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 ``-DGMX_MPI=on`` 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
+another using ``-DGMX_MPI=on``.
+The latter will install binaries and libraries named using
+a default suffix of ``_mpi`` ie ``gmx_mpi``. Hence it is safe
and common practice to install this into the same location where
the non-MPI build is installed.
* ``-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_MPI=on`` to build using `MPI support`_
* ``-DGMX_GPU=CUDA`` to build with NVIDIA CUDA support enabled.
* ``-DGMX_GPU=OpenCL`` to build with OpenCL_ support enabled.
* ``-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``)
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,
+approach. Alternatively, one can use different suffixes to install
+several versions of |Gromacs| in the same location. 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
+in order for simple commands like ``gmx grompp`` to work on all machines,
+then build specialized ``gmx`` 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.
+suffixes (with CMake variables ``-DGMX_BINARY_SUFFIX=xxx`` and
+``-DGMX_LIBS_SUFFIX=xxx``), these can be installed to the same
+location.
Linear algebra libraries
~~~~~~~~~~~~~~~~~~~~~~~~
.. _building just the mdrun binary:
-Building only mdrun
-~~~~~~~~~~~~~~~~~~~
-
-This is now deprecated, but still 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|
^^^^^^^^^^^^^^^^^^^^
your hardware, and the output of ``gmx mdrun -version`` (which contains
valuable diagnostic information in the header).
-Testing for MDRUN_ONLY executables
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-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
- # First, build and install normally to allow full testing of the standalone simulator.
- cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/your/installation/prefix/here
- make -j 4
- make install
- cd ..
- mkdir build-mdrun-only
- cd build-mdrun-only
- # Next, build and install the GMX_BUILD_MDRUN_ONLY version (optional).
- cmake .. -DGMX_MPI=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
-
Non-standard suffix
~~~~~~~~~~~~~~~~~~~
-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
+If your ``gmx`` program has been suffixed in a non-standard way, then
+the ``./gmxtest.pl -suffix`` option will let you specify that suffix 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
-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
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff