[torqueusers] "cp command failed"

Garrick Staples garrick at usc.edu
Wed Dec 12 21:56:31 MST 2007


On Wed, Dec 12, 2007 at 10:57:59PM -0600, Zhiliang Hu alleged:
> Let me re-phrase this problem --
> 
> 1- I can "qsub" to run a "hello" program,
> 2- I can run "mpiblast" with a script,
> 3- but when combine the two I encounter a weird problem:
> 
> > qsub -l nodes=6:ppn=2 mpiblast.sh
> -- Where "mpiblast.sh" contains:
> ----------------
> #!/bin/bash
> /opt/openmpi.gcc/bin/mpirun /usr/local/bin/mpiblast -p blastn -i /home/zhu/tests/mpiblast/datain4 -d bta.genome.chr
> ----------------
> 
> Now it complains (in the torque output file xxxx.e96):
> 
> ----------------------
> cp command failed!
> command: cp /raid/pub/ncbi/blast/mpidb/bta.genome.chr.007.nhr /scratch/tmp/bta.genome.chr.007.nhr
> source = /raid/pub/ncbi/blast/mpidb/bta.genome.chr.007.nhr
> dest = /scratch/tmp/bta.genome.chr.007.nhr
> ret_value = 32512
> ----------------------
> 
> Any idea what could this be?

It doesn't look a torque error.  Is that coming from mpiblast, or your script?
Do both of those directories exist on the compute node?

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