Hi,
Am 03.09.2014 um 12:17 schrieb Donato Pera:
> I'm using Rocks 5.4.3 with SGE 6.1 I installed
> a new version of openMPI 1.6.5 when I run
> a script using SGE+openMPI (1.6.5) in a single node
> I don't have any problems but when I try to use more nodes
> I get this error:
>
>
> A hostfile was provided that contains at least one node not
> present in the allocation:
>
> hostfile: /tmp/21202.1.parallel.q/machines
> node: compute-2-4
>
> 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.
Was Open MPI compiled with SGE support?
$ ompi_info | grep grid
MCA ras: gridengine (MCA v2.0, API v2.0, Component v1.6.5)
In this case you don't need to provide any -machinefile option at all, as Open
MPI will use the SGE generated one automatically.
(Nevertheless the $TMPDIR/machines should be correct - it could be an issue
between the short hostname and the FQDN - can you `cat` the $TMPDIR/machines in
a job script for curiosity - and the output of `hostname` on a node too
therein?).
> --------------------------------------------------------------------------
> rm: cannot remove `/tmp/21202.1.parallel.q/rsh': No such file or directory
> --------------------------------------------------------------------------
The above line comes from "stop_proc_args" defined in the "mpi" PE and can be
ignored. In fact: you don't need any "stop_proc_args" at all. Maybe you can
define a new PE solely for Open MPI, often called "orte":
https://www.open-mpi.org/faq/?category=sge
-- Reuti
> I send also my SGE script:
>
> #!/bin/bash
> #$ -S /bin/bash
> #$ -pe mpi 64
> #$ -cwd
> #$ -o ./file.out
> #$ -e ./file.err
>
> export LD_LIBRARY_PATH=/home/SWcbbc/openmpi-1.6.5/lib:$LD_LIBRARY_PATH
> export OMP_NUM_THREADS=1
>
> CPMD_PATH=/home/tanzi/myroot/X86_66intel-mpi/
> PP_PATH=/home/tanzi
>
> /home/SWcbbc/openmpi-1.6.5/bin/mpirun -np 64 -machinefile
> $TMPDIR/machines
> ${CPMD_PATH}cpmd.x input ${PP_PATH}/PP/ > out
>
>
> I don't understand my mistake
>
> Regards D.
>
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> Link to this post:
> http://www.open-mpi.org/community/lists/users/2014/09/25238.php
