[BioBrew Users] Trouble running mpiBlast

shalini sharon proclaim_jesus at hotmail.com
Wed Mar 10 22:37:45 EST 2004

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 
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 
ew/NCBI/6.1.0/db/ecoil.nt -i/root/test.fas -o /root/output.txt
*** 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
***   $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)?
>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
>>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
>>[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
>>-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,
>>Do you Yahoo!?
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>Glen Otero, Ph.D.
>Linux Prophet
>BioBrew-Users mailing list
>BioBrew-Users at bioinformatics.org

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