Gromacs

Installation Instructions 5.0

    Introduction to building GROMACS

    These instructions pertain to building GROMACS 5.0.7. Up-to-date installation instructions may be found at http://www.gromacs.org/Documentation/Installation_Instructions.

    Quick and dirty installation

    1. Get the latest version of your C and C++ compilers.
    2. Check that you have CMake version 2.8.8 or later.
    3. Get and unpack the latest version of the GROMACS tarball.
    4. Make a separate build directory and change to it.
    5. Run cmake with the path to the source as an argument
    6. Run make, make check, and make install

    Or, as a sequence of commands to execute:

    tar xfz gromacs-5.0.7.tar.gz
    cd gromacs-5.0.7
    mkdir build
    cd build
    cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
    make
    make check
    sudo make install
    source /usr/local/gromacs/bin/GMXRC

    This will download and build first the prerequisite FFT library followed by GROMACS. If you already have FFTW installed, you can remove that argument to cmake. Overall, this build of GROMACS will be correct and reasonably fast on the machine upon which cmake ran. If you want to get the maximum value for your hardware with GROMACS, you will have to read further. Sadly, the interactions of hardware, libraries, and compilers are only going to continue to get more complex.

    Typical GROMACS installation

    As above, and with further details below, but you should consider using the following CMake options with the appropriate value instead of xxx :

    • -DCMAKE_C_COMPILER=xxx equal to the name of the C99 compiler you wish to use (or the environment variable CC)
    • -DCMAKE_CXX_COMPILER=xxx equal to the name of the C++98 compiler you wish to use (or the environment variable CXX)
    • -DGMX_MPI=on to build using an MPI wrapper compiler
    • -DGMX_GPU=on to build using nvcc to run with an NVIDIA GPU
    • -DGMX_SIMD=xxx to specify the level of SIMD support of the node on which mdrun will run
    • -DGMX_BUILD_MDRUN_ONLY=on to build only the mdrun binary, e.g. for compute cluster back-end nodes
    • -DGMX_DOUBLE=on to run GROMACS in double precision (slower, and not normally useful)
    • -DCMAKE_PREFIX_PATH=xxx to add a non-standard location for CMake to search for libraries
    • -DCMAKE_INSTALL_PREFIX=xxx to install GROMACS to a non-standard location (default /usr/local/gromacs)
    • -DBUILD_SHARED_LIBS=off to turn off the building of shared libraries
    • -DGMX_FFT_LIBRARY=xxx to select whether to use fftw, mkl or fftpack libraries for FFT support
    • -DCMAKE_BUILD_TYPE=Debug to build GROMACS in debug mode

    Prerequisites

    Platform

    GROMACS can be compiled for many operating systems and architectures. These include any distribution of Linux, Mac OS X or Windows, and architectures including x86, AMD64/x86-64, PPC, ARM v7 and SPARC VIII.

    Compiler

    Technically, GROMACS can be compiled on any platform with an ANSI C99 and C++98 compiler, and their respective standard C/C++ libraries. Getting good performance on an OS and architecture requires choosing a good compiler. In practice, many compilers struggle to do a good job optimizing the GROMACS architecture-optimized SIMD kernels.

    For best performance, the GROMACS team strongly recommends you get the most recent version of your preferred compiler for your platform. There is a large amount of GROMACS code that depends on effective compiler optimization to get high performance. This makes GROMACS performance sensitive to the compiler used, and the binary will often only work on the hardware for which it is compiled.

    • In particular, GROMACS includes a lot of explicit SIMD (single instruction, multiple data) optimization that can use assembly instructions available on most modern processors. This can have a substantial effect on performance, but for recent processors you also need a similarly recent compiler that includes support for the corresponding SIMD instruction set to get this benefit. The configuration does a good job at detecting this, and you will usually get warnings if GROMACS and your hardware support a more recent instruction set than your compiler.

    • On Intel-based x86 hardware, we recommend you to use the GNU compilers version 4.7 or later or Intel compilers version 12 or later for best performance. The Intel compiler has historically been better at instruction scheduling, but recent gcc versions have proved to be as fast or sometimes faster than Intel.

    • The Intel and GNU compilers produce much faster GROMACS executables than the PGI and Cray compilers.

    • On AMD-based x86 hardware up through the "K10" microarchitecture ("Family 10h") Thuban/Magny-Cours architecture (e.g. Opteron 6100-series processors), it is worth using the Intel compiler for better performance, but gcc version 4.7 and later are also reasonable.

    • On the AMD Bulldozer architecture (Opteron 6200), AMD introduced fused multiply-add instructions and an "FMA4" instruction format not available on Intel x86 processors. Thus, on the most recent AMD processors you want to use gcc version 4.7 or later for best performance! The Intel compiler will only generate code for the subset also supported by Intel processors, and that is significantly slower.

