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- <li class="tocentry"><span class="ref toc here">GROMACS installation guide</span>
- <ul class="toc">
- <li class="tocentry"><a href="#S1" title="1. Building GROMACS in GROMACS installation guide" class="ref toc">1 Building GROMACS</a></li>
- <li class="tocentry"><a href="#S2" title="2. Prerequisites in GROMACS installation guide" class="ref toc">2 Prerequisites</a>
- <ul class="toc">
- <li class="tocentry"><a href="#S2.SS1" title="2.1. Platform in 2. Prerequisites in GROMACS installation guide" class="ref toc">2.1 Platform</a></li>
- <li class="tocentry"><a href="#S2.SS2" title="2.2. Compiler in 2. Prerequisites in GROMACS installation guide" class="ref toc">2.2 Compiler</a>
- <ul class="toc">
- <li class="tocentry"><a href="#S2.SS2.SSS1" title="2.2.1. Running in parallel in 2.2. Compiler in 2. Prerequisites in GROMACS installation guide" class="ref toc">2.2.1 Running in parallel</a></li>
- </ul></li>
- <li class="tocentry"><a href="#S2.SS3" title="2.3. CMake in 2. Prerequisites in GROMACS installation guide" class="ref toc">2.3 CMake</a></li>
- <li class="tocentry"><a href="#S2.SS4" title="2.4. Fast Fourier Transform library in 2. Prerequisites in GROMACS installation guide" class="ref toc">2.4 Fast Fourier Transform library</a>
- <ul class="toc">
- <li class="tocentry"><a href="#S2.SS4.SSS1" title="2.4.1. FFTW in 2.4. Fast Fourier Transform library in 2. Prerequisites in GROMACS installation guide" class="ref toc">2.4.1 FFTW</a></li>
- <li class="tocentry"><a href="#S2.SS4.SSS2" title="2.4.2. MKL in 2.4. Fast Fourier Transform library in 2. Prerequisites in GROMACS installation guide" class="ref toc">2.4.2 MKL</a></li>
- </ul></li>
- <li class="tocentry"><a href="#S2.SS5" title="2.5. Optional build components in 2. Prerequisites in GROMACS installation guide" class="ref toc">2.5 Optional build components</a></li>
- </ul></li>
- <li class="tocentry"><a href="#S3" title="3. Doing a build of GROMACS in GROMACS installation guide" class="ref toc">3 Doing a build of GROMACS</a>
- <ul class="toc">
- <li class="tocentry"><a href="#S3.SS1" title="3.1. Configuring with CMake in 3. Doing a build of GROMACS in GROMACS installation guide" class="ref toc">3.1 Configuring with CMake</a></li>
- <li class="tocentry"><a href="#S3.SS2" title="3.2. Using CMake command-line options in 3. Doing a build of GROMACS in GROMACS installation guide" class="ref toc">3.2 Using CMake command-line options</a></li>
- <li class="tocentry"><a href="#S3.SS3" title="3.3. CMake advanced options in 3. Doing a build of GROMACS in GROMACS installation guide" class="ref toc">3.3 CMake advanced options</a></li>
- <li class="tocentry"><a href="#S3.SS4" title="3.4. Helping CMake find the right libraries/headers/programs in 3. Doing a build of GROMACS in GROMACS installation guide" class="ref toc">3.4 Helping CMake find the right libraries/headers/programs</a></li>
- <li class="tocentry"><a href="#S3.SS5" title="3.5. CMake advice during the GROMACS 4.6 beta phase in 3. Doing a build of GROMACS in GROMACS installation guide" class="ref toc">3.5 CMake advice during the GROMACS 4.6 beta phase</a></li>
- <li class="tocentry"><a href="#S3.SS6" title="3.6. Native GPU acceleration in 3. Doing a build of GROMACS in GROMACS installation guide" class="ref toc">3.6 Native GPU acceleration</a></li>
- <li class="tocentry"><a href="#S3.SS7" title="3.7. Static linking in 3. Doing a build of GROMACS in GROMACS installation guide" class="ref toc">3.7 Static linking</a></li>
- <li class="tocentry"><a href="#S3.SS8" title="3.8. Suffixes for binaries and libraries in 3. Doing a build of GROMACS in GROMACS installation guide" class="ref toc">3.8 Suffixes for binaries and libraries</a></li>
- <li class="tocentry"><a href="#S3.SS9" title="3.9. Building GROMACS in 3. Doing a build of GROMACS in GROMACS installation guide" class="ref toc">3.9 Building GROMACS</a></li>
- <li class="tocentry"><a href="#S3.SS10" title="3.10. Installing GROMACS in 3. Doing a build of GROMACS in GROMACS installation guide" class="ref toc">3.10 Installing GROMACS</a></li>
- <li class="tocentry"><a href="#S3.SS11" title="3.11. Getting access to GROMACS after installation in 3. Doing a build of GROMACS in GROMACS installation guide" class="ref toc">3.11 Getting access to GROMACS after installation</a></li>
- <li class="tocentry"><a href="#S3.SS12" title="3.12. Testing GROMACS for correctness in 3. Doing a build of GROMACS in GROMACS installation guide" class="ref toc">3.12 Testing GROMACS for correctness</a></li>
- <li class="tocentry"><a href="#S3.SS13" title="3.13. Testing GROMACS for performance in 3. Doing a build of GROMACS in GROMACS installation guide" class="ref toc">3.13 Testing GROMACS for performance</a></li>
- <li class="tocentry"><a href="#S3.SS14" title="3.14. Having difficulty? in 3. Doing a build of GROMACS in GROMACS installation guide" class="ref toc">3.14 Having difficulty?</a></li>
