[Bioclusters] new on using clusters: problem running mpiblast

[Aaron Darling]

Hi Zhiliang,

the command-line looks reasonable, does mpiblast generate any additional 
output when the --debug option is added to the command-line?
Is the /usr/local/bin filesystem replicated on each node?  i.e. does 
every node have a copy of mpiblast located at /usr/local/bin/mpiblast?
I personally have not tested mpiBLAST with OpenMPI, although mpiBLAST 
doesn't do anything too fancy with MPI so it really ought to work. 

-Aaron


Zhiliang Hu wrote:
> I am new on using clusters.
>
> I have just installed mpiblast 1.4.0 with ncbi toolbox (June 2005)
> from source codes on a linux cluster [x86_64/x86_64 (GNU/Linux), CentOS].
> The installation seemed to be successful.
>
> Now when I try the following:
>
> > /opt/openmpi.gcc/bin/mpirun -np 14
>       /usr/local/bin/mpiblast -p blastn
>                               -i /raid/pub/ncbi/blast/db/BTrsSNP
>                               -d bta.genome.chr
>                               -o out1
>                               -e 0.0000000001
>                               -W 38 -v 1 -b 1
>
> and immediately got following errors:
> ----------------
> MPI_ABORT invoked on rank 0 in communicator MPI_COMM_WORLD with 
> errorcode 0
> mpirun noticed that job rank 1 with PID 28131 on node xxxx.xxxxxx.xxx 
> exited on signal 15 (Terminated).
> 12 additional processes aborted (not shown)
> --------------------------------
>
> Maybe I am missing something obvious?  Could anyone point to the right 
> place for tracing the problem? ...
>
> Zhiliang
>
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