Hi, Glen I also faced the similar situation but I am running mpiBlast with lam-mpi You can look thru the error I got maybe u might be able to figure it out how to solve this error. ********************************************************************************************************** [guest at frontend-0 root]$ /usr/local/mpich-vmi2/bin/mpirun -np 1 -machinefile /u sr/local/share/machine.list /opt/BioBrew/NCBI/6.1.0/bin/mpiblast -d /opt/BioBre w/NCBI/6.1.0/db/ecoil.nt -i/root/test.fas -o /root/output.txt Sorry, mpiBLAST must be run on 2 or more nodes [guest at frontend-0 root]$ /usr/local/mpich-vmi2/bin/mpirun -np 2 -machinefile / usr/local/share/machine.list /opt/BioBrew/NCBI/6.1.0/bin/mpiblast -d /opt/BioBr ew/NCBI/6.1.0/db/ecoil.nt -i/root/test.fas -o /root/output.txt So----------------------------------------------------------------------------- *** Oops -- I cannot open the LAM help file. *** I tried looking for it in the following places: rry, mpiBLAST must be run on 2 or more nodes *** *** $LAMHELPFILE *** $HOME/lam-helpfile *** $HOME/lam-6.5.9-helpfile *** $HOME/etc/lam-helpfile *** $HOME/etc/lam-6.5.9-helpfile *** $LAMHELPDIR/lam-helpfile *** $LAMHELPDIR/lam-6.5.9-helpfile *** $LAMHOME/etc/lam-helpfile *** $LAMHOME/etc/lam-6.5.9-helpfile *** $SYSCONFDIR/lam-helpfile *** $SYSCONFDIR/lam-6.5.9-helpfile *** *** You were supposed to get help on the program "MPI" *** about the topic "no-lamd" *** *** Sorry! ----------------------------------------------------------------------------- Rgs, Sharon >From: Glen Otero <gotero at linuxprophet.com> >Reply-To: BioBrew-Users at bioinformatics.org >To: BioBrew-Users at bioinformatics.org >Subject: Re: [BioBrew Users] Trouble running mpiBlast >Date: Wed, 10 Mar 2004 17:10:25 -0800 > >Hmmm...I'm getting the same error. I'll need some time to look into this. >Anyone else seen this problem, or running mpiBLAST properly with a >different mpi (like lam)? > >Glen > >On Mar 9, 2004, at 11:16 PM, Soumyadeep nandi wrote: > >> >>Thanks Glen and Kip for your instructions. >> >>We could troubleshoot the earlier troubles.While >>working with pvm we found contirb-pvm is installed in >>the frontend and no pvm was installed in the slave >>nodes. So we installed the normal pvm present in the >>distro and it is working fine. >>Now we are trying to run blast on the cluster. We >>could ran the normal blast without any hiccups. But >>the problem started with mpiblast. >>We have downloaded some of the example scripts from >>http://www.llnl.gov/computing/tutorials/mpi/samples/C/. >>Compiled the programs with "/usr/bin/mpicc", created >>the machines file (with only two nodes, compute-0-0, >>compute-0-1), started up ssh-agent and ran the sample >>program. That ran fine in all the compute nodes >>without any error. >>As we try to run the mpiBlast with the following >>command: >>[andrew at frontend-0 mpi_test_blast]$ >>/usr/local/mpich-vmi2/bin/mpirun -np 2 -machinefile >>../machines /opt/BioBrew/NCBI/6.1.0/bin/mpiblast >>--config-file=/opt/BioBrew/NCBI/6.1.0/etc/mpiblast.conf >>-p blastp -d ../db/nr -i test.seq >>We get the error as bellow: >>Sorry, mpiBLAST must be run on 2 or more nodes. >> >>With Regards, >>Soumyadeep >> >>__________________________________ >>Do you Yahoo!? >>Yahoo! Search - Find what youre looking for faster >>http://search.yahoo.com >>_______________________________________________ >>BioBrew-Users mailing list >>BioBrew-Users at bioinformatics.org >>https://bioinformatics.org/mailman/listinfo/BioBrew-Users >> >> >Glen Otero, Ph.D. >Linux Prophet >619.917.1772 > >_______________________________________________ >BioBrew-Users mailing list >BioBrew-Users at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/BioBrew-Users _________________________________________________________________ Keep track of Singapore & Malaysia stock prices. http://www.msn.com.sg/money/