- </ul></li>
- <li class="tocentry"><a href="#S4" title="4. Special instructions for some platforms in GROMACS installation guide" class="ref toc">4 Special instructions for some platforms</a>
- <ul class="toc">
- <li class="tocentry"><a href="#S4.SS1" title="4.1. Building on Windows in 4. Special instructions for some platforms in GROMACS installation guide" class="ref toc">4.1 Building on Windows</a></li>
- <li class="tocentry"><a href="#S4.SS2" title="4.2. Building on Cray in 4. Special instructions for some platforms in GROMACS installation guide" class="ref toc">4.2 Building on Cray</a></li>
- <li class="tocentry"><a href="#S4.SS3" title="4.3. Building on BlueGene in 4. Special instructions for some platforms in GROMACS installation guide" class="ref toc">4.3 Building on BlueGene</a>
- <ul class="toc">
- <li class="tocentry"><a href="#S4.SS3.SSS1" title="4.3.1. BlueGene/P in 4.3. Building on BlueGene in 4. Special instructions for some platforms in GROMACS installation guide" class="ref toc">4.3.1 BlueGene/P</a></li>
- <li class="tocentry"><a href="#S4.SS3.SSS2" title="4.3.2. BlueGene/Q in 4.3. Building on BlueGene in 4. Special instructions for some platforms in GROMACS installation guide" class="ref toc">4.3.2 BlueGene/Q</a></li>
- </ul></li>
- </ul></li>
- <li class="tocentry"><a href="#S5" title="5. Tested platforms in GROMACS installation guide" class="ref toc">5 Tested platforms</a></li>
- <li class="tocentry"><a href="#S6" title="6. Other issues in GROMACS installation guide" class="ref toc">6 Other issues</a></li>
- </ul></li>
- </ul>
- </div>
- <div class="main">
- <div class="content">
- <div class="document">
- <h1 class="title document-title">GROMACS installation guide</h1>
- <div class="section" id="S1">
- <h2 class="title section-title"> 1. Building GROMACS</h2>
- <div class="para" id="S1.p1">
- <p class="p">These instructions pertain to building GROMACS 4.6 beta releases
-and newer. For installations instructions for old GROMACS versions,
-see here
-<a href="http://www.gromacs.org/Documentation/Installation_Instructions_4.5" title="" class="ref url"><span style="" class="text typewriter">http://www.gromacs.org/Documentation/Installation_Instructions_4.5</span></a>.</p>
- </div>
-
- </div>
-
- <div class="section" id="S2">
- <h2 class="title section-title"> 2. Prerequisites</h2>
- <div class="subsection" id="S2.SS1">
- <h3 class="title subsection-title"> 2.1. Platform</h3>
- <div class="para" id="S2.SS1.p1">
- <p class="p">GROMACS can be compiled for any distribution of Linux, Mac OS X,
-Windows (native, Cygwin or MinGW), BlueGene, Cray and probably others.
-Technically, it can be compiled on any platform with an ANSI C
-compiler and supporting libraries, such as the GNU C library. It can
-even compile on an iPhone! Later, there will be a detailed list of
-hardware, platform and compilers upon which we do build and regression
-testing.</p>
- </div>
-
- </div>
-
- <div class="subsection" id="S2.SS2">
- <h3 class="title subsection-title"> 2.2. Compiler</h3>
- <div class="para" id="S2.SS2.p1">
- <p class="p">GROMACS requires an ANSI C compiler that complies with the C89
-standard. For best performance, the GROMACS team strongly
-recommends you get the most recent version of your preferred compiler
-for your platform (e.g. GCC 4.7 or Intel 12.0 or newer on x86
-hardware). There is a large amount of GROMACS code introduced in
-version 4.6 that depends on effective compiler optimization to get
-high performance - the old assembly-language routines have all
-gone. For other platforms, use the vendor's compiler, and check for
-specialized information below.</p>
- </div>
-
- <div class="subsubsection" id="S2.SS2.SSS1">
- <h4 class="title subsubsection-title"> 2.2.1. Running in parallel</h4>
- <div class="para" id="S2.SS2.SSS1.p1">
- <p class="p">GROMACS can run in parallel on multiple cores of a single
-workstation using its built-in ThreadMPI. No user action is required
-in order to enable this.</p>
- </div>
-
- <div class="para" id="S2.SS2.SSS1.p2">
- <p class="p">If you wish to use the excellent new native GPU support in GROMACS,
-NVIDIA's CUDA
-<a href="http://www.nvidia.com/object/cuda_home_new.html" title="" class="ref url"><span style="" class="text typewriter">http://www.nvidia.com/object/cuda_home_new.html</span></a> version
-3.2 software development kit is required, and the latest
-version is encouraged. NVIDIA GPUs with at least NVIDIA compute
-capability 2.0 are required, e.g. Fermi or Kepler cards.</p>
- </div>
-
- <div class="para" id="S2.SS2.SSS1.p3">
- <p class="p">The GPU support from GROMACS version 4.5 using OpenMM
-<a href="https://simtk.org/home/openmm" title="" class="ref url"><span style="" class="text typewriter">https://simtk.org/home/openmm</span></a> is still available, also requires
-CUDA, and remains the only hardware-based acceleration available
-for implicit solvent simulations in GROMACS. This parallelization
