5/11/2015

GPUacceleratedmoleculardynamicsSHARPEN

GPUacceleratedmoleculardynamics
FromSHARPEN
ThefollowingstepsweretakentoinstallGPUacceleratedGROMACswithOpenMMusingaNVIDIA
GTX580ona64bitUbuntusystemandonaNVIDIAGeForce9600GTona32bitUbuntusystem.

Contents
132bitUbuntuinstallofGPUacceleratedGROMACSviaOpenMM
264bitUbuntuinstallofGPUacceleratedGROMACSviaOpenMM
3Troubleshooting
4Gromacs4.6
5OpenMMPython

32bitUbuntuinstallofGPUacceleratedGROMACSviaOpenMM
CUDA

gccv
sudoaptgetinstallcmake
sudoaptgetinstallfftw3dev
sudoaptgetinstalllibxml2dev
sudoaptgetinstalllibx11dev
sudoaptgetinstalllibxmudev
sudoaptgetinstallfreeglut3dev
sudoaptgetinstalllibxidev
sudoaptgetinstallbuildessential
sudoaptgetinstalllibgl1mesaglx
sudoaptgetinstalllibgl1mesadev
sudoaptgetinstalllibglu1mesa
sudoaptgetinstalllibglu1mesadev
sudoaptgetinstalllibglewdev
wgethttp://developer.download.nvidia.com/compute/cuda/4_2/rel/toolkit/cudatoolkit_4.2.9_linux_32_ubuntu11.04.run
wgethttp://developer.download.nvidia.com/compute/cuda/4_2/rel/drivers/devdriver_4.2_linux_32_295.41.run
wgethttp://developer.download.nvidia.com/compute/cuda/4_2/rel/sdk/gpucomputingsdk_4.2.9_linux.run
chmod+xcudatoolkit_4.2.9_linux_32_ubuntu11.04.run
chmod+xdevdriver_4.2_linux_32_295.41.run
chmod+xgpucomputingsdk_4.2.9_linux.run
sudo./cudatoolkit_4.2.9_linux_32_ubuntu11.04.run
echo'exportPATH="$PATH:/usr/local/cuda/bin"'>sourceme_gromacs
echo'exportLD_LIBRARY_PATH="/usr/local/cuda/lib"'>>sourceme_gromacs
Ctrl+Alt+F1(toswitchtoconsolemode),Login
sudoservicelightdmstop
sudo./devdriver_4.2_linux_32_295.41.run
sudo/sbin/shutdownrnow
./gpucomputingsdk_4.2.9_linux.run
cd../NVIDIA_GPU_Computing_SDK/C
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###Tofixanerrorintheupcomingcompile:undefinedreferenceto`gluErrorString'
sed's/{OPENGLLIB}$(PARAMGLLIB)$(RENDERCHECKGLLIB)/(RENDERCHECKGLLIB)$(PARAMGLLIB)${OPENGLLIB}/'icommon/common.mk

FinishCUDA&OpenMM

makej8
./bin/linux/release/deviceQuery
./bin/linux/release/bandwidthTest
cd~/code
##DownloadtheOpenMMsourcecode
mv../Downloads/OpenMM4.1Source.zip.
unzipOpenMM4.1Source.zip
sudoaptgetinstallgfortran
sudoaptgetinstallgccxml
sudoaptgetinstalldoxygen
sudoaptgetinstallswig
sudoaptgetinstallcmakecursesgui
mkdirbuild_openmm
cdbuild_openmm
sudoccmakei../OpenMM4.1Source
#Pressctoconfigure
#Pressgtogenerate
cd..
sudochownRcsnow:csnowbuild_openmm
cdbuild_openmm
makej8
maketest
###Note:inbothinstalls,sometestsfail.
sudomakeinstall

