Download - GPU Accelerated Molecular Dynamics - SHARPEN

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



###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



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



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



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.