    • If you are running on Mac OS X, the best option is the Intel compiler. Both clang and gcc will work, but they produce lower performance and each have some shortcomings. Current Clang does not support OpenMP. This may change when clang 3.5 becomes available.

    • For all non-x86 platforms, your best option is typically to use the vendor's default or recommended compiler, and check for specialized information below.

    Compiling with parallelization options

    GROMACS can run in parallel on multiple cores of a single workstation using its built-in thread-MPI. No user action is required in order to enable this.

    GPU support

    If you wish to use the excellent native GPU support in GROMACS, NVIDIA's CUDA version 4.0 software development kit is required, and the latest version is strongly encouraged. NVIDIA GPUs with at least NVIDIA compute capability 2.0 are required, e.g. Fermi or Kepler cards. You are strongly recommended to get the latest CUDA version and driver supported by your hardware, but beware of possible performance regressions in newer CUDA versions on older hardware. Note that while some CUDA compilers (nvcc) might not officially support recent versions of gcc as the back-end compiler, we still recommend that you at least use a gcc version recent enough to get the best SIMD support for your CPU, since GROMACS always runs some code on the CPU. It is most reliable to use the same C++ compiler version for GROMACS code as used as the back-end compiler for nvcc, but it could be faster to mix compiler versions to suit particular contexts.

    MPI support

    If you wish to run in parallel on multiple machines across a network, you will need to have

    • an MPI library installed that supports the MPI 1.3 standard, and
    • wrapper compilers that will compile code using that library.

    The GROMACS team recommends OpenMPI version 1.6 (or higher), MPICH version 1.4.1 (or higher), or your hardware vendor's MPI installation. The most recent version of either of these is likely to be the best. More specialized networks might depend on accelerations only available in the vendor's library. LAMMPI might work, but since it has been deprecated for years, it is not supported.

    Often OpenMP parallelism is an advantage for GROMACS, but support for this is generally built into your compiler and detected automatically.

    In summary, for maximum performance you will need to examine how you will use GROMACS, what hardware you plan to run on, and whether you can afford a non-free compiler for slightly better performance. Unfortunately, the only way to find out is to test different options and parallelization schemes for the actual simulations you want to run. You will still get good, performance with the default build and runtime options, but if you truly want to push your hardware to the performance limit, the days of just blindly starting programs with mdrun are gone.

    CMake

    GROMACS 5.0.7 uses the CMake build system, and requires version 2.8.8 or higher. Lower versions will not work. You can check whether CMake is installed, and what version it is, with cmake --version. If you need to install CMake, then first check whether your platform's package management system provides a suitable version, or visit http://www.cmake.org/cmake/help/install.html for pre-compiled binaries, source code and installation instructions. The GROMACS team recommends you install the most recent version of CMake you can.

    Fast Fourier Transform library

    Many simulations in GROMACS make extensive use of fast Fourier transforms, and a software library to perform these is always required. We recommend FFTW (version 3 or higher only) or Intel MKL. The choice of library can be set with cmake -DGMX_FFT_LIBRARY=<name>, where <name> is one of fftw, mkl, or fftpack. FFTPACK is bundled with GROMACS as a fallback, and is acceptable if mdrun performance is not a priority.

    FFTW

    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 "mixed" floating-point precision, which is suited for the use of single precision in FFTW. 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

    • that you permit the GROMACS installation to download and build FFTW from source automatically for you (use cmake -DGMX_BUILD_OWN_FFTW=ON), or
    • that you build FFTW from the source code.

    If you build FFTW from source yourself, get the most recent version and follow its installation guide. Choose the precision for FFTW (i.e. single or float vs. double) to match whether you will later use mixed or double precision for GROMACS. There is no need to compile FFTW with threading or MPI support, but it does no harm. On x86 hardware, compile only with --enable-sse2 (regardless of precision) even if your processors can take advantage of AVX extensions. Since GROMACS uses fairly short transform lengths we do not benefit from the FFTW AVX acceleration, and because of memory system performance limitations, it can even degrade GROMACS performance by around 20%. There is no way for GROMACS to limit the use to SSE2 SIMD at run time if AVX support has been compiled into FFTW, so you need to set this at compile time.

    MKL

    Using MKL with the Intel Compilers version 11 or higher is very simple. Set up your compiler environment correctly, perhaps with a command like source /path/to/compilervars.sh intel64 (or consult your local documentation). Then set -DGMX_FFT_LIBRARY=mkl when you run cmake. In this case, GROMACS will also use MKL for BLAS and LAPACK (see linear algebra libraries). Generally, there is no advantage in using MKL with GROMACS, and FFTW is often faster.