GROMACS

cd~/code
wgetftp://ftp.gromacs.org/pub/gromacs/gromacs4.5.5.tar.gz
tarxvfzgromacs4.5.5.tar.gz
mkdirbuild_gromacs_gpu
cdbuild_gromacs_gpu
exportOPENMM_ROOT_DIR=/usr/local/openmm
cmakeDGMX_OPENMM=ON../gromacs4.5.5
makeclean
makemdrun
sudomakeinstallmdrun

cd~/code
mkdirbuild_gromacs
cdbuild_gromacs
cmake../gromacs4.5.5
makeclean
makej8
sudomakeinstall
echo'exportPATH="$PATH:/usr/local/gromacs/bin"'>>~/code/sourceme_gromacs

DHFRBenchmark

wgethttp://www.gromacs.org/@api/deki/files/128/=gromacsgpubenchdhfr.tar.gz
mv\=gromacsgpubenchdhfr.tar.gzgromacsgpubenchdhfr.tar.gz
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tarxvfzgromacsgpubenchdhfr.tar.gz

./build_gromacs_gpu/src/kernel/mdrungpusdhfr/GPU/dhfrimpl2nm.bench/topol.tprdeviceOpenMM:forcedevice=yes

64bitUbuntuinstallofGPUacceleratedGROMACSviaOpenMM
Note:besidesthedifferentCUDAfiles,anotherdifferenceisthe$LD_LIBRARY_PATH.Also,to
surmounta32bitvs.64bitissue,wehadtoplaceasymboliclinktodirect/usr/local/cuda/libtopointto
/usr/local/cuda/lib64.
CUDA

gccv
sudoaptgetinstallcmake
sudoaptgetinstallfftw3dev
sudoaptgetinstalllibxml2dev
sudoaptgetinstalllibx11dev
sudoaptgetinstalllibxmudev
sudoaptgetinstallfreeglut3dev
sudoaptgetinstalllibxidev
sudoaptgetinstallbuildessential
sudoaptgetinstalllibgl1mesaglx
sudoaptgetinstalllibgl1mesadev
sudoaptgetinstalllibglu1mesa
sudoaptgetinstalllibglu1mesadev
sudoaptgetinstalllibglewdev
wgethttp://developer.download.nvidia.com/compute/cuda/4_2/rel/toolkit/cudatoolkit_4.2.9_linux_64_ubuntu11.04.run
wgethttp://developer.download.nvidia.com/compute/cuda/4_2/rel/drivers/devdriver_4.2_linux_64_295.41.run
wgethttp://developer.download.nvidia.com/compute/cuda/4_2/rel/sdk/gpucomputingsdk_4.2.9_linux.run
chmod+xcudatoolkit_4.2.9_linux_64_ubuntu11.04.run
chmod+xdevdriver_4.2_linux_64_295.41.run
chmod+xgpucomputingsdk_4.2.9_linux.run
sudo./cudatoolkit_4.2.9_linux_64_ubuntu11.04.run
echo'exportPATH="$PATH:/usr/local/cuda/bin"'>sourceme_gromacs
echo'exportLD_LIBRARY_PATH="/usr/local/cuda/lib64:/usr/local/cuda/lib"'>>sourceme_gromacs
Ctrl+Alt+F1(toswitchtoconsolemode),Login
sudoservicelightdmstop
sudo./devdriver_4.2_linux_64_295.41.run
sudo/sbin/shutdownrnow
./gpucomputingsdk_4.2.9_linux.run
cd../NVIDIA_GPU_Computing_SDK/C
###Tofixanerrorintheupcomingcompile:undefinedreferenceto`gluErrorString'
sed's/{OPENGLLIB}$(PARAMGLLIB)$(RENDERCHECKGLLIB)/(RENDERCHECKGLLIB)$(PARAMGLLIB)${OPENGLLIB}/'icommon/common.mk