-path may not be maintained in the future.</p>
- </div>
-
- <div class="para" id="S2.SS2.SSS1.p4">
- <p class="p">If you wish to run in parallel on multiple machines across a network,
-you will need to have</p>
-
- <ul class="itemize" id="I1">
-
- <li class="item" id="I1.i1">
-
- <div class="para" id="I1.i1.p1">
- <p class="p">an MPI library installed that supports the MPI 1.3
-standard, and</p>
- </div>
-
- </li>
-
- <li class="item" id="I1.i2">
-
- <div class="para" id="I1.i2.p1">
- <p class="p">wrapper compilers that will compile code using that library.</p>
- </div>
-
- </li>
-
- </ul>
-
- <p class="p">The GROMACS team recommends OpenMPI
-<a href="http://www.open-mpi.org/" title="" class="ref url"><span style="" class="text typewriter">http://www.open-mpi.org/</span></a> version 1.4.1 (or higher), MPICH
-<a href="http://www.mpich.org/" title="" class="ref url"><span style="" class="text typewriter">http://www.mpich.org/</span></a> version 1.4.1 (or higher), or your
-hardware vendor's MPI installation. The most recent version of
-either of this is likely to be the best. LAM/MPI
-<a href="http://www.lam-mpi.org/" title="" class="ref url"><span style="" class="text typewriter">http://www.lam-mpi.org/</span></a> may work, but since it has been
-deprecated for years, it is not supported.</p>
- </div>
-
- <div class="para" id="S2.SS2.SSS1.p5">
- <p class="p">In some cases, OpenMP parallelism is an advantage for GROMACS,
-but support for this is generally built into your compiler and you
-need to make no advance preparation for this. The performance gain you
-might achieve can vary with the compiler.</p>
- </div>
-
- <div class="para" id="S2.SS2.SSS1.p6">
- <p class="p">It is important to examine how you will use GROMACS and upon what
-hardware and with what compilers in deciding which parallelization
-paths to make available. Testing the performance of different options
-is unfortunately mandatory. The days of being able to just build and
-run '<code class="verbatim">mdrun</code>' and get decent performance by default on your
-hardware are long gone. GROMACS will always run correctly, and does
-a decent job of trying to maximize your performance, but if you want
-to approach close to the optimum, you will need to do some work for
-it!</p>
- </div>
-
- </div>
-
- </div>
-
- <div class="subsection" id="S2.SS3">
- <h3 class="title subsection-title"> 2.3. CMake</h3>
- <div class="para" id="S2.SS3.p1">
- <p class="p">From version 4.6, GROMACS has moved to use the build system
-CMake. The previous build system that used <span style="" class="text typewriter">configure</span> from
-the GNU autotools package has been removed permanently. CMake
-permits the GROMACS team to support a very wide range of hardware,
-compilers and build configurations while continuing to provide the
-portability, robustness and performance for which GROMACS is known.</p>
- </div>
-
- <div class="para" id="S2.SS3.p2">
- <p class="p">GROMACS requires CMake version 2.8.0 or higher. Lower
-versions will not work. You can check whether CMake is installed,
-and what version it is, with <span style="" class="text typewriter">cmake --version</span>. If you need to
-install CMake, then first check whether your platform's package
-management system provides a suitable version, or visit
-<a href="http://www.cmake.org/cmake/help/install.html" title="" class="ref url"><span style="" class="text typewriter">http://www.cmake.org/cmake/help/install.html</span></a> for pre-compiled
-binaries, source code and installation instructions. The GROMACS
-team recommends you install the most recent version of CMake you
-can.
-</p>
- </div>
-
- </div>
-
- <div class="subsection" id="S2.SS4">
- <h3 class="title subsection-title"> 2.4. Fast Fourier Transform library</h3>
- <div class="para" id="S2.SS4.p1">
- <p class="p">Many simulations in GROMACS make extensive use of Fourier transforms,
-and a software library to perform these is always required. We
-recommend FFTW <a href="http://www.fftw.org/" title="" class="ref url"><span style="" class="text typewriter">http://www.fftw.org/</span></a> (version 3 or higher
-only) or Intel's MKL
-<a href="http://software.intel.com/en-us/intel-mkl" title="" class="ref url"><span style="" class="text typewriter">http://software.intel.com/en-us/intel-mkl</span></a>.</p>
- </div>
-
- <div class="subsubsection" id="S2.SS4.SSS1">
- <h4 class="title subsubsection-title"> 2.4.1. FFTW</h4>
- <div class="para" id="S2.SS4.SSS1.p1">
- <p class="p">FFTW is likely to be available for your platform via its package
-management system, but there can be compatibility and significant
-performance issues associated with these packages. In particular,
-GROMACS simulations are normally run in single floating-point
-precision whereas the default FFTW package is normally in double
-precision, and good compiler options to use for FFTW when linked to
-GROMACS may not have been used. Accordingly, the GROMACS team
