ergatis-users Mailing List for ergatis

ergatis-users — For user communication and general help

You can subscribe to this list here.

2008	Jan	Feb	Mar	Apr	May (18)	Jun (21)	Jul (26)	Aug (10)	Sep (17)	Oct (36)	Nov (3)	Dec (6)
2009	Jan (3)	Feb (51)	Mar (15)	Apr (10)	May (17)	Jun (18)	Jul (34)	Aug (37)	Sep (39)	Oct (48)	Nov (14)	Dec
2010	Jan (6)	Feb (10)	Mar (5)	Apr (16)	May (16)	Jun (20)	Jul (11)	Aug (25)	Sep (65)	Oct (23)	Nov (10)	Dec (10)
2011	Jan (21)	Feb (25)	Mar (8)	Apr (9)	May (39)	Jun (32)	Jul (8)	Aug (10)	Sep (20)	Oct (15)	Nov (5)	Dec (3)
2012	Jan (19)	Feb (3)	Mar (6)	Apr (23)	May (25)	Jun	Jul	Aug	Sep	Oct	Nov	Dec
2015	Jan	Feb	Mar	Apr (1)	May	Jun	Jul	Aug	Sep	Oct	Nov	Dec
2023	Jan	Feb	Mar (1)	Apr	May	Jun	Jul	Aug	Sep	Oct	Nov	Dec

Flat | Threaded

1 2 3 .. 36 > >> (Page 1 of 36)

[Ergatis-users] make install fail

From: Alessandro B. <ale...@gm...> - 2023-03-31 10:42:08

Dear all,

I need to install ergatis to reproduce the results of BMC genomics 2019 D Mello et al.

make install fails because 
clusters_lists_defs.h multiple definition of PAIR_LIST_FIRST 

Thank you

A


Inviato da iPhone

[Ergatis-users] Ergatis Error

From: Wimalanathan K. <kok...@gm...> - 2015-04-16 14:44:20

Hi,


When I try to create a project and edit the config file, this error pops
up. I have verified the existence of this file via ssh/terminal. Am I doing
something wrong?

The config file below does not exist:

/diag/home/kokulapalan/argot2//workflow/project.config

try again
<http://ergatis.diagcomputing.org/cgi/edit_config.cgi?config=/diag/home/kokulapalan/argot2//workflow/project.config>

Thanks
-- 
Regards

Gokul
Wimalanathan Kokulapalan

Re: [Ergatis-users] dynamic queue name

From: Jaysheel B. <bja...@gm...> - 2012-05-24 16:28:07

Hey Anup,
	Attached at the files you requested.  I think the problem is in 
		logger.debug("Queue name specified as: " + config.getCmdClass());
	if (config.getCmdClass() != null ) {
		p_out.println(SGE_DIRECTIVE + " -q " + config.getCmdClass());
	}

	This value config.getCmdClass isn't null.  To test I created two more parameters in htc.conf and added appropriate statements in SgeRunner, they are set correctly (see h_vmem, and h_stack in pipeline.xml.log)

Jaysheel



On May 23, 2012, at 12:25 PM, Mahurkar, Anup wrote:

> Can you send me the pipeline and log file. 
> 
> Anup
> 
> On May 23, 2012, at 1:02 PM, "Jaysheel Bhavsar" <bja...@gm...> wrote:
> 
>> Hey Anup,
>> I got latest version of tigr-htc and confirmed that the code snippet is there, compiled and replaced new jar file.  Now however, I get an error 
>> 
>> sge_submit result Unable to read script file because of error:
>> ERROR! -q option must have queue list argument
>> In sge_submit.sh file I see SGE_DIRECTIVE -q but there is not value for queue
>> 
>> # config variables #SGE_DIRECTIVE -l arch=lx* #SGE_DIRECTIVE -l mem_total=1024M #SGE_DIRECTIVE -p -20 #SGE_DIRECTIVE -q #SGE_DIRECTIVE -r y #SGE_DIRECTIVE -N RunWorkflow
>> 
>> I have confirmed that $WORKFLOW_HOME/server-conf/htc.conf has properties 
>> 
>> # Configuration parameters used by the SGERunner class sge_def_queue=centos6-ergatis-test sge_pri_queue=centos6-ergatis-test
>> 
>> 
>> Jaysheel
>> 
>> 
>> On May 22, 2012, at 8:33 PM, Mahurkar, Anup wrote:
>> 
>>> Jaysheel,
>>> 
>>> Could you confirm that this snippet of code exists in the SgeRunner class? It should be in the createSubmitFile method.
>>> 
>>> I do not see the debugging lines in the log file you sent me. Hence the question.
>>> 
>>> Anup
>>> 
>>> // If the user has specified a particular queue (Config.CmdClass), then set the queue name
>>> // with the -q directive else use the default configured in the htc.conf
>>> logger.debug("Queue name specified as: " + config.getCmdClass());
>>> if (config.getCmdClass() != null ) {
>>> p_out.println(SGE_DIRECTIVE + " -q " + config.getCmdClass());
>>> }
>>> else if (HTCConfig.getProperty("sge_def_queue") != null) {
>>> p_out.println(SGE_DIRECTIVE + " -q " + HTCConfig.getProperty("sge_def_queue"));
>>> }
>>> else {
>>> logger.warn("No queue specified in config file. Jobs might fail if epilog/prolog not on all queues");
>>> }
>>> 
>>> 
>>> From: Jaysheel Bhavsar <bja...@gm...>
>>> Reply-To: "erg...@li..." <erg...@li...>
>>> Date: Tue, 22 May 2012 11:40:44 -0500
>>> To: "erg...@li..." <erg...@li...>
>>> Subject: Re: [Ergatis-users] dynamic queue name
>>> 
>>> Hey Anup,
>>> Attached is the pipeline.xml.log and sge_job.sh file.
>>> 
>>> Jaysheel
>>> 
>>> ------------------------------------------------------------------------------ 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 Erg...@li... https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>> ------------------------------------------------------------------------------
>>> 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
>>> Erg...@li...
>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>> 
>> ------------------------------------------------------------------------------
>> 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
>> Erg...@li...
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
> ------------------------------------------------------------------------------
> 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
> Erg...@li...
> https://lists.sourceforge.net/lists/listinfo/ergatis-users

Re: [Ergatis-users] dynamic queue name

From: Mahurkar, A. <ama...@so...> - 2012-05-23 17:25:48

Can you send me the pipeline and log file.

Anup

On May 23, 2012, at 1:02 PM, "Jaysheel Bhavsar" <bja...@gm...<mailto:bja...@gm...>> wrote:

Hey Anup,
I got latest version of tigr-htc and confirmed that the code snippet is there, compiled and replaced new jar file.  Now however, I get an error

sge_submit result Unable to read script file because of error: ERROR! -q option must have queue list argument
In sge_submit.sh file I see SGE_DIRECTIVE -q but there is not value for queue

# config variables #SGE_DIRECTIVE -l arch=lx* #SGE_DIRECTIVE -l mem_total=1024M #SGE_DIRECTIVE -p -20 #SGE_DIRECTIVE -q #SGE_DIRECTIVE -r y #SGE_DIRECTIVE -N RunWorkflow

I have confirmed that $WORKFLOW_HOME/server-conf/htc.conf has properties

# Configuration parameters used by the SGERunner class sge_def_queue=centos6-ergatis-test sge_pri_queue=centos6-ergatis-test


Jaysheel


On May 22, 2012, at 8:33 PM, Mahurkar, Anup wrote:

Jaysheel,

Could you confirm that this snippet of code exists in the SgeRunner class? It should be in the createSubmitFile method.

I do not see the debugging lines in the log file you sent me. Hence the question.

Anup

// If the user has specified a particular queue (Config.CmdClass), then set the queue name
// with the -q directive else use the default configured in the htc.conf
logger.debug("Queue name specified as: " + config.getCmdClass());
if (config.getCmdClass() != null ) {
p_out.println(SGE_DIRECTIVE + " -q " + config.getCmdClass());
}
else if (HTCConfig.getProperty("sge_def_queue") != null) {
p_out.println(SGE_DIRECTIVE + " -q " + HTCConfig.getProperty("sge_def_queue"));
}
else {
logger.warn("No queue specified in config file. Jobs might fail if epilog/prolog not on all queues");
}


From: Jaysheel Bhavsar <bja...@gm...<mailto:bja...@gm...>>
Reply-To: "erg...@li...<mailto:erg...@li...>" <erg...@li...<mailto:erg...@li...>>
Date: Tue, 22 May 2012 11:40:44 -0500
To: "erg...@li...<mailto:erg...@li...>" <erg...@li...<mailto:erg...@li...>>
Subject: Re: [Ergatis-users] dynamic queue name

Hey Anup,
Attached is the pipeline.xml.log and sge_job.sh file.

Jaysheel

------------------------------------------------------------------------------ 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 Erg...@li...<mailto:Erg...@li...> https://lists.sourceforge.net/lists/listinfo/ergatis-users
------------------------------------------------------------------------------
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
Erg...@li...<mailto:Erg...@li...>
https://lists.sourceforge.net/lists/listinfo/ergatis-users

------------------------------------------------------------------------------
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
Erg...@li...<mailto:Erg...@li...>
https://lists.sourceforge.net/lists/listinfo/ergatis-users

Re: [Ergatis-users] dynamic queue name

From: Jaysheel B. <bja...@gm...> - 2012-05-23 17:02:09

Hey Anup,
	I got latest version of tigr-htc and confirmed that the code snippet is there, compiled and replaced new jar file.  Now however, I get an error 

		sge_submit result Unable to read script file because of error: ERROR! -q option must have queue list argument
	
	In sge_submit.sh file I see SGE_DIRECTIVE -q but there is not value for queue

		# config variables
		#SGE_DIRECTIVE -l arch=lx*

		#SGE_DIRECTIVE -l mem_total=1024M
		#SGE_DIRECTIVE -p -20
		#SGE_DIRECTIVE -q 
		#SGE_DIRECTIVE -r y 
		#SGE_DIRECTIVE -N RunWorkflow

	I have confirmed that $WORKFLOW_HOME/server-conf/htc.conf has properties 

		# Configuration parameters used by the SGERunner class
		sge_def_queue=centos6-ergatis-test
		sge_pri_queue=centos6-ergatis-test


Jaysheel


On May 22, 2012, at 8:33 PM, Mahurkar, Anup wrote:

> Jaysheel,
> 
> Could you confirm that this snippet of code exists in the SgeRunner class? It should be in the createSubmitFile method.
> 
> I do not see the debugging lines in the log file you sent me. Hence the question.
> 
> Anup
> 
> // If the user has specified a particular queue (Config.CmdClass), then set the queue name
> // with the -q directive else use the default configured in the htc.conf
> logger.debug("Queue name specified as: " + config.getCmdClass());
> if (config.getCmdClass() != null ) {
> p_out.println(SGE_DIRECTIVE + " -q " + config.getCmdClass());
> }
> else if (HTCConfig.getProperty("sge_def_queue") != null) {
> p_out.println(SGE_DIRECTIVE + " -q " + HTCConfig.getProperty("sge_def_queue"));
> }
> else {
> logger.warn("No queue specified in config file. Jobs might fail if epilog/prolog not on all queues");
> }
> 
> 
> From: Jaysheel Bhavsar <bja...@gm...>
> Reply-To: "erg...@li..." <erg...@li...>
> Date: Tue, 22 May 2012 11:40:44 -0500
> To: "erg...@li..." <erg...@li...>
> Subject: Re: [Ergatis-users] dynamic queue name
> 
> Hey Anup,
> Attached is the pipeline.xml.log and sge_job.sh file.
> 
> Jaysheel
> 
> ------------------------------------------------------------------------------ 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 Erg...@li... https://lists.sourceforge.net/lists/listinfo/ergatis-users
> ------------------------------------------------------------------------------
> 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
> Erg...@li...
> https://lists.sourceforge.net/lists/listinfo/ergatis-users

Re: [Ergatis-users] dynamic queue name

From: Mahurkar, A. <ama...@so...> - 2012-05-23 01:33:20

Jaysheel,

Could you confirm that this snippet of code exists in the SgeRunner class? It should be in the createSubmitFile method.

I do not see the debugging lines in the log file you sent me. Hence the question.

