGPL v2.1 or later). You are guaranteed full access to the source code and are encouraged to help in the further development of the library. + Follow + this link for detailed information. - Please note: - - - Detailed license information can be found following - this link. - - - As a contributor to this project, you agree that any of your + Please note: + + + Detailed license information can be found following + this link. + + + As a contributor to this project, you agree that any of your contributions be licensed under the same terms and conditions as the license of the deal.II project granted to you. - + + + We, the deal.II Authors, do not require copyright assignments for contributions. This means that the copyright for code contributions in the deal.II project is held by its respective + contributors who have each agreed to release their contributed code under the terms of the LGPL v2.1 or later. + - We, the deal.II Authors, do not require copyright - assignments for contributions. This means that the copyright for - code contributions in the deal.II project is held by its - respective contributors who have each agreed to release their - contributed code under the terms of the LGPL v2.1 or later. - - - In addition to the terms imposed by the LGPL (version 2.1 or - later), we ask for the courtesy that scientific publications - presenting results obtained with this libraries acknowledge its - use. Please cite one of the papers referenced - here. - - - deal.II can interface with a number of other packages that you either - have to install yourself. They are, of course, covered by their - own licenses. In addition, deal.II comes bundled with copies of - + In addition to the terms imposed by the LGPL (version 2.1 or later), we ask for the courtesy that scientific publications presenting results obtained with this libraries acknowledge its use. Please cite one of the papers referenced + here. + + + deal.II can interface with a number of other packages that you either have to install yourself. They are, of course, covered by their own licenses. In addition, deal.II comes bundled with + copies of + UMFPACK, - Threading Building Blocks, - BOOST and - muparser, courtesy of their authors. - These are also covered by their own licenses; please refer to - their webpages for more information. - - - - - - + Threading Building Blocks, + BOOST and + muparser, courtesy of their authors. These are also covered by their own licenses; please refer to their webpages for more information. + + + + + + - + - + + + - -- 2.39.5

Installation instructions and further information - on deal.II

Installation instructions and further information on deal.II

System requirements

Supported platforms

System requirements

Supported platforms

Additional software requirements

Additional software requirements

Unpacking

Configuring and building the library

Configuring and building the documentation

Configuration options

Selecting optional compilation features

Selecting optional compilation features

Selecting optional library features

Selecting optional library features

Optional interfaces to other software packages

More information on configuring and building the library

License