[gmx-users] problem: gromacs run on gpu

leila karami karami.leila1 at gmail.com
Fri Jul 7 13:13:55 CEST 2017

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:
    #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
      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:
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.

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