-recommends either</p>
-
- <ul class="itemize" id="I2">
-
- <li class="item" id="I2.i1">
-
- <div class="para" id="I2.i1.p1">
- <p class="p">that you permit the GROMACS installation to download and
-build FFTW 3.3.2 from source automatically
-for you, or</p>
- </div>
-
- </li>
-
- <li class="item" id="I2.i2">
-
- <div class="para" id="I2.i2.p1">
- <p class="p">that you build FFTW from the source code.</p>
- </div>
-
- </li>
-
- </ul>
- </div>
-
- <div class="para" id="S2.SS4.SSS1.p2">
- <p class="p">If you build FFTW from source yourself, get the most recent version
-and follow its installation guide
-(e.g. <a href="http://www.fftw.org/fftw3_doc/Installation-and-Customization.html" title="" class="ref url"><span style="" class="text typewriter">http://www.fftw.org/fftw3_doc/Installation-and-Customization.html</span></a>). Choose
-the precision (i.e. single or float vs double) to match what you will
-later require for GROMACS. There is no need to compile with
-threading or MPI support, but it does no harm. On x86 hardware,
-compile <em class="emph">only</em> with <span style="" class="text typewriter">--enable-sse2</span> (regardless of
-precision) even if your processors can take advantage of AVX
-extensions to SSE. The way GROMACS uses Fourier transforms
-cannot take advantage of this feature in FFTW because of memory
-system performance limitations, it can degrade performance by around
-20%, and there is no way for GROMACS to require the use of the
-SSE2 at run time if AVX support has been compiled into FFTW.</p>
- </div>
-
- </div>
-
- <div class="subsubsection" id="S2.SS4.SSS2">
- <h4 class="title subsubsection-title"> 2.4.2. MKL</h4>
- <div class="para" id="S2.SS4.SSS2.p1">
- <p class="p">Using MKL requires a set of linker flags that GROMACS is not
-able to detect for you, so setting up optimal linking is tricky at the
-moment. Need better documentation later.</p>
- </div>
-
- </div>
-
- </div>
-
- <div class="subsection" id="S2.SS5">
- <h3 class="title subsection-title"> 2.5. Optional build components</h3>
- <div class="para" id="S2.SS5.p1">
- <ul class="itemize" id="I3">
-
- <li class="item" id="I3.i1">
-
- <div class="para" id="I3.i1.p1">
- <p class="p">A hardware-optimized BLAS or LAPACK library is useful for
-some of the GROMACS utilities, but is not needed for running
-simulations.</p>
- </div>
-
- </li>
-
- <li class="item" id="I3.i2">
-
- <div class="para" id="I3.i2.p1">
- <p class="p">The built-in GROMACS trajectory viewer <span style="" class="text typewriter">ngmx</span> requires
-X11 and Motif/Lesstif libraries and header files. Generally, the
-GROMACS team recommends you use third-party software for
-visualization, such as VMD
-<a href="http://www.ks.uiuc.edu/Research/vmd/" title="" class="ref url"><span style="" class="text typewriter">http://www.ks.uiuc.edu/Research/vmd/</span></a> or PyMOL
-<a href="http://www.pymol.org/" title="" class="ref url"><span style="" class="text typewriter">http://www.pymol.org/</span></a>.</p>
- </div>
-
- </li>
-
- </ul>
- </div>
-
- </div>
-
- </div>
-
- <div class="section" id="S3">
- <h2 class="title section-title"> 3. Doing a build of GROMACS</h2>
- <div class="para" id="S3.p1">
- <p class="p">This section will cover a general build of GROMACS with CMake,
-but it is not an exhaustive discussion of how to use CMake. There
-are many resources available on the web, which we suggest you search
-for when you encounter problems not covered here. The material below
-applies specifically to builds on Unix-like systems, including Linux,
-Mac OS X, MinGW and Cygwin. For other platforms, see the specialist
-instructions below.</p>
- </div>
-
- <div class="subsection" id="S3.SS1">
- <h3 class="title subsection-title"> 3.1. Configuring with CMake</h3>
- <div class="para" id="S3.SS1.p1">
- <p class="p">CMake will run many tests on your system and do its best to work
-out how to build GROMACS for you. If you are building GROMACS on
-hardware that is identical to that where you will run <span style="" class="text typewriter">mdrun</span>,
-then you can be sure that the defaults will be pretty good. Howver, if
-you want to control aspects of the build, there's plenty of things you
-can set, too.</p>
- </div>
-
- <div class="para" id="S3.SS1.p2">
- <p class="p">The best way to use CMake to configure GROMACS is to do an
-“out-of-source” build, by making another directory from which you
-will run CMake. This can be a subdirectory or not, it doesn't
-matter. It also means you can never corrupt your source code by trying
-to build it! So, the only required argument on the CMake command
-line is the name of the directory containing the
-<span style="" class="text typewriter">CMakeLists.txt</span> file of the code you want to build. For
-example, download the source tarball and use
-</p>
- <pre class="verbatim">
-$ tar xfz gromacs-4.6-beta1-src.tgz
-$ cd gromacs-4.6-beta1
-$ mkdir build-cmake
-$ cd build-cmake
-$ cmake ..
