[torqueusers] "cp command failed"

Zhiliang Hu zhu at iastate.edu
Thu Dec 13 04:49:00 MST 2007


At 10:56 PM 12/12/2007, you wrote:

>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?

and 

At 11:06 PM 12/12/2007, Chris Samuel <csamuel at vpac.org> wrote:

>Looks like an application error message rather than a Torque error.
>
>It appears that blast is trying (and failing) to stage some files from 
>your RAID system to local scratch - but it's not saying why..


Yes indeed that's what appears.  Thanks for hints on mpiblast -- but 
the mpiblast.sh script works fine on its own.  I manually checked 
folders, permissions, ssh, etc on all suspected directives and 
everything appears fine as before.  As a matter of fact there are 
more than 10 similar files in the same location that got copied over,
no problem, so it appears "weird".

That's why I ask here -- (my first 3 lines in the post) -- any possible
known conflict when a working script and working qsub put together?

Thanks,
Zhiliang



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