Re: Re: new on using clusters: problem running mpiblast (2)
Joe Landman <[email protected]> Fri, 21 Sep 2007 11:20:10 -0400
| Newsgroups | gmane.science.biology.informatics.clusters |
|---|---|
| Organization | Scalable Informatics |
| Message-ID | <[email protected]> |
Zhiliang Hu wrote: > Thanks Joe! > > I tested with 'which' and 'whereis', they do find 'orted' on my system. > So I tried again with full path to "mpirun" (i am sorry I should have > done this earlier): > >> /opt/openmpi.gcc/bin/mpirun -np 3 -machinefile machines > /home/local/bin/mpiblast -p blastp -i ./bait.fasta -d ecoli.aa Lets have you add '-d 4' to the mpirun line in both cases. Also, I might suggest forcing it to use the ethernet if possible. You would need to add in -mca btl tcp to make that happen. -- Joseph Landman, Ph.D Founder and CEO Scalable Informatics LLC, email: [email protected] web : http://www.scalableinformatics.com http://jackrabbit.scalableinformatics.com phone: +1 734 786 8423 fax : +1 866 888 3112 cell : +1 734 612 4615