-</pre></div>
-
- <div class="para" id="S3.SS1.p3">
- <p class="p">You will see <span style="" class="text typewriter">cmake</span> report the results of a large number of
-tests on your system made by CMake and by GROMACS. These are
-written to the CMake cache, kept in <span style="" class="text typewriter">CMakeCache.txt</span>. You
-can edit this file by hand, but this is not recommended because it is
-easy to reach an inconsistent state. You should not attempt to move or
-copy this file to do another build, because the paths are hard-coded
-within it. If you mess things up, just delete this file and start
-again with '<code class="verbatim">cmake</code>'.</p>
- </div>
-
- <div class="para" id="S3.SS1.p4">
- <p class="p">If there's a serious problem detected at this stage, then you will see
-a fatal error and some suggestions for how to overcome it. If you're
-not sure how to deal with that, please start by searching on the web
-(most computer problems already have known solutions!) and then
-consult the <span style="" class="text typewriter">gmx-users</span> mailing list. There are also
-informational warnings that you might like to take on board or
-not. Piping the output of <span style="" class="text typewriter">cmake</span> through <span style="" class="text typewriter">less</span> or
-<span style="" class="text typewriter">tee</span> can be useful, too.</p>
- </div>
-
- <div class="para" id="S3.SS1.p5">
- <p class="p">CMake works in an iterative fashion, re-running each time a setting
-is changed to try to make sure other things are consistent. Once
-things seem consistent, the iterations stop. Once <span style="" class="text typewriter">cmake</span>
-returns, you can see all the settings that were chosen and information
-about them by using</p>
- <pre class="verbatim">
-$ ccmake ..
-</pre>
- <p class="p">Check out <a href="http://www.cmake.org/cmake/help/runningcmake.html" title="" class="ref url"><span style="" class="text typewriter">http://www.cmake.org/cmake/help/runningcmake.html</span></a> for
-general advice on what you are seeing and how to navigate and change
-things. The settings you might normally want to change are already
-presented. If you make any changes, then <span style="" class="text typewriter">ccmake</span> will notice
-that and require that you re-configure (using '<code class="verbatim">c</code>'), so that it
-gets a chance to make changes that depend on yours and perform more
-checking. This might require several configuration stages when you are
-using <span style="" class="text typewriter">ccmake</span> - when you are using <span style="" class="text typewriter">cmake</span> the
-iteration is done behind the scenes.</p>
- </div>
-
- <div class="para" id="S3.SS1.p6">
- <p class="p">A key thing to consider here is the setting of
-<span style="" class="text typewriter">GMX_INSTALL_PREFIX</span>. You will need to be able to write to this
-directory in order to install GROMACS later, and if you change your
-mind later, changing it in the cache triggers a full re-build,
-unfortunately. So if you do not have super-user privileges on your
-machine, then you will need to choose a sensible location within your
-home directory for your GROMACS installation.</p>
- </div>
-
- <div class="para" id="S3.SS1.p7">
- <p class="p">When <span style="" class="text typewriter">cmake</span> or <span style="" class="text typewriter">ccmake</span> have completed iterating, the
-cache is stable and a build tree can be generated, with '<code class="verbatim">g</code>' in
-<span style="" class="text typewriter">ccmake</span> or automatically with <span style="" class="text typewriter">cmake</span>.</p>
- </div>
-
- </div>
-
- <div class="subsection" id="S3.SS2">
- <h3 class="title subsection-title"> 3.2. Using CMake command-line options</h3>
- <div class="para" id="S3.SS2.p1">
- <p class="p">Once you become comfortable with setting and changing options, you
-may know in advance how you will configure GROMACS. If so, you can
-speed things up by invoking <span style="" class="text typewriter">cmake</span> with a command like:</p>
- <pre class="verbatim">
-$ cmake .. -DGMX_GPU=ON -DGMX_MPI=ON -DGMX_INSTALL_PREFIX=/home/marydoe/programs
-</pre>
- <p class="p">to build with GPUs, MPI and install in a custom location. You can even
-save that in a shell script to make it even easier next time. You can
-also do this kind of thing with <span style="" class="text typewriter">ccmake</span>, but you should avoid
-this, because the options set with '<code class="verbatim">-D</code>' will not be able to be
-changed interactively in that run of <span style="" class="text typewriter">ccmake</span>.</p>
- </div>
-
- </div>
-
- <div class="subsection" id="S3.SS3">
- <h3 class="title subsection-title"> 3.3. CMake advanced options</h3>
- <div class="para" id="S3.SS3.p1">
- <p class="p">The options that can be seen with <span style="" class="text typewriter">ccmake</span> are ones that we
-think a reasonable number of users might want to consider
-changing. There are a lot more options available, which you can see by
-toggling the advanced mode in <span style="" class="text typewriter">ccmake</span> on and off with
-'<code class="verbatim">t</code>'. Even there, most of the variables that you might want to
-change have a '<code class="verbatim">CMAKE_</code>' or '<code class="verbatim">GMX_</code>' prefix.</p>
- </div>
-
- </div>
-
- <div class="subsection" id="S3.SS4">
- <h3 class="title subsection-title"> 3.4. Helping CMake find the right libraries/headers/programs</h3>
- <div class="para" id="S3.SS4.p1">
- <p class="p">If libraries are installed in non-default locations their location can
-be specified using the following environment variables:</p>
-
- <ul class="itemize" id="I4">
-
- <li class="item" id="I4.i1">
-
- <div class="para" id="I4.i1.p1">
- <p class="p"><span style="" class="text typewriter">CMAKE_INCLUDE_PATH</span> for header files</p>
- </div>
-
- </li>
-
- <li class="item" id="I4.i2">
-
- <div class="para" id="I4.i2.p1">
- <p class="p"><span style="" class="text typewriter">CMAKE_LIBRARY_PATH</span> for libraries</p>
- </div>
-
- </li>
-
- <li class="item" id="I4.i3">
-
- <div class="para" id="I4.i3.p1">
- <p class="p"><span style="" class="text typewriter">CMAKE_PREFIX_PATH</span> for header, libraries and binaries
-(e.g. '<code class="verbatim">/usr/local</code>').</p>
- </div>
-
- </li>
-
- </ul>
-
- <p class="p">The respective '<code class="verbatim">include</code>', '<code class="verbatim">lib</code>', or '<code class="verbatim">bin</code>' is
-appended to the path. For each of these variables, a list of paths can
-be specified (on Unix seperated with ”:”). Note that these are
-enviroment variables (and not CMake command-line arguments) and in
-a '<code class="verbatim">bash</code>' shell are used like:</p>
- <pre class="verbatim">
-$ CMAKE_PREFIX_PATH=/opt/fftw:/opt/cuda cmake ..