Anup


// If the user has specified a particular queue (Config.CmdClass), then set the queue name

// with the -q directive else use the default configured in the htc.conf

logger.debug("Queue name specified as: " + config.getCmdClass());

if (config.getCmdClass() != null ) {

p_out.println(SGE_DIRECTIVE + " -q " + config.getCmdClass());

}

else if (HTCConfig.getProperty("sge_def_queue") != null) {

p_out.println(SGE_DIRECTIVE + " -q " + HTCConfig.getProperty("sge_def_queue"));

}

else {

logger.warn("No queue specified in config file. Jobs might fail if epilog/prolog not on all queues");

}


From: Jaysheel Bhavsar <bja...@gm...<mailto:bja...@gm...>>
Reply-To: "erg...@li...<mailto:erg...@li...>" <erg...@li...<mailto:erg...@li...>>
Date: Tue, 22 May 2012 11:40:44 -0500
To: "erg...@li...<mailto:erg...@li...>" <erg...@li...<mailto:erg...@li...>>
Subject: Re: [Ergatis-users] dynamic queue name

Hey Anup,
Attached is the pipeline.xml.log and sge_job.sh file.

Jaysheel

------------------------------------------------------------------------------ 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 Erg...@li...<mailto:Erg...@li...> https://lists.sourceforge.net/lists/listinfo/ergatis-users

Re: [Ergatis-users] dynamic queue name

From: Jaysheel B. <bja...@gm...> - 2012-05-22 21:31:58

ooop please disregard my previous email.

Jaysheel


On May 22, 2012, at 10:59 AM, Mahurkar, Anup wrote:

> Can you send me the log file an the shell script?
> 
> Anup
> 
> On May 22, 2012, at 11:54 AM, "Jaysheel Bhavsar" <bja...@gm...> wrote:
> 
>> Hey Anup,
>> I don't see any -q option in sge_job.sh script  written in mock_server_base.  In the log file I see a call to she_job.sh which looks like this
>> 
>> qsub -b n -C '#SGE_DIRECTIVE' /projects/bsi/RandD/ngs/ergatis/mock_server_base/working/0/4521/sge_job.sh
>> 
>> Which come from sge_submitter.sh from what I can tell.
>> 
>> Jaysheel
>> 
>> 
>> On May 21, 2012, at 8:22 PM, Mahurkar, Anup wrote:
>> 
>>> Jaysheel,
>>> 
>>> The -q will be specified in the sge_job.sh script for each of the jobs. Is
>>> it not there? If not could you send me the log file?
>>> 
>>> Anup
>>> 
>>> On 5/21/12 3:52 PM, "Jaysheel Bhavsar" <bja...@gm...> wrote:
>>> 
>>>> Hey Anup,
>>>> I got the workflow-3.1.x branch and re-installed workflow.  I updated
>>>> sge_def_queue and sge_pri_queue in ${WORKFLOW_HOME}/server-conf/htc.conf
>>>> file but jobs are still being submitted to default queue.  I don't see -q
>>>> option in the qsub command in sge_submitter.sh. Is there something I
>>>> missed?
>>>> 
>>>> Jaysheel
>>>> 
>>>> 
>>>> On May 18, 2012, at 2:30 PM, Mahurkar, Anup wrote:
>>>> 
>>>>> Jaysheel,
>>>>> 
>>>>> I have added the code to configure the default queue name that workflow
>>>>> uses as well as specifying a queue name in the workflow that will be
>>>>> honored. You will need to update the HTC and Workflow code. In the
>>>>> htc.conf file specify the default queue name to be used for workflow
>>>>> jobs.
>>>>> If nothing is specified in the command, it will look for the property
>>>>> "sge_def_queue" in the config file.
>>>>> 
>>>>> We have made slight changes to epilog, prolog, and sge_submitter scripts
>>>>> as well. So your best bet is to reinstall workflow.
>>>>> 
>>>>> Anup
>>>>> 
>>>>> 
>>>>> On 5/11/12 4:44 PM, "Mahurkar, Anup" <ama...@so...>
>>>>> wrote:
>>>>> 
>>>>>> Jaysheel,
>>>>>> 
>>>>>> I am working on this feature right now. Should have it ready early next
>>>>>> week. 
>>>>>> 
>>>>>> Anup
>>>>>> 
>>>>>> On May 11, 2012, at 4:39 PM, "Jaysheel Bhavsar" <bja...@gm...>
>>>>>> wrote:
>>>>>> 
>>>>>>> Hey guys,
>>>>>>>  I there a way to dynamically define queue name?  Currently queue
>>>>>>> name is set in $WORKFLOW_HOME/bin/sge_submitter.sh.  I would like to
>>>>>>> pass the queue name based on the pipeline I am executing, along with
>>>>>>> h_vmem and h_stack parameters.
>>>>>>> 
>>>>>>> Thanks
>>>>>>> Jaysheel
>>>>>>> 
>>>>>>> 
>>>>>>> -----------------------------------------------------------------------
>>>>>>> --
>>>>>>> -----
>>>>>>> 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
>>>>>>> Erg...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>>> 
>>>>>> 
>>>>>> ------------------------------------------------------------------------
>>>>>> --
>>>>>> ----
>>>>>> 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
>>>>>> Erg...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>> 
>>>>> 
>>>>> 
>>>>> -------------------------------------------------------------------------
>>>>> -----
>>>>> 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
>>>>> Erg...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>> 
>>>> 
>>>> --------------------------------------------------------------------------
>>>> ----
>>>> 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
>>>> Erg...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> 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
>>> Erg...@li...
>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>> 
>> ------------------------------------------------------------------------------
>> 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
>> Erg...@li...
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
> ------------------------------------------------------------------------------
> 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
> Erg...@li...
> https://lists.sourceforge.net/lists/listinfo/ergatis-users

Re: [Ergatis-users] dynamic queue name

From: Jaysheel B. <bja...@gm...> - 2012-05-22 20:22:27

Hey Anup, 
	I was looking through Ergatis cgi files to figure out when queue option is set, and looks like in Pipeline.pm if pipeline_submission_queue is set its add to runprefix which is written to pipeline.ID.run.sh file.  None of my pipeline.ID.run.sh have -q option.  I not sure if I am on track here.

	Below is the content of pipeline.ID.run.sh file.

Thanks
Jaysheel


#!/bin/bash

export SCRIPT_NAME="/cgi/run_pipeline.cgi"
export REQUEST_METHOD="POST"
export SCRIPT_FILENAME="/projects/bsi/RandD/ngs/ergatis/html/cgi/run_pipeline.cgi"
export WF_TEMPLATE="/projects/bsi/RandD/ngs/ergatis/workflow/templates"
export QUERY_STRING=""
export REMOTE_PORT="56650"
export WF_ROOT="/projects/bsi/RandD/ngs/ergatis/workflow"
export SGE_CELL="default"
export vappio_data_placement="0"
export HMMER_NCPU="1"
export CONTENT_TYPE="application/x-www-form-urlencoded"
export PERL5LIB="/home/m101236/perl5/lib/perl5/x86_64-linux-thread-multi:/home/m101236/perl5/lib/perl5::/usr/local/biotools/perl/5.14.2/lib/site_perl/5.14.2/x86_64-linux-thread-multi:/usr/local/biotools/perl/5.14.2/lib/site_perl/5.14.2:/usr/local/biotools/perl/5.14.2/lib/5.14.2/x86_64-linux-thread-multi:/usr/local/biotools/perl/5.14.2/lib/5.14.2"
export PATH="/projects/bsi/RandD/ngs/ergatis/workflow:/projects/bsi/RandD/ngs/ergatis/workflow/bin:/projects/bsi/RandD/ngs/ergatis/workflow/add-ons/bin:/projects/bsi/RandD/ngs/ergatis/workflow:/projects/bsi/RandD/ngs/ergatis/workflow/bin:/projects/bsi/RandD/ngs/ergatis/workflow/add-ons/bin:/home/m101236/perl5/bin:/usr/local/biotools/blast/blast-2.2.13/bin:/usr/local/biotools/hmmer/hmmer-3.0/bin:/usr/local/biotools/perl/5.14.2/bin:/home/biotools/sas/linux_SAS_9.2/bin:/usr/local/biotools/misc/ver1/bin:/usr/java/jdk1.6.0_05/bin:/usr/local/biotools/emboss/EMBOSS-5.0.0/bin:/usr/local/biotools/subversion/1.4.6/bin:/home/sge6_2/bin/lx24-amd64:/home/sge6_2/bin/lx24-amd64:/usr/local/biotools/python/2.7/bin:/usr/local/biotools/washu/ver1/bin:/usr/lib64/qt-3.3/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/biotools/git/1.7.9.2/bin:/home/m101236/bin:/projects/bsi/bictools/apps/alignment/samtools/samtools-0.1.18:/projects/bsi/bictools/apps/alignment/blat/34"
export GATEWAY_INTERFACE="CGI/1.1"
export DOCUMENT_ROOT="/projects/bsi/RandD/ngs/ergatis/html"
export HMM_SCRIPTS="/usr/local/devel/ANNOTATION/hmm/bin"
export LD_LIBRARY_PATH=""
export CONTENT_LENGTH="708"
export REMOTE_ADDR="172.31.194.244"
export WISECONFIGDIR="/usr/local/devel/ANNOTATION/EGC_utilities/WISE2/wise2.2.0/wisecfg"
export SGE_EXECD_PORT="537"
export REQUEST_URI="/cgi/run_pipeline.cgi"
export SGE_ARCH="lx26-amd64"
export WF_ROOT_INSTALL="/projects/bsi/RandD/ngs/ergatis/workflow"
export TMPDIR="/tmp"
export SGE_ROOT="/home/sge6_2"
export TERMCAP=""
export vappio_root="/opt/vappio_scripts"

  /projects/bsi/RandD/ngs/ergatis/workflow/RunWorkflow -i /projects/bsi/RandD/ngs/ergatis/projects/etest/workflow/runtime/pipeline/22/pipeline.xml -m 1 --init-heap=100m --max-heap=1024m  --logconf=/projects/bsi/RandD/ngs/ergatis/workflow/log4j.properties >& /projects/bsi/RandD/ngs/ergatis/projects/etest/workflow/runtime/pipeline/22/pipeline.xml.run.out




On May 22, 2012, at 10:59 AM, Mahurkar, Anup wrote:

> Can you send me the log file an the shell script?
> 
> Anup
> 
> On May 22, 2012, at 11:54 AM, "Jaysheel Bhavsar" <bja...@gm...> wrote:
> 
>> Hey Anup,
>> I don't see any -q option in sge_job.sh script  written in mock_server_base.  In the log file I see a call to she_job.sh which looks like this
>> 
>> qsub -b n -C '#SGE_DIRECTIVE' /projects/bsi/RandD/ngs/ergatis/mock_server_base/working/0/4521/sge_job.sh
>> 
>> Which come from sge_submitter.sh from what I can tell.
>> 
>> Jaysheel
>> 
>> 
>> On May 21, 2012, at 8:22 PM, Mahurkar, Anup wrote:
>> 
>>> Jaysheel,
>>> 
>>> The -q will be specified in the sge_job.sh script for each of the jobs. Is
>>> it not there? If not could you send me the log file?
>>> 
>>> Anup
>>> 
>>> On 5/21/12 3:52 PM, "Jaysheel Bhavsar" <bja...@gm...> wrote:
>>> 
>>>> Hey Anup,
>>>> I got the workflow-3.1.x branch and re-installed workflow.  I updated
>>>> sge_def_queue and sge_pri_queue in ${WORKFLOW_HOME}/server-conf/htc.conf
>>>> file but jobs are still being submitted to default queue.  I don't see -q
>>>> option in the qsub command in sge_submitter.sh. Is there something I
>>>> missed?
>>>> 
>>>> Jaysheel
>>>> 
>>>> 
>>>> On May 18, 2012, at 2:30 PM, Mahurkar, Anup wrote:
>>>> 
>>>>> Jaysheel,
>>>>> 
>>>>> I have added the code to configure the default queue name that workflow
>>>>> uses as well as specifying a queue name in the workflow that will be
>>>>> honored. You will need to update the HTC and Workflow code. In the
>>>>> htc.conf file specify the default queue name to be used for workflow
>>>>> jobs.
>>>>> If nothing is specified in the command, it will look for the property
>>>>> "sge_def_queue" in the config file.
>>>>> 
>>>>> We have made slight changes to epilog, prolog, and sge_submitter scripts
>>>>> as well. So your best bet is to reinstall workflow.
>>>>> 
>>>>> Anup
>>>>> 
>>>>> 
>>>>> On 5/11/12 4:44 PM, "Mahurkar, Anup" <ama...@so...>
>>>>> wrote:
>>>>> 
>>>>>> Jaysheel,
>>>>>> 
>>>>>> I am working on this feature right now. Should have it ready early next
>>>>>> week. 
>>>>>> 
>>>>>> Anup
>>>>>> 
>>>>>> On May 11, 2012, at 4:39 PM, "Jaysheel Bhavsar" <bja...@gm...>
>>>>>> wrote:
>>>>>> 
>>>>>>> Hey guys,
>>>>>>>  I there a way to dynamically define queue name?  Currently queue
>>>>>>> name is set in $WORKFLOW_HOME/bin/sge_submitter.sh.  I would like to
>>>>>>> pass the queue name based on the pipeline I am executing, along with
>>>>>>> h_vmem and h_stack parameters.
>>>>>>> 
>>>>>>> Thanks
>>>>>>> Jaysheel
>>>>>>> 
>>>>>>> 
>>>>>>> -----------------------------------------------------------------------
>>>>>>> --
>>>>>>> -----
>>>>>>> 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
>>>>>>> Erg...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>>> 
>>>>>> 
>>>>>> ------------------------------------------------------------------------
>>>>>> --
>>>>>> ----
>>>>>> 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
>>>>>> Erg...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>> 
>>>>> 
>>>>> 
>>>>> -------------------------------------------------------------------------
>>>>> -----
>>>>> 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
>>>>> Erg...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>> 
>>>> 
>>>> --------------------------------------------------------------------------
>>>> ----
>>>> 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
>>>> Erg...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> 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
>>> Erg...@li...
>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>> 
>> ------------------------------------------------------------------------------
>> 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
>> Erg...@li...
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
> ------------------------------------------------------------------------------
> 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
> Erg...@li...
> https://lists.sourceforge.net/lists/listinfo/ergatis-users

