Installation guide

Introduction to building GROMACS

These instructions pertain to building GROMACS 2019-beta1. You might also want to check the up-to-date installation instructions.

Quick and dirty installation

  1. Get the latest version of your C and C++ compilers.
  2. Check that you have CMake version 3.4.3 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
  7. Source GMXRC to get access to GROMACS

Or, as a sequence of commands to execute:

tar xfz gromacs-2019-beta1.tar.gz
cd gromacs-2019-beta1
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. On another machine, it may not run, or may not run fast. 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.

Quick and dirty cluster installation

On a cluster where users are expected to be running across multiple nodes using MPI, make one installation similar to the above, and another using an MPI wrapper compiler and which is building only mdrun, because that is the only component of GROMACS that uses MPI. The latter will install a single simulation engine binary, i.e. mdrun_mpi when the default suffix is used. Hence it is safe and common practice to install this into the same location where the non-MPI build is installed.

Typical 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 MPI support (generally good to combine with building only mdrun)
  • -DGMX_GPU=on to build using nvcc to run using NVIDIA CUDA GPU acceleration or an OpenCL GPU
  • -DGMX_USE_OPENCL=on to build with OpenCL support enabled. GMX_GPU must also be set.
  • -DGMX_SIMD=xxx to specify the level of SIMD support of the node on which GROMACS will run
  • -DGMX_BUILD_MDRUN_ONLY=on for building only mdrun, e.g. for compute cluster back-end nodes
  • -DGMX_DOUBLE=on to build 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, headers or programs
  • -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 to help with static linking
  • -DGMX_FFT_LIBRARY=xxx to select whether to use fftw3, mkl or fftpack libraries for FFT support
  • -DCMAKE_BUILD_TYPE=Debug to build GROMACS in debug mode

Building with MiMiC QM/MM support

MiMiC QM/MM interface integration will require linking against MiMiC communication library, that establishes the communication channel between GROMACS and CPMD. Check that the installation folder of the library is added to CMAKE_PREFIX_PATH if it is installed in non-standard location. Building QM/MM-capable version requires double-precision version of GROMACS compiled with MPI support:

  • -DGMX_DOUBLE=ON -DGMX_MPI -DGMX_MIMIC=ON

Building older versions

Installation instructions for old GROMACS versions can be found at the GROMACS documentation page.

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, several PowerPC including POWER8, ARM v7, ARM v8, and SPARC VIII.

Compiler

GROMACS can be compiled on any platform with ANSI C99 and C++11 compilers, and their respective standard C/C++ libraries. Good performance on an OS and architecture requires choosing a good compiler. We recommend gcc, because it is free, widely available and frequently provides the best performance.

You should strive to use the most recent version of your compiler. Since we require full C++11 support the minimum supported compiler versions are

  • GNU (gcc) 4.8.1
  • Intel (icc) 17.0.1
  • LLVM (clang) 3.3
  • Microsoft (MSVC) 2017 (C++14 is used)

Other compilers may work (Cray, Pathscale, older clang) but do not offer competitive performance. We recommend against PGI because the performance with C++ is very bad.

The xlc compiler is not supported and has not been tested on POWER architectures for GROMACS-2019-beta1. We recommend to use the gcc compiler instead, as it is being extensively tested.

You may also need the most recent version of other compiler toolchain components beside the compiler itself (e.g. assembler or linker); these are often shipped by your OS distribution’s binutils package.

C++11 support requires adequate support in both the compiler and the C++ library. The gcc and MSVC compilers include their own standard libraries and require no further configuration. For configuration of other compilers, read on.

On Linux, both the Intel and clang compiler use the libstdc++ which comes with gcc as the default C++ library. For GROMACS, we require the compiler to support libstc++ version 4.8.1 or higher. To select a particular libstdc++ library, use:

  • For Intel: -DGMX_STDLIB_CXX_FLAGS=-gcc-name=/path/to/gcc/binary or make sure that the correct gcc version is first in path (e.g. by loading the gcc module). It can also be useful to add -DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/path/to/gcc/lib64 -L/path/to/gcc/lib64" to ensure linking works correctly.
  • For clang: -DCMAKE_CXX_FLAGS=--gcc-toolchain=/path/to/gcc/folder. This folder should contain include/c++.

