[gmx-users] MPI oversubscription
gmx3 at hotmail.com
Tue Feb 5 13:30:02 CET 2013
This looks like our CPU detection code failed and the result is not handled properly.
What hardware are you running on?
Could you mail the 10 lines from the md.log file following: "Detecting CPU-specific acceleration."?
> Date: Tue, 5 Feb 2013 11:38:53 +0100
> From: hypolit at googlemail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] MPI oversubscription
> 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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