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From: Tim Prins (tprins_at_[hidden])
Date: 2007-04-01 09:49:42


Hi Barry,

The problem is the line:
ncpus=`wc -l $PBS_NODEFILE`

wc will print out the file name after the count. So ncpus gets "16 /
var/spool/torque/aux//350.wc01" and your mpirun command will look like:
mpirun -np 16 /var/spool/torque/aux//350.wc01 /home/test/hpcc-1.0.0/hpcc

So mpirun will try to execute /var/spool/torque/aux//350.wc01

A solution to this is that Open MPI will run on every available slot
if -np is not passed. So you could just use the script:

HPCC_HOME=/home/test/hpcc-1.0.0
mpirun $HPCC_HOME/hpcc

This will launch one process on every CPU reported by Torque.

Alternatively, you could have wc read from stdin instead of from a file:
ncpus=`wc -l < $PBS_NODEFILE`

this will avoid the filename being printed.

Hope this helps,

Tim

On Apr 1, 2007, at 9:16 AM, Barry Evans wrote:

> Hello,
>
>
>
> Having a bit of trouble running Open MPI 1.2 under Torque 2.1.8.
>
>
>
> My Script contains the following:
>
> -----------------------------------------------
>
> HPCC_HOME=/home/test/hpcc-1.0.0
>
> ncpus=`wc -l $PBS_NODEFILE`
>
> mpirun -np $ncpus $HPCC_HOME/hpcc
>
> -----------------------------------------------
>
>
>
>
>
> When I try to run on 4 nodes, 4 cpus each I receive the following
> in my err file:
>
>
>
> [node003:04409] [0,0,4] ORTE_ERROR_LOG: Not found in file
> odls_default_module.c at line 1188
>
> [node008:06691] [0,0,1] ORTE_ERROR_LOG: Not found in file
> odls_default_module.c at line 1188
>
> [node007:04352] [0,0,2] ORTE_ERROR_LOG: Not found in file
> odls_default_module.c at line 1188
>
> ----------------------------------------------------------------------
> ----
>
> Failed to find or execute the following executable:
>
>
>
> Host: node007
>
> Executable: /var/spool/torque/aux//350.wc01
>
>
>
> Cannot continue.
>
> ----------------------------------------------------------------------
> ----
>
> [no-------------------------------------------------------------------
> -------
>
> Failed to find or execute the following executable:
>
>
>
> Host: node004
>
> Executable: /var/spool/torque/aux//350.wc01
>
>
>
> Cannot continue.
>
> ----------------------------------------------------------------------
> ----
>
> de004:04364] [0,0,3] ORTE_ERROR_LOG: Not found in file
> odls_default_module.c at line 1188
>
> ----------------------------------------------------------------------
> ----
>
> Failed to find or execute the following executable:
>
>
>
> Host: node003
>
> Executable: /var/spool/torque/aux//350.wc01
>
>
>
> Cannot continue.
>
> ----------------------------------------------------------------------
> ----
>
> ----------------------------------------------------------------------
> ----
>
> Failed to find or execute the following executable:
>
>
>
> Host: node008
>
> Executable: /var/spool/torque/aux//350.wc01
>
>
>
> Cannot continue.
>
> ----------------------------------------------------------------------
> ----
>
> [node007:04352] [0,0,2] ORTE_ERROR_LOG: Not found in file orted.c
> at line 588
>
> [node008:06691] [0,0,1] ORTE_ERROR_LOG: Not found in file orted.c
> at line 588
>
> [node004:04364] [0,0,3] ORTE_ERROR_LOG: Not found in file orted.c
> at line 588
>
> [node003:04409] [0,0,4] ORTE_ERROR_LOG: Not found in file orted.c
> at line 588
>
>
>
>
>
> Has anyone seen this before? It seems odd that openmpi would be
> trying to execute what is effectively the host file. I stuck a
> sleep in to make sure the file was being distributed, and sure
> enough, it was there. I am able to run mvapich through torque
> without issue and openmpi from the command line.
>
>
>
> Cheers,
>
> Barry Evans
>
> Technical Manager
>
> OCF plc
>
> +44 (0)7970 148 121
>
> bevans_at_[hidden]
>
>
>
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