Error getCommandCount

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Error getCommandCount

Mariette
Hi everyone,

When runing an iterable component, this one crash at the iteration step.
There is no help only the log file with failed steps written like this

FINEST 10:23:28:564 [Thread: ID:1412 - create iterator i1 groupings] CommandSet getCommandCount:1420 Beginning to get the total number of commands with state: failed


Any idea where it can come from ?

thanks,
Jerome

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Re: Error getCommandCount

Mahurkar, Anup
Jerome,

This message is from the underlying Java workflow. It is in a method that
is trying to build a list of commands that failed. Not knowing the later
lines in the log file my best guess is that the XML for the workflows
could not be parsed or command count determined. Can you send me the XML
file for one of these iterators and the log file?

Also, in the log you should see a line that looks like this after the
message you see below:

Total commands with state: failed is xx



On 4/26/12 4:44 AM, "Mariette" <[hidden email]> wrote:

>Hi everyone,
>
>When runing an iterable component, this one crash at the iteration step.
>There is no help only the log file with failed steps written like this
>
>FINEST 10:23:28:564 [Thread: ID:1412 - create iterator i1 groupings]
>CommandSet getCommandCount:1420 Beginning to get the total number of
>commands with state: failed
>
>
>Any idea where it can come from ?
>
>thanks,
>Jerome
>
>--------------------------------------------------------------------------
>----
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>threat landscape has changed and how IT managers can respond. Discussions
>will include endpoint security, mobile security and the latest in malware
>threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>_______________________________________________
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>[hidden email]
>https://lists.sourceforge.net/lists/listinfo/ergatis-users


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Re: Error getCommandCount

Mariette

in attachement the log file,
thanks for your help,

Jerome






Le 26/04/2012 11:56, Mahurkar, Anup a écrit :

> Jerome,
>
> This message is from the underlying Java workflow. It is in a method that
> is trying to build a list of commands that failed. Not knowing the later
> lines in the log file my best guess is that the XML for the workflows
> could not be parsed or command count determined. Can you send me the XML
> file for one of these iterators and the log file?
>
> Also, in the log you should see a line that looks like this after the
> message you see below:
>
> Total commands with state: failed is xx
>
>
>
> On 4/26/12 4:44 AM, "Mariette"<[hidden email]>  wrote:
>
>> Hi everyone,
>>
>> When runing an iterable component, this one crash at the iteration step.
>> There is no help only the log file with failed steps written like this
>>
>> FINEST 10:23:28:564 [Thread: ID:1412 - create iterator i1 groupings]
>> CommandSet getCommandCount:1420 Beginning to get the total number of
>> commands with state: failed
>>
>>
>> Any idea where it can come from ?
>>
>> thanks,
>> Jerome
>>
>> --------------------------------------------------------------------------
>> ----
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond. Discussions
>> will include endpoint security, mobile security and the latest in malware
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> Ergatis-users mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>
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> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: Error getCommandCount

Mariette

oupsss, I forgot the log.
Jerome






Le 26/04/2012 14:44, Mariette a écrit :

in attachement the log file,
thanks for your help,

Jerome






Le 26/04/2012 11:56, Mahurkar, Anup a écrit :
Jerome,

This message is from the underlying Java workflow. It is in a method that
is trying to build a list of commands that failed. Not knowing the later
lines in the log file my best guess is that the XML for the workflows
could not be parsed or command count determined. Can you send me the XML
file for one of these iterators and the log file?

