[Bioclusters] new on using clusters: problem running mpiblast

[Chris Dagdigian]

Have you confirmed that MPI works in general before running MPIBLAST?  
This looks like it may be a problem with your MPI environment.

You'll likely have an easier job debugging if you prove to yourself  
that standard MPI test codes like the simple "cpi.c" example can be  
compiled and run correctly first before you try running any "real"  
parallel apps.

-Chris


On Aug 24, 2007, at 10:57 PM, 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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