-</pre></div>
-
- <div class="para" id="S3.SS4.p2">
- <p class="p">The <span style="" class="text typewriter">CC</span> and <span style="" class="text typewriter">CXX</span> environment variables are also useful
-for indicating to CMake which compilers to use, which can be very
-important for maximising GROMACS performance. Similarly,
-<span style="" class="text typewriter">CFLAGS</span>/<span style="" class="text typewriter">CXXFLAGS</span> can be used to pass compiler
-options, but note that these will be appended to those set by
-GROMACS for your build platform and build type. You can customize
-some of this with advanced options such as <span style="" class="text typewriter">CMAKE_C_FLAGS</span>
-and its relatives.</p>
- </div>
-
- <div class="para" id="S3.SS4.p3">
- <p class="p">See also: <a href="http://cmake.org/Wiki/CMake_Useful_Variables#Environment_Variables" title="" class="ref url"><span style="" class="text typewriter">http://cmake.org/Wiki/CMake_Useful_Variables#Environment_Variables</span></a></p>
- </div>
-
- </div>
-
- <div class="subsection" id="S3.SS5">
- <h3 class="title subsection-title"> 3.5. CMake advice during the GROMACS 4.6 beta phase</h3>
- <div class="para" id="S3.SS5.p1">
- <p class="p">We'd like users to have the ability to change any setting and still
-have the CMake cache stable; ie. not have things you set
-mysteriously change, or (worse) the whole thing breaks. We're not
-there yet. If you know in advance you will want to use a particular
-setting, set that on the initial <span style="" class="text typewriter">cmake</span> command line. If you
-have to change compilers, do that there, or immediately afterwards in
-<span style="" class="text typewriter">ccmake</span>. Gross changes like GPU or shared libraries on/off are
-more likely to work if you do them on the initial command line,
-because that's how we've been doing it while developing and
-testing. If you do make a mess of things, there's a great thing about
-an out-of-source build - you can just do '<code class="verbatim">rm -rf *</code>' and start
-again. Easy!</p>
- </div>
-
- <div class="para" id="S3.SS5.p2">
- <p class="p">We are interested in learning how you managed to break things. If you
-can reproducibly reach a state where CMake can't proceed, or
-subsequent compilation/linking/running fails, then we need to know so
-we can fix it!</p>
- </div>
-
- </div>
-
- <div class="subsection" id="S3.SS6">
- <h3 class="title subsection-title"> 3.6. Native GPU acceleration</h3>
- <div class="para" id="S3.SS6.p1">
- <p class="p">If you have the CUDA SDK installed, you can use CMake
-with:</p>
- <pre class="verbatim">
-cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
-</pre>
- <p class="p">(or whichever path has your installation). Note that this will require
-a working C++ compiler, and in some cases you might need to handle
-this manually, e.g. with the advanced option
-<span style="" class="text typewriter">CUDA_HOST_COMPILER</span>.</p>
- </div>
-
- <div class="para" id="S3.SS6.p2">
- <p class="p">More documentation needed here - particular discussion of fiddly
-details on Windows, Linux and Mac required. Not all compilers on all
-systems can be made to work.</p>
- </div>
-
- </div>
-
- <div class="subsection" id="S3.SS7">
- <h3 class="title subsection-title"> 3.7. Static linking</h3>
- <div class="para" id="S3.SS7.p1">
- <p class="p">Dynamic linking of the GROMACS executables will lead to a smaller
-disk footprint when installed, and so is the default. However, on some
-hardware or under some circumstances you might need to do static
-linking. To link GROMACS binaries statically against the internal
-GROMACS libraries, set <span style="" class="text typewriter">BUILD_SHARED_LIBS=OFF</span>. To link
-statically against external libraries as well, the
-<span style="" class="text typewriter">GMX_PREFER_STATIC_LIBS=ON</span> option can be used. Note, that
-in general CMake picks up whatever is available, so this option
-only instructs CMake to prefer static libraries when both static
-and shared are available. If no static version of an external library
-is available, even when the aforementioned option is ON, the shared
-library will be used. Also note, that the resulting binaries will
-still be dynamically linked against system libraries if that is all
-that is available.</p>
- </div>
-
- </div>
-
- <div class="subsection" id="S3.SS8">
- <h3 class="title subsection-title"> 3.8. Suffixes for binaries and libraries</h3>
- <div class="para" id="S3.SS8.p1">
- <p class="p">It is sometimes convenient to have different versions of the same
-GROMACS libraries installed. The most common use cases have been
-single and double precision, and with and without MPI. By default,
-GROMACS will suffix binaries and libraries for such builds with
-'<code class="verbatim">_d</code>' for double precision and/or '<code class="verbatim">_mpi</code>' for MPI (and
-nothing otherwise). This can be controlled manually with
-<span style="" class="text typewriter">GMX_DEFAULT_SUFFIX</span>, <span style="" class="text typewriter">GMX_BINARY_SUFFIX</span> and
-<span style="" class="text typewriter">GMX_LIBRARY_SUFFIX</span>.</p>
