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Asc
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@AncaSc
AncaSc committed Oct 31, 2014
2 parents 6400ed5 + de78108 commit 8c19c3e
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30 changes: 23 additions & 7 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -215,13 +215,26 @@ gmx_add_cache_dependency(GMX_COOL_QUOTES BOOL "NOT GMX_FAHCORE" OFF)

# Decide on GPU settings based on user-settings and GPU/CUDA detection.
# We support CUDA >=v4.0 on *nix, but <= v4.1 doesn't work with MSVC
if(MSVC)
set(REQUIRED_CUDA_VERSION 4.1)
else()
set(REQUIRED_CUDA_VERSION 4.0)
endif()
set(REQUIRED_CUDA_COMPUTE_CAPABILITY 2.0)
include(gmxManageGPU)
option(GMX_USE_OPENCL "Enable OpenCL accelerators" OFF)
if(NOT GMX_USE_OPENCL)
if(MSVC)
set(REQUIRED_CUDA_VERSION 4.1)
else()
set(REQUIRED_CUDA_VERSION 4.0)
endif()
set(REQUIRED_CUDA_COMPUTE_CAPABILITY 2.0)
include(gmxManageGPU)
else(NOT GMX_USE_OPENCL)
#Now the OpenCL path
if(GMX_GPU)
#1.1 For nvidia, 1.2 for amd/intel. 2.0 cannot test
#set(REQUIRED_OPENCL_MIN_VERSION 1.1)
#set(REQUIRED_OPENCL_MAX_VERSION 1.2)
include(gmxManageOpenCL)
else(GMX_GPU)
message(FATAL_ERROR "OpenCL requested but GPU option is not enabled (try -DGMX_GPU=on) ")
endif(GMX_GPU)
endif(NOT GMX_USE_OPENCL)

# Detect the architecture the compiler is targetting, detect
# SIMD instructions possibilities on that hardware, suggest SIMD instruction set
Expand Down Expand Up @@ -285,6 +298,7 @@ option(GMX_LOAD_PLUGINS "Compile with plugin support, needed to read VMD support
mark_as_advanced(GMX_LOAD_PLUGINS)

option(GMX_GPU "Enable GPU acceleration" ON)
option(GMX_USE_OPENCL "Enable OpenCL accelerators" OFF)
option(GMX_OPENMP "Enable OpenMP-based multithreading" ON)

option(GMX_USE_TNG "Use the TNG library for trajectory I/O" ON)
Expand Down Expand Up @@ -817,6 +831,8 @@ set(LIB_INSTALL_DIR ${GMX_LIB_INSTALL_DIR})
set(BIN_INSTALL_DIR bin)
set(DATA_INSTALL_DIR share/${GMX_DATA_INSTALL_DIR})
set(MAN_INSTALL_DIR share/man)
set(OCL_INSTALL_DIR_NAME opencl) #Used as define in the source
set(OCL_INSTALL_DIR ${BIN_INSTALL_DIR}/${OCL_INSTALL_DIR_NAME})
set(INCL_INSTALL_DIR include)

# These variables get written into config.h for use in finding the data
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237 changes: 159 additions & 78 deletions README
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Original file line number Diff line number Diff line change
@@ -1,78 +1,159 @@

Welcome to the official version of GROMACS!

If you are familiar with Unix, it should be fairly trivial to compile and
install GROMACS. GROMACS uses only the CMake build sytem, and our
installation guide can be found at
http://www.gromacs.org/Documentation/Installation_Instructions.

Of course we will do our utmost to help you with any problems, but PLEASE
READ THE INSTALLATION INSTRUCTIONS BEFORE CONTACTING US!

There are also several other online resources available from the homepage,
and special information for developers.

If you are a developer, or change the source for any other reason, check
out http://www.gromacs.org/Developer_Zone.

* * * * *

GROMACS is free software, distributed under the GNU Lesser General
Public License, version 2.1 However, scientific software is a little
special compared to most other programs. Both you, we, and all other
GROMACS users depend on the quality of the code, and when we find bugs
(every piece of software has them) it is crucial that we can correct
it and say that it was fixed in version X of the file or package
release. For the same reason, it is important that you can reproduce
other people's result from a certain GROMACS version.

The easiest way to avoid this kind of problems is to get your modifications
included in the main distribution. We'll be happy to consider any decent
code. If it's a separate program it can probably be included in the contrib
directory straight away (not supported by us), but for major changes in the
main code we appreciate if you first test that it works with (and without)
MPI, threads, double precision, etc.

If you still want to distribute a modified version or use part of GROMACS
in your own program, remember that the entire project must be licensed
according to the requirements of the LGPL v2.1 license under which you
received this copy of GROMACS. We request that it must clearly be labeled as
derived work. It should not use the name "official GROMACS", and make
sure support questions are directed to you instead of the GROMACS developers.
Sorry for the hard wording, but it is meant to protect YOUR reseach results!

