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 > > >
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