    Otherwise, you can get your hands dirty and configure MKL by setting

    -DGMX_FFT_LIBRARY=mkl
    -DMKL_LIBRARIES="/full/path/to/libone.so;/full/path/to/libtwo.so"
    -DMKL_INCLUDE_DIR="/full/path/to/mkl/include"

    where the full list (and order!) of libraries you require are found in Intel's MKL documentation for your system.

    Optional build components

    • Compiling to run on NVIDIA GPUs requires CUDA
    • An external Boost library can be used to provide better implementation support for smart pointers and exception handling, but the GROMACS source bundles a subset of Boost 1.55.0 as a fallback
    • Hardware-optimized BLAS and LAPACK libraries are useful for a few of the GROMACS utilities focused on normal modes and matrix manipulation, but they do not provide any benefits for normal simulations. Configuring these are discussed at linear algebra libraries.
    • The built-in GROMACS trajectory viewer gmx view requires X11 and Motif/Lesstif libraries and header files. You may prefer to use third-party software for visualization, such as VMD or PyMOL.
    • An external TNG library for trajectory-file handling can be used, but TNG 1.6 is bundled in the GROMACS source already
    • zlib is used by TNG for compressing some kinds of trajectory data
    • Running the GROMACS test suite requires libxml2
    • Building the GROMACS documentation requires ImageMagick, pdflatex, bibtex, doxygen and pandoc.
    • 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.

    Doing a build of GROMACS

    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, and Mac OS X. For other platforms, see the specialist instructions below.

    Configuring with CMake

    CMake will run many tests on your system and do its best to work out how to build GROMACS for you. If your build machine is the same as your target machine, then you can be sure that the defaults will be pretty good. The build configuration will for instance attempt to detect the specific hardware instructions available in your processor. However, if you want to control aspects of the build, or you are compiling on a cluster head node for back-end nodes with a different architecture, there are plenty of things you can set manually.

    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 outside the source directory, or a subdirectory of it. 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 CMakeLists.txt file of the code you want to build. For example, download the source tarball and use

    $ tar xfz gromacs-5.0.7.tgz
    $ cd gromacs-5.0.7
    $ mkdir build-gromacs
    $ cd build-gromacs
    $ cmake ..

    You will see cmake report a sequence of results of tests and detections done by the GROMACS build system. These are written to the cmake cache, kept in CMakeCache.txt. You can edit this file by hand, but this is not recommended because you could make a mistake. You should not attempt to move or copy this file to do another build, because file paths are hard-coded within it. If you mess things up, just delete this file and start again with cmake.

    If there is a serious problem detected at this stage, then you will see a fatal error and some suggestions for how to overcome it. If you are 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 gmx-users mailing list. There are also informational warnings that you might like to take on board or not. Piping the output of cmake through less or tee can be useful, too.

    Once cmake returns, you can see all the settings that were chosen and information about them by using e.g. the curses interface

    $ ccmake ..

    You can actually use ccmake (available on most Unix platforms, if the curses library is supported) directly in the first step, but then most of the status messages will merely blink in the lower part of the terminal rather than be written to standard out. Most platforms including Linux, Windows, and Mac OS X even have native graphical user interfaces for cmake, and it can create project files for almost any build environment you want (including Visual Studio or Xcode). Check out http://www.cmake.org/cmake/help/runningcmake.html 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. You may make changes, then re-configure (using c), so that it gets a chance to make changes that depend on yours and perform more checking. It may take several configuration passes to reach the desired configuration, in particular if you need to resolve errors.

    When you have reached the desired configuration with ccmake, the build system can be generated by pressing g. This requires that the previous configuration pass did not reveal any additional settings (if it did, you need to configure once more with c). With cmake, the build system is generated after each pass that does not produce errors.

    You cannot attempt to change compilers after the initial run of cmake. If you need to change, clean up, and start again.

    Where to install GROMACS

    A key thing to consider is the setting of CMAKE_INSTALL_PREFIX. You will need to be able to write to this directory in order to install GROMACS later, this directory cannot be the same as the build tree, 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. Even if you do have super-user privileges, you should use them only for the installation phase, and never for configuring, building, or running GROMACS!

    Using CMake command-line options

    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 cmake and passing the various options at once on the command line. This can be done by setting cache variable at the cmake invocation using the -DOPTION=VALUE; note that some environment variables are also taken into account, in particular variables like CC, CXX, FCC (which may be familiar to autoconf users).

    For example, the following command line

    $ cmake .. -DGMX_GPU=ON -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/marydoe/programs

    can be used 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 ccmake, but you should avoid this, because the options set with -D will not be able to be changed interactively in that run of ccmake.