Re: [Ergatis-users] dynamic queue name

From: Jaysheel B. <bja...@gm...> - 2012-05-22 16:41:29

Hey Anup,
	Attached is the pipeline.xml.log and sge_job.sh file.

Jaysheel



On May 22, 2012, at 10:59 AM, Mahurkar, Anup wrote:

> Can you send me the log file an the shell script?
> 
> Anup
> 
> On May 22, 2012, at 11:54 AM, "Jaysheel Bhavsar" <bja...@gm...> wrote:
> 
>> Hey Anup,
>> I don't see any -q option in sge_job.sh script  written in mock_server_base.  In the log file I see a call to she_job.sh which looks like this
>> 
>> qsub -b n -C '#SGE_DIRECTIVE' /projects/bsi/RandD/ngs/ergatis/mock_server_base/working/0/4521/sge_job.sh
>> 
>> Which come from sge_submitter.sh from what I can tell.
>> 
>> Jaysheel
>> 
>> 
>> On May 21, 2012, at 8:22 PM, Mahurkar, Anup wrote:
>> 
>>> Jaysheel,
>>> 
>>> The -q will be specified in the sge_job.sh script for each of the jobs. Is
>>> it not there? If not could you send me the log file?
>>> 
>>> Anup
>>> 
>>> On 5/21/12 3:52 PM, "Jaysheel Bhavsar" <bja...@gm...> wrote:
>>> 
>>>> Hey Anup,
>>>> I got the workflow-3.1.x branch and re-installed workflow.  I updated
>>>> sge_def_queue and sge_pri_queue in ${WORKFLOW_HOME}/server-conf/htc.conf
>>>> file but jobs are still being submitted to default queue.  I don't see -q
>>>> option in the qsub command in sge_submitter.sh. Is there something I
>>>> missed?
>>>> 
>>>> Jaysheel
>>>> 
>>>> 
>>>> On May 18, 2012, at 2:30 PM, Mahurkar, Anup wrote:
>>>> 
>>>>> Jaysheel,
>>>>> 
>>>>> I have added the code to configure the default queue name that workflow
>>>>> uses as well as specifying a queue name in the workflow that will be
>>>>> honored. You will need to update the HTC and Workflow code. In the
>>>>> htc.conf file specify the default queue name to be used for workflow
>>>>> jobs.
>>>>> If nothing is specified in the command, it will look for the property
>>>>> "sge_def_queue" in the config file.
>>>>> 
>>>>> We have made slight changes to epilog, prolog, and sge_submitter scripts
>>>>> as well. So your best bet is to reinstall workflow.
>>>>> 
>>>>> Anup
>>>>> 
>>>>> 
>>>>> On 5/11/12 4:44 PM, "Mahurkar, Anup" <ama...@so...>
>>>>> wrote:
>>>>> 
>>>>>> Jaysheel,
>>>>>> 
>>>>>> I am working on this feature right now. Should have it ready early next
>>>>>> week. 
>>>>>> 
>>>>>> Anup
>>>>>> 
>>>>>> On May 11, 2012, at 4:39 PM, "Jaysheel Bhavsar" <bja...@gm...>
>>>>>> wrote:
>>>>>> 
>>>>>>> Hey guys,
>>>>>>>  I there a way to dynamically define queue name?  Currently queue
>>>>>>> name is set in $WORKFLOW_HOME/bin/sge_submitter.sh.  I would like to
>>>>>>> pass the queue name based on the pipeline I am executing, along with
>>>>>>> h_vmem and h_stack parameters.
>>>>>>> 
>>>>>>> Thanks
>>>>>>> Jaysheel
>>>>>>> 
>>>>>>> 
>>>>>>> -----------------------------------------------------------------------
>>>>>>> --
>>>>>>> -----
>>>>>>> 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
>>>>>>> Erg...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>>> 
>>>>>> 
>>>>>> ------------------------------------------------------------------------
>>>>>> --
>>>>>> ----
>>>>>> 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
>>>>>> Erg...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>> 
>>>>> 
>>>>> 
>>>>> -------------------------------------------------------------------------
>>>>> -----
>>>>> 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
>>>>> Erg...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>> 
>>>> 
>>>> --------------------------------------------------------------------------
>>>> ----
>>>> 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
>>>> Erg...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> 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
>>> Erg...@li...
>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>> 
>> ------------------------------------------------------------------------------
>> 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
>> Erg...@li...
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
> ------------------------------------------------------------------------------
> 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
> Erg...@li...
> https://lists.sourceforge.net/lists/listinfo/ergatis-users

Re: [Ergatis-users] dynamic queue name

From: Mahurkar, A. <ama...@so...> - 2012-05-22 15:59:59

Can you send me the log file an the shell script?

Anup

On May 22, 2012, at 11:54 AM, "Jaysheel Bhavsar" <bja...@gm...<mailto:bja...@gm...>> wrote:

Hey Anup,
I don't see any -q option in sge_job.sh script written in mock_server_base. In the log file I see a call to she_job.sh which looks like this

qsub -b n -C '#SGE_DIRECTIVE' /projects/bsi/RandD/ngs/ergatis/mock_server_base/working/0/4521/sge_job.sh

Which come from sge_submitter.sh from what I can tell.

Jaysheel

On May 21, 2012, at 8:22 PM, Mahurkar, Anup wrote:

Jaysheel,

The -q will be specified in the sge_job.sh script for each of the jobs. Is
it not there? If not could you send me the log file?

Anup

On 5/21/12 3:52 PM, "Jaysheel Bhavsar" <bja...@gm...<mailto:bja...@gm...>> wrote:

Hey Anup,
I got the workflow-3.1.x branch and re-installed workflow. I updated
sge_def_queue and sge_pri_queue in ${WORKFLOW_HOME}/server-conf/htc.conf
file but jobs are still being submitted to default queue. I don't see -q
option in the qsub command in sge_submitter.sh. Is there something I
missed?

Jaysheel

On May 18, 2012, at 2:30 PM, Mahurkar, Anup wrote:

Jaysheel,

I have added the code to configure the default queue name that workflow
uses as well as specifying a queue name in the workflow that will be
honored. You will need to update the HTC and Workflow code. In the
htc.conf file specify the default queue name to be used for workflow
jobs.
If nothing is specified in the command, it will look for the property
"sge_def_queue" in the config file.

We have made slight changes to epilog, prolog, and sge_submitter scripts
as well. So your best bet is to reinstall workflow.

Anup

On 5/11/12 4:44 PM, "Mahurkar, Anup" <ama...@so...<mailto:ama...@so...>>
wrote:

Jaysheel,

I am working on this feature right now. Should have it ready early next
week.

Anup

On May 11, 2012, at 4:39 PM, "Jaysheel Bhavsar" <bja...@gm...<mailto:bja...@gm...>>
wrote:

Hey guys,
I there a way to dynamically define queue name? Currently queue
name is set in $WORKFLOW_HOME/bin/sge_submitter.sh. I would like to
pass the queue name based on the pipeline I am executing, along with
h_vmem and h_stack parameters.

Thanks
Jaysheel

-----------------------------------------------------------------------
--
-----
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
Erg...@li...<mailto:Erg...@li...>
https://lists.sourceforge.net/lists/listinfo/ergatis-users

------------------------------------------------------------------------
--
----
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
Erg...@li...<mailto:Erg...@li...>
https://lists.sourceforge.net/lists/listinfo/ergatis-users

-------------------------------------------------------------------------
-----
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
Erg...@li...<mailto:Erg...@li...>
https://lists.sourceforge.net/lists/listinfo/ergatis-users

--------------------------------------------------------------------------
----
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
Erg...@li...<mailto:Erg...@li...>
https://lists.sourceforge.net/lists/listinfo/ergatis-users

------------------------------------------------------------------------------
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
Erg...@li...<mailto:Erg...@li...>
https://lists.sourceforge.net/lists/listinfo/ergatis-users

------------------------------------------------------------------------------
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
Erg...@li...<mailto:Erg...@li...>
https://lists.sourceforge.net/lists/listinfo/ergatis-users

Re: [Ergatis-users] dynamic queue name

From: Jaysheel B. <bja...@gm...> - 2012-05-22 15:54:41

Hey Anup,
	I don't see any -q option in sge_job.sh script  written in mock_server_base.  In the log file I see a call to she_job.sh which looks like this

		qsub -b n -C '#SGE_DIRECTIVE' /projects/bsi/RandD/ngs/ergatis/mock_server_base/working/0/4521/sge_job.sh

	Which come from sge_submitter.sh from what I can tell.

Jaysheel


On May 21, 2012, at 8:22 PM, Mahurkar, Anup wrote:

> Jaysheel,
> 
> The -q will be specified in the sge_job.sh script for each of the jobs. Is
> it not there? If not could you send me the log file?
> 
> Anup
> 
> On 5/21/12 3:52 PM, "Jaysheel Bhavsar" <bja...@gm...> wrote:
> 
>> Hey Anup,
>> 	I got the workflow-3.1.x branch and re-installed workflow.  I updated
>> sge_def_queue and sge_pri_queue in ${WORKFLOW_HOME}/server-conf/htc.conf
>> file but jobs are still being submitted to default queue.  I don't see -q
>> option in the qsub command in sge_submitter.sh. Is there something I
>> missed?
>> 
>> Jaysheel
>> 
>> 
>> On May 18, 2012, at 2:30 PM, Mahurkar, Anup wrote:
>> 
>>> Jaysheel,
>>> 
>>> I have added the code to configure the default queue name that workflow
>>> uses as well as specifying a queue name in the workflow that will be
>>> honored. You will need to update the HTC and Workflow code. In the
>>> htc.conf file specify the default queue name to be used for workflow
>>> jobs.
>>> If nothing is specified in the command, it will look for the property
>>> "sge_def_queue" in the config file.
>>> 
>>> We have made slight changes to epilog, prolog, and sge_submitter scripts
>>> as well. So your best bet is to reinstall workflow.
>>> 
>>> Anup
>>> 
>>> 
>>> On 5/11/12 4:44 PM, "Mahurkar, Anup" <ama...@so...>
>>> wrote:
>>> 
>>>> Jaysheel,
>>>> 
>>>> I am working on this feature right now. Should have it ready early next
>>>> week. 
>>>> 
>>>> Anup
>>>> 
>>>> On May 11, 2012, at 4:39 PM, "Jaysheel Bhavsar" <bja...@gm...>
>>>> wrote:
>>>> 
>>>>> Hey guys,
>>>>>  I there a way to dynamically define queue name?  Currently queue
>>>>> name is set in $WORKFLOW_HOME/bin/sge_submitter.sh.  I would like to
>>>>> pass the queue name based on the pipeline I am executing, along with
>>>>> h_vmem and h_stack parameters.
>>>>> 
>>>>> Thanks
>>>>> Jaysheel
>>>>> 
>>>>> 
>>>>> -----------------------------------------------------------------------
>>>>> --
>>>>> -----
>>>>> 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
>>>>> Erg...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>> 
>>>> 
>>>> ------------------------------------------------------------------------
>>>> --
>>>> ----
>>>> 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
>>>> Erg...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>> 
>>> 
>>> 
>>> -------------------------------------------------------------------------
>>> -----
>>> 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
>>> Erg...@li...
>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>> 
>> 
>> --------------------------------------------------------------------------
>> ----
>> 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
>> Erg...@li...
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
> 
> 
> ------------------------------------------------------------------------------
> 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
> Erg...@li...
> https://lists.sourceforge.net/lists/listinfo/ergatis-users

Re: [Ergatis-users] dynamic queue name

From: Mahurkar, A. <ama...@so...> - 2012-05-22 01:22:18

Jaysheel,

The -q will be specified in the sge_job.sh script for each of the jobs. Is
it not there? If not could you send me the log file?

