[BioBrew Users] Trouble running mpiBlast

Thu Mar 11 16:04:43 EST 2004

On Mar 11, 2004, at 3:57 AM, Soumyadeep nandi wrote:

> 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.

Did you have to rebuild HMMER, or were you able to use it with pvm as  
it was in 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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>>>>> BioBrew-Users at bioinformatics.org
>>>>>
>>>>
>>>
>>
> 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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>
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Glen Otero, Ph.D.
Linux Prophet
619.917.1772