Re: [gmx-users] gmx 2019 running problems
Hi, Thanks for the feed-backs. Yes, I could build gmx 2019 on a hosts running with nvidia driver 4.10 Tamas On 01/14/2019 09:06 PM, Tamas Hegedus wrote: Hi, I tried to install and use gmx 2019 on a single node computer with 4 GPUs. I think that the build was ok, but the running is... There is only workload on 4 cores (-nt 16) and there is no workload on the GPUs at all. gmx 2018 was deployed on the same computer with the same tools and libraries. CPU 16cores + 16threads GPU 1080Ti cmake -j 16 -DCMAKE_C_COMPILER=gcc-6 -DCMAKE_CXX_COMPILER=g++-6 -DCMAKE_INSTALL_PREFIX=$HOME/opt/gromacs-2019-gpu -DGMX_GPU=ON -DCMAKE_PREFIX_PATH=$HOME/opt/OpenBLAS-0.2.20 -DFFTWF_LIBRARY=$HOME/opt/fftw-3.3.7/lib/libfftw3f.so -DFFTWF_INCLUDE_DIR=$HOME/opt/fftw-3.3.7/include ../ | tee out.cmake -- Looking for NVIDIA GPUs present in the system -- Number of NVIDIA GPUs detected: 4 -- Found CUDA: /usr (found suitable version "9.1", minimum required is "7.0") make -j16 make -j16 install # note: a lot of building happened also in this step ** gmx mdrun -nt 16 -ntmpi 4 -gputasks 0123 -nb gpu -bonded gpu -pme gpu -npme 1 -pin on -v -deffnm md_2 -s md_2_500ns.tpr -cpi md_2.1.cpt -noappend +-+ | NVIDIA-SMI 390.48 Driver Version: 390.48 | |---+--+--+ | GPU NamePersistence-M| Bus-IdDisp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 GeForce GTX 108... Off | :02:00.0 Off | N/A | | 0% 28CP819W / 250W |179MiB / 11178MiB | 0% Default | +---+--+--+ | 1 GeForce GTX 108... Off | :03:00.0 Off | N/A | | 0% 28CP8 8W / 250W |179MiB / 11178MiB | 0% Default | +---+--+--+ | 2 GeForce GTX 108... Off | :83:00.0 Off | N/A | | 0% 28CP8 9W / 250W |179MiB / 11178MiB | 0% Default | +---+--+--+ | 3 GeForce GTX 108... Off | :84:00.0 Off | N/A | | 0% 27CP8 9W / 250W |237MiB / 11178MiB | 0% Default | +---+--+--+ +-+ | Processes: GPU Memory | | GPU PID Type Process name Usage | |=| |0 20243 C gmx 161MiB | |1 20243 C gmx 161MiB | |2 20243 C gmx 161MiB | |3 20243 C gmx 219MiB | +-+ Thanks for your suggestions, Tamas -- Tamas Hegedus, PhD Senior Research Fellow Department of Biophysics and Radiation Biology Semmelweis University | phone: (36) 1-459 1500/60233 Tuzolto utca 37-47| mailto:ta...@hegelab.org Budapest, 1094, Hungary | http://www.hegelab.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx 2019 running problems
Hi, On Mon, Jan 14, 2019 at 9:06 PM Tamas Hegedus wrote: > Hi, > > I tried to install and use gmx 2019 on a single node computer with 4 GPUs. > > I think that the build was ok, but the running is... > There is only workload on 4 cores (-nt 16) and > there is no workload on the GPUs at all. > Sounds like your driver might be incompatible with either the GPUs or the CUDA version found. Check out the log file written by mdrun, and probably plan to reinstall CUDA 10 and get the latest drivers. Mark > gmx 2018 was deployed on the same computer with the same tools and > libraries. > > CPU 16cores + 16threads > GPU 1080Ti > > cmake -j 16 -DCMAKE_C_COMPILER=gcc-6 -DCMAKE_CXX_COMPILER=g++-6 > -DCMAKE_INSTALL_PREFIX=$HOME/opt/gromacs-2019-gpu -DGMX_GPU=ON > -DCMAKE_PREFIX_PATH=$HOME/opt/OpenBLAS-0.2.20 > -DFFTWF_LIBRARY=$HOME/opt/fftw-3.3.7/lib/libfftw3f.so > -DFFTWF_INCLUDE_DIR=$HOME/opt/fftw-3.3.7/include ../ | tee out.cmake > > -- Looking for NVIDIA GPUs present in the system > -- Number of NVIDIA GPUs detected: 4 > -- Found CUDA: /usr (found suitable version "9.1", minimum required is > "7.0") > > make -j16 > make -j16 install # note: a lot of building happened also in this step > > ** > gmx mdrun -nt 16 -ntmpi 4 -gputasks 0123 -nb gpu -bonded gpu -pme gpu > -npme 1 -pin on -v -deffnm md_2 -s md_2_500ns.tpr -cpi md_2.1.cpt -noappend > > > +-+ > | NVIDIA-SMI 390.48 Driver Version: 390.48 > | > > |---+--+--+ > | GPU NamePersistence-M| Bus-IdDisp.A | Volatile > Uncorr. ECC | > | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util > Compute M. | > > |===+==+==| > | 0 GeForce GTX 108... Off | :02:00.0 Off | > N/A | > | 0% 28CP819W / 250W |179MiB / 11178MiB | 0% > Default | > > +---+--+--+ > | 1 GeForce GTX 108... Off | :03:00.0 Off | > N/A | > | 0% 28CP8 8W / 250W |179MiB / 11178MiB | 0% > Default | > > +---+--+--+ > | 2 GeForce GTX 108... Off | :83:00.0 Off | > N/A | > | 0% 28CP8 9W / 250W |179MiB / 11178MiB | 0% > Default | > > +---+--+--+ > | 3 GeForce GTX 108... Off | :84:00.0 Off | > N/A | > | 0% 27CP8 9W / 250W |237MiB / 11178MiB | 0% > Default | > > +---+--+--+ > > > > +-+ > | Processes: GPU > Memory | > | GPU PID Type Process name Usage > | > > |=| > |0 20243 C gmx > 161MiB | > |1 20243 C gmx > 161MiB | > |2 20243 C gmx > 161MiB | > |3 20243 C gmx > 219MiB | > > +-+ > > Thanks for your suggestions, > Tamas > > -- > Tamas Hegedus, PhD > Senior Research Fellow > MTA-SE Molecular Biophysics Research Group > Hungarian Academy of Sciences | phone: (36) 1-459 1500/60233 > Semmelweis University | fax: (36) 1-266 6656 > Tuzolto utca 37-47 | mailto:ta...@hegelab.org > Budapest, 1094, Hungary| http://www.hegelab.org > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx 2019 running problems
One other suggestion: from the PPA repository, install the Nvidia 410 driver. Your Cuda 9 install may work with the 410 driver but more likely you will need to reinstall. cuda If so, install the CUDA 10 toolkit, but DO NOT use the toolkit to install the driver when asked, it will revert to the Nvidia v384 driver Hope it works out for your monster Paul > On Jan 14, 2019, at 2:06 PM, Tamas Hegedus wrote: > > Hi, > > I tried to install and use gmx 2019 on a single node computer with 4 GPUs. > > I think that the build was ok, but the running is... > There is only workload on 4 cores (-nt 16) and > there is no workload on the GPUs at all. > > gmx 2018 was deployed on the same computer with the same tools and libraries. > > CPU 16cores + 16threads > GPU 1080Ti > > cmake -j 16 -DCMAKE_C_COMPILER=gcc-6 -DCMAKE_CXX_COMPILER=g++-6 > -DCMAKE_INSTALL_PREFIX=$HOME/opt/gromacs-2019-gpu -DGMX_GPU=ON > -DCMAKE_PREFIX_PATH=$HOME/opt/OpenBLAS-0.2.20 > -DFFTWF_LIBRARY=$HOME/opt/fftw-3.3.7/lib/libfftw3f.so > -DFFTWF_INCLUDE_DIR=$HOME/opt/fftw-3.3.7/include ../ | tee out.cmake > > -- Looking for NVIDIA GPUs present in the system > -- Number of NVIDIA GPUs detected: 4 > -- Found CUDA: /usr (found suitable version "9.1", minimum required is "7.0") > > make -j16 > make -j16 install # note: a lot of building happened also