[gmx-users] Cuda not detected
Hey, I am playing with the gpu version of mdrun and could make it run with: ~/gromacs/gpu/bin/mdrun-gpu -s topol.tpr -device OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes However after reboot of the machine ( which is a testing machine) I get the following error: --- Program mdrun-gpu, VERSION 4.5.5 Source code file: /home/weber/gromacs/gromacs-4.5.5_gpu/src/kernel/ openmm_wrapper.cpp, line: 1272 Fatal error: The requested platform Cuda could not be found. echo $LD_LIBRARY_PATH:/opt/software/ganglia-3.1.7/lib64:/opt/software/ htop-0.8.3:/usr/local/cuda/lib64:/usr/local/cuda/lib:/home/weber/ OpenMM3.1.1-Linux64/lib echo $PATH/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/usr/games:/usr/ lib64/jvm/jre/bin:/opt/software/nvidia/3.2.16/cuda/bin:/opt/software/ ganglia-3.1.7/bin:/opt/software/htop-0.8.3/bin:/usr/lib/mit/bin:/usr/ lib/mit/sbin:.:/usr/local/cuda/bin:/home/weber/cmake-2.8.6/bin I run a simple gpu test program and it works. I believe something is not linked correctly, maybe someone can give me a hint. Thank You Andrzej -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Cuda not detected
try nvidia-smi -a to see whether the GPU card has been correctly configured. This happens on my GPU node. Every time I reboot the computer, I must reconfigure the GPU cards with nvidia-smi -a using root account. Ye 2011-11-17 From： Andrzej Rzepiela Date： 2011-11-17 21:01:07 To： gmx-users CC： Subject： [gmx-users] Cuda not detected Hey, I am playing with the gpu version of mdrun and could make it run with: ~/gromacs/gpu/bin/mdrun-gpu -s topol.tpr -device OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes However after reboot of the machine ( which is a testing machine) I get the following error: --- Program mdrun-gpu, VERSION 4.5.5 Source code file: /home/weber/gromacs/gromacs-4.5.5_gpu/src/kernel/ openmm_wrapper.cpp, line: 1272 Fatal error: The requested platform Cuda could not be found. echo $LD_LIBRARY_PATH:/opt/software/ganglia-3.1.7/lib64:/opt/software/ htop-0.8.3:/usr/local/cuda/lib64:/usr/local/cuda/lib:/home/weber/ OpenMM3.1.1-Linux64/lib echo $PATH/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/usr/games:/usr/ lib64/jvm/jre/bin:/opt/software/nvidia/3.2.16/cuda/bin:/opt/software/ ganglia-3.1.7/bin:/opt/software/htop-0.8.3/bin:/usr/lib/mit/bin:/usr/ lib/mit/sbin:.:/usr/local/cuda/bin:/home/weber/cmake-2.8.6/bin I run a simple gpu test program and it works. I believe something is not linked correctly, maybe someone can give me a hint. Thank You Andrzej -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Cuda not detected
On 11/17/11 10:10 PM, Andrzej Rzepiela wrote: Hey, thank you for the hint. I just finished the tests. The machine is Intel xeon R, 12 cores , 4 Teslas M2090 and 96 gb of memory. I used the most demanding PME dhfr benchmark system ( 7000w + protein) and obtained the following results: 1 cpu core run: 2.135 ns a day 12 cpu cores run: 21.478 ns a day 1 gpu unit run ( how many cpu cores are used, one ? ): 13.0 ns/day 4 parallel gpu runs on the node, performance: 12.884, 10.296, 8.290 and 6.953 ns/day, which is on average about 9.6 ns for one gpu. From your experience, are this expected numbers ? From the benchmarks on the website I had e feeling that the gpu runs will be faster. GPU is faster with implicit solvent and other constraints up to now. They are optimizing everything for the next version of gromacs http://www.gromacs.org/Developer_Zone/Roadmap/GROMACS_4.6 More detailed info on the gromacs manual. -- Gianluca Santoni, Institut de Biologie Structurale 41 rue Horowitz Grenoble _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
