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Thread: sequest cluster problem
sequest cluster problem
user name
 2006-05-24 11:17:53 
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  -  Bioclustersbioinformatics.org
https://bioinformatics.org/mailman/listinfo/bioclusters
sequest cluster problem
user name
 2006-05-24 13:31:45 
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.hesseespci.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  -  Bioclustersbioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
>


-- 
Jeremy
_______________________________________________
Bioclusters maillist  -  Bioclustersbioinformatics.org
https://bioinformatics.org/mailman/listinfo/bioclusters
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