Differences

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--- mpiblast [2010/01/19 09:17] – 172.26.0.166
+++ mpiblast [2010/01/19 12:59] – 172.26.0.166
@@ Line 8: / Line 8: @@
   * **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.
-http://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl
@@ Line 59: / Line 57: @@
 user    12m13.891s
 sys     0m56.631s</code>
+With 12 jobs, sge, mpiblast, 6 nodes did it in:
+<code>$ less mpiblast_sge.sh.o5515
+Total Execution Time: 98.3068</code>
+<code>$ time pb blastall -d alan_drosoph -p blastn -i sequences/drosoph.seq -o drosoph.result
+real    3m6.163s
+user    0m0.046s
+sys     0m1.423s</code>
 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.
 ===== Links =====
   * Submitting MPI jobs using SGE: http://www.shef.ac.uk/wrgrid/documents/gridengine.html
+  * mpiBLAST Guide: http://www.mpiblast.org/Docs/Guide
-<code>$ sudo mkdir -p /state/
+  * Updating the BLAST databases: http://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl
-$ sudo ln -s /scratch/ /state/partition1
+  * Rocks documentation on mpiBLAST: http://www.rocksclusters.org/roll-documentation/bio/5.2/mpiblast_usage.html
-$ sudo chmod 777 /scratch/
-$ sudo chmod o+t /scratch/</code>