[Bioclusters] sequest cluster problem

[Jeremy Mann]

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