    SIMD support

    GROMACS has extensive support for detecting and using the SIMD capabilities of many modern HPC CPU architectures. If you are building GROMACS on the same hardware you will run it on, then you don't need to read more about this, unless you are getting configuration warnings you do not understand. By default, the GROMACS build system will detect the SIMD instruction set supported by the CPU architecture (on which the configuring is done), and thus pick the best available SIMD parallelization supported by GROMACS. The build system will also check that the compiler and linker used also support the selected SIMD instruction set and issue a fatal error if they do not.

    Valid values are listed below, and the applicable value lowest on the list is generally the one you should choose:

    1. None For use only on an architecture either lacking SIMD, or to which GROMACS has not yet been ported and none of the options below are applicable.
    2. SSE2 This SIMD instruction set was introduced in Intel processors in 2001, and AMD in 2003. Essentially all x86 machines in existence have this, so it might be a good choice if you need to support dinosaur x86 computers too.
    3. SSE4.1 Present in all Intel core processors since 2007, but notably not in AMD magny-cours. Still, almost all recent processors support this, so this can also be considered a good baseline if you are content with portability between reasonably modern processors.
    4. AVX_128_FMA AMD bulldozer processors (2011) have this. Unfortunately Intel and AMD have diverged the last few years; If you want good performance on modern AMD processors you have to use this since it also allows the reset of the code to use AMD 4-way fused multiply-add instructions. The drawback is that your code will not run on Intel processors at all.
    5. AVX_256 This instruction set is present on Intel processors since Sandy Bridge (2011), where it is the best choice unless you have an even more recent CPU that supports AVX2. While this code will work on recent AMD processors, it is significantly less efficient than the AVX_128_FMA choice above - do not be fooled to assume that 256 is better than 128 in this case.
    6. AVX2_256 Present on Intel Haswell processors released in 2013, and it will also enable Intel 3-way fused multiply-add instructions. This code will not work on AMD CPUs.
    7. IBM_QPX BlueGene/Q A2 cores have this.
    8. Sparc64_HPC_ACE Fujitsu machines like the K computer have this.

    The CMake configure system will check that the compiler you have chosen can target the architecture you have chosen. mdrun will check further at runtime, so if in doubt, choose the lowest setting you think might work, and see what mdrun says. The configure system also works around many known issues in many versions of common HPC compilers. However, since the options also enable general compiler flags for the platform in question, you can end up in situations where e.g. an AVX_128_FMA binary will just crash on any Intel machine, since the code will try to execute general illegal instructions (inserted by the compiler) before mdrun gets to the architecture detection routines.

    A further GMX_SIMD=Reference option exists, which is a special SIMD-like implementation written in plain C that developers can use when developing support in GROMACS for new SIMD architectures. It is not designed for use in production simulations, but if you are using an architecture with SIMD support to which GROMACS has not yet been ported, you may wish to try this option instead of the default GMX_SIMD=None, as it can often out-perform this when the auto-vectorization in your compiler does a good job. And post on the GROMACS mailing lists, because GROMACS can probably be ported for new SIMD architectures in a few days.

    CMake advanced options

    The options that are displayed in the default view of ccmake 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 ccmake on and off with t. Even there, most of the variables that you might want to change have a CMAKE_ or GMX_ prefix. There are also some options that will be visible or not according to whether their preconditions are satisfied.

    Helping CMake find the right libraries/headers/programs

    If libraries are installed in non-default locations their location can be specified using the following environment variables:

    • CMAKE_INCLUDE_PATH for header files
    • CMAKE_LIBRARY_PATH for libraries
    • CMAKE_PREFIX_PATH for header, libraries and binaries (e.g. /usr/local).

    The respective include, lib, or bin is appended to the path. For each of these variables, a list of paths can be specified (on Unix, separated with ":"). Note that these are enviroment variables (and not cmake command-line arguments) and in a bash shell are used like:

    $ CMAKE_PREFIX_PATH=/opt/fftw:/opt/cuda cmake ..

    Alternatively, these variables are also cmake options, so they can be set like -DCMAKE_PREFIX_PATH=/opt/fftw:/opt/cuda.

    The CC and CXX environment variables are also useful for indicating to cmake which compilers to use, which can be very important for maximising GROMACS performance. Similarly, CFLAGS/CXXFLAGS 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 CMAKE_C_FLAGS and its relatives.

    See also: http://cmake.org/Wiki/CMake_Useful_Variables#Environment_Variables

    Native GPU acceleration

    If you have the CUDA Toolkit installed, you can use cmake with:

    $ cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda

    (or whichever path has your installation). In some cases, you might need to specify manually which of your C++ compilers should be used, e.g. with the advanced option CUDA_HOST_COMPILER.

