[Bioclusters] mpiBLAST question

Joseph Landman bioclusters@bioinformatics.org
Tue, 06 May 2003 19:15:14 -0400


Jeremy Mann wrote:

>I am playing around with mpiblast again and have somewhat of a problem.
>Last time I played with it, mpiformatdb moved the segments to the shared
>directory. Then when I ran mpirun -np 20 mpiblast for the first time, I
>remember it moved the individual segments to each nodes local storage,
>then it ran blastall under MPI.
>

One thing I recommend is a healthy network connection, and lots of nfsd's...

>I just updated to 1.1.0 of mpiBLAST, and just mpiformatdb works. When I
>start my *job* mpirun just hangs and prints to STDOUT. I have to manually
>kill it with CTRL-Z. What am I missing here?
>
>Oh... instant brainstorm here. I think its a permissions issue, let me run
>it and chown the local storage. I remember I used /tmp before, now its a
>dedicated hard drive.
>

When in doubt, insert an strace into the mix...


-- 
Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman@scalableinformatics.com
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