Differences

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--- mpiblast [2010/01/29 09:39] – 172.26.0.166
+++ mpiblast [2010/01/29 09:42] – 172.26.0.166
@@ Line 41: / 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 46: / Line 48: @@
 user    7m40.775s
 sys     0m6.732s</code>
+==== MPI Blast with 4 jobs, 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 54: / Line 56: @@
 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 66: / Line 69: @@
 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 =====
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   * wwwblast: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/wwwblast/
   * OpenMPI FAQ: http://www.open-mpi.org/faq/