Also, in the log you should see a line that looks like this after the
message you see below:

Total commands with state: failed is xx



On 4/26/12 4:44 AM, "Mariette"[hidden email]  wrote:

Hi everyone,

When runing an iterable component, this one crash at the iteration step.
There is no help only the log file with failed steps written like this

FINEST 10:23:28:564 [Thread: ID:1412 - create iterator i1 groupings]
CommandSet getCommandCount:1420 Beginning to get the total number of
commands with state: failed


Any idea where it can come from ?

thanks,
Jerome

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Re: Error getCommandCount

Mariette

Hi again,
I have hard time understanding and I'm running out of idea to get an idea of what's going wrong. The job is sent to the cluster, however, the only jobs running are :

ng6@ceri004:~$ ps aux | grep ng6
ng6       1262  0.0  0.0 106668  1312 ?        Ss   17:04   0:00 /bin/bash /var/spool/sge/ceri004/job_scripts/25293
ng6       1263  0.0  0.0 122988  2524 ?        S    17:04   0:00 /usr/bin/perl /usr/local/bioinfo/src/workflowng6/current/RunWorkflow -i=/work/ng6/ergatis//workflow/runtime/ncbi-blastn/24_default/i1/g1/g1.xml.gz -m=1 --delaybuild=true --max-heap=1024m
ng6       1265  0.0  0.0 122988  1444 ?        S    17:04   0:00 /usr/bin/perl /usr/local/bioinfo/src/workflowng6/current/RunWorkflow -i=/work/ng6/ergatis//workflow/runtime/ncbi-blastn/24_default/i1/g1/g1.xml.gz -m=1 --delaybuild=true --max-heap=1024m
ng6       1266  0.0  0.0 106408  1488 ?        S    17:04   0:00 /bin/bash /usr/local/bioinfo/src/workflowng6/current/run_workflow -i=/work/ng6/ergatis//workflow/runtime/ncbi-blastn/24_default/i1/g1/g1.xml.gz -m=1 --delaybuild=true --max-heap=1024m --pidfile .workflow.ng6.1263
ng6       1351  2.6  0.0 5116488 179940 ?      Sl   17:04   0:02 java -classpath .:/usr/local/bioinfo/src/workflowng6/current/jars/castor-1.0.4.jar:/usr/local/bioinfo/src/workflowng6/current/jars/commons-logging.jar:/usr/local/bioinfo/src/workflowng6/current/jars/drmaa.jar:/usr/local/bioinfo/src/workflowng6/current/jars/EUIDService.jar:/usr/local/bioinfo/src/workflowng6/current/jars/icons.jar:/usr/local/bioinfo/src/workflowng6/current/jars/jconn2.jar:/usr/local/bioinfo/src/workflowng6/current/jars/jdom.jar:/usr/local/bioinfo/src/workflowng6/current/jars/junit-addons-1.4.jar:/usr/local/bioinfo/src/workflowng6/current/jars/junit.jar:/usr/local/bioinfo/src/workflowng6/current/jars/log4j-1.2.8.jar:/usr/local/bioinfo/src/workflowng6/current/jars/mysql-connector-java-5.1.5-bin.jar:/usr/local/bioinfo/src/workflowng6/current/jars/postgresql-8.2-505.jdbc3.jar:/usr/local/bioinfo/src/workflowng6/current/jars/tigr-htc-2.0.4.jar:/usr/local/bioinfo/src/workflowng6/current/jars/tigr-shared-2.0.9.jar:/usr/local/bioinfo/src/workflowng6/current/jars/wf-3.1.4.jar:/usr/! local/bioi nfo/src/workflowng6/current/jars/wf-3.1.5.jar:/usr/local/bioinfo/src/workflowng6/current/jars/xercesImpl.jar:/usr/local/bioinfo/src/workflowng6/current/jars/xerces.jar:/usr/local/bioinfo/src/workflowng6/current/jars/xmlParserAPIs.jar:/usr/local/bioinfo/src/workflowng6/current/jars/xmlrpc-1.1.jar -Xms100m -Xmx1024m -XX:+UseAltSigs -Dwf.instance.file=/work/ng6/ergatis//workflow/runtime/ncbi-blastn/24_default/i1/g1/g1.xml.gz -Dproject.config.file=/usr/local/bioinfo/src/workflowng6/current/workflow.config -Did.config.file=/usr/local/bioinfo/src/workflowng6/current/workflow.config -Dorg.xml.sax.parser=org.apache.xerces.parsers.SAXParser -Djava.library.path=/SGE/GE2011.11/lib/linux-x64 -Dorg.tigr.htc.config=/usr/local/bioinfo/src/workflowng6/current/server-conf/htc.conf org.tigr.workflow.common.WorkflowEngine -i=/work/ng6/ergatis//workflow/runtime/ncbi-blastn/24_default/i1/g1/g1.xml.gz -m=1 --delaybuild=true --pidfile .workflow.ng6.1263 --max-heap=1024m
ng6       5144  0.2  0.0 115752  2512 pts/0    Ss   17:05   0:00 -tcsh
ng6       6264  5.0  0.0 112388  1176 pts/0    R+   17:06   0:00 ps aux
ng6       6265  0.0  0.0 103304   852 pts/0    S+   17:06   0:00 grep ng6

