[BioBrew Users] Trouble running mpiBlast

[Soumyadeep nandi]

Hi Glen,

> What application were you running with pvm, HMMER?
> If it was HMMER, which version?

We ran HMMER version hmmer-2.3.2 in cluster. As pvm is
a prerequisit for running hmmer-2.3.2 in cluster we
were starting up the pvm in the cluster running with
BioBrew. 

> And I think the problem with mpiBLAST (must be run
> on more than two nodes error) is that mpiBLAST is 
> built with lam-mpi and hasn't been tested with  
> vmi-mpich. Can you try using lam-mpi with mpiBLAST 
> and let me know how it goes?

We tried to run lam-mpi with mpiblast with the
following command:
[andrew at frontend-0 andrew]$
/opt/lam-mpi/7.0.3/bin/mpirun C
/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 mpi_test_blast/test.seq

What we could see is our lamd is not running. So to 
start lamd in frontend and slave nodes we tried
"lamboot -v" after editing /etc/lam/lam-bhost.def
file.

The lamd seems to be running now as we can see from
"tping".
Still we are getting the same error as lamd is not
running.

The outpu is as bellow:
-----------------------------------------------------------------------------
It seems that there is no lamd running on this host,
which indicates
that the LAM/MPI runtime environment is not operating.
 The LAM/MPI
runtime environment is necessary for the "mpirun"
command.
 
Please run the "lamboot" command the start the LAM/MPI
runtime
environment.  See the LAM/MPI documentation for how to
invoke
"lamboot" across multiple machines.
-----------------------------------------------------------------------------

Regards Soumyadeep

--- Glen Otero <gotero at linuxprophet.com> wrote:
> Hi Soumyadeep-
> 
> What application were you running with pvm, HMMER?
> If it was HMMER, 
> which version?
> 
> And I think the problem with mpiBLAST (must be run
> on more than two 
> nodes error) is that mpiBLAST is built with lam-mpi
> and hasn't been 
> tested with vmi-mpich. Can you try using lam-mpi
> with mpiBLAST and let 
> me know how it goes?
> 
> Glen
> 
> 
> On Mar 10, 2004, at 3:26 AM, Soumyadeep nandi wrote:
> 
> > Hi Glen,
> >
> > We made no changes in the local .bashrc or profile
> > files. The /etc/profile.d directory had two sets
> of
> > pvm paths - one pvm_profile.csh and .sh and the
> other
> > pvm.csh and .sh. The pvm_profile.sh had the
> following
> > contents
> >
> > export PVM_ROOT=/usr/share/pvm3
> > export PVM_RSH=/usr/bin/ssh
> >
> > while the pvm.sh had
> >
> > PVM_RSH=/usr/bin/rsh
> > PVM_ROOT=/usr/share/pvm3
> > export PVM_RSH PVM_ROOT
> >
> > as we require PVM_RSH to be ssh (rsh is not yet
> setup
> > on the cluster) we removed the pvm.sh.
> >
> > We did have problems extracting the PVM
> environmental
> > variables when setting up pvm on a cluster of
> > workstations and got around it by sending these
> > directives as part of the hostfile used to start
> pvm.
> > This is our hostfile:
> >
> > * dx=/usr/share/pvm3/lib/pvmd
> > ep=/usr/share/pvm3/bin/LINUX sp=2000
> > frontend-0
> > compute-0-0
> > compute-0-1
> >
> >
> >> Where did you install PVM on the compute nodes?
> > We installed
> >
>
/home/install/7.3/en/os/i386/RedHat/RPMS/pvm-3.4.4-2.i386.rpm
> > as "rpm -ivh pvm-3.4.4-2.i386.rpm"
> > and it was installed by default in /usr/share/pvm3
> >
> > Regards,
> > Soumyadeep
> >
> > --- Glen Otero <gotero at linuxprophet.com> wrote:
> >> I'll try to duplicate your mpiBLAST scenario
> >> tomorrow. In the meantime,
> >> can you send me an example of a user's .bashrc
> and
> >> .bash_profile from
> >> your cluster? I'd like to see how you set the PVM
> >> environment variables
> >> for your users. Or did you put them in
> /etc/profile?
> >> Where did you
> >> install PVM on the compute nodes?
> >>
> >> 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
> >>>
> >>> __________________________________
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> >>>
> >>
> >
>
https://bioinformatics.org/mailman/listinfo/BioBrew-Users
> >>>
> >>>
> >> Glen Otero, Ph.D.
> >> Linux Prophet
> >> 619.917.1772
> >>
> >
> >
> > __________________________________
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> >
> >
> Glen Otero, Ph.D.
> Linux Prophet
> 619.917.1772
> 
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>
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