On Jul 16, 2004, at 6:22 PM, kenix y wrote: > mpiBLAST is ready to run in BioBrew. > > 1)I had set up .ncbirc > > [NCBI] > Data=/opt/BioBrew/NCBI/6.1.0/data > [BLAST] > BLASTDB=/tmp/blast > > 2) and mpiblast.conf > > /mnt/pvfs > /tmp/blast > /opt/BioBrew/NCBI/6.1.0/bin > > 3) edit my /etc/profile > export BLASTPATH=/opt/BioBrew/NCBI/6.1.0/bin > export MPIBLASTCONFIG=/home/bigcpuguest/mpiblast.conf > export MPIRUN=/usr/bin/mpirun > > 4) my $HOME/machines contains > comp-pvfs-0-0 > > Can anyone tell me what is the correct command if I want to run > mpiblast against ecoli.nt? We have to know what directory you keep the input file and the db in on the frontend, but here is the general idea: $MPIRUN -np <number of procs> -machinefile $ /path/to/file/with/nodelist $BLASTPATH/mpiblast --config-file=$MPIBLASTCONFIG -p blastn -i /path/to/query -d /path/to/ecoli.nt -o /path/to/results_file > > _________________________________________________________________ > Get 10mb of inbox space with MSN Hotmail Extra Storage > http://join.msn.com/?pgmarket=en-sg > > _______________________________________________ > Bioclusters maillist - Bioclusters@bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bioclusters > > Glen Otero, Ph.D. Linux Prophet 619.917.1772