On Windows with the Intel compiler, the MSVC standard library is used, and at least MSVC 2017 is required. Load the enviroment variables with vcvarsall.bat.

To build with any compiler and clang’s libcxx standard library, use -DGMX_STDLIB_CXX_FLAGS=-stdlib=libc++ -DGMX_STDLIB_LIBRARIES='-lc++abi -lc++'.

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. clang 3.8 now offers support for OpenMP, and so may provide decent performance.

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

For updated versions of gcc to add to your Linux OS, see

Compiling with parallelization options

For maximum performance you will need to examine how you will use GROMACS and what hardware you plan to run on. Often OpenMP parallelism is an advantage for GROMACS, but support for this is generally built into your compiler and detected automatically.

GPU support

GROMACS has excellent support for NVIDIA GPUs supported via CUDA. On Linux, NVIDIA CUDA toolkit with minimum version 7.0 is required, and the latest version is strongly encouraged. Using Microsoft MSVC compiler requires version 9.0. NVIDIA GPUs with at least NVIDIA compute capability 3.0 are required. You are strongly recommended to get the latest CUDA version and driver that supports your hardware, but beware of possible performance regressions in newer CUDA versions on older hardware. 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 host compiler for nvcc.

To make it possible to use other accelerators, GROMACS also includes OpenCL support. The minimum OpenCL version required is 1.2. The current OpenCL implementation is recommended for use with GCN-based AMD GPUs, on Linux we recommend the ROCm runtime. For Intel GPUs it is required to compile with -DGMX_OCL_NB_CLUSTER_SIZE=4 and the Neo driver is recommended. It is also supported with NVIDIA GPUs, but using the latest NVIDIA driver (which includes the NVIDIA OpenCL runtime) is recommended. Also note that there are performance limitations (inherent to the NVIDIA OpenCL runtime). It is not possible to configure both CUDA and OpenCL support in the same version of GROMACS.

MPI support

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.

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. LAM-MPI might work, but since it has been deprecated for years, it is not supported.

CMake

GROMACS builds with the CMake build system, requiring at least version 3.4.3. 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 the CMake installation page 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 fftw3, mkl, or fftpack. FFTPACK is bundled with GROMACS as a fallback, and is acceptable if simulation performance is not a priority. When choosing MKL, 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. With PME GPU offload support using CUDA, a GPU-based FFT library is required. The CUDA-based GPU FFT library cuFFT is part of the CUDA toolkit (required for all CUDA builds) and therefore no additional software component is needed when building with CUDA GPU acceleration.

Using 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 the FFTW installation guide. Choose the precision for FFTW (i.e. single/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 with both --enable-sse2 and --enable-avx for FFTW-3.3.4 and earlier. From FFTW-3.3.5, you should also add --enable-avx2 also. On Intel processors supporting 512-wide AVX, including KNL, add --enable-avx512 also. FFTW will create a fat library with codelets for all different instruction sets, and pick the fastest supported one at runtime. On ARM architectures with NEON SIMD support and IBM Power8 and later, you definitely want version 3.3.5 or later, and to compile it with --enable-neon and --enable-vsx, respectively, for SIMD support. If you are using a Cray, there is a special modified (commercial) version of FFTs using the FFTW interface which can be slightly faster.

Using MKL

Use MKL bundled with Intel compilers by setting up the compiler environment, e.g., through source /path/to/compilervars.sh intel64 or similar before running CMake including setting -DGMX_FFT_LIBRARY=mkl.

If you need to customize this further, use

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

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

Other optional build components

  • Run-time detection of hardware capabilities can be improved by linking with hwloc, which is automatically enabled if detected.
  • 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 is 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 by setting -DGMX_EXTERNAL_TNG=yes, but TNG 1.7.10 is bundled in the GROMACS source already.
  • The lmfit library for Levenberg-Marquardt curve fitting is used in GROMACS. Only lmfit 7.0 is supported. A reduced version of that library is bundled in the GROMACS distribution, and the default build uses it. That default may be explicitly enabled with -DGMX_USE_LMFIT=internal. To use an external lmfit library, set -DGMX_USE_LMFIT=external, and adjust CMAKE_PREFIX_PATH as needed. lmfit support can be disabled with -DGMX_USE_LMFIT=none.
  • zlib is used by TNG for compressing some kinds of trajectory data
  • Building the GROMACS documentation is optional, and requires ImageMagick, pdflatex, bibtex, doxygen, python 2.7, sphinx 1.6.1, and pygments.
  • 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 and detection will be pretty good. 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 a few things you should consider specifying.

