Hi Joe, Here's an example of one of the commands I've used:
/usr/local/mpi/bin/mpirun -np 32 -nolocal -machinefile machines /usr/local/mpiblast/bin/mpiblast -p blastn -i PT_7G4_00005_fil.fas -d tigr -m 7 -v 3 -b 3 -a 2 Generally I'll submit this to SGE but I seem to get the same response whether I run it through SGE or straight on the command line The tigr database is 4GB divided up using mpiformatdb into 32 pieces. Thanks, Stephen On Tue, 2006-01-10 at 10:17, Joe Landman wrote: > Stephen Ficklin wrote: > > I may be wrong on my assessment, but it appears that when I try to run an > > mpiblast that the master node (chosen by the algorithm) does all the work. > > I'll get a constant load average of 1 on that node while the program is > > running. On the other nodes I barely register any activity. For small > > database searches I will get results, but for larger ones it takes too long > > and patience gives out or it finishes with errors. The last large job I ran > > ended with this message after giving a few results: > > > > NULL_Caption] FATAL ERROR: CoreLib [002.005] 000049_0498_0531: File write > > error 0 34645.5 Bailing out with signal -1 > > [0] MPI Abort by user Aborting program ! > > [0] Aborting program! > > > > In any case it always seems to overload the master node but the workers > > seem to be doing nothing. I've compiled MPIBlast for OSX, Linux and > > Solaris and I get the samre response on all three platforms. Before I try > > an debugging I just wanted to check to see if anyone had experienced > > something similar. > > > > Hi Stephen: > > Could you tell us how you are launching the job? > > Joe > > -- > Joseph Landman, Ph.D > Founder and CEO > Scalable Informatics LLC, > email: [EMAIL PROTECTED] > web : http://www.scalableinformatics.com > phone: +1 734 786 8423 > fax : +1 734 786 8452 > cell : +1 734 612 4615 > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Mpiblast-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/mpiblast-users -- ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click _______________________________________________ Mpiblast-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mpiblast-users
