GROMACS can be compiled for any distribution of Linux, Mac OS X, Windows (native, Cygwin or MinGW), BlueGene, Cray and many other architectures. Technically, it can be compiled on any platform with an ANSI C compiler and supporting libraries, such as the GNU C library. However, Gromacs also comes with many hardware-specific extensions to provide very high performance on those platforms, and to enable these we have slightly more specific requirements since old compilers do not support new features, or they can be buggy.

GROMACS requires an ANSI C compiler that complies with the C89 standard. For best performance, the GROMACS team strongly recommends you get the most recent version of your preferred compiler for your platform (e.g. GCC 4.7 or Intel 12.0 or newer on x86 hardware). There is a large amount of GROMACS code introduced in version 4.6 that depends on effective compiler optimization to get high performance - the old raw assembly-language kernel routines are all gone. Unfortunately this makes GROMACS more sensitive to the compiler used, and the binary will only work on the hardware for which it is compiled, but the good news is that it has enabled us to significantly accelerate performance compared to version 4.5.

• On Intel-based x86 hardware, we recommend you to use the Intel compiler for best performance. It is usually better at instruction scheduling, although it does not hurt to try gcc too. Recent versions can give icc a run for the money.

• On AMD-based x86 hardware up through the Magny-Cours architecture (e.g. Opteron 6100-series processors), it is worth using the Intel compiler for better performance, but gcc-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-4.7 or later for better performance! icc will only generate code for the subset also supported by Intel processors, and that is significantly slower right now.

• 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 does not fully support OpenMP, and the current gcc ports do not support AVX instructions.

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

From version 4.6, GROMACS uses the build system CMake. The previous build system that used configure from the GNU autotools package has been removed permanently. CMake permits the GROMACS team to support a very wide range of hardware, compilers and build configurations while continuing to provide the portability, robustness and performance for which GROMACS is known.

GROMACS requires CMake version 2.8.0 or higher. Lower versions will not work. You can check whether CMake is installed, and what version it is, with 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. If you need to compile CMake yourself and have a really old environment, you might first have to compile a moderately recent version (say, 2.6) to bootstrap version 2.8. This is a one-time job, and you can find lots of documentation on the CMake website if you run into problems.

Many simulations in GROMACS make extensive use of fast Fourier transforms, and a software library to perform these is always required. We recommend FFTW http://www.fftw.org/ (version 3 or higher only) or Intel's MKL http://software.intel.com/en-us/intel-mkl.

• Hardware-optimized BLAS and LAPACK libraries are useful for a few of the GROMACS utilities focused on normal modes and matrix manipulation, but they does not provide any benefits for normal simulations.

• The built-in GROMACS trajectory viewer ngmx requires X11 and Motif/Lesstif libraries and header files. Generally, the GROMACS team rather recommends you use third-party software for visualization, such as VMD http://www.ks.uiuc.edu/Research/vmd/ or PyMOL http://www.pymol.org/.

• A few GROMACS tools get some extra functionality when linked with the GNU scientific library GSL.

CMake will run many tests on your system and do its best to work out how to build GROMACS for you. If you are building GROMACS on hardware that is identical to that where you will run mdrun, 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, 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 a subdirectory or not, it doesn't matter. It also means you can never corrupt your source code by trying to build it! So, the only required argument on the CMake command line is the name of the directory containing the CMakeLists.txt file of the code you want to build. For example, download the source tarball and use

$ tar xfz gromacs-4.6.tgz
$ cd gromacs-4.6
$ mkdir build-cmake
$ cd build-cmake
$ cmake ..

You will see cmake report the results of a large number of tests on your system made by CMake and by GROMACS. These are written to the CMake cache, kept in CMakeCache.txt. You can edit this file by hand, but this is not recommended because it is easy to reach an inconsistent state. You should not attempt to move or copy this file to do another build, because file paths are hard-coded within it. If you mess things up, just delete this file and start again with 'cmake'.

If there's a serious problem detected at this stage, then you will see a fatal error and some suggestions for how to overcome it. If you're not sure how to deal with that, please start by searching on the web (most computer problems already have known solutions!) and then consult the 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.

