[Bioclusters] sequest cluster problem

[Bernard Li]

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
>