Dear Gromacs users, I installed Gromacs 5.1.3. on GPU in Rocks cluster system.
After using command: gmx_mpi mdrun -nb gpu -v -deffnm old_gpu, I encountered with: ============================================================= GROMACS: gmx mdrun, VERSION 5.1.3 Executable: /home/karami_leila1/513/gromacs/bin/gmx_mpi Data prefix: /home/karami_leila1/513/gromacs Command line: gmx_mpi mdrun -nb gpu -v -deffnm new_gpu Running on 1 node with total 96 cores, 192 logical cores, 3 compatible GPUs Hardware detected on host cschpc.ut.ac.ir (the node of MPI rank 0): CPU info: Vendor: GenuineIntel Brand: Intel(R) Xeon(R) CPU E7-8890 v4 @ 2.20GHz SIMD instructions most likely to fit this hardware: AVX2_256 SIMD instructions selected at GROMACS compile time: AVX2_256 GPU info: Number of GPUs detected: 3 #0: NVIDIA TITAN X (Pascal), compute cap.: 6.1, ECC: no, stat: compatible #1: NVIDIA Tesla K40c, compute cap.: 3.5, ECC: no, stat: compatible #2: NVIDIA Tesla K40c, compute cap.: 3.5, ECC: no, stat: compatible Reading file new_gpu.tpr, VERSION 5.1.3 (single precision) Using 1 MPI process Using 192 OpenMP threads 3 compatible GPUs are present, with IDs 0,1,2 1 GPU auto-selected for this run. Mapping of GPU ID to the 1 PP rank in this node: 0 NOTE: potentially sub-optimal launch configuration, gmx_mpi started with less PP MPI process per node than GPUs available. Each PP MPI process can use only one GPU, 1 GPU per node will be used. ------------------------------------------------------- Program gmx mdrun, VERSION 5.1.3 Source code file: /root/gromacs_source/gromacs-5.1.3/src/programs/mdrun/resource-division.cpp, line: 571 Fatal error: Your choice of 1 MPI rank and the use of 192 total threads leads to the use of 192 OpenMP threads, whereas we expect the optimum to be with more MPI ranks with 2 to 6 OpenMP threads. If you want to run with this many OpenMP threads, specify the -ntomp option. But we suggest to increase the number of MPI ranks. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- Halting program gmx mdrun -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. ============================================================= How to resolve this problem? Any help will be highly appreciated. -- 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.