[Bioclusters] sequest cluster problem

[Anne-Marie HESSE]

thank you everyone
 this libraries missed :compat-libstdc++-33- 3.2.3-47.3.i386.rpm

now almost everything is ok
our last problem is that we lose nodes from time to time ; From the conf command in the pvm window there is a kind of bug because the nodes disappear sometimes andI have to add them manually

Anne-marie
Jeremy Mann a écrit :
> 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
>>
>
>