[BioBrew Users] Unable to get mpiblast running

[Glen Otero]

Bastian-

Any progress running mpiBLAST?

Glen

On Apr 6, 2006, at 2:27 PM, Bastian Friedrich wrote:

> Hi Glen,
>
> thank you for your quick response.
>
> On Thursday 06 April 2006 15:53, Glen Otero wrote:
>>
>> I usually don't see these types of errors. Here are a few questions:
>>
>> How did you format the database for mpiblast?
>
> /usr/local/bin/mpiformatdb --nfrags=28 -i Hs.seq.uniq
> was the latest call, but I had used
> mpiformatdb -N 28 -i Hs.seq.uniq
> earlier.
>
>> Is the mpiblast database on a shared filesystem, like NFS (I don't
>> think symlinks will work)?
>
> Currently, I have created a /export/data/blastdb/ on the frontend;  
> this
> was rsynced to /state/partition1/blastdb on the compute nodes; on the
> frontend, I had a directory /state/partition1 (on the root
> partition...) containing a symlink to /export/data/blastdb.
>
> I have just used a bind mount on the frontend (no more symlinking),  
> but
> this was not successful, either.
>
> The first tests were done via NFS, which did not work either.
>
>> How did you launch the job, SGE?
>
> In the future, we surely want to use mpiblast in an SGE environment;
> currently, it was started from the command line.
>
>> Can you try a smaller job using just the 6 compute nodes (and
>> formatting the db into 6 pieces)?
>
> Wow, I get a new one now:
> ===============================
> bastian at frontend:/state/partition1/blastdb> mpiformatdb -N 6 -i
> Hs.seq.uniq
> [...]
> [... semi-manual distributing data to /state/partiton1/blastdb of all
> nodes ...]
> bastian at frontend:/state/partition1/blastdb> cd ~/tmp03
> bastian at frontend:~/tmp03> /opt/mpich/gnu/sbin/cleanipcs
> bastian at frontend:~/tmp03> cluster-fork /opt/mpich/gnu/sbin/cleanipcs
> [...]
> bastian at frontend:~/tmp03> mpirun -np 6 /usr/local/bin/mpiblast -p  
> blastn
> -d Hs.seq.uniq -i IL2RA -o blast_results
> 54p3_2934:  p4_error: : 0
> 3       0.078125        Bailing out with signal 11
> [3] MPI Abort by user Aborting program !
> [3] Aborting program!
> 2p1_28697:  p4_error: interrupt SIGx: 13
>  p5_17962:  p4_error: : 0
>         0.0742188       Bailing out with signal 11
> [5] MPI Abort by user Aborting program !
> [5] Aborting program!
> p4_21219:  p4_error: : 0
> rm_l_4_21279: (0.367188) net_send: could not write to fd=5, errno =  
> 104
>         0.078125        Bailing out with signal 11
> [4] MPI Abort by user Aborting program !
> [4] Aborting program!
> p2_13443:  p4_error: : 0
>         0.078125        Bailing out with signal 11
> [2] MPI Abort by user Aborting program !
> [2] Aborting program!
> rm_l_3_2994: (0.644531) net_send: could not write to fd=5, errno = 104
>
>  p1_28697: (7.242188) net_send: could not write to fd=5, errno = 32
> rm_l_2_13503: (6.929688) net_send: could not write to fd=5, errno =  
> 104
> p2_13443: (6.929688) net_send: could not write to fd=5, errno = 32
> p5_17962: (6.093750) net_send: could not write to fd=5, errno = 32
> ===============================
>
> Signal 11 seems to be a segfault? Something's going awfully wrong
> here...
>
>> Can you try a smaller blast job using p53, p53db from ftp://
>> ftp.bioinformatics.org/pub/biobrew/ and blastp?
>
> This works! :)) The first time I see mpiblast actually working :)
>
> Unfortunately, we are looking forward to blasting against the 17 GB
> genebank... Any more ideas?
>
> Thx again,
>    Bastian
>
> -- 
>  Bastian Friedrich                  bastian at bastian-friedrich.de
>  Adress & Fon available on my HP   http://www.bastian-friedrich.de/
> \~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\
> \ Computers make very fast, very accurate mistakes.
> _______________________________________________
> BioBrew-Users mailing list
> BioBrew-Users at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/BioBrew-Users