    The GPU acceleration has been tested on AMD64/x86-64 platforms with Linux, Mac OS X and Windows operating systems, but Linux is the best-tested and supported of these. Linux running on ARM v7 (32 bit) CPUs also works.

    Static linking

    Dynamic linking of the GROMACS executables will lead to a smaller disk footprint when installed, and so is the default on platforms where we believe it has been tested repeatedly and found to work. In general, this includes Linux, Windows, Mac OS X and BSD systems. Static binaries take much more space, but on some hardware and/or under some conditions they are necessary, most commonly when you are running a parallel simulation using MPI libraries (e.g. BlueGene, Cray).

    • To link GROMACS binaries statically against the internal GROMACS libraries, set -DBUILD_SHARED_LIBS=OFF.
    • To link statically against external (non-system) libraries as well, the -DGMX_PREFER_STATIC_LIBS=ON 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 on platforms where that is the default. To use static system libraries, additional compiler/linker flags are necessary, e.g. -static-libgcc -static-libstdc++.
    • To attempt to link a fully static binary set -DGMX_BUILD_SHARED_EXE=OFF. This will prevent CMake from explicitly setting any dynamic linking flags. This option also sets -DBUILD_SHARED_LIBS=OFF and -DGMX_PREFER_STATIC_LIBS=ON by default, but the above caveats apply. For compilers which don't default to static linking, the required flags have to be specified. On Linux, this is usually CFLAGS=-static CXXFLAGS=-static.

    Portability aspects

    Here, we consider portability aspects related to CPU instruction sets, for details on other topics like binaries with statical vs dynamic linking please consult the relevant parts of this documentation or other non-GROMACS specific resources.

    A GROMACS build will normally not be portable, not even across hardware with the same base instruction set like x86. Non-portable hardware-specific optimizations are selected at configure-time, such as the SIMD instruction set used in the compute-kernels. This selection will be done by the build system based on the capabilities of the build host machine or based on cross-compilation information provided to cmake at configuration.

    Often it is possible to ensure portability by choosing the least common denominator of SIMD support, e.g. SSE2 for x86, and ensuring the you use cmake -DGMX_USE_RDTSCP=off if any of the target CPU architectures does not support the RDTSCP instruction. However, we discourage attempts to use a single GROMACS installation when the execution environment is heterogeneous, such as a mix of AVX and earlier hardware, because this will lead to programs (especially mdrun) that run slowly on the new hardware. Building two full installations and locally managing how to call the correct one (e.g. using the module system) is the recommended approach. Alternatively, as at the moment the GROMACS tools do not make strong use of SIMD acceleration, it can be convenient to create an installation with tools portable across different x86 machines, but with separate mdrun binaries for each architecture. To achieve this, one can first build a full installation with the least-common-denominator SIMD instruction set, e.g. -DGMX_SIMD=SSE2, then build separate mdrun binaries for each architecture present in the heterogeneous environment. By using custom binary and library suffixes for the mdrun-only builds, these can be installed to the same location as the "generic" tools installation. Building only the mdrun binary is possible by setting the -DGMX_BUILD_MDRUN_ONLY=ON option.

    Linear algebra libraries

    As mentioned above, sometimes vendor BLAS and LAPACK libraries can provide performance enhancements for GROMACS when doing normal-mode analysis or covariance analysis. For simplicity, the text below will refer only to BLAS, but the same options are available for LAPACK. By default, CMake will search for BLAS, use it if it is found, and otherwise fall back on a version of BLAS internal to GROMACS. The cmake option -DGMX_EXTERNAL_BLAS=on will be set accordingly. The internal versions are fine for normal use. If you need to specify a non-standard path to search, use -DCMAKE_PREFIX_PATH=/path/to/search. If you need to specify a library with a non-standard name (e.g. ESSL on AIX or BlueGene), then set -DGMX_BLAS_USER=/path/to/reach/lib/libwhatever.a.

    If you are using Intel MKL for FFT, then the BLAS and LAPACK it provides are used automatically. This could be over-ridden with GMX_BLAS_USER, etc.

    On Apple platforms where the Accelerate Framework is available, these will be automatically used for BLAS and LAPACK. This could be over-ridden with GMX_BLAS_USER, etc.

    Changing the names of GROMACS binaries and libraries

    It is sometimes convenient to have different versions of the same GROMACS programs installed. The most common use cases have been single and double precision, and with and without MPI. This mechanism can also be used to install side-by-side multiple versions of mdrun optimized for different CPU architectures, as mentioned previously.

