A hostfile was provided that contains at least one node not

        Re: [OMPI users] Problem running an MPI program through the PBS manager
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

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