* * * * *

The development of GROMACS is mainly funded by academic research grants.
To help us fund development, we humbly ask that you cite the GROMACS papers:

* GROMACS: A message-passing parallel molecular dynamics implementation
H.J.C. Berendsen, D. van der Spoel and R. van Drunen
Comp. Phys. Comm. 91, 43-56 (1995)
DOI: 10.1016/0010-4655(95)00042-E

* GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
J. Chem. Theory Comput. 4 (2008) pp. 435-447
DOI: 10.1021/ct700301q

* GROMACS 4.5: a high-throughput and highly parallel open source
molecular simulation toolkit
Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar,
Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith, Peter M. Kasson,
David van der Spoel, Berk Hess, Erik Lindahl.
Bioinformatics 29 (2013) pp. 845-54
DOI: 10.1093/bioinformatics/btt055

There are a lot of cool features we'd like to include in future versions,
but our resources are limited. All kinds of donations are welcome, both in
form of code, hardware and funding! Industrial users who choose to pay
for a license pro bono (it is still LGPL and can be redistributed freely) or
contribute in other ways are listed as GROMACS supporters on our webpages.
Don't hesitate to contact us if you are interested.


Good luck with your simulations!

The GROMACS Crew
This is a modified version of GROMACS 5.1 adding OpenCL support.
All CUDA accelerated features have been ported to OpenCL 1.1.

Official GROMACS website: http://www.gromacs.org/

TABLE OF CONTENTS
1. SUPPORTED OPENCL DEVICES
2. GENERAL PROJECT SETUP
3. OPENCL SETUP
4. KNOWN LIMITATIONS
5. TESTED CONFIGURATIONS

1. SUPPORTED OPENCL DEVICES
========================
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.

2. GENERAL PROJECT SETUP
=====================
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

3. OPENCL SETUP
============
Build Gromacs with OpenCL support enabled
-----------------------------------------
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.

Run Gromacs with OpenCL accelerations enabled
---------------------------------------------
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 OCL_FILE_PATH=/path-to-gromacs/src/

OpenCL Device Selection
-----------------------
The same option used to select a CUDA device can be used to select an OpenCL
GPU device: -gpu_id.
For the example below, running mdrun with -gpu_id 1 will select the NVIDIA GPU.

gmx mdrun -gpu_id 1

3 GPUs detected:
#0: name: Bonaire, vendor: Advanced Micro Devices, Inc. device version: OpenCL 1.2 AMD-APP (1411.4), comp. units: 12, stat: compatible
#1: name: GeForce GTX 750 Ti, vendor: NVIDIA Corporation device version: OpenCL 1.1 CUDA, comp. units: 5, stat: compatible
#2: name: Intel(R) HD Graphics 4600, vendor: Intel(R) Corporation device version: OpenCL 1.2 , comp. units: 20, stat: compatible

1 GPU user-selected for this run.
Mapping of GPU ID to the 1 PP rank in this node: GeForce GTX 750 Ti

Environment Variables For OpenCL
--------------------------------
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.

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.

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.

OCL_NOFASTGEN - Generates and compiles all algorithm flavors, otherwise
only the flavor required for the simulation is generated and compiled.

OCL_DEBUG - Use in conjunction with OCL_FORCE_CPU or with an AMD device.
It adds the debug flag to the compiler options (-g).

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)

OCL_NOOPT - Disable optimisations. Adds the option cl-opt-disable to the
compiler options.

4. KNOWN LIMITATIONS
=================
- Intel CPUs are not supported
- Intel GPUs are not supported
- The current implementation is not compatible with OpenCL devices that are not using warp/wavefronts or for which the warp/wavefront size is not a multiple of 32
- The following kernels are known to produce incorrect results:
nbnxn_kernel_ElecEwQSTab_VdwLJ_VF_prune_opencl
nbnxn_kernel_ElecEwQSTab_VdwLJ_F_prune_opencl

5. TESTED CONFIGURATIONS
=====================
Tested devices:
NVIDIA GPUs: GeForce GTX 660M, GeForce GTX 750Ti
AMD GPUs: FirePro W5100, HD 7950, FirePro W9100, Radeon R7 M260

Tested kernels:
Kernel |Benchmark test |Remarks
--------------------------------------------------------------------------------------------------------
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

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
Teemu Virolainen
Anca Hamuraru
Contributors
Dimitris Karkoulis
* * * * *

GROMACS is free software, distributed under the GNU Lesser General
Public License, version 2.1 However, scientific software is a little
special compared to most other programs. Both you, we, and all other
GROMACS users depend on the quality of the code, and when we find bugs
(every piece of software has them) it is crucial that we can correct
it and say that it was fixed in version X of the file or package
release. For the same reason, it is important that you can reproduce
other people's result from a certain GROMACS version.

The easiest way to avoid this kind of problems is to get your modifications
included in the main distribution. We'll be happy to consider any decent
code. If it's a separate program it can probably be included in the contrib
directory straight away (not supported by us), but for major changes in the
main code we appreciate if you first test that it works with (and without)
MPI, threads, double precision, etc.

If you still want to distribute a modified version or use part of GROMACS
in your own program, remember that the entire project must be licensed
according to the requirements of the LGPL v2.1 license under which you
received this copy of GROMACS. We request that it must clearly be labeled as
derived work. It should not use the name "official GROMACS", and make
sure support questions are directed to you instead of the GROMACS developers.
Sorry for the hard wording, but it is meant to protect YOUR reseach results!

* * * * *
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