    By default, GROMACS will suffix programs and libraries for such builds with _d for double precision and/or _mpi for MPI (and nothing otherwise). This can be controlled manually with GMX_DEFAULT_SUFFIX (ON/OFF), GMX_BINARY_SUFFIX (takes a string) and GMX_LIBS_SUFFIX (also takes a string). For instance, to set a custom suffix for programs and libraries, one might specify:

    cmake .. -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_mod -DGMX_LIBS_SUFFIX=_mod

    Thus the names of all programs and libraries will be appended with _mod.

    Changing installation tree structure

    By default, a few different directories under CMAKE_INSTALL_PREFIX are used when when GROMACS is installed. Some of these can be changed, which is mainly useful for packaging GROMACS for various distributions. The directories are listed below, with additional notes about some of them. Unless otherwise noted, the directories can be renamed by editing the installation paths in the main CMakeLists.txt.

    bin/
    The standard location for executables, some scripts, and some symlinks. Some of the scripts hardcode the absolute installation prefix, which needs to be changed if the scripts are relocated.
    include/gromacs/
    The standard location for installed headers.
    lib/
    The standard location for libraries. The default depends on the system, and is determined by CMake. The name of the directory can be changed using GMX_LIB_INSTALL_DIR CMake variable.
    share/gromacs/
    Various data files and some documentation go here. The gromacs part can be changed using GMX_DATA_INSTALL_DIR. Using this CMake variable is the preferred way of changing the installation path for share/gromacs/top/, since the path to this directory is built into libgromacs as well as some scripts, both as a relative and as an absolute path (the latter as a fallback if everything else fails).
    share/man/
    Installed man pages go here.

    Compiling and linking

    Once you have configured with cmake, you can build GROMACS with make. It is expected that this will always complete successfully, and give few or no warnings. The CMake-time tests GROMACS makes on the settings you choose are pretty extensive, but there are probably a few cases we have not thought of yet. Search the web first for solutions to problems, but if you need help, ask on gmx-users, being sure to provide as much information as possible about what you did, the system you are building on, and what went wrong. This may mean scrolling back a long way through the output of make to find the first error message!

    If you have a multi-core or multi-CPU machine with N processors, then using

    $ make -j N

    will generally speed things up by quite a bit. Other build generator systems supported by cmake (e.g. ninja) also work well.

    Building only mdrun

    Past versions of the build system offered "mdrun" and "install-mdrun" targets (similarly for other programs too) to build and install only the mdrun program, respectively. Such a build is useful when the configuration is only relevant for mdrun (such as with parallelization options for MPI, SIMD, GPUs, or on BlueGene or Cray), or the length of time for the compile-link-install cycle is relevant when developing.

    This is now supported with the cmake option -DGMX_BUILD_MDRUN_ONLY=ON, which will build a cut-down version of libgromacs and/or the mdrun program (according to whether shared or static). Naturally, now make install installs only those products. By default, mdrun-only builds will default to static linking against GROMACS libraries, because this is generally a good idea for the targets for which an mdrun-only build is desirable. If you re-use a build tree and change to the mdrun-only build, then you will inherit the setting for BUILD_SHARED_LIBS from the old build, and will be warned that you may wish to manage BUILD_SHARED_LIBS yourself.

    Installing GROMACS

    Finally, make install will install GROMACS in the directory given in CMAKE_INSTALL_PREFIX. If this is a system directory, then you will need permission to write there, and you should use super-user privileges only for make install and not the whole procedure.

    Getting access to GROMACS after installation

    GROMACS installs the script GMXRC in the bin subdirectory of the installation directory (e.g. /usr/local/gromacs/bin/GMXRC), which you should source from your shell:

    $ source /your/installation/prefix/here/bin/GMXRC

    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.

    Many of the GROMACS programs rely on data installed in the share/gromacs subdirectory of the installation directory. By default, the programs will use the environment variables set in the GMXRC script, and if this is not available they will try to guess the path based on their own location. This usually works well unless you change the names of directories inside the install tree. If you still need to do that, you might want to recompile with the new install location properly set, or edit the GMXRC script.

    Testing GROMACS for correctness

    Since 2011, the GROMACS development uses an automated system where every new code change is subject to regression testing on a number of platforms and software combinations. While this improves reliability quite a lot, not everything is tested, and since we increasingly rely on cutting edge compiler features there is non-negligible risk that the default compiler on your system could have bugs. We have tried our best to test and refuse to use known bad versions in cmake, but we strongly recommend that you run through the tests yourself. It only takes a few minutes, after which you can trust your build.

    The simplest way to run the checks is to build GROMACS with -DREGRESSIONTEST_DOWNLOAD, and run make check. GROMACS will automatically download and run the tests for you. Alternatively, you can download and unpack the tarball yourself from http://gerrit.gromacs.org/download/regressiontests-5.0.7.tar.gz, and use the advanced cmake option REGRESSIONTEST_PATH to specify the path to the unpacked tarball, which will then be used for testing. If the above does not work, then please read on.