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-2019-beta1.tgz
cd gromacs-2019-beta1
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) 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 output. 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 running CMake 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

GROMACS is installed in the directory to which CMAKE_INSTALL_PREFIX points. It may not be the source directory or the build directory. You require write permissions to this directory. Thus, without super-user privileges, CMAKE_INSTALL_PREFIX will have to be within your home directory. 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 -DOPTION=VALUE. Note that some environment variables are also taken into account, in particular variables like CC and CXX.

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 CUDA 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 with the largest number in the list is generally the one you should choose. In most cases, choosing an inappropriate higher number will lead to compiling a binary that will not run. However, on a number of processor architectures choosing the highest supported value can lead to performance loss, e.g. on Intel Skylake-X/SP and AMD Zen.

  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 slow simulations and prefer portability between reasonably modern processors.
  4. AVX_128_FMA AMD Bulldozer, Piledriver (and later Family 15h) processors have this.
  5. AVX_256 Intel processors since Sandy Bridge (2011). While this code will work on the AMD Bulldozer and Piledriver 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_128 AMD Zen microarchitecture processors (2017); it will enable AVX2 with 3-way fused multiply-add instructions. While the Zen microarchitecture does support 256-bit AVX2 instructions, hence AVX2_256 is also supported, 128-bit will generally be faster, in particular when the non-bonded tasks run on the CPU – hence the default AVX2_128. With GPU offload however AVX2_256 can be faster on Zen processors.
  7. AVX2_256 Present on Intel Haswell (and later) processors (2013), and it will also enable Intel 3-way fused multiply-add instructions.
  8. AVX_512 Skylake-X desktop and Skylake-SP Xeon processors (2017); it will generally be fastest on the higher-end desktop and server processors with two 512-bit fused multiply-add units (e.g. Core i9 and Xeon Gold). However, certain desktop and server models (e.g. Xeon Bronze and Silver) come with only one AVX512 FMA unit and therefore on these processors AVX2_256 is faster (compile- and runtime checks try to inform about such cases). Additionally, with GPU accelerated runs AVX2_256 can also be faster on high-end Skylake CPUs with both 512-bit FMA units enabled.
  9. AVX_512_KNL Knights Landing Xeon Phi processors
  10. Sparc64_HPC_ACE Fujitsu machines like the K computer have this.
  11. IBM_VMX Power6 and similar Altivec processors have this.
  12. IBM_VSX Power7, Power8 and later have this.
  13. ARM_NEON 32-bit ARMv7 with NEON support.
  14. ARM_NEON_ASIMD 64-bit ARMv8 and later.

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 number 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.

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, or programs

If libraries are installed in non-default locations their location can be specified using the following 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 “:”). These can be set as enviroment variables like:

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

(assuming bash shell). 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. 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 CMake options such as CMAKE_C_FLAGS and its relatives.

See also the page on CMake environment variables.

CUDA 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.

By default, code will be generated for the most common CUDA architectures. However, to reduce build time and binary size we do not generate code for every single possible architecture, which in rare cases (say, Tegra systems) can result in the default build not being able to use some GPUs. If this happens, or if you want to remove some architectures to reduce binary size and build time, you can alter the target CUDA architectures. This can be done either with the GMX_CUDA_TARGET_SM or GMX_CUDA_TARGET_COMPUTE CMake variables, which take a semicolon delimited string with the two digit suffixes of CUDA (virtual) architectures names, for instance “35;50;51;52;53;60”. For details, see the “Options for steering GPU code generation” section of the nvcc man / help or Chapter 6. of the nvcc manual.

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 POWER 8, ARM v7 and v8 CPUs also works well.