Anup

On 5/21/12 3:52 PM, "Jaysheel Bhavsar" <bja...@gm...> wrote:

>Hey Anup,
>	I got the workflow-3.1.x branch and re-installed workflow.  I updated
>sge_def_queue and sge_pri_queue in ${WORKFLOW_HOME}/server-conf/htc.conf
>file but jobs are still being submitted to default queue.  I don't see -q
>option in the qsub command in sge_submitter.sh. Is there something I
>missed?
>
>Jaysheel
>
>
>On May 18, 2012, at 2:30 PM, Mahurkar, Anup wrote:
>
>> Jaysheel,
>> 
>> I have added the code to configure the default queue name that workflow
>> uses as well as specifying a queue name in the workflow that will be
>> honored. You will need to update the HTC and Workflow code. In the
>> htc.conf file specify the default queue name to be used for workflow
>>jobs.
>> If nothing is specified in the command, it will look for the property
>> "sge_def_queue" in the config file.
>> 
>> We have made slight changes to epilog, prolog, and sge_submitter scripts
>> as well. So your best bet is to reinstall workflow.
>> 
>> Anup
>> 
>> 
>> On 5/11/12 4:44 PM, "Mahurkar, Anup" <ama...@so...>
>>wrote:
>> 
>>> Jaysheel,
>>> 
>>> I am working on this feature right now. Should have it ready early next
>>> week. 
>>> 
>>> Anup
>>> 
>>> On May 11, 2012, at 4:39 PM, "Jaysheel Bhavsar" <bja...@gm...>
>>> wrote:
>>> 
>>>> Hey guys,
>>>>   I there a way to dynamically define queue name?  Currently queue
>>>> name is set in $WORKFLOW_HOME/bin/sge_submitter.sh.  I would like to
>>>> pass the queue name based on the pipeline I am executing, along with
>>>> h_vmem and h_stack parameters.
>>>> 
>>>> Thanks
>>>> Jaysheel
>>>> 
>>>> 
>>>>-----------------------------------------------------------------------
>>>>--
>>>> -----
>>>> 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
>>>> Erg...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>> 
>>> 
>>>------------------------------------------------------------------------
>>>--
>>> ----
>>> 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
>>> Erg...@li...
>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>> 
>> 
>> 
>>-------------------------------------------------------------------------
>>-----
>> 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
>> Erg...@li...
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>
>
>--------------------------------------------------------------------------
>----
>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
>Erg...@li...
>https://lists.sourceforge.net/lists/listinfo/ergatis-users

Re: [Ergatis-users] dynamic queue name

From: Jaysheel B. <bja...@gm...> - 2012-05-21 19:52:33

Hey Anup,
	I got the workflow-3.1.x branch and re-installed workflow.  I updated sge_def_queue and sge_pri_queue in ${WORKFLOW_HOME}/server-conf/htc.conf file but jobs are still being submitted to default queue.  I don't see -q option in the qsub command in sge_submitter.sh. Is there something I missed?

Jaysheel


On May 18, 2012, at 2:30 PM, Mahurkar, Anup wrote:

> Jaysheel,
> 
> I have added the code to configure the default queue name that workflow
> uses as well as specifying a queue name in the workflow that will be
> honored. You will need to update the HTC and Workflow code. In the
> htc.conf file specify the default queue name to be used for workflow jobs.
> If nothing is specified in the command, it will look for the property
> "sge_def_queue" in the config file.
> 
> We have made slight changes to epilog, prolog, and sge_submitter scripts
> as well. So your best bet is to reinstall workflow.
> 
> Anup
> 
> 
> On 5/11/12 4:44 PM, "Mahurkar, Anup" <ama...@so...> wrote:
> 
>> Jaysheel,
>> 
>> I am working on this feature right now. Should have it ready early next
>> week. 
>> 
>> Anup
>> 
>> On May 11, 2012, at 4:39 PM, "Jaysheel Bhavsar" <bja...@gm...>
>> wrote:
>> 
>>> Hey guys,
>>>   I there a way to dynamically define queue name?  Currently queue
>>> name is set in $WORKFLOW_HOME/bin/sge_submitter.sh.  I would like to
>>> pass the queue name based on the pipeline I am executing, along with
>>> h_vmem and h_stack parameters.
>>> 
>>> Thanks
>>> Jaysheel
>>> 
>>> -------------------------------------------------------------------------
>>> -----
>>> 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
>>> Erg...@li...
>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>> 
>> --------------------------------------------------------------------------
>> ----
>> 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
>> Erg...@li...
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
> 
> 
> ------------------------------------------------------------------------------
> 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
> Erg...@li...
> https://lists.sourceforge.net/lists/listinfo/ergatis-users

Re: [Ergatis-users] dynamic queue name

From: Mahurkar, A. <ama...@so...> - 2012-05-21 18:45:46

Yes. It is in the branch.

-----Original Message-----
From: Jaysheel Bhavsar [mailto:bja...@gm...] 
Sent: Monday, May 21, 2012 1:44 PM
To: erg...@li...
Subject: Re: [Ergatis-users] dynamic queue name

Hey
	Anup, I don't see a releaser version should I download workflow-3.1.x branch?

Jaysheel


On May 18, 2012, at 2:30 PM, Mahurkar, Anup wrote:

> Jaysheel,
> 
> I have added the code to configure the default queue name that 
> workflow uses as well as specifying a queue name in the workflow that 
> will be honored. You will need to update the HTC and Workflow code. In 
> the htc.conf file specify the default queue name to be used for workflow jobs.
> If nothing is specified in the command, it will look for the property 
> "sge_def_queue" in the config file.
> 
> We have made slight changes to epilog, prolog, and sge_submitter 
> scripts as well. So your best bet is to reinstall workflow.
> 
> Anup
> 
> 
> On 5/11/12 4:44 PM, "Mahurkar, Anup" <ama...@so...> wrote:
> 
>> Jaysheel,
>> 
>> I am working on this feature right now. Should have it ready early 
>> next week.
>> 
>> Anup
>> 
>> On May 11, 2012, at 4:39 PM, "Jaysheel Bhavsar" <bja...@gm...>
>> wrote:
>> 
>>> Hey guys,
>>>   I there a way to dynamically define queue name?  Currently queue 
>>> name is set in $WORKFLOW_HOME/bin/sge_submitter.sh.  I would like to 
>>> pass the queue name based on the pipeline I am executing, along with 
>>> h_vmem and h_stack parameters.
>>> 
>>> Thanks
>>> Jaysheel
>>> 
>>> --------------------------------------------------------------------
>>> -----
>>> -----
>>> 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
>>> Erg...@li...
>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>> 
>> ---------------------------------------------------------------------
>> -----
>> ----
>> 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
>> Erg...@li...
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
> 
> 
> ----------------------------------------------------------------------
> --------
> 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
> Erg...@li...
> https://lists.sourceforge.net/lists/listinfo/ergatis-users


------------------------------------------------------------------------------
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
Erg...@li...
https://lists.sourceforge.net/lists/listinfo/ergatis-users

Re: [Ergatis-users] dynamic queue name

From: Jaysheel B. <bja...@gm...> - 2012-05-21 17:44:12

Hey
	Anup, I don't see a releaser version should I download workflow-3.1.x branch?

Jaysheel


On May 18, 2012, at 2:30 PM, Mahurkar, Anup wrote:

> Jaysheel,
> 
> I have added the code to configure the default queue name that workflow
> uses as well as specifying a queue name in the workflow that will be
> honored. You will need to update the HTC and Workflow code. In the
> htc.conf file specify the default queue name to be used for workflow jobs.
> If nothing is specified in the command, it will look for the property
> "sge_def_queue" in the config file.
> 
> We have made slight changes to epilog, prolog, and sge_submitter scripts
> as well. So your best bet is to reinstall workflow.
> 
> Anup
> 
> 
> On 5/11/12 4:44 PM, "Mahurkar, Anup" <ama...@so...> wrote:
> 
>> Jaysheel,
>> 
>> I am working on this feature right now. Should have it ready early next
>> week. 
>> 
>> Anup
>> 
>> On May 11, 2012, at 4:39 PM, "Jaysheel Bhavsar" <bja...@gm...>
>> wrote:
>> 
>>> Hey guys,
>>>   I there a way to dynamically define queue name?  Currently queue
>>> name is set in $WORKFLOW_HOME/bin/sge_submitter.sh.  I would like to
>>> pass the queue name based on the pipeline I am executing, along with
>>> h_vmem and h_stack parameters.
>>> 
>>> Thanks
>>> Jaysheel
>>> 
>>> -------------------------------------------------------------------------
>>> -----
>>> 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
>>> Erg...@li...
>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>> 
>> --------------------------------------------------------------------------
>> ----
>> 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
>> Erg...@li...
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
> 
> 
> ------------------------------------------------------------------------------
> 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
> Erg...@li...
> https://lists.sourceforge.net/lists/listinfo/ergatis-users

Re: [Ergatis-users] dynamic queue name

From: Mahurkar, A. <ama...@so...> - 2012-05-18 19:30:43

Jaysheel,

I have added the code to configure the default queue name that workflow
uses as well as specifying a queue name in the workflow that will be
honored. You will need to update the HTC and Workflow code. In the
htc.conf file specify the default queue name to be used for workflow jobs.
If nothing is specified in the command, it will look for the property
"sge_def_queue" in the config file.

We have made slight changes to epilog, prolog, and sge_submitter scripts
as well. So your best bet is to reinstall workflow.

Anup


On 5/11/12 4:44 PM, "Mahurkar, Anup" <ama...@so...> wrote:

>Jaysheel,
>
>I am working on this feature right now. Should have it ready early next
>week. 
>
>Anup
>
>On May 11, 2012, at 4:39 PM, "Jaysheel Bhavsar" <bja...@gm...>
>wrote:
>
>> Hey guys,
>>    I there a way to dynamically define queue name?  Currently queue
>>name is set in $WORKFLOW_HOME/bin/sge_submitter.sh.  I would like to
>>pass the queue name based on the pipeline I am executing, along with
>>h_vmem and h_stack parameters.
>> 
>> Thanks
>> Jaysheel
>> 
>>-------------------------------------------------------------------------
>>-----
>> 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
>> Erg...@li...
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>
>--------------------------------------------------------------------------
>----
>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
>Erg...@li...
>https://lists.sourceforge.net/lists/listinfo/ergatis-users

Re: [Ergatis-users] dynamic queue name

From: Mahurkar, A. <ama...@so...> - 2012-05-11 20:45:04

Jaysheel,

I am working on this feature right now. Should have it ready early next week. 

Anup

On May 11, 2012, at 4:39 PM, "Jaysheel Bhavsar" <bja...@gm...> wrote:

> Hey guys,
>    I there a way to dynamically define queue name?  Currently queue name is set in $WORKFLOW_HOME/bin/sge_submitter.sh.  I would like to pass the queue name based on the pipeline I am executing, along with h_vmem and h_stack parameters.
> 
> Thanks
> Jaysheel
> ------------------------------------------------------------------------------
> 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
> Erg...@li...
> https://lists.sourceforge.net/lists/listinfo/ergatis-users

[Ergatis-users] dynamic queue name

From: Jaysheel B. <bja...@gm...> - 2012-05-11 20:39:36

Hey guys,
	I there a way to dynamically define queue name?  Currently queue name is set in $WORKFLOW_HOME/bin/sge_submitter.sh.  I would like to pass the queue name based on the pipeline I am executing, along with h_vmem and h_stack parameters.

Thanks
Jaysheel

[Ergatis-users] workflow setup.

From: Jaysheel B. <bja...@gm...> - 2012-05-03 19:47:02

Attachments: error.txt workflow.config.txt unittest.log

Hey guys,
	I am setting up a new instance of Ergatis-Workflow.  I have installed workflow but can't run a successful test (RunIDTest mode=text).  Error I get is 
		
			testGenerateID(org.tigr.workflow.common.test.TestIDGenerator)org.tigr.antware.shared.exceptions.IDGenerationException: Could not create an instance of ID generator class. null

	full error is attached.  I created a small java test program to check if I can connect to db, and that works fine.  My workflow.config file and log file generated in wf_test is attached.


Thanks
Jaysheel

Re: [Ergatis-users] PERL5LIB

From: Mariette <jma...@to...> - 2012-05-03 15:09:14

Hi again,

we have some other informations. From the Pipeline.pm, we changed the 
sudo command by:
   sudo -s -E -u <user> ... instead of sudo -E -u <user>: here it's 
working when running the pipeline.X.run.sh script within a terminal.
However I got a "no tty error" from the ergatis website, as ergatis is 
run as apache, this does sound right. My guess would be that
our apache user should have in is env the LD_LIBRARY_PATH correctly 
settled.

Does this make sense to you ?

Jerome




Le 03/05/2012 16:03, Mariette a écrit :
>
> Joshua,
>
> We got the same behaviour for both!
>
> On our old system, we did the same (adding sudo -E -u ng6 echo 
> $LD_LIBRARY_PATH > /work/tmp/tt.ld; sudo -E -u ng6 env > 
> /work/tmp/tt.env on the pipeline.X.run.sh script) and we got the same 
> result (nothing on the env, but ok when using the $LD_LIBRARY_PATH)
>
> We run the same component (executing the 'env') on our old system what 
> lead to a correct LD_LIBARY_PATH.
>
> What we tested also is to take off the sudo prefix from the 
> pipeline.X.run.sh script, here the LD_LIBARY_PATH is ok! So we are 
> pretty sure it's coming from the sudo. What we did is to add the 
> LD_LIBRARY_PATH to the env_keep variable without any success!
>
> Defaults    env_reset
> Defaults    env_keep =  "COLORS DISPLAY HOSTNAME HISTSIZE INPUTRC 
> KDEDIR LS_COLORS"
> ...
> Defaults    env_keep += "LC_TIME LC_ALL LANGUAGE LINGUAS _XKB_CHARSET 
> XAUTHORITY LD_LIBRARY_PATH"
> Defaults    env_keep += "PATH "
>
> Something weird is that the PATH is ok in the pipeline execution, but 
> not the LD_LIBARY_PATH and PERL5LIB variables, even if we did the same 
> with those variables !
>
> How this variables are retreived within tigr workflow ? There is any 
> changed since last workflow version using those variables ?
>
> Jerome
>
>
>
>
>
>
>
> Le 03/05/2012 15:44, Joshua Orvis a écrit :
>> Jerome -
>>
>> This information is helpful.  In the last test that you mentioned, 
>> when running in Ergatis, was that step distributed on the grid at all 
>> or just run locally?
>>
>> JO
>>
>> On Thu, May 3, 2012 at 7:31 AM, Mariette <jma...@to... 
>> <mailto:jma...@to...>> wrote:
>>
>>
>>     Joshua,
>>
>>     Just so you know, we are running ergatis on a red hat 6 system,
>>     have you make it run on it ?
>>
>>     I get a litle further. From the pipeline.X.run.sh
>>     <http://pipeline.X.run.sh> file, I added the folowing lines:
>>
>>     sudo -E -u ng6 echo $LD_LIBRARY_PATH > /work/tmp/tt.ld
>>     sudo -E -u ng6 env > /work/tmp/tt.env
>>
>>     the /work/tmp/tt.ld file does contain the right path! However the
>>     /work/tmp/tt.env does not contain the LD_LIBARY_PATH at all!
>>
>>     An other point, within ergatis, a simple component running a
>>     'env' command return a LD_LIBRARY_PATH set to:
>>
>>     LD_LIBRARY_PATH=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64/server:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../lib/amd64
>>
>>     I tryed to figure out where that path could come from ... any idea ?
>>
>>
>>     thanks for your time!
>>
>>     Jérôme
>>
>>
>>
>>
>>
>>     Le 03/05/2012 10:02, Mariette a écrit :
>>>
>>>     Joshua,
>>>
>>>     they are pretty close, SGE adds some variables (SGE_BINARY_PATH,
>>>     SGE_CWD_PATH ...), but the PATH, the LD_LIBRARY_PATH are the
>>>     same within or not a qsub.
>>>
>>>     Jerome
>>>
>>>
>>>
>>>
>>>     Le 02/05/2012 17:29, Joshua Orvis a écrit :
>>>>     Jerome -
>>>>
>>>>     I think you should take a step back here.  Take Ergatis and
>>>>     Workflow Engine completely out of this.  What happens if you
>>>>     write a shell script that sets an ENV variable and then does
>>>>     the equivalent of a qsub to run your script that prints your
>>>>     environment to a file?  Is the ENV retained?
>>>>
>>>>     Joshua
>>>>
>>>>     On Wed, May 2, 2012 at 10:05 AM, Mariette
>>>>     <jma...@to... <mailto:jma...@to...>>
>>>>     wrote:
>>>>
>>>>
>>>>         Hi again,
>>>>
>>>>         so I made a component with just a env as execution, and the
>>>>         paths are not right !
>>>>         What are the steps after the execution of the script ?
>>>>
>>>>         Jerome
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>         Le 02/05/2012 16:48, Mariette a écrit :
>>>>>
>>>>>         Hi everyone,
>>>>>
>>>>>         I'm still facing the same probleme ... I moved on by
>>>>>         making a sed to all ergatis scripts to add the right
>>>>>         PERL5LIB path, but this is just a patch! I need to do the
>>>>>         same with the
>>>>>         LD_LIBRARY_PATH and the PATH variables ... but it's
>>>>>         working with non of them!
>>>>>
>>>>>         The script produced (pipeline.*.run.sh) is correctly
>>>>>         written down, and the execution with an echo right after
>>>>>         display the right path !
>>>>>
>>>>>         What we changed is the full cluster, so we are running the
>>>>>         open sge version and no longer the sun sge.
>>>>>
>>>>>         any idea on debugging ?
>>>>>         thanks,
>>>>>
>>>>>         Jerome
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>         Le 20/04/2012 17:08, Joshua Orvis a écrit :
>>>>>>         Jérôme -
>>>>>>
>>>>>>         The script looks right, and that was going to be my next
>>>>>>         question.  Yes, Ergatis writes that shell script and then
>>>>>>         executes it, and within that script RunWorkflow is
>>>>>>         called.  Has anything else changed in your SGE
>>>>>>         configuration?  You could replace the RunWorkflow line in
>>>>>>         the script with your own qsub test that just prints out
>>>>>>         the environment once it's placed on a node.  This would
>>>>>>         allow you to see if it's within the SGE job submission
>>>>>>         that your job is being lost.  Out of curiosity, do you
>>>>>>         have the 'submit_pipelines_as_jobs' option turned on in
>>>>>>         the ergatis.ini file?
>>>>>>
>>>>>>         Joshua
>>>>>>
>>>>>>
>>>>>>
>>>>>>         2012/4/20 Mariette <jma...@to...
>>>>>>         <mailto:jma...@to...>>
>>>>>>
>>>>>>
>>>>>>             Joshua,
>>>>>>
>>>>>>             there is something I'm missing. I did modified the
>>>>>>             Pipeline.pm so the PERL5LIB is settled. When I take a
>>>>>>             look at the pipeline.XXX.run.sh
>>>>>>             <http://pipeline.XXX.run.sh> script written down,
>>>>>>             the variable is correctly set ! Is this script used
>>>>>>             to process the workflow ?
>>>>>>
>>>>>>             Jérôme
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>             Le 19/04/2012 10:16, Mariette a écrit :
>>>>>>>
>>>>>>>             Joshua,
>>>>>>>             the file is in attachement. The error returned is:
>>>>>>>
>>>>>>>             Can't locate Config/IniFiles.pm in @INC (@INC
>>>>>>>             contains:
>>>>>>>             /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5//x86_64-linux-thread-multi
>>>>>>>             /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5/
>>>>>>>             /usr/local/lib64/perl5 /usr/local/share/perl5
>>>>>>>             /usr/lib64/perl5/vendor_perl
>>>>>>>             /usr/share/perl5/vendor_perl /usr/lib64/perl5/5.10.0
>>>>>>>             /usr/lib64/perl5 /usr/share/perl5 .
>>>>>>>             /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/5.8.8/x86_64-linux-thread-multi
>>>>>>>             /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/5.8.8)
>>>>>>>             at
>>>>>>>             /usr/local/bioinfo/src/ergatisng6/v2r17b2/bin/replace_template_keys.pl
>>>>>>>             <http://replace_template_keys.pl> line 17
>>>>>>>
>>>>>>>             Paths I provided to Pipeline.pm are not in @INC.
>>>>>>>
>>>>>>>             thanks for your time!
>>>>>>>             Jérôme
>>>>>>>
>>>>>>>
>>>>>>>             Le 13/04/2012 20:32, Joshua Orvis a écrit :
>>>>>>>>             Jerome -
>>>>>>>>
>>>>>>>>             Do you mind sending me your modified Pipeline.pm
>>>>>>>>             file?  I don't see any changes here that would
>>>>>>>>             cause the ENV changes you make in the
>>>>>>>>             _setup_environment() method of Pipeline.pm to not
>>>>>>>>             make it to the execution of the
>>>>>>>>             create_template_keys.pl
>>>>>>>>             <http://create_template_keys.pl> script.  I'd like
>>>>>>>>             to test it locally.
>>>>>>>>
>>>>>>>>             Joshua
>>>>>>>>
>>>>>>>>
>>>>>>>>             On Fri, Apr 13, 2012 at 1:14 PM, Joshua Orvis
>>>>>>>>             <jo...@gm... <mailto:jo...@gm...>> wrote:
>>>>>>>>
>>>>>>>>                 Jérôme -
>>>>>>>>
>>>>>>>>                 I'm taking a look at this.
>>>>>>>>
>>>>>>>>                 Joshua
>>>>>>>>
>>>>>>>>                 On Fri, Apr 13, 2012 at 10:24 AM, Mariette
>>>>>>>>                 <jma...@to...
>>>>>>>>                 <mailto:jma...@to...>> wrote:
>>>>>>>>
>>>>>>>>                     Hi everyone,
>>>>>>>>
>>>>>>>>                     the environment we are running ergatis on
>>>>>>>>                     is a bit tricky. The perl libs
>>>>>>>>                     are not located on the usual perl path.
>>>>>>>>                     usually when I have this kind of trouble
>>>>>>>>                     with ergatis, I set the path
>>>>>>>>                     within the Pipeline.pm file. However it doesn't
>>>>>>>>                     work with the new version.
>>>>>>>>
>>>>>>>>                     The script crashing is the
>>>>>>>>                     create_template_keys, when I add the correct
>>>>>>>>                     lib path to this wrapper line:
>>>>>>>>                     export
>>>>>>>>                     PERL5LIB=/usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5/:/path/....
>>>>>>>>
>>>>>>>>                     it does work! I would have guessed the
>>>>>>>>                     Pipeline.pm was adding what I
>>>>>>>>                     wanted bu this one is not called in the
>>>>>>>>                     create_template_keys.pl
>>>>>>>>                     <http://create_template_keys.pl> script ...
>>>>>>>>
>>>>>>>>                     How can I manage to fix this problem,
>>>>>>>>                     without adding to all the wrapper
>>>>>>>>                     my path ?
>>>>>>>>                     thanks,
>>>>>>>>
>>>>>>>>                     Jérôme
>>>>>>>>
>>>>>>>>
>>>>>>>>                     ------------------------------------------------------------------------------
>>>>>>>>                     For Developers, A Lot Can Happen In A Second.
>>>>>>>>                     Boundary is the first to Know...and Tell You.
>>>>>>>>                     Monitor Your Applications in Ultra-Fine
>>>>>>>>                     Resolution. Try it FREE!
>>>>>>>>                     http://p.sf.net/sfu/Boundary-d2dvs2
>>>>>>>>                     _______________________________________________
>>>>>>>>                     Ergatis-users mailing list
>>>>>>>>                     Erg...@li...
>>>>>>>>                     <mailto:Erg...@li...>
>>>>>>>>                     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>             ------------------------------------------------------------------------------
>>>>>>>>             For Developers, A Lot Can Happen In A Second.
>>>>>>>>             Boundary is the first to Know...and Tell You.
>>>>>>>>             Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>>>>>>>             http://p.sf.net/sfu/Boundary-d2dvs2
>>>>>>>>
>>>>>>>>
>>>>>>>>             _______________________________________________
>>>>>>>>             Ergatis-users mailing list
>>>>>>>>             Erg...@li...  <mailto:Erg...@li...>
>>>>>>>>             https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>             ------------------------------------------------------------------------------
>>>>>>>             For Developers, A Lot Can Happen In A Second.
>>>>>>>             Boundary is the first to Know...and Tell You.
>>>>>>>             Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>>>>>>             http://p.sf.net/sfu/Boundary-d2dvs2
>>>>>>>
>>>>>>>
>>>>>>>             _______________________________________________
>>>>>>>             Ergatis-users mailing list
>>>>>>>             Erg...@li...  <mailto:Erg...@li...>
>>>>>>>             https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>>>
>>>>>>
>>>>>>             ------------------------------------------------------------------------------
>>>>>>             For Developers, A Lot Can Happen In A Second.
>>>>>>             Boundary is the first to Know...and Tell You.
>>>>>>             Monitor Your Applications in Ultra-Fine Resolution.
>>>>>>             Try it FREE!
>>>>>>             http://p.sf.net/sfu/Boundary-d2dvs2
>>>>>>             _______________________________________________
>>>>>>             Ergatis-users mailing list
>>>>>>             Erg...@li...
>>>>>>             <mailto:Erg...@li...>
>>>>>>             https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>         ------------------------------------------------------------------------------
>>>>>>         For Developers, A Lot Can Happen In A Second.
>>>>>>         Boundary is the first to Know...and Tell You.
>>>>>>         Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>>>>>         http://p.sf.net/sfu/Boundary-d2dvs2
>>>>>>
>>>>>>
>>>>>>         _______________________________________________
>>>>>>         Ergatis-users mailing list
>>>>>>         Erg...@li...  <mailto:Erg...@li...>
>>>>>>         https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>>
>>>>>
>>>>>
>>>>>         ------------------------------------------------------------------------------
>>>>>         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
>>>>>         Erg...@li...  <mailto:Erg...@li...>
>>>>>         https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>
>>>>
>>>>         ------------------------------------------------------------------------------
>>>>         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
>>>>         Erg...@li...
>>>>         <mailto:Erg...@li...>
>>>>         https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>
>>>>
>>>>
>>>>
>>>>     ------------------------------------------------------------------------------
>>>>     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
>>>>     Erg...@li...  <mailto:Erg...@li...>
>>>>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>
>>>
>>>
>>>     ------------------------------------------------------------------------------
>>>     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
>>>     Erg...@li...  <mailto:Erg...@li...>
>>>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>
>>
>>     ------------------------------------------------------------------------------
>>     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
>>     Erg...@li...
>>     <mailto:Erg...@li...>
>>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>> Erg...@li...
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>
>
>
> ------------------------------------------------------------------------------
> 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
> Erg...@li...
> https://lists.sourceforge.net/lists/listinfo/ergatis-users