    The regression tests are available from the GROMACS website and ftp site. Once you have downloaded them, unpack the tarball, source GMXRC as described above, and run ./gmxtest.pl all inside the regression tests folder. You can find more options (e.g. adding double when using double precision, or -only expanded to run just the tests whose names match "expanded") if you just execute the script without options.

    Hopefully, you will get a report that all tests have passed. If there are individual failed tests it could be a sign of a compiler bug, or that a tolerance is just a tiny bit too tight. Check the output files the script directs you too, and try a different or newer compiler if the errors appear to be real. If you cannot get it to pass the regression tests, you might try dropping a line to the gmx-users mailing list, but then you should include a detailed description of your hardware, and the output of mdrun -version (which contains valuable diagnostic information in the header).

    A build with -DGMX_BUILD_MDRUN_ONLY cannot be tested with make check from the build tree, because most of the tests require a full build to run things like grompp. To test such an mdrun fully requires installing it to the same location as a normal build of GROMACS, downloading the regression tests tarball manually as described above, sourcing the correct GMXRC and running the perl script manually. For example, from your GROMACS source directory:

    $ mkdir build-normal
    $ cd build-normal
    $ cmake .. -DCMAKE_INSTALL_PREFIX=/your/installation/prefix/here
    $ make -j 4
    $ make install
    $ cd ..
    $ mkdir build-mdrun-only
    $ cd build-mdrun-only
    $ cmake .. -DGMX_MPI=ON -DGMX_GPU=ON -DGMX_BUILD_MDRUN_ONLY=ON -DCMAKE_INSTALL_PREFIX=/your/installation/prefix/here
    $ make -j 4
    $ make install
    $ cd /to/your/unpacked/regressiontests
    $ source /your/installation/prefix/here/bin/GMXRC
    $ ./gmxtest.pl all -np 2

    If your mdrun program has been suffixed in a non-standard way, then the ./gmxtest.pl -mdrun option will let you specify that name to the test machinery. You can use ./gmxtest.pl -double to test the double-precision version. You can use ./gmxtest.pl -crosscompiling to stop the test harness attempting to check that the programs can be run.

    Testing GROMACS for performance

    We are still working on a set of benchmark systems for testing the performance of GROMACS. Until that is ready, we recommend that you try a few different parallelization options, and experiment with tools such as gmx tune_pme.

    Having difficulty?

    You are 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:

    1. Read the installation instructions again, taking note that you have followed each and every step correctly.

    2. Search the GROMACS website and users emailing list for information on the error. Adding "site:https://mailman-1.sys.kth.se/piperma....org_gmx-users" to a Google search may help filter better results.

    3. Search the internet using a search engine such as Google.

    4. Post to the GROMACS users emailing list gmx-users for assistance. Be sure to give a full description of what you have done and why you think it did not 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. In particular, please try to include at least the header from the mdrun logfile, and preferably the entire file. 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. High quality bug reports tend to receive rapid high quality answers.

    Special instructions for some platforms

    Building on Windows

    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. 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-gromacs.

    For CMake, you can either use the graphical user interface provided on Windows, or you can use a command line shell with instructions similar to the UNIX ones above. If you open a shell from within your IDE (e.g. Microsoft Visual Studio), it will configure the environment for you, but you might need to tweak this in order to get either a 32-bit or 64-bit build environment. The latter provides the fastest executable. 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 vcvarsall.bat batch script provided by MSVC (just like sourcing a bash script under Unix).

    With the graphical user interface, you will be asked about what compilers to use at the initial configuration stage, and if you use the command line they can be set in a similar way as under UNIX. You will probably make your life easier and faster by using the new facility to download and install FFTW automatically.

    For the build, you can either load the generated solutions file into e.g. Visual Studio, or use the command line with cmake --build so the right tools get used.

    Building on Cray

    GROMACS builds mostly out of the box on modern Cray machines, but * you may need to specify the use of static binaries with -DGMX_BUILD_SHARED_EXE=off, * you may need to set the F77 environmental variable to ftn when compiling FFTW,

    Building on BlueGene

    BlueGene/Q

    There is currently native acceleration on this platform for the Verlet cut-off scheme. There are no plans to provide accelerated kernels for the group cut-off scheme, but the default plain C kernels will work (slowly).

    Only static linking with XL compilers is supported by GROMACS. Dynamic linking would be supported by the architecture and GROMACS, but has no advantages other than disk space, and is generally discouraged on BlueGene for performance reasons.