The command is a simple blast, but no blast are executed!
Any idea how to debug this ?

Jerome


Le 26/04/2012 17:18, Mariette a écrit :

oupsss, I forgot the log.
Jerome






Le 26/04/2012 14:44, Mariette a écrit :

in attachement the log file,
thanks for your help,

Jerome






Le 26/04/2012 11:56, Mahurkar, Anup a écrit :
Jerome,

This message is from the underlying Java workflow. It is in a method that
is trying to build a list of commands that failed. Not knowing the later
lines in the log file my best guess is that the XML for the workflows
could not be parsed or command count determined. Can you send me the XML
file for one of these iterators and the log file?

Also, in the log you should see a line that looks like this after the
message you see below:

Total commands with state: failed is xx



On 4/26/12 4:44 AM, "Mariette"[hidden email]  wrote:

Hi everyone,

When runing an iterable component, this one crash at the iteration step.
There is no help only the log file with failed steps written like this

FINEST 10:23:28:564 [Thread: ID:1412 - create iterator i1 groupings]
CommandSet getCommandCount:1420 Beginning to get the total number of
commands with state: failed


Any idea where it can come from ?

thanks,
Jerome

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Re: Error getCommandCount

Mariette

ok I solved the problem ... it was a database ID retrivial problem from the cluster nodes.
Jerome





Le 27/04/2012 17:09, Mariette a écrit :

Hi again,
I have hard time understanding and I'm running out of idea to get an idea of what's going wrong. The job is sent to the cluster, however, the only jobs running are :