Re: [Ergatis-users] PERL5LIB

From: Mariette <jma...@to...> - 2012-05-03 14:03:34

Joshua,

We got the same behaviour for both!

On our old system, we did the same (adding sudo -E -u ng6 echo 
$LD_LIBRARY_PATH > /work/tmp/tt.ld; sudo -E -u ng6 env > 
/work/tmp/tt.env on the pipeline.X.run.sh script) and we got the same 
result (nothing on the env, but ok when using the $LD_LIBRARY_PATH)

We run the same component (executing the 'env') on our old system what 
lead to a correct LD_LIBARY_PATH.

What we tested also is to take off the sudo prefix from the 
pipeline.X.run.sh script, here the LD_LIBARY_PATH is ok! So we are 
pretty sure it's coming from the sudo. What we did is to add the 
LD_LIBRARY_PATH to the env_keep variable without any success!

Defaults    env_reset
Defaults    env_keep =  "COLORS DISPLAY HOSTNAME HISTSIZE INPUTRC KDEDIR 
LS_COLORS"
...
Defaults    env_keep += "LC_TIME LC_ALL LANGUAGE LINGUAS _XKB_CHARSET 
XAUTHORITY LD_LIBRARY_PATH"
Defaults    env_keep += "PATH "

Something weird is that the PATH is ok in the pipeline execution, but 
not the LD_LIBARY_PATH and PERL5LIB variables, even if we did the same 
with those variables !

How this variables are retreived within tigr workflow ? There is any 
changed since last workflow version using those variables ?

Jerome







Le 03/05/2012 15:44, Joshua Orvis a écrit :
> Jerome -
>
> This information is helpful.  In the last test that you mentioned, 
> when running in Ergatis, was that step distributed on the grid at all 
> or just run locally?
>
> JO
>
> On Thu, May 3, 2012 at 7:31 AM, Mariette <jma...@to... 
> <mailto:jma...@to...>> wrote:
>
>
>     Joshua,
>
>     Just so you know, we are running ergatis on a red hat 6 system,
>     have you make it run on it ?
>
>     I get a litle further. From the pipeline.X.run.sh
>     <http://pipeline.X.run.sh> file, I added the folowing lines:
>
>     sudo -E -u ng6 echo $LD_LIBRARY_PATH > /work/tmp/tt.ld
>     sudo -E -u ng6 env > /work/tmp/tt.env
>
>     the /work/tmp/tt.ld file does contain the right path! However the
>     /work/tmp/tt.env does not contain the LD_LIBARY_PATH at all!
>
>     An other point, within ergatis, a simple component running a 'env'
>     command return a LD_LIBRARY_PATH set to:
>
>     LD_LIBRARY_PATH=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64/server:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../lib/amd64
>
>     I tryed to figure out where that path could come from ... any idea ?
>
>
>     thanks for your time!
>
>     Jérôme
>
>
>
>
>
>     Le 03/05/2012 10:02, Mariette a écrit :
>>
>>     Joshua,
>>
>>     they are pretty close, SGE adds some variables (SGE_BINARY_PATH,
>>     SGE_CWD_PATH ...), but the PATH, the LD_LIBRARY_PATH are the same
>>     within or not a qsub.
>>
>>     Jerome
>>
>>
>>
>>
>>     Le 02/05/2012 17:29, Joshua Orvis a écrit :
>>>     Jerome -
>>>
>>>     I think you should take a step back here.  Take Ergatis and
>>>     Workflow Engine completely out of this.  What happens if you
>>>     write a shell script that sets an ENV variable and then does the
>>>     equivalent of a qsub to run your script that prints your
>>>     environment to a file?  Is the ENV retained?
>>>
>>>     Joshua
>>>
>>>     On Wed, May 2, 2012 at 10:05 AM, Mariette
>>>     <jma...@to... <mailto:jma...@to...>>
>>>     wrote:
>>>
>>>
>>>         Hi again,
>>>
>>>         so I made a component with just a env as execution, and the
>>>         paths are not right !
>>>         What are the steps after the execution of the script ?
>>>
>>>         Jerome
>>>
>>>
>>>
>>>
>>>
>>>
>>>         Le 02/05/2012 16:48, Mariette a écrit :
>>>>
>>>>         Hi everyone,
>>>>
>>>>         I'm still facing the same probleme ... I moved on by making
>>>>         a sed to all ergatis scripts to add the right PERL5LIB
>>>>         path, but this is just a patch! I need to do the same with the
>>>>         LD_LIBRARY_PATH and the PATH variables ... but it's working
>>>>         with non of them!
>>>>
>>>>         The script produced (pipeline.*.run.sh) is correctly
>>>>         written down, and the execution with an echo right after
>>>>         display the right path !
>>>>
>>>>         What we changed is the full cluster, so we are running the
>>>>         open sge version and no longer the sun sge.
>>>>
>>>>         any idea on debugging ?
>>>>         thanks,
>>>>
>>>>         Jerome
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>         Le 20/04/2012 17:08, Joshua Orvis a écrit :
>>>>>         Jérôme -
>>>>>
>>>>>         The script looks right, and that was going to be my next
>>>>>         question.  Yes, Ergatis writes that shell script and then
>>>>>         executes it, and within that script RunWorkflow is called.
>>>>>          Has anything else changed in your SGE configuration?  You
>>>>>         could replace the RunWorkflow line in the script with your
>>>>>         own qsub test that just prints out the environment once
>>>>>         it's placed on a node.  This would allow you to see if
>>>>>         it's within the SGE job submission that your job is being
>>>>>         lost.  Out of curiosity, do you have the
>>>>>         'submit_pipelines_as_jobs' option turned on in the
>>>>>         ergatis.ini file?
>>>>>
>>>>>         Joshua
>>>>>
>>>>>
>>>>>
>>>>>         2012/4/20 Mariette <jma...@to...
>>>>>         <mailto:jma...@to...>>
>>>>>
>>>>>
>>>>>             Joshua,
>>>>>
>>>>>             there is something I'm missing. I did modified the
>>>>>             Pipeline.pm so the PERL5LIB is settled. When I take a
>>>>>             look at the pipeline.XXX.run.sh
>>>>>             <http://pipeline.XXX.run.sh> script written down,
>>>>>             the variable is correctly set ! Is this script used to
>>>>>             process the workflow ?
>>>>>
>>>>>             Jérôme
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>             Le 19/04/2012 10:16, Mariette a écrit :
>>>>>>
>>>>>>             Joshua,
>>>>>>             the file is in attachement. The error returned is:
>>>>>>
>>>>>>             Can't locate Config/IniFiles.pm in @INC (@INC
>>>>>>             contains:
>>>>>>             /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5//x86_64-linux-thread-multi
>>>>>>             /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5/
>>>>>>             /usr/local/lib64/perl5 /usr/local/share/perl5
>>>>>>             /usr/lib64/perl5/vendor_perl
>>>>>>             /usr/share/perl5/vendor_perl /usr/lib64/perl5/5.10.0
>>>>>>             /usr/lib64/perl5 /usr/share/perl5 .
>>>>>>             /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/5.8.8/x86_64-linux-thread-multi
>>>>>>             /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/5.8.8)
>>>>>>             at
>>>>>>             /usr/local/bioinfo/src/ergatisng6/v2r17b2/bin/replace_template_keys.pl
>>>>>>             <http://replace_template_keys.pl> line 17
>>>>>>
>>>>>>             Paths I provided to Pipeline.pm are not in @INC.
>>>>>>
>>>>>>             thanks for your time!
>>>>>>             Jérôme
>>>>>>
>>>>>>
>>>>>>             Le 13/04/2012 20:32, Joshua Orvis a écrit :
>>>>>>>             Jerome -
>>>>>>>
>>>>>>>             Do you mind sending me your modified Pipeline.pm
>>>>>>>             file?  I don't see any changes here that would cause
>>>>>>>             the ENV changes you make in the _setup_environment()
>>>>>>>             method of Pipeline.pm to not make it to the
>>>>>>>             execution of the create_template_keys.pl
>>>>>>>             <http://create_template_keys.pl> script.  I'd like
>>>>>>>             to test it locally.
>>>>>>>
>>>>>>>             Joshua
>>>>>>>
>>>>>>>
>>>>>>>             On Fri, Apr 13, 2012 at 1:14 PM, Joshua Orvis
>>>>>>>             <jo...@gm... <mailto:jo...@gm...>> wrote:
>>>>>>>
>>>>>>>                 Jérôme -
>>>>>>>
>>>>>>>                 I'm taking a look at this.
>>>>>>>
>>>>>>>                 Joshua
>>>>>>>
>>>>>>>                 On Fri, Apr 13, 2012 at 10:24 AM, Mariette
>>>>>>>                 <jma...@to...
>>>>>>>                 <mailto:jma...@to...>> wrote:
>>>>>>>
>>>>>>>                     Hi everyone,
>>>>>>>
>>>>>>>                     the environment we are running ergatis on is
>>>>>>>                     a bit tricky. The perl libs
>>>>>>>                     are not located on the usual perl path.
>>>>>>>                     usually when I have this kind of trouble
>>>>>>>                     with ergatis, I set the path
>>>>>>>                     within the Pipeline.pm file. However it doesn't
>>>>>>>                     work with the new version.
>>>>>>>
>>>>>>>                     The script crashing is the
>>>>>>>                     create_template_keys, when I add the correct
>>>>>>>                     lib path to this wrapper line:
>>>>>>>                     export
>>>>>>>                     PERL5LIB=/usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5/:/path/....
>>>>>>>
>>>>>>>                     it does work! I would have guessed the
>>>>>>>                     Pipeline.pm was adding what I
>>>>>>>                     wanted bu this one is not called in the
>>>>>>>                     create_template_keys.pl
>>>>>>>                     <http://create_template_keys.pl> script ...
>>>>>>>
>>>>>>>                     How can I manage to fix this problem,
>>>>>>>                     without adding to all the wrapper
>>>>>>>                     my path ?
>>>>>>>                     thanks,
>>>>>>>
>>>>>>>                     Jérôme
>>>>>>>
>>>>>>>
>>>>>>>                     ------------------------------------------------------------------------------
>>>>>>>                     For Developers, A Lot Can Happen In A Second.
>>>>>>>                     Boundary is the first to Know...and Tell You.
>>>>>>>                     Monitor Your Applications in Ultra-Fine
>>>>>>>                     Resolution. Try it FREE!
>>>>>>>                     http://p.sf.net/sfu/Boundary-d2dvs2
>>>>>>>                     _______________________________________________
>>>>>>>                     Ergatis-users mailing list
>>>>>>>                     Erg...@li...
>>>>>>>                     <mailto:Erg...@li...>
>>>>>>>                     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>             ------------------------------------------------------------------------------
>>>>>>>             For Developers, A Lot Can Happen In A Second.
>>>>>>>             Boundary is the first to Know...and Tell You.
>>>>>>>             Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>>>>>>             http://p.sf.net/sfu/Boundary-d2dvs2
>>>>>>>
>>>>>>>
>>>>>>>             _______________________________________________
>>>>>>>             Ergatis-users mailing list
>>>>>>>             Erg...@li...  <mailto:Erg...@li...>
>>>>>>>             https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>>>
>>>>>>
>>>>>>
>>>>>>             ------------------------------------------------------------------------------
>>>>>>             For Developers, A Lot Can Happen In A Second.
>>>>>>             Boundary is the first to Know...and Tell You.
>>>>>>             Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>>>>>             http://p.sf.net/sfu/Boundary-d2dvs2
>>>>>>
>>>>>>
>>>>>>             _______________________________________________
>>>>>>             Ergatis-users mailing list
>>>>>>             Erg...@li...  <mailto:Erg...@li...>
>>>>>>             https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>>
>>>>>
>>>>>             ------------------------------------------------------------------------------
>>>>>             For Developers, A Lot Can Happen In A Second.
>>>>>             Boundary is the first to Know...and Tell You.
>>>>>             Monitor Your Applications in Ultra-Fine Resolution.
>>>>>             Try it FREE!
>>>>>             http://p.sf.net/sfu/Boundary-d2dvs2
>>>>>             _______________________________________________
>>>>>             Ergatis-users mailing list
>>>>>             Erg...@li...
>>>>>             <mailto:Erg...@li...>
>>>>>             https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>         ------------------------------------------------------------------------------
>>>>>         For Developers, A Lot Can Happen In A Second.
>>>>>         Boundary is the first to Know...and Tell You.
>>>>>         Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>>>>         http://p.sf.net/sfu/Boundary-d2dvs2
>>>>>
>>>>>
>>>>>         _______________________________________________
>>>>>         Ergatis-users mailing list
>>>>>         Erg...@li...  <mailto:Erg...@li...>
>>>>>         https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>
>>>>
>>>>
>>>>         ------------------------------------------------------------------------------
>>>>         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
>>>>         Erg...@li...  <mailto:Erg...@li...>
>>>>         https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>
>>>
>>>         ------------------------------------------------------------------------------
>>>         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
>>>         Erg...@li...
>>>         <mailto:Erg...@li...>
>>>         https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>
>>>
>>>
>>>
>>>     ------------------------------------------------------------------------------
>>>     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
>>>     Erg...@li...  <mailto:Erg...@li...>
>>>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>
>>
>>
>>     ------------------------------------------------------------------------------
>>     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
>>     Erg...@li...  <mailto:Erg...@li...>
>>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>
>
>     ------------------------------------------------------------------------------
>     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
>     Erg...@li...
>     <mailto:Erg...@li...>
>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>
>
>
>
> ------------------------------------------------------------------------------
> 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
> Erg...@li...
> https://lists.sourceforge.net/lists/listinfo/ergatis-users

