Differences

This shows you the differences between two versions of the page.

--- mpiblast [2010/01/29 09:37] – 172.26.0.166
+++ mpiblast [2010/01/29 09:41] – 172.26.0.166
@@ Line 3: / Line 3: @@
   * http://wiki.bioinformatics.ucdavis.edu/index.php/MPI_Blast
-  * OpenMPI FAQ: http://www.open-mpi.org/faq/
 <code>$ mpiformatdb -i drosoph.nt -p F --nfrags=12</code>
@@ Line 42: / Line 41: @@
                  MCA ras: gridengine (MCA v2.0, API v2.0, Component v1.3.2)</code>
 ===== Benchmarks =====
+==== Standard BLAST ====
 <code>$ time blastall -d drosoph.nt -p blastn -i drosoph.seq -o drosoph.result
@@ Line 48: / Line 49: @@
 sys     0m6.732s</code>
+==== MPI Blast on 1 node ====
 <code>$ 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
@@ Line 55: / Line 57: @@
 sys     0m56.631s</code>
-With 12 jobs, sge, mpiblast, 6 nodes did it in:
+==== MPI Blast with 12 jobs, 6 nodes ====
 <code>$ less mpiblast_sge.sh.o5515
 Total Execution Time: 98.3068</code>
+==== Paracel Blast ====
 <code>$ time pb blastall -d alan_drosoph -p blastn -i sequences/drosoph.seq -o drosoph.result
@@ Line 67: / Line 70: @@
 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 =====
@@ Line 91: / Line 95: @@
 </code>
 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
 ===== Links =====
   * Submitting MPI jobs using SGE: http://www.shef.ac.uk/wrgrid/documents/gridengine.html
@@ Line 98: / Line 101: @@
   * Rocks documentation on mpiBLAST: http://www.rocksclusters.org/roll-documentation/bio/5.2/mpiblast_usage.html
   * wwwblast: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/wwwblast/
+  * OpenMPI FAQ: http://www.open-mpi.org/faq/