compiler versions are
* GNU (gcc/libstdc++) 7
-* LLVM (clang/libc++) 5
-* Microsoft (MSVC) 2017 15.7
+* LLVM (clang/libc++) 8
+* Microsoft (MSVC) 2019
Other compilers may work (Cray, Pathscale, older clang) but do
not offer competitive performance. We recommend against PGI because
the compiler to the MPI compiler wrapper but it is neither necessary
nor recommended.
+CUDA-Aware MPI support
+~~~~~~~~~~~~~~~~~~~~~~
+
+In simulations using multiple NVIDIA GPUs, an MPI implementation with CUDA support
+(also called "CUDA-aware") allows communication to be performed directly between the
+distinct GPU memory spaces without staging through CPU memory, often
+resulting in higher bandwidth and lower latency communication. For
+more details, see `Introduction to CUDA-aware MPI
+<https://developer.nvidia.com/blog/introduction-cuda-aware-mpi/>`_.
+
+To use CUDA-aware MPI for direct GPU communication we recommend
+using the latest OpenMPI version (>=4.1.0) with the latest UCX version
+(>=1.10), since most GROMACS internal testing on CUDA-aware support has
+been performed using these versions. OpenMPI with CUDA-aware support can
+be built following the procedure in `these OpenMPI build instructions
+<https://www.open-mpi.org/faq/?category=buildcuda>`_.
+
+With ``GPU_MPI=ON``, GROMACS attempts to automatically detect CUDA support
+in the underlying MPI library at compile time, and enables direct GPU
+communication when this is detected. However, there are some cases when
+GROMACS may fail to detect existing CUDA-aware support, in which case
+it can be manually enabled by setting environment variable ``GMX_FORCE_CUDA_AWARE_MPI=1``
+at runtime (although such cases still lack substantial
+testing, so we urge the user to carefully check correctness of results
+against those using default build options, and report any issues).
+
CMake
^^^^^
cmake .. -DGMX_GPU=OpenCL
To build with support for Intel integrated GPUs, it is required
-to add ``-DGMX_OPENCL_NB_CLUSTER_SIZE=4`` to the cmake command line,
+to add ``-DGMX_GPU_NB_CLUSTER_SIZE=4`` to the cmake command line,
so that the GPU kernels match the characteristics of the hardware.
The `Neo driver <https://github.com/intel/compute-runtime/releases>`_
is recommended.
* ``-DGMX_DOUBLE=ON -DGMX_MPI -DGMX_MIMIC=ON``
+.. _installing with CP2K:
+
+Building with CP2K QM/MM support
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+CP2K QM/MM interface integration will require linking against libcp2k
+library, that incorporates CP2K functionality into |Gromacs|.
+
+1. Download, compile and install CP2K (version 8.1 or higher is required).
+CP2K latest distribution can be downloaded `here <https://github.com/cp2k/cp2k/releases/>`_.
+For CP2K specific instructions please `follow <https://github.com/cp2k/cp2k/blob/master/INSTALL.md>`_.
+You can also check instructions on the `oficial CP2K web-page <https://www.cp2k.org/howto>`_.
+
+2. Make :file:`libcp2k.a` library by executing the following command::
+ make ARCH=<your arch file> VERSION=<your version like psmp> libcp2k
+
+The library archive (*e.g.* :file:`libcp2k.a`) should appear in the :file:`{<cp2k dir>}/lib/{<arch>}/{<version>}/` directory.
+
+3. Configure |Gromacs| with :command:`cmake`, adding the following flags.
+
+Build should be static:
+* ``-DBUILD_SHARED_LIBS=OFF -DGMXAPI=OFF -DGMX_INSTALL_NBLIB_API=OFF``
+
+Double precision in general is better than single for QM/MM
+(however both options are viable):
+* ``-DGMX_DOUBLE=ON``
+
+FFT, BLAS and LAPACK libraries should be the same between CP2K and |Gromacs|.
+Use the following flags to do so:
+
+* ``-DGMX_FFT_LIBRARY=<your library like fftw3> -DFFTWF_LIBRARY=<path to library> -DFFTWF_INCLUDE_DIR=<path to directory with headers>``
+* ``-DGMX_BLAS_USER=<path to your BLAS>``
+* ``-DGMX_LAPACK_USER=<path to your LAPACK>``
+
+4. Compilation of QM/MM interface is controled by the following flags.
+
+``-DGMX_CP2K=ON``
+ Activates QM/MM interface compilation
+``-DCP2K_DIR="<path to cp2k>/lib/local/psmp``
+ Directory with libcp2k.a library
+``-DCP2K_LINKER_FLAGS="<combination of LDFLAGS and LIBS>"``
+ Other libraries used by CP2K. Typically that should be combination
+ of LDFLAGS and LIBS from the ARCH file used for CP2K compilation.
+ Sometimes ARCH file could have several lines defining LDFLAGS and LIBS
+ or even split one line into several using "\". In that case all of them
+ should be concatenated into one long string without any extra slashes
+ or quotes.
+
.. _suffixes:
Changing the names of |Gromacs| binaries and libraries
it works because we have tested it.
Every commit in our git source code repository
is currently tested with a range of configuration options on x86 with
-gcc versions 7 and 8,
-clang versions 8 and 9,
+gcc versions including 7 and 11,
+clang versions including 8 and 13,
+CUDA versions 11.0 and 11.4.2,
and
a version of oneAPI containing Intel's clang-based compiler.
-For this testing, we use Ubuntu 18.04 or 20.04 operating system.
+For this testing, we use Ubuntu 20.04 operating system.
Other compiler, library, and OS versions are tested less frequently.
For details, you can have a look at the
`continuous integration server used by GROMACS <https://gitlab.com/gromacs/gromacs/>`_,
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff