Benchmarking: Gromacs-5.0 - Revision history

K mouza: /* MPI + GPU */

2015-07-30T13:07:51Z

MPI + GPU

K mouza: /* CMake */

2015-02-06T10:04:39Z

CMake

K mouza: /* MPI + GPU */

2015-01-16T16:20:00Z

MPI + GPU

K mouza: /* MPI + GPU */

2015-01-16T16:05:28Z

MPI + GPU

K mouza: /* GPU */

2015-01-16T16:05:01Z

GPU

K mouza: /* Download */

2015-01-16T16:04:14Z

Download

Roshan at 11:57, 8 July 2014

2014-07-08T11:57:12Z

Roshan: Created page with "==Requirements== cmake 2.8 (for build)
CUDA 5.0 ==Download== wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz ==Build== module load cmake/2.8.10.2 module..."

2014-07-08T11:46:46Z

Created page with "==Requirements== cmake 2.8 (for build) <br> CUDA 5.0 ==Download== wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz ==Build== module load cmake/2.8.10.2 module..."

New page

==Requirements==

cmake 2.8 (for build) <br>
CUDA 5.0

==Download==

wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz

==Build==

module load cmake/2.8.10.2
module load cuda/5.0

cmake ../gromacs-4.6 -DGMX_GPU=ON -DGMX_BUILD_OWN_FFTW=ON \
-DCUDA_TOOLKIT_ROOT_DIR=/shared/apps/cuda/cuda-5.0 \
-DLIB_INSTALL_DIR=/shared/apps/cuda/gromacs/4.6/lib \
-DCMAKE_INSTALL_PREFIX=/shared/apps/cuda/gromacs/4.6

make -j 24

==Modulefiles==
File location: /shared/modulefiles <br>
File name: gpu/gromacs/4.6

#%Module 1.0
#
prereq cuda/5.0
system "source /shared/apps/cuda/gromacs/4.6/bin/GMXRC.bash"
prepend-path PATH /shared/apps/cuda/gromacs/4.6/bin
prepend-path LD_LIBRARY_PATH /shared/apps/cuda/gromacs/4.6/lib

==Run==
module load gpu/gromacs/4.6
mdrun -s <input file>

==Build Errors==
===Intel Compilers===
'''Error'''
<pre>
/home/boston/gromacs-4.6.3/include/gmx_math_x86_avx_128_fma_double.h(674): error: a value of type "int" cannot be assigned to an entity of type "__m128d"
PolyCP0 = _mm_macc_pd(PolyCP1, w, PolyCP0);
^

compilation aborted for /home/boston/gromacs-4.6.3/src/gmxlib/bondfree.c (code 4)
make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/bondfree.c.o] Error 4
make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
make: *** [all] Error 2
</pre>
'''Fix'''
<pre>
You can fix the error by updating the CMakeCache.txt after you cmake Gromacs.

Update GMX_CPU_ACCELERATION:STRING=AVX_128_FMA to

//Accelerated CPU kernels. Pick one of: None, SSE2, SSE4.1, AVX_128_FMA,
// AVX_256, IBM_QPX, Sparc64_HPC_ACE
GMX_CPU_ACCELERATION:STRING=None

After which you can proceed with
$ make
$ make install

It’s probably because Intel compilers do not understand the intrinsic types of AMD (AVX_128_FMA as identified by Gromacs)
Meaning: the Intel compiler cannot produce optimized code for AMD.
</pre>

@@ Line 49: / Line 49: @@
   -DCMAKE_INSTALL_PREFIX=/cm/shared/apps/Gromacs-5/gpu \
   -DBUILD_SHARED_LIBS=OFF
 </syntaxhighlight>

← Older revision		Revision as of 10:04, 6 February 2015
Line 8:		Line 8:

	GROMACS 5.0 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 http://www.cmake.org/cmake/help/install.html for pre-compiled binaries, source code and installation instructions. The GROMACS team recommends you install the most recent version of CMake you can.		GROMACS 5.0 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 http://www.cmake.org/cmake/help/install.html for pre-compiled binaries, source code and installation instructions. The GROMACS team recommends you install the most recent version of CMake you can.
		+
		+	'''Note''' that CMake 3.1.0 generated a faulty Makefile, which prevents the NVIDIA components to be compiled. Version 2.8.12.2 works fine.

	===MPI support===		===MPI support===

@@ Line 65: / Line 65: @@
   -DBUILD_SHARED_LIBS=OFF
-  make -j 16
+  make
   make install
 </syntaxhighlight>

@@ Line 50: / Line 50: @@
 ===MPI + GPU===
   module load cuda60/toolkit/6.0.37
   module load openmpi/gcc/64/1.8.1
@@ Line 65: / Line 67: @@
   make -j 16
   make install

@@ Line 35: / Line 35: @@
 ===GPU===
   module load cuda60/toolkit/6.0.37
@@ Line 44: / Line 46: @@
   -DGMX_GPU=ON \
   -DCMAKE_INSTALL_PREFIX=/cm/shared/apps/Gromacs-5/gpu \
   -DBUILD_SHARED_LIBS=OFF
 ===MPI + GPU===

@@ Line 24: / Line 24: @@
 ==Download==
- wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz
+<syntaxhighlight>
 ==Build==

@@ Line 1: / Line 1: @@
 ==Requirements==
-cmake 2.8 (for build) <br>
+===GPU support===
-==Download==
+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.
- wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz
+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. LAMMPI might work, but since it has been deprecated for years, it is not supported.
-==Build==
+Often OpenMP parallelism is an advantage for GROMACS, but support for this is generally built into your compiler and detected automatically.
- module load cmake/2.8.10.2
+In summary, for maximum performance you will need to examine how you will use GROMACS, what hardware you plan to run on, and whether you can afford a non-free compiler for slightly better performance. 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 mdrun are gone.
- cmake ../gromacs-4.6 -DGMX_GPU=ON -DGMX_BUILD_OWN_FFTW=ON \
+==Download==
-  make -j 24
+  wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz
-==Modulefiles==
+===GPU===
-File location: /shared/modulefiles <br>
+ module load cuda60/toolkit/6.0.37
-  #%Module 1.0
+  /cm/shared/apps/cmake/2.8.12.1/bin/cmake .. \
+  -DCUDA_TOOLKIT_ROOT_DIR=/cm/shared/apps/cuda60/toolkit/current \
- prereq  cuda/5.0
+ -DGMX_BUILD_OWN_FFTW=ON \
- system "source /shared/apps/cuda/gromacs/4.6/bin/GMXRC.bash"
+ -DCMAKE_C_COMPILER=gcc \
-  prepend-path  PATH      /shared/apps/cuda/gromacs/4.6/bin
+ -DCMAKE_CXX_COMPILER=g++ \
-  prepend-path  LD_LIBRARY_PATH /shared/apps/cuda/gromacs/4.6/lib
+  -DGMX_GPU=ON \
-==Run==
+===MPI + GPU===
-  module load gpu/gromacs/4.6
+  module load cuda60/toolkit/6.0.37
-  mdrun -s <input file>
+  module load openmpi/gcc/64/1.8.1
-==Build Errors==
+ /cm/shared/apps/cmake/2.8.12.1/bin/cmake .. \
-===Intel Compilers===
+ -DCUDA_TOOLKIT_ROOT_DIR=/cm/shared/apps/cuda60/toolkit/current \
-'''Error'''
+ -DGMX_BUILD_OWN_FFTW=ON \
-<pre>
+ -DCMAKE_C_COMPILER=mpicc \
-/home/boston/gromacs-4.6.3/include/gmx_math_x86_avx_128_fma_double.h(674): error: a value of type "int" cannot be assigned to an entity of type "__m128d"
+ -DCMAKE_CXX_COMPILER=mpic++ \
-      PolyCP0  = _mm_macc_pd(PolyCP1, w, PolyCP0);
+ -DGMX_GPU=ON \
+ -DGMX_MPI=ON \
-compilation aborted for /home/boston/gromacs-4.6.3/src/gmxlib/bondfree.c (code 4)
+ make -j 16
-make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/bondfree.c.o] Error 4
+  make install

Benchmarking: Gromacs-5.0 - Revision history

K mouza: /* MPI + GPU */

K mouza: /* CMake */

K mouza: /* MPI + GPU */

K mouza: /* MPI + GPU */

K mouza: /* GPU */

K mouza: /* Download */

Roshan at 11:57, 8 July 2014

Roshan: Created page with "==Requirements== cmake 2.8 (for build) CUDA 5.0 ==Download== wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz ==Build== module load cmake/2.8.10.2 module..."

Roshan: Created page with "==Requirements== cmake 2.8 (for build)
CUDA 5.0 ==Download== wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz ==Build== module load cmake/2.8.10.2 module..."