Re: MPI on linux Exit status=1
Nick,
There is also a run#.log file that shows the parallelization as it occurs. You
can verify that the running is working as expected by looking at the file and
seeing that parts of the data are being sent out to the nodes and back. We also
use SGE with linux for parallel runs and have not had any major issues.
Bill
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Quoted reply history
On Friday, September 28, 2012 at 7:41 AM, Elassaiss - Schaap, J (Jeroen) wrote:
> Hi Nick,
>
> We have a working nm7 parallel setup using MPI on linux over our SGE cluster.
> Based on your e-mail I found a match somewhere in the SGE stdout capture:
>
> CREATING MUMODEL ROUTINE...
> Recompiling certain components
>
> USING PARALLEL PROFILE mpihydra.pnm
> MPI TRANSFER TYPE SELECTED
> Exit status = 1
> IN MPI
> Starting MPI version of nonmem execution ...
>
> And thereafter I had a decent parallel run. Does the system create
> subdirectories for each worker etc in your situation?
> You might also want to look for this kind of statement in nonmem's report:
> #PARA: PARAFILE=mpihydra.pnm, PROTOCOL=MPI, NODES= 16
>
> Hope this helps,
> Jeroen
>
> J. Elassaiss-Schaap Senior Principal Scientist Phone: + 31 412 66 9320
> MSD | PK, PD and Drug Metabolism | Clinical PK-PD Mail stop KR 4406 | PO Box
> 20, 5340 BH Oss, NL
>
>
>
> -----Original Message-----
> From: [email protected] [mailto:[email protected]] On
> Behalf Of Nick Holford
> Sent: Friday, September 28, 2012 10:25
> To: nmusers
> Subject: [NMusers] MPI on linux Exit status=1
>
> Hi,
>
> I'm trying to help our local grid computing guys to get NONMEM running
> with MPI on a Linux based grid.
>
> We have NONMEM running with a pnm file asking for 8 nodes but the actual
> run time is 10% longer than with a regular 'transfer' run. The only clue
> I can see to the problem is the "Exit status=1" after the "MPI TRANSFER
> TYPE SELECTED" message. The NONMEM runs appears to execute OK except for
> no evidence that MPI is operating. Can anybody tell me if this exit
> status is normal under Linux? If not what might it mean?
>
> Nick
>
> Recompiling certain components
>
> USING PARALLEL PROFILE wfn_mpi8.pnm
> MPI TRANSFER TYPE SELECTED
> Exit status = 1
> IN MPI
> Starting MPI version of nonmem execution ...
>
> --
> Nick Holford, Professor Clinical Pharmacology
> Dept Pharmacology & Clinical Pharmacology, Bldg 503 Room 302A
> University of Auckland,85 Park Rd,Private Bag 92019,Auckland,New Zealand
> tel:+64(9)923-6730 fax:+64(9)373-7090 mobile:+64(21)46 23 53
> email: [email protected] (mailto:[email protected])
> http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
>
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