    Computation on BlueGene floating-point units is always done in double-precision. However, mixed-precision builds of GROMACS are still normal and encouraged since they use cache more efficiently. The BlueGene hardware automatically converts values stored in single precision in memory to double precision in registers for computation, converts the results back to single precision correctly, and does so for no additional cost. As with other platforms, doing the whole computation in double precision normally shows no improvement in accuracy and costs twice as much time moving memory around.

    You need to arrange for FFTW to be installed correctly, following the above instructions.

    MPI wrapper compilers should be used for compiling and linking. Both xlc and bgclang are supported back ends - either might prove to be faster in practice. The MPI wrapper compilers can make it awkward to attempt to use IBM's optimized BLAS/LAPACK called ESSL (see the section on linear algebra libraries). Since mdrun is the only part of GROMACS that should normally run on the compute nodes, and there is nearly no need for linear algebra support for mdrun, it is recommended to use the GROMACS built-in linear algebra routines - this is never a problem for normal simulations.

    The recommended configuration is to use

    cmake .. -DCMAKE_C_COMPILER=mpicc \
             -DCMAKE_CXX_COMPILER=mpicxx \
             -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-CXX.cmake \
             -DCMAKE_PREFIX_PATH=/your/fftw/installation/prefix \
             -DGMX_MPI=ON \
             -DGMX_BUILD_MDRUN_ONLY=ON
    make
    make install

    which will build a statically-linked MPI-enabled mdrun for the compute nodes. Or use the Platform/BlueGeneQ-static-bgclang-cxx toolchain file if compiling with bgclang. Otherwise, GROMACS default configuration behaviour applies.

    It is possible to configure and make the remaining GROMACS tools with the compute-node toolchain, but as none of those tools are MPI-aware and could then only run on the compute nodes, this would not normally be useful. Instead, these should be planned to run on the login node, and a separate GROMACS installation performed for that using the login node's toolchain - not the above platform file, or any other compute-node toolchain.

    Note that only the MPI build is available for the compute-node toolchains. The GROMACS thread-MPI or no-MPI builds are not useful at all on BlueGene/Q.

    BlueGene/P

    There is currently no SIMD support on this platform and no plans to add it. The default plain C kernels will work.

    Fujitsu PRIMEHPC

    This is the architecture of the K computer, which uses Fujitsu Sparc64VIIIfx chips. On this platform, GROMACS 5.0.7 has accelerated group kernels using the HPC-ACE instructions, no accelerated Verlet kernels, and a custom build toolchain. Since this particular chip only does double precision SIMD, the default setup is to build Gromacs in double. Since most users only need single, we have added an option GMX_RELAXED_DOUBLE_PRECISION to accept single precision square root accuracy in the group kernels; unless you know that you really need 15 digits of accuracy in each individual force, we strongly recommend you use this. Note that all summation and other operations are still done in double.

    The recommended configuration is to use

    cmake .. -DCMAKE_TOOLCHAIN_FILE=Toolchain-Fujitsu-Sparc64-mpi.cmake \
             -DCMAKE_PREFIX_PATH=/your/fftw/installation/prefix \
             -DCMAKE_INSTALL_PREFIX=/where/gromacs/should/be/installed \
             -DGMX_MPI=ON \
             -DGMX_BUILD_MDRUN_ONLY=ON \
             -DGMX_RELAXED_DOUBLE_PRECISION=ON
    make
    make install

    Intel Xeon Phi

    GROMACS 5.0.7 has preliminary support for Intel Xeon Phi. Only symmetric (aka native) mode is supported. GROMACS is functional on Xeon Phi, but it has so far not been optimized to the same level as other architectures have. The performance depends among other factors on the system size, and for now the performance might not be faster than CPUs. Building for Xeon Phi works almost as any other Unix. See the instructions above for details. The recommended configuration is

    cmake .. -DCMAKE_TOOLCHAIN_FILE=Platform/XeonPhi
    make
    make install

    Tested platforms

    While it is our best belief that GROMACS will build and run pretty much everywhere, it is important that we tell you where we really know it works because we have 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 git source code repository is currently tested on x86 with gcc versions ranging from 4.4 through 4.7, and versions 12 and 13 of the Intel compiler as well as Clang version 3.1 through 3.4. For this, we use a variety of GNU/Linux flavors and versions as well as recent version of Mac OS X. Under Windows we test both MSVC and the Intel compiler. For details, you can have a look at the continuous integration server at http://jenkins.gromacs.org.

    We test irregularly on ARM v7, BlueGene/Q, Cray, Fujitsu PRIMEHPC, Google Native Client and other environments, and with other compilers and compiler versions, too.

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    Page last modified 14:41, 14 Oct 2015 by mabraham