Experimental support is available for compiling CUDA code, both for host and device, using clang (version 3.9 or later). A CUDA toolkit (>= v7.0) is still required but it is used only for GPU device code generation and to link against the CUDA runtime library. The clang CUDA support simplifies compilation and provides benefits for development (e.g. allows the use code sanitizers in CUDA host-code). Additionally, using clang for both CPU and GPU compilation can be beneficial to avoid compatibility issues between the GNU toolchain and the CUDA toolkit. clang for CUDA can be triggered using the GMX_CLANG_CUDA=ON CMake option. Target architectures can be selected with GMX_CUDA_TARGET_SM, virtual architecture code is always embedded for all requested architectures (hence GMX_CUDA_TARGET_COMPUTE is ignored). Note that this is mainly a developer-oriented feature and it is not recommended for production use as the performance can be significantly lower than that of code compiled with nvcc (and it has also received less testing). However, note that with clang 5.0 the performance gap is significantly narrowed (at the time of writing, about 20% slower GPU kernels), so this version could be considered in non performance-critical use-cases.

OpenCL GPU acceleration

The primary target of the GROMACS OpenCL support is accelerating simulations on AMD hardware, both discrete GPUs and APUs (integrated CPU+GPU chips). The GROMACS OpenCL on NVIDIA GPUs works, but performance and other limitations make it less practical (for details see the user guide).

To build GROMACS with OpenCL support enabled, two components are required: the OpenCL headers and the wrapper library that acts as a client driver loader (so-called ICD loader). The additional, runtime-only dependency is the vendor-specific GPU driver for the device targeted. This also contains the OpenCL compiler. As the GPU compute kernels are compiled on-demand at run time, this vendor-specific compiler and driver is not needed for building GROMACS. The former, compile-time dependencies are standard components, hence stock versions can be obtained from most Linux distribution repositories (e.g. opencl-headers and ocl-icd-libopencl1 on Debian/Ubuntu). Only the compatibility with the required OpenCL version 1.2 needs to be ensured. Alternatively, the headers and library can also be obtained from vendor SDKs (e.g. from AMD), which must be installed in a path found in CMAKE_PREFIX_PATH (or via the environment variables AMDAPPSDKROOT or CUDA_PATH).

To trigger an OpenCL build the following CMake flags must be set

cmake .. -DGMX_GPU=ON -DGMX_USE_OPENCL=ON

On Mac OS, an AMD GPU can be used only with OS version 10.10.4 and higher; earlier OS versions are known to run incorrectly.

By default, any clFFT library on the system will be used with GROMACS, but if none is found then the code will fall back on a version bundled with GROMACS. To require GROMACS to link with an external library, use

cmake .. -DGMX_GPU=ON -DGMX_USE_OPENCL=ON -DclFFT_ROOT_DIR=/path/to/your/clFFT -DGMX_EXTERNAL_CLFFT=TRUE

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 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. 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, set -DGMX_PREFER_STATIC_LIBS=ON. 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.

gmxapi external API

For dynamic linking builds and on non-Windows platforms, an extra library and headers are installed by setting -DGMXAPI=ON (default). Build targets gmxapi_cppdocs and gmxapi_cppdocs_dev produce documentation in docs/api-user and docs/api-dev, respectively. For more project information and use cases, refer to the tracked Issue 2585, associated GitHub gmxapi projects, or DOI 10.1093/bioinformatics/bty484.

gmxapi is not yet tested on Windows or with static linking, but these use cases are targeted for future versions.

Portability aspects

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 otherwise specified to cmake during 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 a 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 just 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 Power machines), 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 and some scripts. Some of the scripts hardcode the absolute installation prefix, which needs to be changed if the scripts are relocated. The name of the directory can be changed using CMAKE_INSTALL_BINDIR CMake variable.
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 CMAKE_INSTALL_LIBDIR CMake variable.
lib/pkgconfig/
Information about the installed libgromacs library for pkg-config is installed here. The lib/ part adapts to the installation location of the libraries. The installed files contain the installation prefix as absolute paths.
share/cmake/
CMake package configuration files are installed here.
share/gromacs/
Various data files and some documentation go here. The first part can be changed using CMAKE_INSTALL_DATADIR, and the second by using GMX_INSTALL_DATASUBDIR Using these CMake variables 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

This is now supported with the cmake option -DGMX_BUILD_MDRUN_ONLY=ON, which will build a different version of libgromacs and the mdrun program. 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.

