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mpi:mpiblast

MPI Blast

Parallel implementation of NCBI's BLAST algorithm.

$ mpiformatdb -i drosoph.nt -p F --nfrags=12
  • nfrags specifies how many database fragments you want to split the original database into. This should be equal to how many different nodes you want to run mpiblast on.

Notes on .ncbirc

Notes on setting up the ~/.ncbirc file from the mpiBLAST installation page: http://www.mpiblast.org/Docs/Install#unix

Before running mpiBLAST, it is necessary to configure the shared and local storage paths that each node will use to access the database. A shared storage path is usually a path to a directory residing on a file server, such as NFS, AFS, or samba. The local storage path is typically a subdirectory within the /tmp directory, e.g. /tmp/mpiblast. As worker nodes search the database, they will copy fragments to the local storage directory. During subsequent searches of the same database, the fragments will already reside in local storage and thus will not need to be copied. Note that diskless nodes can be supported by setting the local storage path to be the same as the shared storage path. To configure mpiBLAST create a .ncbirc file in your home directory that looks like:

[NCBI]
Data=/path/to/ncbi/data

[BLAST]
BLASTDB=/path/to/shared/storage
BLASTMAT=/path/to/ncbi/data

[mpiBLAST]
Shared=/path/to/shared/storage
Local=/path/to/local/storage

The Data variable gives the location of the NCBI Data directory containing BLOSUM and PAM scoring matrices, among other things. The scoring matrix files are necessary for any type of protein BLAST search and should be accessible by all cluster nodes. The BLASTMAT variable also specifies the path to the scoring matrices, and will usually be identical to the Data variable. The BLASTDB variable tells standard NCBI blastall (not mpiBLAST) where to find BLAST databases. As previously mentioned, the Shared and Local variables give the shared and local database paths, respectively. By setting BLASTDB to the same path as Shared, it is possible for NCBI blastall to share the same databases that mpiBLAST uses. In such a configuration, be sure to format all databases with mpiformatdb rather than formatdb.

Frequently Asked Questions

Collection of the more-helpful questions and answers from the mpiBLAST FAQ.

How do I format a huge database?

Large databases like nt can consume several gigabytes of disk space and it is preferable to store them in compressed form. Starting with mpiBLAST 1.4.0 it is possible to pipe FastA formatted sequence data into mpiformatdb. This feature provides the ability to directly format a compressed (gzip/bzip etc.) database using command line syntax like:

$ zcat nt.gz | mpiformatdb -i stdin -N 100 -t nt -p F

SGE Support

See this FAQ entry: http://www.open-mpi.org/faq/?category=running#run-n1ge-or-sge

$ ompi_info | grep gridengine
                 MCA ras: gridengine (MCA v2.0, API v2.0, Component v1.3.2)

Benchmarks

Standard BLAST

$ time blastall -d drosoph.nt -p blastn -i drosoph.seq -o drosoph.result
        
real    7m48.052s
user    7m40.775s
sys     0m6.732s

MPI Blast with 4 jobs, 1 node

$ time /opt/openmpi/bin/mpirun -np 4 /opt/Bio/mpiblast/bin/mpiblast -d drosoph.nt -i drosoph.seq -p blastn -o mpi_drosoph_result.txt
Total Execution Time: 395.754

real    6m36.841s
user    12m13.891s
sys     0m56.631s

MPI Blast with 12 jobs, 6 nodes

$ less mpiblast_sge.sh.o5515
Total Execution Time: 98.3068

Paracel Blast

$ time pb blastall -d alan_drosoph -p blastn -i sequences/drosoph.seq -o drosoph.result
                                                                               
real    3m6.163s
user    0m0.046s
sys     0m1.423s

The number of processes for an MPI job should be +1 of the number of CPUs because one process is used as the master to control the other jobs.

Random Notes

Number of Jobs

https://lists.sdsc.edu/pipermail/npaci-rocks-discussion/2005-July/012726.html

With formatdb, the number of nodes refers to compute node number. With mpiBLAST, np refers to number of processes, which isn't necessarily linked to compute node or processor number. You can run 10 processes on 4 processors. But it's recommended to run a single process per processor. But the minimum number of processes for mpiBLAST is 3, no matter what your compute node number is.

Number of Fragments

Incorrect mpiBLAST Version

$ rpmquery -a mpiblast    
mpiblast-1.5.0-pio
$ mpiblast --version
mpiblast version 1.4.0

You're not crazy, it's a known issue. 1.5.0 reports as 1.4.0: http://lists.mpiblast.org/pipermail/users_lists.mpiblast.org/2009-February/000933.html

mpi/mpiblast.txt · Last modified: 2011/01/23 13:31 by aorth