Hi, thanks for this information. I wonder if PME offload has been implemented for more than one node simulations? I tried the following command for running on two nodes (with 4 ranks each and 4 OpenMP threads)
mpirun -np 8 gmx_mpi mdrun -nb gpu -pme gpu -npme 1 -ntomp 4 -dlb yes the log files when the simulation finishes says: On 7 MPI ranks doing PP, each using 4 OpenMP threads, and on 1 MPI rank doing PME, using 4 OpenMP threads Thus, it seems that only 1 PME rank (on a single node was offloaded)? El mié., 6 feb. 2019 a las 15:42, Kevin Boyd (<kevin.b...@uconn.edu>) escribió: > Hi, > > Your log file will definitely tell you whether PME was offloaded. > > The performance gains depend on your hardware, particularly the CPU/GPU > balance. There have been a number of threads on this forum discussing this > topic, if you search back through the gmx_user archives. The gist of it is > that with you can balance a good GPU with ~4 CPU cores, though that's > dependent on the CPU quality as well. > > The docs in Gromacs 2019 have been updated to include examples on running > PME on GPUs > http://manual.gromacs.org/current/user-guide/mdrun-performance.html > Search for "-pme gpu". The examples should mostly apply if you're using > Gromacs 2018 as well (although you won't have the -bonded options). > > Kevin > > > On Wed, Feb 6, 2019 at 9:29 AM jing liang <jingliang2...@gmail.com> wrote: > > > Hello, > > > > I understood from the documentation: > > > > > > > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmanual.gromacs.org%2Fdocumentation%2F2018-current%2Fuser-guide%2Fmdrun-performance.html&data=02%7C01%7Ckevin.boyd%40uconn.edu%7Caec25493f30d483d29e008d68c3f8aad%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636850601922827903&sdata=QvfmUT6Ua70zXuDezkO%2Bzunj8WX72qyGBpQvcIRm%2BgA%3D&reserved=0 > > > > that PME can be now offloaded to GPUs in v2018. I'm using SLURM in a > > machine with 24 > > cores, I wonder if the following script would be able to offload PME to > > GPUs > > > > #SBATCH -n 2 > > #SBATCH -c 12 > > #SBATCH --gpu:2 > > > > slurun gmx_mpi mdrun -ntomp 12 -npme 0 -dlb yes -v -deffnm step1 > > > > Is there some information in the log files which can allow me to see if > PME > > has been > > offloaded and what was the performance gain upon using GPUs? > > > > Thanks. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%7C01%7Ckevin.boyd%40uconn.edu%7Caec25493f30d483d29e008d68c3f8aad%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636850601922837913&sdata=W9R%2BATbN5LSgPIdhIxzxUIZ1q5aW9SaVXHmSUbMwgIw%3D&reserved=0 > > before posting! > > > > * Can't post? Read > > > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&data=02%7C01%7Ckevin.boyd%40uconn.edu%7Caec25493f30d483d29e008d68c3f8aad%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636850601922837913&sdata=7HobuqWxVukzkfhWJMv1XLxNqDvHWVkfkQktV49ncaQ%3D&reserved=0 > > > > * For (un)subscribe requests visit > > > > > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&data=02%7C01%7Ckevin.boyd%40uconn.edu%7Caec25493f30d483d29e008d68c3f8aad%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636850601922837913&sdata=4QOcG5jH%2BnoNwiAjdReKq4hWmuDy7zVweAA2yPVzR%2Bg%3D&reserved=0 > > 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. > -- 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.