ng6@ceri004:~$ ps aux | grep ng6
ng6       1262  0.0  0.0 106668  1312 ?        Ss   17:04   0:00 /bin/bash /var/spool/sge/ceri004/job_scripts/25293
ng6       1263  0.0  0.0 122988  2524 ?        S    17:04   0:00 /usr/bin/perl /usr/local/bioinfo/src/workflowng6/current/RunWorkflow -i=/work/ng6/ergatis//workflow/runtime/ncbi-blastn/24_default/i1/g1/g1.xml.gz -m=1 --delaybuild=true --max-heap=1024m
ng6       1265  0.0  0.0 122988  1444 ?        S    17:04   0:00 /usr/bin/perl /usr/local/bioinfo/src/workflowng6/current/RunWorkflow -i=/work/ng6/ergatis//workflow/runtime/ncbi-blastn/24_default/i1/g1/g1.xml.gz -m=1 --delaybuild=true --max-heap=1024m
ng6       1266  0.0  0.0 106408  1488 ?        S    17:04   0:00 /bin/bash /usr/local/bioinfo/src/workflowng6/current/run_workflow -i=/work/ng6/ergatis//workflow/runtime/ncbi-blastn/24_default/i1/g1/g1.xml.gz -m=1 --delaybuild=true --max-heap=1024m --pidfile .workflow.ng6.1263
ng6       1351  2.6  0.0 5116488 179940 ?      Sl   17:04   0:02 java -classpath .:/usr/local/bioinfo/src/workflowng6/current/jars/castor-1.0.4.jar:/usr/local/bioinfo/src/workflowng6/current/jars/commons-logging.jar:/usr/local/bioinfo/src/workflowng6/current/jars/drmaa.jar:/usr/local/bioinfo/src/workflowng6/current/jars/EUIDService.jar:/usr/local/bioinfo/src/workflowng6/current/jars/icons.jar:/usr/local/bioinfo/src/workflowng6/current/jars/jconn2.jar:/usr/local/bioinfo/src/workflowng6/current/jars/jdom.jar:/usr/local/bioinfo/src/workflowng6/current/jars/junit-addons-1.4.jar:/usr/local/bioinfo/src/workflowng6/current/jars/junit.jar:/usr/local/bioinfo/src/workflowng6/current/jars/log4j-1.2.8.jar:/usr/local/bioinfo/src/workflowng6/current/jars/mysql-connector-java-5.1.5-bin.jar:/usr/local/bioinfo/src/workflowng6/current/jars/postgresql-8.2-505.jdbc3.jar:/usr/local/bioinfo/src/workflowng6/current/jars/tigr-htc-2.0.4.jar:/usr/local/bioinfo/src/workflowng6/current/jars/tigr-shared-2.0.9.jar:/usr/local/bioinfo/src/workflowng6/current/jars/wf-3.1.4.jar:/us! r/! local/bioi nfo/src/workflowng6/current/jars/wf-3.1.5.jar:/usr/local/bioinfo/src/workflowng6/current/jars/xercesImpl.jar:/usr/local/bioinfo/src/workflowng6/current/jars/xerces.jar:/usr/local/bioinfo/src/workflowng6/current/jars/xmlParserAPIs.jar:/usr/local/bioinfo/src/workflowng6/current/jars/xmlrpc-1.1.jar -Xms100m -Xmx1024m -XX:+UseAltSigs -Dwf.instance.file=/work/ng6/ergatis//workflow/runtime/ncbi-blastn/24_default/i1/g1/g1.xml.gz -Dproject.config.file=/usr/local/bioinfo/src/workflowng6/current/workflow.config -Did.config.file=/usr/local/bioinfo/src/workflowng6/current/workflow.config -Dorg.xml.sax.parser=org.apache.xerces.parsers.SAXParser -Djava.library.path=/SGE/GE2011.11/lib/linux-x64 -Dorg.tigr.htc.config=/usr/local/bioinfo/src/workflowng6/current/server-conf/htc.conf org.tigr.workflow.common.WorkflowEngine -i=/work/ng6/ergatis//workflow/runtime/ncbi-blastn/24_default/i1/g1/g1.xml.gz -m=1 --delaybuild=true --pidfile .workflow.ng6.1263 --max-heap=1024m
ng6       5144  0.2  0.0 115752  2512 pts/0    Ss   17:05   0:00 -tcsh
ng6       6264  5.0  0.0 112388  1176 pts/0    R+   17:06   0:00 ps aux
ng6       6265  0.0  0.0 103304   852 pts/0    S+   17:06   0:00 grep ng6

The command is a simple blast, but no blast are executed!
Any idea how to debug this ?

Jerome


Le 26/04/2012 17:18, Mariette a écrit :

oupsss, I forgot the log.
Jerome






Le 26/04/2012 14:44, Mariette a écrit :

in attachement the log file,
thanks for your help,

Jerome






Le 26/04/2012 11:56, Mahurkar, Anup a écrit :
Jerome,

This message is from the underlying Java workflow. It is in a method that
is trying to build a list of commands that failed. Not knowing the later
lines in the log file my best guess is that the XML for the workflows
could not be parsed or command count determined. Can you send me the XML
file for one of these iterators and the log file?

Also, in the log you should see a line that looks like this after the
message you see below:

Total commands with state: failed is xx



On 4/26/12 4:44 AM, "Mariette"[hidden email]  wrote:

Hi everyone,

When runing an iterable component, this one crash at the iteration step.
There is no help only the log file with failed steps written like this

FINEST 10:23:28:564 [Thread: ID:1412 - create iterator i1 groupings]
CommandSet getCommandCount:1420 Beginning to get the total number of
commands with state: failed


Any idea where it can come from ?

thanks,
Jerome

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