[gmx-users] NaN error for mdrun-gpu
Hi! I have a Palit 3GB GTX 580 GPU card to simulate about ~ 140 000 atoms. However, after an mdrun-gpu simulation of 5000 timesteps (each time step = 0.002), the log file starts to show NaN in the energy values. How do I fix this? Regards, Adam ps. The same system runs well in a conventional CPU-based mdrun. So I don't think its due to the system blowing up. pps. The GPU card reaches a temperature of ~ 88 degrees celsius after 5 minutes of simulation. Could this be the problem? However, I have another GPU card (MSI 1.5GB GTX 580) that works well with a smaller system (100 000 atoms) even at 85 degrees celsius.-- 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] NaN error using mdrun-gpu
Hi! I have a Palit 3GB GTX 580 GPU card to simulate about ~ 140 000 atoms. However, after an mdrun-gpu simulation of 5000 timesteps (each time step = 0.002), the log file starts to show NaN in the energy values. How do I fix this? Regards, Adam ps. The same system runs well in a conventional CPU-based mdrun. So I don't think its due to the system blowing up. pps. The GPU card reaches a temperature of ~ 88 degrees celsius after 5 minutes of simulation. Could this be the problem? However, I have another GPU card (MSI 1.5GB GTX 580) that works well with a smaller system (100 000 atoms) even at 85 degrees celsius.-- 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] BornSum: cudaMalloc in CUDAStream::Allocate failed out of memory
Hi! I'm trying to run a mdrun-gpu simulation on a 64-bit Ubuntu system. I'm using a 15GB GTX 580 NVIDIA GPU card with all the appropriate drivers and cuda toolkit. However, when I run the command: mdrun-gpu -s inpufile.tpr -c inputfile.gro -x outputfile.xtc -g outputfile.log -nice - 0 I get the following error message: BornSum: cudaMalloc in CUDAStream::Allocate failed out of memory What is the problem? Is my 15GB GPU card insufficient for my 138596 atom system? Appreciate any help, Adam-- 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
