This is a modified version of GROMACS 5.0 adding OpenCL support. All CUDA accelerated features have been ported to OpenCL 1.1.
Official GROMACS website: http://www.gromacs.org/
TABLE OF CONTENTS
SUPPORTED OPENCL DEVICES
GENERAL PROJECT SETUP
OPENCL SETUP
KNOWN LIMITATIONS
TESTED CONFIGURATIONS
The current version works with NVIDIA GPUs and GCN based AMD GPUs. Make sure that you have the latest drivers installed. Also check "Known Limitations" chapter.
Check GROMACS website for how to build the project: http://www.gromacs.org/Documentation/Installation_Instructions You can find additional information here: https://github.com/StreamComputing/gromacs/wiki/GROMACS-GPU-ACCELERATION-USING-OPENCL#General_Project_Setup
To build Gromacs with OpenCL support enabled, an OpenCL SDK must be installed and the following cmake flags must be set: GMX_GPU GMX_USE_OPENCL After setting these flags, if an OpenCL implementation has been detected on your system, the following cmake entries will be defined: OPENCL_INCLUDE_DIR - the OpenCL include directory OPENCL_LIBRARY - the OpenCL library directory The two paths will be automatically used to configure the project.
Gromacs loads and builds at runtime the OpenCL kernels. To do so, it needs to know the location of the OpenCL source files. If you want to run the installed version, the path to the OpenCL files is automatically defined. If you do not wish to install Gromacs, but run the version built from sources, you need to provide the path to the source tree with the OpenCL kernels like below: export GMX_OCL_FILE_PATH=/path-to-gromacs/src/
Building an OpenCL program can take a significant amount of time. NVIDIA implements a mechanism to cache the result of the build. As a consequence, only the first build of the OpenCL kernels will take longer, the following builds will be very fast. AMD drivers, on the other hand, implement no caching and building a program can be very slow. That's why we have started implementing our own caching. Caching for OpenCL kernel builds is by default enabled. To disable it, set GMX_OCL_NOGENCACHE environment variable.
If you plan to modify the OpenCL kernels, you should disable any caching:
The same option used to select CUDA devices or to define a mapping of GPUs to PP ranks can also be used for OpenCL devices: -gpu_id
Currently, several environment variables exist that help customize some aspects of the OpenCL version of Gromacs. They are mostly related to the runtime compilation of OpenCL kernels, but they are also used on the device selection.
GXM_OCL_FILE_PATH: Is the full path to Gromacs src folder. Useful when gmx is called from a folder other than the installation/bin folder.
GMX_OCL_NOGENCACHE: Disable caching for OpenCL kernel builds.
GMX_OCL_NOFASTGEN: Generates and compiles all algorithm flavors, otherwise only the flavor required for the simulation is generated and compiled.
GMX_OCL_FASTMATH: Adds the option cl-fast-relaxed-math to the compiler options (in the CUDA version this is enabled by default, it is likely that the same will happen with the OpenCL version soon)
GMX_OCL_DUMP_LOG: If defined, the OpenCL build log is always written to file. The file is saved in the current directory with the name OpenCL_kernel_file_name.build_status where OpenCL_kernel_file_name is the name of the file containing the OpenCL source code (usually nbnxn_ocl_kernels.cl) and build_status can be either SUCCEEDED or FAILED. If this environment variable is not defined, the default behavior is the following:
Release build: build log is written to file only in case of errors.
GMX_OCL_VERBOSE: If defined, it enables verbose mode for OpenCL kernel build. Currently available only for NVIDIA GPUs. See GMX_OCL_DUMP_LOG for details about how to obtain the OpenCL build log.
GMX_OCL_DUMP_INTERM_FILES: If defined, intermediate language code corresponding to the OpenCL build process is saved to file. Caching has to be turned off in order for this option to take effect (see GMX_OCL_NOGENCACHE).
AMD GPUs: .IL/.ISA files will be created for each OpenCL kernel built. For details about where these files are created check AMD documentation for -save-temps compiler option.
GMX_OCL_DEBUG: Use in conjunction with OCL_FORCE_CPU or with an AMD device. It adds the debug flag to the compiler options (-g).
GMX_OCL_NOOPT: Disable optimisations. Adds the option cl-opt-disable to the compiler options.
GMX_OCL_FORCE_CPU: Force the selection of a CPU device instead of a GPU. This exists only for debugging purposes. Do not expect Gromacs to function properly with this option on, it is solely for the simplicity of stepping in a kernel and see what is happening.
GMX_OCL_NB_ANA_EWALD: Forces the use of analytical Ewald kernels. Equivalent of CUDA env var GMX_CUDA_NB_ANA_EWALD
GMX_OCL_NB_TAB_EWALD: Forces the use of tabulated Ewald kernel. Equivalent of CUDA env var GMX_OCL_NB_TAB_EWALD
GMX_OCL_NB_EWALD_TWINCUT: Forces the use of twin-range cutoff kernel. Equivalent of CUDA env var GMX_CUDA_NB_EWALD_TWINCUT
GMX_DISABLE_OCL_TIMING: Disables timing for OpenCL operations
Tested devices: NVIDIA GPUs: GeForce GTX 660M, GeForce GTX 750Ti, GeForce GTX 780 AMD GPUs: FirePro W5100, HD 7950, FirePro W9100, Radeon R7 M260, R9 290
nbnxn_kernel_ElecCut_VdwLJ_VF_prune_opencl |d.poly-ch2 | nbnxn_kernel_ElecCut_VdwLJ_F_opencl |d.poly-ch2 | nbnxn_kernel_ElecCut_VdwLJ_F_prune_opencl |d.poly-ch2 | nbnxn_kernel_ElecCut_VdwLJ_VF_opencl |d.poly-ch2 | nbnxn_kernel_ElecRF_VdwLJ_VF_prune_opencl |adh_cubic with rf_verlet.mdp | nbnxn_kernel_ElecRF_VdwLJ_F_opencl |adh_cubic with rf_verlet.mdp | nbnxn_kernel_ElecRF_VdwLJ_F_prune_opencl |adh_cubic with rf_verlet.mdp | nbnxn_kernel_ElecEwQSTab_VdwLJ_VF_prune_opencl |adh_cubic_vsites with pme_verlet_vsites.mdp |Failed nbnxn_kernel_ElecEwQSTab_VdwLJ_F_prune_opencl |adh_cubic_vsites with pme_verlet_vsites.mdp |Failed nbnxn_kernel_ElecEw_VdwLJ_VF_prune_opencl |adh_cubic_vsites with pme_verlet_vsites.mdp | nbnxn_kernel_ElecEw_VdwLJ_F_opencl |adh_cubic_vsites with pme_verlet_vsites.mdp | nbnxn_kernel_ElecEw_VdwLJ_F_prune_opencl |adh_cubic_vsites with pme_verlet_vsites.mdp | nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_prune_opencl |adh_cubic_vsites with pme_verlet_vsites.mdp | nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_opencl |adh_cubic_vsites with pme_verlet_vsites.mdp |
Input data used for testing - Benchmark data sets available here: ftp://ftp.gromacs.org/pub/benchmarks
* * * * *The GROMACS OpenCL team StreamComputing - www.streamcomputing.eu Vincent Hindriksen - vincent@streamcomputing.eu Teemu Virolainen - teemu@streamcomputing.eu Anca Hamuraru - anca@streamcomputing.eu Contributors Dimitrios Karkoulis - dimitris.karkoulis@gmail.com
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