in this step > > ** > gmx mdrun -nt 16 -ntmpi 4 -gputasks 0123 -nb gpu -bonded gpu -pme gpu -npme 1 > -pin on -v -deffnm md_2 -s md_2_500ns.tpr -cpi md_2.1.cpt -noappend > > +-+ > | NVIDIA-SMI 390.48 Driver Version: 390.48 | > |---+--+--+ > | GPU NamePersistence-M| Bus-IdDisp.A | Volatile Uncorr. ECC > | > | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | > |===+==+==| > | 0 GeForce GTX 108... Off | :02:00.0 Off | N/A | > | 0% 28CP819W / 250W |179MiB / 11178MiB | 0% Default | > +---+--+--+ > | 1 GeForce GTX 108... Off | :03:00.0 Off | N/A | > | 0% 28CP8 8W / 250W |179MiB / 11178MiB | 0% Default | > +---+--+--+ > | 2 GeForce GTX 108... Off | :83:00.0 Off | N/A | > | 0% 28CP8 9W / 250W |179MiB / 11178MiB | 0% Default | > +---+--+--+ > | 3 GeForce GTX 108... Off | :84:00.0 Off | N/A | > | 0% 27CP8 9W / 250W |237MiB / 11178MiB | 0% Default | > +---+--+--+ > > +-+ > | Processes: GPU Memory > | > | GPU PID Type Process name Usage > | > |=| > |0 20243 C gmx 161MiB | > |1 20243 C gmx 161MiB | > |2 20243 C gmx 161MiB | > |3 20243 C gmx 219MiB | > +-+ > > Thanks for your suggestions, > Tamas > > -- > Tamas Hegedus, PhD > Senior Research Fellow > MTA-SE Molecular Biophysics Research Group > Hungarian Academy of Sciences | phone: (36) 1-459 1500/60233 > Semmelweis University | fax: (36) 1-266 6656 > Tuzolto utca 37-47 | mailto:ta...@hegelab.org > Budapest, 1094, Hungary| http://www.hegelab.org > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx 2019 running problems
Tamas I’ve the same build as you (almost… 2 gpus ) I found good results using one change : from -nt 16 to-ntomp 4 which should map the GPU’s and tasks in the same manner, but may be handled differently by mdrun. These two versions run with different efficiency on my rig. Paul > On Jan 14, 2019, at 2:06 PM, Tamas Hegedus wrote: > > Hi, > > I tried to install and use gmx 2019 on a single node computer with 4 GPUs. > > I think that the build was ok, but the running is... > There is only workload on 4 cores (-nt 16) and > there is no workload on the GPUs at all. > > gmx 2018 was deployed on the same computer with the same tools and libraries. > > CPU 16cores + 16threads > GPU 1080Ti > > cmake -j 16 -DCMAKE_C_COMPILER=gcc-6 -DCMAKE_CXX_COMPILER=g++-6 > -DCMAKE_INSTALL_PREFIX=$HOME/opt/gromacs-2019-gpu -DGMX_GPU=ON > -DCMAKE_PREFIX_PATH=$HOME/opt/OpenBLAS-0.2.20 > -DFFTWF_LIBRARY=$HOME/opt/fftw-3.3.7/lib/libfftw3f.so > -DFFTWF_INCLUDE_DIR=$HOME/opt/fftw-3.3.7/include ../ | tee out.cmake > > -- Looking for NVIDIA GPUs present in the system > -- Number of NVIDIA GPUs detected: 4 > -- Found CUDA: /usr (found suitable version "9.1", minimum required is "7.0") > > make -j16 > make -j16 install # note: a lot of building happened also in this step > > ** > gmx mdrun -nt 16 -ntmpi 4 -gputasks 0123 -nb gpu -bonded gpu -pme gpu -npme 1 > -pin on -v -deffnm md_2 -s md_2_500ns.tpr -cpi md_2.1.cpt -noappend > > +-+ > | NVIDIA-SMI 390.48 Driver Version: 390.48 | > |---+--+--+ > | GPU NamePersistence-M| Bus-IdDisp.A | Volatile Uncorr. ECC > | > | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | > |===+==+==| > | 0 GeForce GTX 108... Off | :02:00.0 Off | N/A | > | 0% 28CP819W / 250W |179MiB / 11178MiB | 0% Default | > +---+--+--+ > | 1 GeForce GTX 108... Off | :03:00.0 Off | N/A | > | 0% 28CP8 8W / 250W |179MiB / 11178MiB | 0% Default | > +---+--+--+ > | 2 GeForce GTX 108... Off | :83:00.0 Off | N/A | > | 0% 28CP8 9W / 250W |179MiB / 11178MiB | 0% Default | > +---+--+--+ > | 3 GeForce GTX 108... Off | :84:00.0 Off | N/A | > | 0% 27CP8 9W / 250W |237MiB / 11178MiB | 0% Default | > +---+--+--+ > > +-+ > | Processes: GPU Memory > | > | GPU PID Type Process name Usage > | > |=| > |0 20243 C gmx 161MiB | > |1 20243 C gmx 161MiB | > |2 20243 C gmx 161MiB | > |3 20243 C gmx 219MiB | > +-+ > > Thanks for your suggestions, > Tamas > > -- > Tamas Hegedus, PhD > Senior Research Fellow > MTA-SE Molecular Biophysics Research Group > Hungarian Academy of Sciences | phone: (36) 1-459 1500/60233 > Semmelweis University | fax: (36) 1-266 6656 > Tuzolto utca 37-47 | mailto:ta...@hegelab.org > Budapest, 1094, Hungary| http://www.hegelab.org > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gmx 2019 running problems
Hi, I tried to install and use gmx 2019 on a single node computer with 4 GPUs. I think that the build was ok, but the running is... There is only workload on 4 cores (-nt 16) and there is no workload on the GPUs at all. gmx 2018 was deployed on the same computer with the same tools and libraries. CPU 16cores + 16threads GPU 1080Ti cmake -j 16 -DCMAKE_C_COMPILER=gcc-6 -DCMAKE_CXX_COMPILER=g++-6 -DCMAKE_INSTALL_PREFIX=$HOME/opt/gromacs-2019-gpu -DGMX_GPU=ON -DCMAKE_PREFIX_PATH=$HOME/opt/OpenBLAS-0.2.20 -DFFTWF_LIBRARY=$HOME/opt/fftw-3.3.7/lib/libfftw3f.so -DFFTWF_INCLUDE_DIR=$HOME/opt/fftw-3.3.7/include ../ | tee out.cmake -- Looking for NVIDIA GPUs present in the system -- Number of NVIDIA GPUs detected: 4 -- Found CUDA: /usr (found suitable version "9.1", minimum required is "7.0") make -j16 make -j16 install # note: a lot of building happened also in this step ** gmx mdrun -nt 16 -ntmpi 4 -gputasks 0123 -nb gpu -bonded gpu -pme gpu -npme 1 -pin on -v -deffnm md_2 -s md_2_500ns.tpr -cpi md_2.1.cpt -noappend +-+ | NVIDIA-SMI 390.48 Driver Version: 390.48 | |---+--+--+ | GPU NamePersistence-M| Bus-IdDisp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 GeForce GTX 108... Off | :02:00.0 Off | N/A | | 0% 28CP819W / 250W |179MiB / 11178MiB | 0% Default | +---+--+--+ | 1 GeForce GTX 108... Off | :03:00.0 Off | N/A | | 0% 28CP8 8W / 250W |179MiB / 11178MiB | 0% Default | +---+--+--+ | 2 GeForce GTX 108... Off | :83:00.0 Off | N/A | | 0% 28CP8 9W / 250W |179MiB / 11178MiB | 0% Default | +---+--+--+ | 3 GeForce GTX 108... Off | :84:00.0 Off | N/A | | 0% 27CP8 9W / 250W |237MiB / 11178MiB | 0% Default | +---+--+--+ +-+ | Processes: GPU Memory | | GPU PID Type Process name Usage | |=| |0 20243 C gmx 161MiB | |1 20243 C gmx 161MiB | |2 20243 C gmx 161MiB | |3 20243 C gmx 219MiB | +-+ Thanks for your suggestions, Tamas -- Tamas Hegedus, PhD Senior Research Fellow MTA-SE Molecular Biophysics Research Group Hungarian Academy of Sciences | phone: (36) 1-459 1500/60233 Semmelweis University | fax: (36) 1-266 6656 Tuzolto utca 37-47 | mailto:ta...@hegelab.org Budapest, 1094, Hungary| http://www.hegelab.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
