[gmx-users] Trouble running 4.6.4. on cpu+gpu but not on gpu alone

rajat desikan rajatdesikan at gmail.com
Tue Dec 10 10:30:59 CET 2013

Dear all,
I recently installed gromacs 4.6.4 on our cluster. The configuration is 12
cpus and 2 gpus per node. The build details are given below.

I am able to run gromacs on the 2 gpus alone. However, running a job with
cpu+gpu fails with a fatal error (given below).

Gromacs build:


*Job1) Pure GPUs:Running*


mpirun  –np 2 mdrun-mpi  ./

running on 2 GPU cards of the same node.

*Job2) CPU+GPUs:Crashed*


mpirun  –np 12 mdrun-mpi

FATAL error

“Using 12 MPI processes

Using 2 OpenMP threads per MPI process

Compiled acceleration: SSE2 (Gromacs could use SSE4.1 on this machine,
which is better)

2 GPUs detected on host cn1.local:

  #0: NVIDIA Tesla M2090, compute cap.: 2.0, ECC:  no, stat: compatible

  #1: NVIDIA Tesla M2090, compute cap.: 2.0, ECC:  no, stat: compatible

2 GPUs auto-selected for this run.

Mapping of GPUs to the 12 PP ranks in this node: #0, #1


Program mdrun_mpi, VERSION 4.6.4

Source code file:
/home/rajat/softback/gromacs-4.6.4/src/gmxlib/gmx_detect_hardware.c, line:

Fatal error:

Incorrect launch configuration: mismatching number of PP MPI processes and
GPUs per node.

mdrun_mpi was started with 12 PP MPI processes per node, but only 2 GPUs
were detected.
For more information and tips for troubleshooting, please check the GROMACS”

Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore

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