INSTALL

Installation guide
******************


Introduction to building GROMACS
================================

These instructions pertain to building GROMACS 5.1.2. 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 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"

7. Source "GMXRC" to get access to GROMACS

Or, as a sequence of commands to execute:

   tar xfz gromacs-5.1.2.tar.gz
   cd gromacs-5.1.2
   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 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

* "-DGMX_GPU=on" to build using nvcc to run using NVIDIA native 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 "fftw", "mkl" or
  "fftpack" libraries for FFT support

* "-DCMAKE_BUILD_TYPE=Debug" to build GROMACS in debug mode


Building older versions
-----------------------

For installation instructions for old GROMACS versions, see the
documentation for installing GROMACS 4.5, GROMACS 4.6, and GROMACS
5.0.


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.

On Linux, a 64-bit operating system is strongly recommended, since
currently GROMACS cannot operate on large trajectories when compiled
on a 32-bit system.


Compiler
--------

Technically, GROMACS can be compiled on any platform with an ANSI C99
and C++98 compiler, and their respective standard C/C++ libraries. We
use only a few C99 features, but note that the C++ compiler also needs
to support these C99 features (notably, int64_t and related things),
which are not part of the C++98 standard. 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. You may also need
the most recent version compiler toolchain components beside the
compiler itself (e.g. assembler or linker); these are often shipped by
the distribution's binutils package.

* In particular, GROMACS includes a lot of explicit SIMD (single
  instruction, multiple data) optimization that suits modern
  processors. This can greatly increase performance, but for recent
  processors you also need a similarly recent compiler 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 3.7 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
--------------------------------------

For maximum performance you will need to examine how you will use
GROMACS and what hardware you plan to run on. 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 "gmx mdrun" are gone.


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.

To make it possible to use other accelerators, GROMACS also includes
OpenCL support. The current version is recommended for use with GCN-
based AMD GPUs. It does work with NVIDIA GPUs, but using the latest
NVIDIA driver (which includes the NVIDIA OpenCL runtime) is
recommended, and please see the known limitations in the GROMACS user
guide. The minimum OpenCL version required is 1.1.

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.

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


CMake
-----

GROMACS 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 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 "fftw", "mkl", or
"fftpack". FFTPACK is bundled with GROMACS as a fallback, and is
acceptable if mdrun performance is not a priority.


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. Note that we have recently
contributed new SIMD optimization for several extra platforms to FFTW,
which will appear in FFTW-3.3.5 (for now it is available in the FFTW
repository on github, or you can find a very unofficial prerelease
version at ftp://ftp.gromacs.org/pub/prerequisite_software ). 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. As of FFTW-3.3.5 you should
also add "--enable-avx2". FFTW will create a fat library with codelets
for all different instruction sets, and pick the fastest supported one
at runtime. On IBM Power8, you definitely want the upcoming FFTW-3.3.5
and use "--enable-vsx" for SIMD support. If you are using a Cray,
there is a special modified (commercial) version of FFTs using the
FFTW interface which might be faster, but we have not yet tested this
extensively.


Using 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

* Compiling to run on AMD GPUs requires OpenCL

* 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 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,
  but TNG 1.7.6 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, python 2.7, sphinx 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 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-5.1.2.tgz
   cd gromacs-5.1.2
   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
~~~~~~~~~~~~~~~~~~~~~~~~

A key thing to consider here is the setting of "CMAKE_INSTALL_PREFIX"
to control where GROMACS will be installed. You will need permissions
to be able to write to this directory. 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 "-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:

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 rest 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 (and later) processors
   (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.

9. "IBM_VMX" Power6 and similar Altivec processors have this.

10. "IBM_VSX" Power7 and Power8 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 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, 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 the page on CMake environment variables.


Native 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".

To make it possible to get best performance from NVIDIA Tesla and
Quadro GPUs, you should install the GPU Deployment Kit and configure
GROMACS to use it by setting the CMake variable
"-DGPU_DEPLOYMENT_KIT_ROOT_DIR=/path/to/your/kit". The NVML support is
most useful if "nvidia-smi --applications-clocks-
permission=UNRESTRICTED" is run (as root). When application clocks
permissions are unrestricted, the GPU clock speed can be increased
automatically, which increases the GPU kernel performance roughly
proportional to the clock increase. When using GROMACS on suitable
GPUs under restricted permissions, clocks cannot be changed, and in
that case informative log file messages will be produced. Background
details can be found at this NVIDIA blog post. NVML support is only
available if detected, and may be disabled by turning off the
"GMX_USE_NVML" CMake advanced option.

By default, optimized code will be generated for CUDA architectures
supported by the nvcc compiler (and the GROMACS build system).
However, it can be beneficial to manually pick the specific CUDA
architecture(s) to generate code for either to reduce compilation time
(and binary size) or to target a new architecture not yet supported by
the GROMACS build system. Setting the desired CUDA architecture(s) and
virtual architecture(s) can be done using the "GMX_CUDA_TARGET_SM" and
"GMX_CUDA_TARGET_COMPUTE" variables, respectively. These take a
semicolon delimited string with the two digit suffixes of CUDA
(virtual) architectures names (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 ARM v7 (32 bit) CPUs
also works.


OpenCL GPU acceleration
~~~~~~~~~~~~~~~~~~~~~~~

To build Gromacs with OpenCL support enabled, an OpenCL SDK (e.g. from
AMD) must be installed in a path found in "CMAKE_PREFIX_PATH" (or via
the environment variables "AMDAPPSDKROOT" or "CUDA_PATH"), and the
following CMake flags must be set

   cmake .. -DGMX_GPU=ON -DGMX_USE_OPENCL=ON

Building GROMACS OpenCL support for a CUDA GPU works, but see the
known limitations in the user guide. If you want to do so anyway,
because NVIDIA OpenCL support is part of the CUDA package, a C++
compiler supported by your CUDA installation is required.

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.


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, 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".


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 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 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 and some scripts. 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.

"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 "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. 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 GROMACS regression test suite
http://gerrit.gromacs.org/download/regressiontests-5.1.2.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, you may need to
set the CMake variables "MPIEXEC", "MPIEXEC_NUMPROC_FLAG", "NUMPROC",
"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

Typically, one might use variable values "mpirun", "-np", "2", "''",
"''" respectively, in order to run on two ranks.


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. 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 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 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 4.1 through
5.1, and versions 12 through 15 of the Intel compiler as well as Clang
version 3.4 through 3.6. For this, we use a variety of GNU/Linux
flavors and versions as well as recent versions of Mac OS X and
Windows.  Under Windows we test both MSVC and 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, BlueGene/Q, Cray, Fujitsu
PRIMEHPC, Power8, Google Native Client and other environments, and
with other compilers and compiler versions, too.