Re: [Ergatis-users] PERL5LIB

From: Joshua O. <jo...@gm...> - 2012-05-03 13:44:15

Jerome -

This information is helpful.  In the last test that you mentioned, when
running in Ergatis, was that step distributed on the grid at all or just
run locally?

JO

On Thu, May 3, 2012 at 7:31 AM, Mariette <jma...@to...> wrote:

>
> Joshua,
>
> Just so you know, we are running ergatis on a red hat 6 system, have you
> make it run on it ?
>
> I get a litle further. From the pipeline.X.run.sh file, I added the
> folowing lines:
>
> sudo -E -u ng6 echo $LD_LIBRARY_PATH > /work/tmp/tt.ld
> sudo -E -u ng6 env > /work/tmp/tt.env
>
> the /work/tmp/tt.ld file does contain the right path! However the
> /work/tmp/tt.env does not contain the LD_LIBARY_PATH at all!
>
> An other point, within ergatis, a simple component running a 'env' command
> return a LD_LIBRARY_PATH set to:
>
> LD_LIBRARY_PATH=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64/server:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../lib/amd64
>
> I tryed to figure out where that path could come from ... any idea ?
>
>
> thanks for your time!
>
> Jérôme
>
>
>
>
>
> Le 03/05/2012 10:02, Mariette a écrit :
>
>
> Joshua,
>
> they are pretty close, SGE adds some variables (SGE_BINARY_PATH,
> SGE_CWD_PATH ...), but the PATH, the LD_LIBRARY_PATH are the same within or
> not a qsub.
>
> Jerome
>
>
>
>
> Le 02/05/2012 17:29, Joshua Orvis a écrit :
>
> Jerome -
>
>  I think you should take a step back here.  Take Ergatis and Workflow
> Engine completely out of this.  What happens if you write a shell script
> that sets an ENV variable and then does the equivalent of a qsub to run
> your script that prints your environment to a file?  Is the ENV retained?
>
>  Joshua
>
> On Wed, May 2, 2012 at 10:05 AM, Mariette <jma...@to...>wrote:
>
>>
>> Hi again,
>>
>> so I made a component with just a env as execution, and the paths are not
>> right !
>> What are the steps after the execution of the script ?
>>
>> Jerome
>>
>>
>>
>>
>>
>>
>> Le 02/05/2012 16:48, Mariette a écrit :
>>
>>
>> Hi everyone,
>>
>> I'm still facing the same probleme ... I moved on by making a sed to all
>> ergatis scripts to add the right PERL5LIB path, but this is just a patch! I
>> need to do the same with the
>> LD_LIBRARY_PATH and the PATH variables ... but it's working with non of
>> them!
>>
>> The script produced (pipeline.*.run.sh) is correctly written down, and
>> the execution with an echo right after display the right path !
>>
>> What we changed is the full cluster, so we are running the open sge
>> version and no longer the sun sge.
>>
>> any idea on debugging ?
>> thanks,
>>
>> Jerome
>>
>>
>>
>>
>>
>>
>> Le 20/04/2012 17:08, Joshua Orvis a écrit :
>>
>> Jérôme -
>>
>>  The script looks right, and that was going to be my next question.
>>  Yes, Ergatis writes that shell script and then executes it, and within
>> that script RunWorkflow is called.  Has anything else changed in your SGE
>> configuration?  You could replace the RunWorkflow line in the script with
>> your own qsub test that just prints out the environment once it's placed on
>> a node.  This would allow you to see if it's within the SGE job submission
>> that your job is being lost.  Out of curiosity, do you have the
>> 'submit_pipelines_as_jobs' option turned on in the ergatis.ini file?
>>
>>  Joshua
>>
>>
>>
>> 2012/4/20 Mariette <jma...@to...>
>>
>>>
>>> Joshua,
>>>
>>> there is something I'm missing. I did modified the Pipeline.pm so the
>>> PERL5LIB is settled. When I take a look at the pipeline.XXX.run.shscript written down,
>>> the variable is correctly set ! Is this script used to process the
>>> workflow ?
>>>
>>> Jérôme
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Le 19/04/2012 10:16, Mariette a écrit :
>>>
>>>
>>> Joshua,
>>> the file is in attachement. The error returned is:
>>>
>>> Can't locate Config/IniFiles.pm in @INC (@INC contains:
>>> /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5//x86_64-linux-thread-multi
>>> /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5/ /usr/local/lib64/perl5
>>> /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl
>>> /usr/share/perl5/vendor_perl /usr/lib64/perl5/5.10.0 /usr/lib64/perl5
>>> /usr/share/perl5 .
>>> /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/5.8.8/x86_64-linux-thread-multi
>>> /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/5.8.8) at
>>> /usr/local/bioinfo/src/ergatisng6/v2r17b2/bin/replace_template_keys.plline 17
>>>
>>> Paths I provided to Pipeline.pm are not in @INC.
>>>
>>> thanks for your time!
>>> Jérôme
>>>
>>>
>>> Le 13/04/2012 20:32, Joshua Orvis a écrit :
>>>
>>> Jerome -
>>>
>>>  Do you mind sending me your modified Pipeline.pm file?  I don't see
>>> any changes here that would cause the ENV changes you make in the
>>> _setup_environment() method of Pipeline.pm to not make it to the execution
>>> of the create_template_keys.pl script.  I'd like to test it locally.
>>>
>>>  Joshua
>>>
>>>
>>> On Fri, Apr 13, 2012 at 1:14 PM, Joshua Orvis <jo...@gm...> wrote:
>>>
>>>> Jérôme -
>>>>
>>>>  I'm taking a look at this.
>>>>
>>>>  Joshua
>>>>
>>>> On Fri, Apr 13, 2012 at 10:24 AM, Mariette <jma...@to...>wrote:
>>>>
>>>>> Hi everyone,
>>>>>
>>>>> the environment we are running ergatis on is a bit tricky. The perl
>>>>> libs
>>>>> are not located on the usual perl path.
>>>>> usually when I have this kind of trouble with ergatis, I set the path
>>>>> within the Pipeline.pm file. However it doesn't
>>>>> work with the new version.
>>>>>
>>>>> The script crashing is the create_template_keys, when I add the correct
>>>>> lib path to this wrapper line:
>>>>> export
>>>>>
>>>>> PERL5LIB=/usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5/:/path/....
>>>>>
>>>>> it does work! I would have guessed the Pipeline.pm was adding what I
>>>>> wanted bu this one is not called in the
>>>>> create_template_keys.pl script ...
>>>>>
>>>>> How can I manage to fix this problem, without adding to all the wrapper
>>>>> my path ?
>>>>> thanks,
>>>>>
>>>>> Jérôme
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> For Developers, A Lot Can Happen In A Second.
>>>>> Boundary is the first to Know...and Tell You.
>>>>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>>>> http://p.sf.net/sfu/Boundary-d2dvs2
>>>>> _______________________________________________
>>>>> Ergatis-users mailing list
>>>>> Erg...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>>
>>>>
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> For Developers, A Lot Can Happen In A Second.
>>> Boundary is the first to Know...and Tell You.
>>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!http://p.sf.net/sfu/Boundary-d2dvs2
>>>
>>>
>>>
>>> _______________________________________________
>>> Ergatis-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> For Developers, A Lot Can Happen In A Second.
>>> Boundary is the first to Know...and Tell You.
>>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!http://p.sf.net/sfu/Boundary-d2dvs2
>>>
>>>
>>>
>>> _______________________________________________
>>> Ergatis-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> For Developers, A Lot Can Happen In A Second.
>>> Boundary is the first to Know...and Tell You.
>>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>> http://p.sf.net/sfu/Boundary-d2dvs2
>>> _______________________________________________
>>> Ergatis-users mailing list
>>> Erg...@li...
>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> For Developers, A Lot Can Happen In A Second.
>> Boundary is the first to Know...and Tell You.
>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!http://p.sf.net/sfu/Boundary-d2dvs2
>>
>>
>>
>> _______________________________________________
>> Ergatis-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>
>>
>>
>>
>>  ------------------------------------------------------------------------------
>> 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 lis...@li...https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>> Erg...@li...
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>
>>
>
>
> ------------------------------------------------------------------------------
> 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 lis...@li...https://lists.sourceforge.net/lists/listinfo/ergatis-users
>
>
>
>
> ------------------------------------------------------------------------------
> 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 lis...@li...https://lists.sourceforge.net/lists/listinfo/ergatis-users
>
>
>
>
> ------------------------------------------------------------------------------
> 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
> Erg...@li...
> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>
>

Re: [Ergatis-users] PERL5LIB

From: Mariette <jma...@to...> - 2012-05-03 13:16:01

Joshua,

Just so you know, we are running ergatis on a red hat 6 system, have you 
make it run on it ?

