[gmx-users] MPI oversubscription

Christian H. hypolit at googlemail.com
Tue Feb 5 11:38:53 CET 2013


I am using the latest git version of gromacs, compiled with gcc 4.6.2 and
openmpi 1.6.3.
I start the program using the usual mpirun -np 8 mdrun_mpi ...
This always leads to a warning:

Using 1 MPI process
WARNING: On node 0: oversubscribing the available 0 logical CPU cores per
node with 1 MPI processes.

Checking the processes confirms that there is only one of the 8 available
cores used.
Running mdrun_mpi with an additional debug -1:

Detected 0 processors, will use this as the number of supported hardware
hw_opt: nt 0 ntmpi 0 ntomp 1 ntomp_pme 1 gpu_id ''
0 CPUs detected, but 8 was returned by CPU_COUNTIn gmx_setup_nodecomm:
hostname 'myComputerName', hostnum 0
0 CPUs detected, but 8 was returned by CPU_COUNTOn rank  0, thread  0, core
 0 the affinity setting returned 0

I also made another try by compiling  gromacs using some experimental
version of gcc 4.8, which did not help in this case.
Is this a known problem? Obviously gromacs detects the right value with
CPU_COUNT, why is it not just taking that value?

Best regards,

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