- </div>
-
- </div>
-
- <div class="subsection" id="S3.SS9">
- <h3 class="title subsection-title"> 3.9. Building GROMACS</h3>
- <div class="para" id="S3.SS9.p1">
- <p class="p">Once you have a stable cache, you can build GROMACS. If you're not
-sure the cache is stable, you can re-run <code class="verbatim">cmake ..</code> or
-<code class="verbatim">ccmake ..</code>' to see. Then you can run <span style="" class="text typewriter">make</span> to start the
-compilation. Before actual compilation starts, <span style="" class="text typewriter">make</span> checks
-that the cache is stable, so if it isn't you will see CMake run
-again.</p>
- </div>
-
- <div class="para" id="S3.SS9.p2">
- <p class="p">So long as any changes you've made to the configuration are sensible,
-it is expected that the <span style="" class="text typewriter">make</span> procedure will always complete
-successfully. The tests GROMACS makes on the settings you choose
-are pretty extensive, but there are probably a few cases we haven't
-thought of yet. Search the web first for solutions to problems,
-but if you need help, ask on <span style="" class="text typewriter">gmx-users</span>, being sure to provide
-as much information as possible about what you did, the system you are
-building on, and what went wrong.</p>
- </div>
-
- <div class="para" id="S3.SS9.p3">
- <p class="p">If you have a multi-core or multi-CPU machine with <span style="" class="text typewriter">N</span>
-processors, then using
-</p>
- <pre class="verbatim">
-$ make -j N
-</pre>
- <p class="p">will generally speed things up by quite a bit.</p>
- </div>
-
- </div>
-
- <div class="subsection" id="S3.SS10">
- <h3 class="title subsection-title"> 3.10. Installing GROMACS</h3>
- <div class="para" id="S3.SS10.p1">
- <p class="p">Finally, <span style="" class="text typewriter">make install</span> will install GROMACS in the
-directory given in <span style="" class="text typewriter">GMX_INSTALL_PREFIX</span>. If this is an system
-directory, then you will need permission to write there, and you
-should use super-user privileges only for <span style="" class="text typewriter">make install</span> and
-not the whole procedure.</p>
- </div>
-
- </div>
-
- <div class="subsection" id="S3.SS11">
- <h3 class="title subsection-title"> 3.11. Getting access to GROMACS after installation</h3>
- <div class="para" id="S3.SS11.p1">
- <p class="p">GROMACS installs the script <span style="" class="text typewriter">GMXRC</span> in the <span style="" class="text typewriter">bin</span>
-subdirectory of the installation directory
-(e.g. <span style="" class="text typewriter">/usr/local/gromacs/bin/GMXRC</span>), which you should source
-from your shell:</p>
- <pre class="verbatim">
-$ source your-installation-prefix-here/bin/GMXRC
-</pre></div>
-
- <div class="para" id="S3.SS11.p2">
- <p class="p">It will detect what kind of shell you are running and
-set up your environment for using GROMACS. You may wish to arrange
-for your login scripts to do this automatically; please search the web
-for instructions on how to do this for your shell.</p>
- </div>
-
- </div>
-
- <div class="subsection" id="S3.SS12">
- <h3 class="title subsection-title"> 3.12. Testing GROMACS for correctness</h3>
- <div class="para" id="S3.SS12.p1">
- <p class="p">TODO install and use regression set</p>
- </div>
-
- </div>
-
- <div class="subsection" id="S3.SS13">
- <h3 class="title subsection-title"> 3.13. Testing GROMACS for performance</h3>
- <div class="para" id="S3.SS13.p1">
- <p class="p">TODO benchmarks</p>
- </div>
-
- </div>
-
- <div class="subsection" id="S3.SS14">
- <h3 class="title subsection-title"> 3.14. Having difficulty?</h3>
- <div class="para" id="S3.SS14.p1">
- <p class="p">You're not alone, this can be a complex task. If you encounter a
-problem with installing GROMACS, then there are a number of
-locations where you can find assistance. It is recommended that you
-follow these steps to find the solution:</p>
- </div>
-
- <div class="para" id="S3.SS14.p2">
- <ol class="enumerate" id="I5">
-
- <li class="item" id="I5.i1">
-
- <div class="para" id="I5.i1.p1">
- <p class="p">Read the installation instructions again, taking note that you
-have followed each and every step correctly.</p>
- </div>
-
- </li>
-
- <li class="item" id="I5.i2">
-
- <div class="para" id="I5.i2.p1">
- <p class="p">Search the GROMACS website and users emailing list for
-information on the error.</p>
- </div>
-
- </li>
-
- <li class="item" id="I5.i3">
-
- <div class="para" id="I5.i3.p1">
- <p class="p">Search the internet using a search engine such as Google.</p>
- </div>
-
- </li>
-
- <li class="item" id="I5.i4">
-
- <div class="para" id="I5.i4.p1">
- <p class="p">Post to the GROMACS users emailing list <span style="" class="text typewriter">gmx-users</span>
-for assistance. Be sure to give a full description of what you have
-done and why you think it didn't work. Give details about the system
-on which you are installing. Copy and paste your command line and as
-much of the output as you think might be relevant - certainly from
-the first indication of a problem. Describe the machine and
-operating system you are running on. People who might volunteer to