CMake works in an iterative fashion, re-running each time a setting is changed to try to make sure other things are consistent. Once things seem consistent, the iterations stop. Once 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 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. Some platforms like Windows or Mac 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. If you make any changes, then ccmake will notice that and require that you re-configure (using 'c'), so that it gets a chance to make changes that depend on yours and perform more checking. This might require several configuration stages when you are using ccmake - when you are using cmake the iteration is done behind the scenes.

A key thing to consider here is the setting of CMAKE_INSTALL_PREFIX. You will need to be able to write to this directory in order to install GROMACS later, and if you change your mind later, changing it in the cache triggers a full re-build, unfortunately. So if you do not have super-user privileges on your machine, then you will need to choose a sensible location within your home directory for your GROMACS installation.

When cmake or ccmake have completed iterating, the cache is stable and a build tree can be generated, with 'g' in ccmake or automatically with cmake.

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

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 with a command like:

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

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.

The options that can be seen with 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.

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 seperated 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 ..

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

If you have the CUDA Software Development Kit installed, you can use CMake with:

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

(or whichever path has your installation). Note that this will require a working C++ compiler, and in some cases you might need to handle this manually, e.g. with the advanced option CUDA_HOST_COMPILER.

Historically, Linux GPU builds have received most testing, but we want to support GPU builds both under x86 Linux, Windows, Mac OS X and in the future ARM. Any feedback on this build process (and fixes in particular) are very welcome!

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.

• To link GROMACS binaries statically against the internal GROMACS libraries, set BUILD_SHARED_LIBS=OFF.

• To link statically against external libraries as well, the GMX_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 if that is all that is available (common on Mac OS X).

It is sometimes convenient to have different versions of the same GROMACS libraries installed. The most common use cases have been single and double precision, and with and without MPI. By default, GROMACS will suffix binaries and libraries for such builds with '_d' for double precision and/or '_mpi' for MPI (and nothing otherwise). Naming can be controlled manually with GMX_DEFAULT_SUFFIX (ON/OFF), GMX_BINARY_SUFFIX (takes a string) and GMX_LIBS_SUFFIX (also takes a string). This can also be useful for resolving libary-naming conflicts with existing packges (GMX_PREFIX_LIBMD also can be useful).  For instance, to set a custom suffix for binaries and libraries, one might specify:

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

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

Once you have a stable cache, you can build GROMACS. If you're not sure the cache is stable, you can re-run cmake .. or ccmake ..' to see. Then you can run make to start the compilation. Before actual compilation starts, make checks that the cache is stable, so if it isn't you will see CMake run again.

So long as any changes you've made to the configuration are sensible, it is expected that the make procedure will always complete successfully. The tests GROMACS makes on the settings you choose are pretty extensive, but there are probably a few cases we haven't thought of yet. Search the web first for solutions to problems, but if you need help, ask on 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.

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.

Finally, make install will install GROMACS in the directory given in GMX_INSTALL_PREFIX. If this is an 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.

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 our share/gromacs 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.

Since 2011, the GROMACS development uses an automated system where every new patch is subject to regression testing. 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 regression 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-4.6.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 this doesn't 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) 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 an example logfile from mdrun (which contains valuable information in the header).

We are still working on a set of benchmark systems for testing the performance of GROMACS. Until that is ready, we recommend that you start by comparing the performance to release 4.5, and also try a few different parallelization options.

You're not alone - this can be a complex task! If you encounter a problem with installing GROMACS, then there are a number of locations where you can find assistance. It is recommended that you follow these steps to find the solution:

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.

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 didn't work. Give details about the system on which you are installing. Copy and paste your command line and as much of the output as you think might be relevant - certainly from the first indication of a problem. 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.

Building on Cygwin/MinGW/etc. works just like Unix. Please see the instructions above.

Building on Windows using native compilers is rather similar to building on Unix, so please start by reading the above. Then, download and unpack the GROMACS source archive. The UNIX-standard .tar.gz format can be managed on Windows, but you may prefer to browse ftp://ftp.gromacs.org/pub/gromacs to obtain a zip format file, which doesn't need any external tools to unzip on recent Windows systems. Make a folder in which to do the out-of-source build of GROMACS. For example, make it within the folder unpacked from the source archive, and call it “build-cmake”.

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.

Gromacs builds mostly out of the box on modern Cray machines, but you want to use static libraries due to the peculiarities with parallel job execution.