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 >>>>> >>>>> __________________________________ >>>>> 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 >>>> >>> >>> >>> __________________________________ >>> Do you Yahoo!? >>> Yahoo! Search - Find what youre looking for >> faster >>> http://search.yahoo.com >>> >>> >> 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 > > > __________________________________ > 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