OK thank you very much. It is now running... Regards, Mahmood
On Mon, Sep 26, 2016 at 2:04 PM, Gilles Gouaillardet < gilles.gouaillar...@gmail.com> wrote: > Mahmood, > > The node is defined in the PBS config, however it is not part of the > allocation (e.g. job) so it cannot be used, and hence the error message. > > In your PBS script, you do not need -np nor -host parameters to your > mpirun command. > Open MPI mpirun will automatically detect it is launched from a PBS job, > and get the needed information directly from PBS. > > FWIW, the list of allocated nodes is in the file $PBS_NODEFILE, but you > should not need that. > > Cheers, > > Gilles > > > On Monday, September 26, 2016, Mahmood Naderan <mahmood...@gmail.com> > wrote: > >> Hi, >> When I run an MPI command through the terminal the programs runs fine on >> the compute node specified in hosts.txt. >> >> However, when I put that command in a PBS script, if says that the >> compute node is not defined in the job manager's list. However, that node >> is actually defined in the job manager. >> >> Please see the output below >> >> >> mahmood@cluster:tran-bt-o-40$ cat submit.tor >> #!/bin/bash >> #PBS -V >> #PBS -q default >> #PBS -j oe >> #PBS -l nodes=1:ppn=15 >> #PBS -N job-1 >> #PBS -o /home/mahmood/tran-bt-o-40/cc-bt-cc-163-20.out >> cd $PBS_O_WORKDIR >> /share/apps/computer/openmpi-2.0.0/bin/mpirun -hostfile hosts.txt -np 15 >> /share/apps/chemistry/siesta-4.0/tpar/transiesta < >> trans-cc-bt-cc-163-20.fdf >> mahmood@cluster:tran-bt-o-40$ cat cc-bt-cc-163-20.out >> ------------------------------------------------------------ >> -------------- >> A hostfile was provided that contains at least one node not >> present in the allocation: >> >> hostfile: hosts.txt >> node: compute-0-1 >> >> If you are operating in a resource-managed environment, then only >> nodes that are in the allocation can be used in the hostfile. You >> may find relative node syntax to be a useful alternative to >> specifying absolute node names see the orte_hosts man page for >> further information. >> ------------------------------------------------------------ >> -------------- >> mahmood@cluster:tran-bt-o-40$ cat hosts.txt >> compute-0-1 >> compute-0-2 >> mahmood@cluster:tran-bt-o-40$ pbsnodes -l all >> compute-0-0 down >> compute-0-1 free >> compute-0-2 free >> compute-0-3 free >> >> >> >> As you can see, compute-0-1 has free cores and it is defined for the >> manager. >> >> Any idea? >> Regards, >> Mahmood >> >> >> > _______________________________________________ > users mailing list > users@lists.open-mpi.org > https://rfd.newmexicoconsortium.org/mailman/listinfo/users >
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