[Bioclusters] sequest cluster problem

[Jeremy Mann]

Oops, you're right Bernard, thank you for the correction.


On 5/24/06, Bernard Li <bli at bcgsc.ca> wrote:
> I think you meant:
>
> rpm -qa | grep compat
>
> Cheers,
>
> Bernard
>
> > -----Original Message-----
> > From: bioclusters-bounces+bli=bcgsc.ca at bioinformatics.org
> > [mailto:bioclusters-bounces+bli=bcgsc.ca at bioinformatics.org]
> > On Behalf Of Jeremy Mann
> > Sent: Wednesday, May 24, 2006 6:32
> > To: Clustering, compute farming & distributed computing in
> > life science informatics
> > Subject: Re: [Bioclusters] sequest cluster problem
> >
> > Anne, the library errors on your Fedora nodes I think are the cause of
> > a missing RPM called compat-libs. Can you remote access a good node
> > and run as root:
> >
> > rpm -qa compat
> >
> > Look for anything compat-libs
> >
> > If a good node has those, then I can assume that the bad nodes don't
> > have the RPM installed. So remote access a bad node and run the same
> > command.
> >
> >
> > On 5/24/06, Anne-Marie Hesse <anne-marie.hesse at espci.fr> wrote:
> > > Hi,
> > >
> > > We have some problems while running Sequest Cluster.  Our cluster is
> > > configured as follows:
> > >
> > > Master Node:
> > >  Dell Precision 2670, with 2 Xeon 2.4GHz CPUs and 2 gb of RAM
> > >  Microsoft Windows 2003, with Service Pack 1
> > >
> > > Slave Nodes 1 to 8:
> > >  Dell Precision 2670, with 2 Xeon 2.4GHz CPUs and 2 gb of RAM
> > >  Linux Fedora Core 4
> > >
> > >
> > > We are using BioWorks version 3.2 SR1.
> > >
> > >
> > > The first problem we have is when we start the PVM (by
> > clicking "Start
> > > PVM" in the Cluster Manager), we always get the following
> > error for Node
> > > 2, even if "Cleanup Nodes" has been clicked prior to starting PVM:
> > >
> > > "Error connecting to the stderr server port!error in
> > receive on socket:
> > > Socket shutdown by remote." three times the same line
> > >
> > > When starting PVM, node2, node6 and node 7 are not started and the
> > > message states we started only 6 hosts.
> > >
> > > Here is the pvml.proteomics file contents: (joel2 is the name of the
> > > master)
> > >
> > > [t80040000] JOEL2 (192.168.66.250:1073) WIN32 3.4.3
> > > [t80040000] ready Wed May 24 11:59:36 2006
> > > [t80040000] startack() host node2 expected version, got ""
> > > [t80040000] startack() host node4 expected version, got ""
> > > [t80040000] startack() host node7 expected version, got ""
> > > [t80040000] [t80001]
> > /usr/share/pvm3/bin/LINUXI386/sequest27_slave: error
> > > while loading shared libraries: libstdc++.so.5: cannot open
> > shared object
> > > file: No such file or directory
> > > [t80040000] [t80002]
> > /usr/share/pvm3/bin/LINUXI386/sequest27_slave: error
> > > while loading shared libraries: libstdc++.so.5: cannot open
> > shared object
> > > file: No such file or directory
> > > [t80040000] [t100001]
> > /usr/share/pvm3/bin/LINUXI386/sequest27_slave: error
> > > while loading shared libraries: libstdc++.so.5: cannot open
> > shared object
> > > file: No such file or directory
> > > [t80040000] [t100002]
> > /usr/share/pvm3/bin/LINUXI386/sequest27_slave: error
> > > while loading shared libraries: libstdc++.so.5: cannot open
> > shared object
> > > file: No such file or directory
> > > [t80040000] [t180001]
> > /usr/share/pvm3/bin/LINUXI386/sequest27_slave: error
> > > while loading shared libraries: libstdc++.so.5: cannot open
> > shared object
> > > file: No such file or directory
> > > [t80040000] [t180002]
> > /usr/share/pvm3/bin/LINUXI386/sequest27_slave: error
> > > while loading shared libraries: libstdc++.so.5: cannot open
> > shared object
> > > file: No such file or directory
> > > [t80040000] [t1c0001]
> > /usr/share/pvm3/bin/LINUXI386/sequest27_slave: error
> > > while loading shared libraries: libstdc++.so.5: cannot open
> > shared object
> > > file: No such file or directory
> > > [t80040000] [t1c0002]
> > /usr/share/pvm3/bin/LINUXI386/sequest27_slave: error
> > > while loading shared libraries: libstdc++.so.5: cannot open
> > shared object
> > > file: No such file or directory
> > > [t80040000] [t240001]
> > /usr/share/pvm3/bin/LINUXI386/sequest27_slave: error
> > > while loading shared libraries: libstdc++.so.5: cannot open
> > shared object
> > > file: No such file or directory
> > > [t80040000] [t240002]
> > /usr/share/pvm3/bin/LINUXI386/sequest27_slave: error
> > > while loading shared libraries: libstdc++.so.5: cannot open
> > shared object
> > > file: No such file or directory
> > > [t80040000] loclinput() read: 10054
> > > [t80040000] loclinput() marking t40003 dead
> > >
> > > Do you have any suggestion ?
> > > Thank you in advance
> > > sincerely
> > >
> > > Anne-Marie HESSE
> > >
> > > --
> > >
> > > Anne-Marie HESSE
> > > Laboratoire de Neurobiologie et Diversité Cellulaire UMR 7637
> > > ESPCI
> > > 10 rue Vauquelin
> > > 75005 Paris
> > > FRANCE
> > >
> > >
> > > _______________________________________________
> > > Bioclusters maillist  -  Bioclusters at bioinformatics.org
> > > https://bioinformatics.org/mailman/listinfo/bioclusters
> > >
> >
> >
> > --
> > Jeremy
> > _______________________________________________
> > Bioclusters maillist  -  Bioclusters at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bioclusters
> >
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
>


-- 
Jeremy