Hello Szilárd Páll Thank you for you reply. I tried your command:
gmx mdrun -ntmpi 7 -npme 1 -nb gpu -pme gpu -bonded gpu -gpuid 0,2,4,6 -gputask 001122334 but got the following error information: Using 7 MPI threads Using 10 OpenMP threads per tMPI thread Program: gmx mdrun, version 2019.3 Source file: src/gromacs/taskassignment/taskassignment.cpp (line 255) Function: std::vector<std::vector<gmx::GpuTaskMapping> >::value_type gmx::runTaskAssignment(const std::vector<int>&, const std::vector<int>&, const gmx_hw_info_t&, const gmx::MDLogger&, const t_commrec*, const gmx_multisim_t*, const gmx::PhysicalNodeCommunicator&, const std::vector<gmx::GpuTask>&, bool, PmeRunMode) MPI rank: 0 (out of 7) Inconsistency in user input: There were 7 GPU tasks found on node localhost.localdomain, but 4 GPUs were available. If the GPUs are equivalent, then it is usually best to have a number of tasks that is a multiple of the number of GPUs. You should reconsider your GPU task assignment, number of ranks, or your use of the -nb, -pme, and -npme options, perhaps after measuring the performance you can get. Could you tell me how to correct this? Best regards, Yeping ------------------------------------------------------------------ Hi, You have 2x Xeon Gold 6150 which is 2x 18 = 36 cores; Intel CPUs support 2 threads/core (HyperThreading), hence the 72. https://ark.intel.com/content/www/us/en/ark/products/120490/intel-xeon-gold-6150-processor-24-75m-cache-2-70-ghz.html You will not be able to scale efficiently over 8 GPUs in a single simulation with the current code; while performance will likely improve in the next release, due to PCI bus and PME scaling limitations, even with GROMACS 2020 it is unlikely you will see much benefit beyond 4 GPUs. Try running on 3-4 GPUs with at least 2 ranks on each, and one separate PME rank. You might also want to use every second GPU rather than the first four to avoid overloading the PCI bus; e.g. gmx mdrun -ntmpi 7 -npme 1 -nb gpu -pme gpu -bonded gpu -gpuid 0,2,4,6 -gputask 001122334 Cheers, -- Szilárd -- 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.