Differences

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--- mpiblast [2010/01/18 14:32] – 172.26.0.166
+++ mpiblast [2010/01/19 06:11] – 172.26.0.166
@@ Line 7: / Line 7: @@
 <code>$ mpiformatdb -i drosoph.nt -p F --nfrags=12</code>
-  * **--nfrags=10** 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.
+  * **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 41: / Line 41: @@
 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:
 <code>$ zcat nt.gz | mpiformatdb -i stdin -N 100 -t nt -p F</code>
+==== SGE Support ====
+See this FAQ entry: http://www.open-mpi.org/faq/?category=running#run-n1ge-or-sge
+<code>$ ompi_info | grep gridengine
+                 MCA ras: gridengine (MCA v2.0, API v2.0, Component v1.3.2)</code>
 ===== Benchmarks =====
 <code>$ time blastall -d drosoph.nt -p blastn -i drosoph.seq -o drosoph.result