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

[Mahmood Naderan]

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


***@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 $PBS_O_WORKDIR
/share/apps/computer/openmpi-2.0.0/bin/mpirun -hostfile hosts.txt -np 15
/share/apps/chemistry/siesta-4.0/tpar/transiesta < trans-cc-bt-cc-163-20.fdf
***@cluster:tran-bt-o-40$ 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.
--------------------------------------------------------------------------
***@cluster:tran-bt-o-40$ cat hosts.txt
compute-0-1
compute-0-2
***@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

[Gilles Gouaillardet]

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

Post by Mahmood Naderan
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
#!/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
--------------------------------------------------------------------------
A hostfile was provided that contains at least one node not
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.
--------------------------------------------------------------------------
compute-0-1
compute-0-2
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

[Mahmood Naderan]

OK thank you very much. It is now running...

Regards,
Mahmood



On Mon, Sep 26, 2016 at 2:04 PM, Gilles Gouaillardet <

Post by Gilles Gouaillardet
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

Post by Mahmood Naderan
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
#!/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
------------------------------------------------------------
--------------
A hostfile was provided that contains at least one node not
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.
------------------------------------------------------------
--------------
compute-0-1
compute-0-2
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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