-help you do not have time to ask you interactive detailed follow-up
-questions, so you will get an answer faster if you provide as much
-information as you think could possibly help.</p>
- </div>
-
- </li>
-
- </ol>
- </div>
-
- </div>
-
- </div>
-
- <div class="section" id="S4">
- <h2 class="title section-title"> 4. Special instructions for some platforms</h2>
- <div class="subsection" id="S4.SS1">
- <h3 class="title subsection-title"> 4.1. Building on Windows</h3>
- <div class="para" id="S4.SS1.p1">
- <p class="p">Building on Cygwin/MinGW/etc. works just like Unix. Please see the
-instructions above.</p>
- </div>
-
- <div class="para" id="S4.SS1.p2">
- <p class="p">Building on Windows using native compilers is rather similar to
-building on Unix, so please start by reading the above. Then, download
-and unpack the GROMACS source archive. The UNIX-standard
-<span style="" class="text typewriter">.tar.gz</span> format can be managed on Windows, but you may prefer
-to browse <a href="ftp://ftp.gromacs.org/pub/gromacs" title="" class="ref url"><span style="" class="text typewriter">ftp://ftp.gromacs.org/pub/gromacs</span></a> to obtain a
-<span style="" class="text typewriter">.zip</span> format file, which doesn't need any external tools to
-unzip on recent Windows systems. Make a folder in which to do the
-out-of-source build of GROMACS. For example, make it within the
-folder unpacked from the source archive, and call it “build-cmake”.
-</p>
- </div>
-
- <div class="para" id="S4.SS1.p3">
- <p class="p">Next, you need to open a command shell. If you do this from within
-your IDE (e.g. Microsoft Visual Studio), it will configure the
-environment for you. If you use a normal Windows command shell, then
-you will need to either set up the environment to find your compilers
-and libraries yourself, or run the <span style="" class="text typewriter">vcvarsall.bat</span> batch script
-provided by MSVC (just like sourcing a bash script under
-Unix). Presumably Intel's IDE has a similar functionality.</p>
- </div>
-
- <div class="para" id="S4.SS1.p4">
- <p class="p">Within that command shell, change to the folder you created above. Run
-<code class="verbatim">cmake ..</code>, where the folder you point CMake towards is the
-folder created by the GROMACS installer. Resolve issues as
-above. You will probably make your life easier and faster by using the
-new facility to download and install FFTW automatically. After the
-initial run of <code class="verbatim">cmake</code>, you may wish to use <code class="verbatim">cmake</code>,
-<code class="verbatim">ccmake</code> or the GUI version of CMake until your configuration
-is complete.</p>
- </div>
-
- <div class="para" id="S4.SS1.p5">
- <p class="p">To compile GROMACS, you then use <code class="verbatim">cmake --build .</code> so the
-right tools get used.</p>
- </div>
-
- </div>
-
- <div class="subsection" id="S4.SS2">
- <h3 class="title subsection-title"> 4.2. Building on Cray</h3>
- <div class="para" id="S4.SS2.p1">
- <p class="p">Probably you need to build static libraries only? Volunteer needed.</p>
- </div>
-
- </div>
-
- <div class="subsection" id="S4.SS3">
- <h3 class="title subsection-title"> 4.3. Building on BlueGene</h3>
- <div class="subsubsection" id="S4.SS3.SSS1">
- <h4 class="title subsubsection-title"> 4.3.1. BlueGene/P</h4>
- <div class="para" id="S4.SS3.SSS1.p1">
- <p class="p">Mark to write later. There is currently no native acceleration on this
-platform, but the default plain C kernels will work.</p>
- </div>
-
- </div>
-
- <div class="subsubsection" id="S4.SS3.SSS2">
- <h4 class="title subsubsection-title"> 4.3.2. BlueGene/Q</h4>
- <div class="para" id="S4.SS3.SSS2.p1">
- <p class="p">Mark to write later. There is currently no native acceleration on this
-platform, but the default plain C kernels will work.</p>
- </div>
-
- </div>
-
- </div>
-
- </div>
-
- <div class="section" id="S5">
- <h2 class="title section-title"> 5. Tested platforms</h2>
- <div class="para" id="S5.p1">
- <p class="p">While it is our best belief that GROMACS will build and run pretty
-much everywhere, it's important that we tell you where we really know
-it works because we've tested it. We do test on Linux, Windows, and
-Mac with a range of compilers and libraries for a range of our
-configuration options. Every commit in our <span style="" class="text typewriter">git</span> source code
-repository is tested on … We test irregularly on…</p>
- </div>
-
- <div class="para" id="S5.p2">
- <p class="p">Contributions to this section are welcome.</p>
- </div>
-
- <div class="para" id="S5.p3">
- <p class="p">Later we might set up the ability for users to contribute test results
-to Jenkins.
-</p>
- </div>
-
- </div>
-
- <div class="section" id="S6">
- <h2 class="title section-title"> 6. Other issues</h2>
- <div class="para" id="S6.p1">
- <p class="p">The GROMACS utility programs often write data files in formats
-suitable for the Grace plotting tool, but it is straightforward to
-use these files in other plotting programs, too.</p>
- </div>
-
- </div>
-
- </div>
-
- </div>
- </div>
- </body>
- </html>
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