FinishCUDA&OpenMM

makej8
./bin/linux/release/deviceQuery
./bin/linux/release/bandwidthTest
###Forcedownstreamsoftwaretofindthe64bitversion
cd/usr/local/cuda
http://sharpen.engr.colostate.edu/mediawiki/index.php/GPU_accelerated_molecular_dynamics

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sudomvliblib32
sudolnslib64lib
cd~/code
##DownloadtheOpenMMsourcecode
mv../Downloads/OpenMM4.1Source.zip.
unzipOpenMM4.1Source.zip
sudoaptgetinstallgfortran
sudoaptgetinstallgccxml
sudoaptgetinstalldoxygen
sudoaptgetinstallswig
sudoaptgetinstallcmakecursesgui
mkdirbuild_openmm
cdbuild_openmm
sudoccmakei../OpenMM4.1Source
#Pressctoconfigure
#Pressgtogenerate
cd..
sudochownRcsnow:csnowbuild_openmm
cdbuild_openmm
makej8
maketest
###Note:inbothinstalls,sometestsfail.
sudomakeinstall

GROMACS

cd~/code
wgetftp://ftp.gromacs.org/pub/gromacs/gromacs4.5.5.tar.gz
tarxvfzgromacs4.5.5.tar.gz
mkdirbuild_gromacs_gpu
cdbuild_gromacs_gpu
exportOPENMM_ROOT_DIR=/usr/local/openmm
cmakeDGMX_OPENMM=ON../gromacs4.5.5
makeclean
makemdrun
sudomakeinstallmdrun

cd~/code
mkdirbuild_gromacs
cdbuild_gromacs
cmake../gromacs4.5.5
makeclean
makej8
sudomakeinstall
echo'exportPATH="$PATH:/usr/local/gromacs/bin"'>>~/code/sourceme_gromacs

DHFRBenchmark

wgethttp://www.gromacs.org/@api/deki/files/128/=gromacsgpubenchdhfr.tar.gz
mv\=gromacsgpubenchdhfr.tar.gzgromacsgpubenchdhfr.tar.gz
tarxvfzgromacsgpubenchdhfr.tar.gz

./build_gromacs_gpu/src/kernel/mdrungpusdhfr/GPU/dhfrimpl2nm.bench/topol.tprdeviceOpenMM:forcedevice=yes

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Troubleshooting
Programmdrungpu,VERSION4.6dev201205099f86610
Sourcecodefile:/data/lucasj/code/gromacs/src/kernel/openmm_wrapper.cpp,line:1272
Fatalerror:
Therequestedplatform"CUDA"couldnotbefound.

Thisistheerrorwewerehavingonthe64bitsystembeforeweputalinkto/usr/local/cuda/lib64inplace
of/usr/local/cuda/lib.

Fatalerror:
TheselectedGPU(#0,GeForce9600GT)isnotsupportedbyGromacs!MostprobablyyouhavealowendGPUwhichwouldnotperf
ornewhardwarethathasnotbeentestedwiththecurrentrelease.Ifyoustillwanttotryusingthedevice,usetheforce

Thisistheerrorweget,forbothGPUcards,ifwedonotusetheforcedeviceoption.

Gromacs4.6

sudoaptgetinstallgit
cd~/code
gitclonegit://git.gromacs.org/gromacs.gitgromacs4.6
mkdirbuild_gromacs4.6_gpu
cdbuild_gromacs4.6_gpu
cmakeDGMX_OPENMM=ON../gromacs4.6DCMAKE_INSTALL_PREFIX=/home/csnow/code/gromacs4.6_install
makemdrun
makeinstallmdrun

OpenMMPython
Asroot,incode/build_openmm2,makePythonInstall
Retrievedfrom
"http://sharpen.engr.colostate.edu/mediawiki/index.php/GPU_accelerated_molecular_dynamics"
Thispagewaslastmodifiedon3June2012,at04:17.

http://sharpen.engr.colostate.edu/mediawiki/index.php/GPU_accelerated_molecular_dynamics

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