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--- mpiblast [2010/01/19 11:10] – 172.26.0.166
+++ mpiblast [2010/01/20 13:03] – 172.26.0.166
@@ Line 61: / Line 61: @@
 <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.
+===== 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
+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 ====
+Rule of thumb for large databases, one segment for every gigabyte (144 GB, 144 segments).
+  * http://lists.mpiblast.org/pipermail/users_lists.mpiblast.org/2009-August/000988.html
+  * https://lists.sdsc.edu/pipermail/npaci-rocks-discussion/2008-February/029231.html
 ===== Links =====
@@ Line 68: / Line 93: @@
   * mpiBLAST Guide: http://www.mpiblast.org/Docs/Guide
   * Updating the BLAST databases: http://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl
+  * Rocks documentation on mpiBLAST: http://www.rocksclusters.org/roll-documentation/bio/5.2/mpiblast_usage.html