GPU Accelerated Molecular Dynamics - SHARPEN
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GPU accelerated molecular dynamics From SHARPEN The following steps were taken to install GPUaccelerated GROMACs with OpenMM using a NVIDIA GTX 580 on a 64bit Ubuntu system and on a NVIDIA GeForce 9600 GT on a 32bit Ubuntu system. Contents 1 32 bit Ubuntu install of GPU accelerated GROMACS via OpenMM 2 64 bit Ubuntu install of GPU accelerated GROMACS via OpenMM 3 Troubleshooting 4 Gromacs 4.6 5 OpenMM Python 32 bit Ubuntu install of GPU accelerated GROMACS via OpenMM CUDA gcc ‐v sudo apt‐get install cmake sudo apt‐get install fftw3‐dev sudo apt‐get install libxml2‐dev sudo apt‐get install libx11‐dev sudo apt‐get install libxmu‐dev sudo apt‐get install freeglut3‐dev sudo apt‐get install libxi‐dev sudo apt‐get install build‐essential sudo apt‐get install libgl1‐mesa‐glx sudo apt‐get install libgl1‐mesa‐dev sudo apt‐get install libglu1‐mesa sudo apt‐get install libglu1‐mesa‐dev sudo apt‐get install libglew‐dev wget http://developer.download.nvidia.com/compute/cuda/4_2/rel/toolkit/cudatoolkit_4.2.9_linux_32_ubuntu11.04.run wget http://developer.download.nvidia.com/compute/cuda/4_2/rel/drivers/devdriver_4.2_linux_32_295.41.run wget http://developer.download.nvidia.com/compute/cuda/4_2/rel/sdk/gpucomputingsdk_4.2.9_linux.run chmod +x cudatoolkit_4.2.9_linux_32_ubuntu11.04.run chmod +x devdriver_4.2_linux_32_295.41.run chmod +x gpucomputingsdk_4.2.9_linux.run sudo ./cudatoolkit_4.2.9_linux_32_ubuntu11.04.run echo 'export PATH="$PATH:/usr/local/cuda/bin"' > sourceme_gromacs echo 'export LD_LIBRARY_PATH="/usr/local/cuda/lib"' >> sourceme_gromacs Ctrl + Alt + F1 (to switch to console mode), Login sudo service lightdm stop sudo ./devdriver_4.2_linux_32_295.41.run sudo /sbin/shutdown ‐r now ./gpucomputingsdk_4.2.9_linux.run cd ../NVIDIA_GPU_Computing_SDK/C
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Transcript of GPU Accelerated Molecular Dynamics - SHARPEN
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5/11/2015 GPUacceleratedmoleculardynamicsSHARPEN
http://sharpen.engr.colostate.edu/mediawiki/index.php/GPU_accelerated_molecular_dynamics 1/5
GPUacceleratedmoleculardynamicsFromSHARPEN
ThefollowingstepsweretakentoinstallGPUacceleratedGROMACswithOpenMMusingaNVIDIAGTX580ona64bitUbuntusystemandonaNVIDIAGeForce9600GTona32bitUbuntusystem.
Contents132bitUbuntuinstallofGPUacceleratedGROMACSviaOpenMM264bitUbuntuinstallofGPUacceleratedGROMACSviaOpenMM3Troubleshooting4Gromacs4.65OpenMMPython
32bitUbuntuinstallofGPUacceleratedGROMACSviaOpenMM
CUDA
gccvsudoaptgetinstallcmakesudoaptgetinstallfftw3devsudoaptgetinstalllibxml2devsudoaptgetinstalllibx11devsudoaptgetinstalllibxmudevsudoaptgetinstallfreeglut3devsudoaptgetinstalllibxidevsudoaptgetinstallbuildessentialsudoaptgetinstalllibgl1mesaglxsudoaptgetinstalllibgl1mesadevsudoaptgetinstalllibglu1mesasudoaptgetinstalllibglu1mesadevsudoaptgetinstalllibglewdevwgethttp://developer.download.nvidia.com/compute/cuda/4_2/rel/toolkit/cudatoolkit_4.2.9_linux_32_ubuntu11.04.runwgethttp://developer.download.nvidia.com/compute/cuda/4_2/rel/drivers/devdriver_4.2_linux_32_295.41.runwgethttp://developer.download.nvidia.com/compute/cuda/4_2/rel/sdk/gpucomputingsdk_4.2.9_linux.runchmod+xcudatoolkit_4.2.9_linux_32_ubuntu11.04.runchmod+xdevdriver_4.2_linux_32_295.41.runchmod+xgpucomputingsdk_4.2.9_linux.runsudo./cudatoolkit_4.2.9_linux_32_ubuntu11.04.runecho'exportPATH="$PATH:/usr/local/cuda/bin"'>sourceme_gromacsecho'exportLD_LIBRARY_PATH="/usr/local/cuda/lib"'>>sourceme_gromacsCtrl+Alt+F1(toswitchtoconsolemode),Loginsudoservicelightdmstopsudo./devdriver_4.2_linux_32_295.41.runsudo/sbin/shutdownrnow./gpucomputingsdk_4.2.9_linux.runcd../NVIDIA_GPU_Computing_SDK/C
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5/11/2015 GPUacceleratedmoleculardynamicsSHARPEN
http://sharpen.engr.colostate.edu/mediawiki/index.php/GPU_accelerated_molecular_dynamics 2/5
###Tofixanerrorintheupcomingcompile:undefinedreferenceto`gluErrorString'sed's/{OPENGLLIB}$(PARAMGLLIB)$(RENDERCHECKGLLIB)/(RENDERCHECKGLLIB)$(PARAMGLLIB)${OPENGLLIB}/'icommon/common.mk
FinishCUDA&OpenMM
makej8./bin/linux/release/deviceQuery./bin/linux/release/bandwidthTestcd~/code##DownloadtheOpenMMsourcecodemv../Downloads/OpenMM4.1Source.zip.unzipOpenMM4.1Source.zipsudoaptgetinstallgfortransudoaptgetinstallgccxmlsudoaptgetinstalldoxygensudoaptgetinstallswigsudoaptgetinstallcmakecursesguimkdirbuild_openmmcdbuild_openmmsudoccmakei../OpenMM4.1Source#Pressctoconfigure#Pressgtogeneratecd..sudochownRcsnow:csnowbuild_openmmcdbuild_openmmmakej8maketest###Note:inbothinstalls,sometestsfail.sudomakeinstall
GROMACS
cd~/codewgetftp://ftp.gromacs.org/pub/gromacs/gromacs4.5.5.tar.gztarxvfzgromacs4.5.5.tar.gzmkdirbuild_gromacs_gpucdbuild_gromacs_gpuexportOPENMM_ROOT_DIR=/usr/local/openmmcmakeDGMX_OPENMM=ON../gromacs4.5.5makecleanmakemdrunsudomakeinstallmdruncd~/codemkdirbuild_gromacscdbuild_gromacscmake../gromacs4.5.5makecleanmakej8sudomakeinstallecho'exportPATH="$PATH:/usr/local/gromacs/bin"'>>~/code/sourceme_gromacs
DHFRBenchmark
wgethttp://www.gromacs.org/@api/deki/files/128/=gromacsgpubenchdhfr.tar.gzmv\=gromacsgpubenchdhfr.tar.gzgromacsgpubenchdhfr.tar.gz
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5/11/2015 GPUacceleratedmoleculardynamicsSHARPEN
http://sharpen.engr.colostate.edu/mediawiki/index.php/GPU_accelerated_molecular_dynamics 3/5
tarxvfzgromacsgpubenchdhfr.tar.gz./build_gromacs_gpu/src/kernel/mdrungpusdhfr/GPU/dhfrimpl2nm.bench/topol.tprdeviceOpenMM:forcedevice=yes
64bitUbuntuinstallofGPUacceleratedGROMACSviaOpenMM
Note:besidesthedifferentCUDAfiles,anotherdifferenceisthe$LD_LIBRARY_PATH.Also,tosurmounta32bitvs.64bitissue,wehadtoplaceasymboliclinktodirect/usr/local/cuda/libtopointto/usr/local/cuda/lib64.