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 GROMACS regression test suite http://gerrit.gromacs.org/download/regressiontests-2019-beta1.tar.gz tarball yourself 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 also available from the download section. 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 gmx 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. You can use ./gmxtest.pl -mpirun srun if your command to run an MPI program is called srun.

The make check target also runs integration-style tests that may run with MPI if GMX_MPI=ON was set. To make these work with various possible MPI libraries, you may need to set the CMake variables MPIEXEC, MPIEXEC_NUMPROC_FLAG, MPIEXEC_PREFLAGS and MPIEXEC_POSTFLAGS so that mdrun-mpi-test_mpi would run on multiple ranks via the shell command

${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${NUMPROC} ${MPIEXEC_PREFLAGS} \
      mdrun-mpi-test_mpi ${MPIEXEC_POSTFLAGS} -otherflags

A typical example for SLURM is

cmake .. -DGMX_MPI=on -DMPIEXEC=srun -DMPIEXEC_NUMPROC_FLAG=-n -DMPIEXEC_PREFLAGS= -DMPIEXEC_POSTFLAGS=

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 webpage and users emailing list for information on the error. Adding site:https://mailman-1.sys.kth.se/pipermail/gromacs.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.

Unfortunately -DGMX_BUILD_OWN_FFTW=ON (see Using FFTW) does not work on Windows, because there is no supported way to build FFTW on Windows. You can either build FFTW some other way (e.g. MinGW), or use the built-in fftpack (which may be slow), or using MKL.

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, and you may need to set the F77 environmental variable to ftn when compiling FFTW. The ARM ThunderX2 Cray XC50 machines differ only in that the recommended compiler is the ARM HPC Compiler (armclang).

Building on Solaris

The built-in GROMACS processor detection does not work on Solaris, so it is strongly recommended that you build GROMACS with -DGMX_HWLOC=on and ensure that the CMAKE_PREFIX_PATH includes the path where the hwloc headers and libraries can be found. At least version 1.11.8 of hwloc is recommended.

Oracle Developer Studio is not a currently supported compiler (and does not currently compile GROMACS correctly, perhaps because the thread-MPI atomics are incorrectly implemented in GROMACS).

Fujitsu PRIMEHPC

This is the architecture of the K computer, which uses Fujitsu Sparc64VIIIfx chips. On this platform, GROMACS 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

Xeon Phi processors, hosted or self-hosted, are supported. Only symmetric (aka native) mode is supported on Knights Corner. The performance depends among other factors on the system size, and for now the performance might not be faster than CPUs. When building for it, the recommended configuration is

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

The Knights Landing-based Xeon Phi processors behave like standard x86 nodes, but support a special SIMD instruction set. When cross-compiling for such nodes, use the AVX_512_KNL SIMD flavor. Knights Landing processors support so-called “clustering modes” which allow reconfiguring the memory subsystem for lower latency. GROMACS can benefit from the quadrant or SNC clustering modes. Care needs to be taken to correctly pin threads. In particular, threads of an MPI rank should not cross cluster and NUMA boundaries. In addition to the main DRAM memory, Knights Landing has a high-bandwidth stacked memory called MCDRAM. Using it offers performance benefits if it is ensured that mdrun runs entirely from this memory; to do so it is recommended that MCDRAM is configured in “Flat mode” and mdrun is bound to the appropriate NUMA node (use e.g. numactl --membind 1 with quadrant clustering mode).

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 a number of gcc versions ranging from 4.8.1 through 7, versions 16 and 18 of the Intel compiler, and Clang versions 3.4 through 5. For this, we use a variety of GNU/Linux flavors and versions as well as recent versions of Windows. Under Windows, we test both MSVC 2017 and version 16 of the Intel compiler. For details, you can have a look at the continuous integration server used by GROMACS, which runs Jenkins.

We test irregularly on ARM v7, ARM v8, Cray, Fujitsu PRIMEHPC, Power8, Google Native Client and other environments, and with other compilers and compiler versions, too.