CUDA
gccvsudoaptgetinstallcmakesudoaptgetinstallfftw3devsudoaptgetinstalllibxml2devsudoaptgetinstalllibx11devsudoaptgetinstalllibxmudevsudoaptgetinstallfreeglut3devsudoaptgetinstalllibxidevsudoaptgetinstallbuildessentialsudoaptgetinstalllibgl1mesaglxsudoaptgetinstalllibgl1mesadevsudoaptgetinstalllibglu1mesasudoaptgetinstalllibglu1mesadevsudoaptgetinstalllibglewdevwgethttp://developer.download.nvidia.com/compute/cuda/4_2/rel/toolkit/cudatoolkit_4.2.9_linux_64_ubuntu11.04.runwgethttp://developer.download.nvidia.com/compute/cuda/4_2/rel/drivers/devdriver_4.2_linux_64_295.41.runwgethttp://developer.download.nvidia.com/compute/cuda/4_2/rel/sdk/gpucomputingsdk_4.2.9_linux.runchmod+xcudatoolkit_4.2.9_linux_64_ubuntu11.04.runchmod+xdevdriver_4.2_linux_64_295.41.runchmod+xgpucomputingsdk_4.2.9_linux.runsudo./cudatoolkit_4.2.9_linux_64_ubuntu11.04.runecho'exportPATH="$PATH:/usr/local/cuda/bin"'>sourceme_gromacsecho'exportLD_LIBRARY_PATH="/usr/local/cuda/lib64:/usr/local/cuda/lib"'>>sourceme_gromacsCtrl+Alt+F1(toswitchtoconsolemode),Loginsudoservicelightdmstopsudo./devdriver_4.2_linux_64_295.41.runsudo/sbin/shutdownrnow./gpucomputingsdk_4.2.9_linux.runcd../NVIDIA_GPU_Computing_SDK/C###Tofixanerrorintheupcomingcompile:undefinedreferenceto`gluErrorString'sed's/{OPENGLLIB}$(PARAMGLLIB)$(RENDERCHECKGLLIB)/(RENDERCHECKGLLIB)$(PARAMGLLIB)${OPENGLLIB}/'icommon/common.mk
FinishCUDA&OpenMM
makej8./bin/linux/release/deviceQuery./bin/linux/release/bandwidthTest###Forcedownstreamsoftwaretofindthe64bitversioncd/usr/local/cuda
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5/11/2015 GPUacceleratedmoleculardynamicsSHARPEN
http://sharpen.engr.colostate.edu/mediawiki/index.php/GPU_accelerated_molecular_dynamics 4/5
sudomvliblib32sudolnslib64libcd~/code##DownloadtheOpenMMsourcecodemv../Downloads/OpenMM4.1Source.zip.unzipOpenMM4.1Source.zipsudoaptgetinstallgfortransudoaptgetinstallgccxmlsudoaptgetinstalldoxygensudoaptgetinstallswigsudoaptgetinstallcmakecursesguimkdirbuild_openmmcdbuild_openmmsudoccmakei../OpenMM4.1Source#Pressctoconfigure#Pressgtogeneratecd..sudochownRcsnow:csnowbuild_openmmcdbuild_openmmmakej8maketest###Note:inbothinstalls,sometestsfail.sudomakeinstall
GROMACS
cd~/codewgetftp://ftp.gromacs.org/pub/gromacs/gromacs4.5.5.tar.gztarxvfzgromacs4.5.5.tar.gzmkdirbuild_gromacs_gpucdbuild_gromacs_gpuexportOPENMM_ROOT_DIR=/usr/local/openmmcmakeDGMX_OPENMM=ON../gromacs4.5.5makecleanmakemdrunsudomakeinstallmdruncd~/codemkdirbuild_gromacscdbuild_gromacscmake../gromacs4.5.5makecleanmakej8sudomakeinstallecho'exportPATH="$PATH:/usr/local/gromacs/bin"'>>~/code/sourceme_gromacs
DHFRBenchmark
wgethttp://www.gromacs.org/@api/deki/files/128/=gromacsgpubenchdhfr.tar.gzmv\=gromacsgpubenchdhfr.tar.gzgromacsgpubenchdhfr.tar.gztarxvfzgromacsgpubenchdhfr.tar.gz./build_gromacs_gpu/src/kernel/mdrungpusdhfr/GPU/dhfrimpl2nm.bench/topol.tprdeviceOpenMM:forcedevice=yes
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5/11/2015 GPUacceleratedmoleculardynamicsSHARPEN
http://sharpen.engr.colostate.edu/mediawiki/index.php/GPU_accelerated_molecular_dynamics 5/5
Troubleshooting
Programmdrungpu,VERSION4.6dev201205099f86610Sourcecodefile:/data/lucasj/code/gromacs/src/kernel/openmm_wrapper.cpp,line:1272Fatalerror:Therequestedplatform"CUDA"couldnotbefound.
Thisistheerrorwewerehavingonthe64bitsystembeforeweputalinkto/usr/local/cuda/lib64inplaceof/usr/local/cuda/lib.
Fatalerror:TheselectedGPU(#0,GeForce9600GT)isnotsupportedbyGromacs!MostprobablyyouhavealowendGPUwhichwouldnotperformwell,ornewhardwarethathasnotbeentestedwiththecurrentrelease.Ifyoustillwanttotryusingthedevice,usetheforcedevice=yesoption.
Thisistheerrorweget,forbothGPUcards,ifwedonotusetheforcedeviceoption.
Gromacs4.6
sudoaptgetinstallgitcd~/codegitclonegit://git.gromacs.org/gromacs.gitgromacs4.6mkdirbuild_gromacs4.6_gpucdbuild_gromacs4.6_gpucmakeDGMX_OPENMM=ON../gromacs4.6DCMAKE_INSTALL_PREFIX=/home/csnow/code/gromacs4.6_installmakemdrunmakeinstallmdrun
OpenMMPythonAsroot,incode/build_openmm2,makePythonInstall
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Thispagewaslastmodifiedon3June2012,at04:17.