I get a litle further. From the pipeline.X.run.sh file, I added the 
folowing lines:

sudo -E -u ng6 echo $LD_LIBRARY_PATH > /work/tmp/tt.ld
sudo -E -u ng6 env > /work/tmp/tt.env

the /work/tmp/tt.ld file does contain the right path! However the 
/work/tmp/tt.env does not contain the LD_LIBARY_PATH at all!

An other point, within ergatis, a simple component running a 'env' 
command return a LD_LIBRARY_PATH set to:

LD_LIBRARY_PATH=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64/server:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../lib/amd64

I tryed to figure out where that path could come from ... any idea ?

thanks for your time!

Jérôme





Le 03/05/2012 10:02, Mariette a écrit :
>
> Joshua,
>
> they are pretty close, SGE adds some variables (SGE_BINARY_PATH, 
> SGE_CWD_PATH ...), but the PATH, the LD_LIBRARY_PATH are the same 
> within or not a qsub.
>
> Jerome
>
>
>
>
> Le 02/05/2012 17:29, Joshua Orvis a écrit :
>> Jerome -
>>
>> I think you should take a step back here.  Take Ergatis and Workflow 
>> Engine completely out of this.  What happens if you write a shell 
>> script that sets an ENV variable and then does the equivalent of a 
>> qsub to run your script that prints your environment to a file?  Is 
>> the ENV retained?
>>
>> Joshua
>>
>> On Wed, May 2, 2012 at 10:05 AM, Mariette <jma...@to... 
>> <mailto:jma...@to...>> wrote:
>>
>>
>>     Hi again,
>>
>>     so I made a component with just a env as execution, and the paths
>>     are not right !
>>     What are the steps after the execution of the script ?
>>
>>     Jerome
>>
>>
>>
>>
>>
>>
>>     Le 02/05/2012 16:48, Mariette a écrit :
>>>
>>>     Hi everyone,
>>>
>>>     I'm still facing the same probleme ... I moved on by making a
>>>     sed to all ergatis scripts to add the right PERL5LIB path, but
>>>     this is just a patch! I need to do the same with the
>>>     LD_LIBRARY_PATH and the PATH variables ... but it's working with
>>>     non of them!
>>>
>>>     The script produced (pipeline.*.run.sh) is correctly written
>>>     down, and the execution with an echo right after display the
>>>     right path !
>>>
>>>     What we changed is the full cluster, so we are running the open
>>>     sge version and no longer the sun sge.
>>>
>>>     any idea on debugging ?
>>>     thanks,
>>>
>>>     Jerome
>>>
>>>
>>>
>>>
>>>
>>>
>>>     Le 20/04/2012 17:08, Joshua Orvis a écrit :
>>>>     Jérôme -
>>>>
>>>>     The script looks right, and that was going to be my next
>>>>     question.  Yes, Ergatis writes that shell script and then
>>>>     executes it, and within that script RunWorkflow is called.  Has
>>>>     anything else changed in your SGE configuration?  You could
>>>>     replace the RunWorkflow line in the script with your own qsub
>>>>     test that just prints out the environment once it's placed on a
>>>>     node.  This would allow you to see if it's within the SGE job
>>>>     submission that your job is being lost.  Out of curiosity, do
>>>>     you have the 'submit_pipelines_as_jobs' option turned on in the
>>>>     ergatis.ini file?
>>>>
>>>>     Joshua
>>>>
>>>>
>>>>
>>>>     2012/4/20 Mariette <jma...@to...
>>>>     <mailto:jma...@to...>>
>>>>
>>>>
>>>>         Joshua,
>>>>
>>>>         there is something I'm missing. I did modified the
>>>>         Pipeline.pm so the PERL5LIB is settled. When I take a look
>>>>         at the pipeline.XXX.run.sh <http://pipeline.XXX.run.sh>
>>>>         script written down,
>>>>         the variable is correctly set ! Is this script used to
>>>>         process the workflow ?
>>>>
>>>>         Jérôme
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>         Le 19/04/2012 10:16, Mariette a écrit :
>>>>>
>>>>>         Joshua,
>>>>>         the file is in attachement. The error returned is:
>>>>>
>>>>>         Can't locate Config/IniFiles.pm in @INC (@INC contains:
>>>>>         /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5//x86_64-linux-thread-multi
>>>>>         /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5/
>>>>>         /usr/local/lib64/perl5 /usr/local/share/perl5
>>>>>         /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl
>>>>>         /usr/lib64/perl5/5.10.0 /usr/lib64/perl5 /usr/share/perl5
>>>>>         .
>>>>>         /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/5.8.8/x86_64-linux-thread-multi
>>>>>         /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/5.8.8) at
>>>>>         /usr/local/bioinfo/src/ergatisng6/v2r17b2/bin/replace_template_keys.pl
>>>>>         <http://replace_template_keys.pl> line 17
>>>>>
>>>>>         Paths I provided to Pipeline.pm are not in @INC.
>>>>>
>>>>>         thanks for your time!
>>>>>         Jérôme
>>>>>
>>>>>
>>>>>         Le 13/04/2012 20:32, Joshua Orvis a écrit :
>>>>>>         Jerome -
>>>>>>
>>>>>>         Do you mind sending me your modified Pipeline.pm file?  I
>>>>>>         don't see any changes here that would cause the ENV
>>>>>>         changes you make in the _setup_environment() method of
>>>>>>         Pipeline.pm to not make it to the execution of the
>>>>>>         create_template_keys.pl <http://create_template_keys.pl>
>>>>>>         script.  I'd like to test it locally.
>>>>>>
>>>>>>         Joshua
>>>>>>
>>>>>>
>>>>>>         On Fri, Apr 13, 2012 at 1:14 PM, Joshua Orvis
>>>>>>         <jo...@gm... <mailto:jo...@gm...>> wrote:
>>>>>>
>>>>>>             Jérôme -
>>>>>>
>>>>>>             I'm taking a look at this.
>>>>>>
>>>>>>             Joshua
>>>>>>
>>>>>>             On Fri, Apr 13, 2012 at 10:24 AM, Mariette
>>>>>>             <jma...@to...
>>>>>>             <mailto:jma...@to...>> wrote:
>>>>>>
>>>>>>                 Hi everyone,
>>>>>>
>>>>>>                 the environment we are running ergatis on is a
>>>>>>                 bit tricky. The perl libs
>>>>>>                 are not located on the usual perl path.
>>>>>>                 usually when I have this kind of trouble with
>>>>>>                 ergatis, I set the path
>>>>>>                 within the Pipeline.pm file. However it doesn't
>>>>>>                 work with the new version.
>>>>>>
>>>>>>                 The script crashing is the create_template_keys,
>>>>>>                 when I add the correct
>>>>>>                 lib path to this wrapper line:
>>>>>>                 export
>>>>>>                 PERL5LIB=/usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5/:/path/....
>>>>>>
>>>>>>                 it does work! I would have guessed the
>>>>>>                 Pipeline.pm was adding what I
>>>>>>                 wanted bu this one is not called in the
>>>>>>                 create_template_keys.pl
>>>>>>                 <http://create_template_keys.pl> script ...
>>>>>>
>>>>>>                 How can I manage to fix this problem, without
>>>>>>                 adding to all the wrapper
>>>>>>                 my path ?
>>>>>>                 thanks,
>>>>>>
>>>>>>                 Jérôme
>>>>>>
>>>>>>
>>>>>>                 ------------------------------------------------------------------------------
>>>>>>                 For Developers, A Lot Can Happen In A Second.
>>>>>>                 Boundary is the first to Know...and Tell You.
>>>>>>                 Monitor Your Applications in Ultra-Fine
>>>>>>                 Resolution. Try it FREE!
>>>>>>                 http://p.sf.net/sfu/Boundary-d2dvs2
>>>>>>                 _______________________________________________
>>>>>>                 Ergatis-users mailing list
>>>>>>                 Erg...@li...
>>>>>>                 <mailto:Erg...@li...>
>>>>>>                 https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>         ------------------------------------------------------------------------------
>>>>>>         For Developers, A Lot Can Happen In A Second.
>>>>>>         Boundary is the first to Know...and Tell You.
>>>>>>         Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>>>>>         http://p.sf.net/sfu/Boundary-d2dvs2
>>>>>>
>>>>>>
>>>>>>         _______________________________________________
>>>>>>         Ergatis-users mailing list
>>>>>>         Erg...@li...  <mailto:Erg...@li...>
>>>>>>         https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>>
>>>>>
>>>>>
>>>>>         ------------------------------------------------------------------------------
>>>>>         For Developers, A Lot Can Happen In A Second.
>>>>>         Boundary is the first to Know...and Tell You.
>>>>>         Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>>>>         http://p.sf.net/sfu/Boundary-d2dvs2
>>>>>
>>>>>
>>>>>         _______________________________________________
>>>>>         Ergatis-users mailing list
>>>>>         Erg...@li...  <mailto:Erg...@li...>
>>>>>         https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>
>>>>
>>>>         ------------------------------------------------------------------------------
>>>>         For Developers, A Lot Can Happen In A Second.
>>>>         Boundary is the first to Know...and Tell You.
>>>>         Monitor Your Applications in Ultra-Fine Resolution. Try it
>>>>         FREE!
>>>>         http://p.sf.net/sfu/Boundary-d2dvs2
>>>>         _______________________________________________
>>>>         Ergatis-users mailing list
>>>>         Erg...@li...
>>>>         <mailto:Erg...@li...>
>>>>         https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>
>>>>
>>>>
>>>>
>>>>     ------------------------------------------------------------------------------
>>>>     For Developers, A Lot Can Happen In A Second.
>>>>     Boundary is the first to Know...and Tell You.
>>>>     Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>>>     http://p.sf.net/sfu/Boundary-d2dvs2
>>>>
>>>>
>>>>     _______________________________________________
>>>>     Ergatis-users mailing list
>>>>     Erg...@li...  <mailto:Erg...@li...>
>>>>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>
>>>
>>>
>>>     ------------------------------------------------------------------------------
>>>     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
>>>     Erg...@li...  <mailto:Erg...@li...>
>>>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>
>>
>>     ------------------------------------------------------------------------------
>>     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
>>     Erg...@li...
>>     <mailto:Erg...@li...>
>>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>> Erg...@li...
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>
>
>
> ------------------------------------------------------------------------------
> 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
> Erg...@li...
> https://lists.sourceforge.net/lists/listinfo/ergatis-users

Re: [Ergatis-users] PERL5LIB

From: Mariette <jma...@to...> - 2012-05-03 08:02:35

Joshua,

they are pretty close, SGE adds some variables (SGE_BINARY_PATH, 
SGE_CWD_PATH ...), but the PATH, the LD_LIBRARY_PATH are the same within 
or not a qsub.

Jerome




Le 02/05/2012 17:29, Joshua Orvis a écrit :
> Jerome -
>
> I think you should take a step back here.  Take Ergatis and Workflow 
> Engine completely out of this.  What happens if you write a shell 
> script that sets an ENV variable and then does the equivalent of a 
> qsub to run your script that prints your environment to a file?  Is 
> the ENV retained?
>
> Joshua
>
> On Wed, May 2, 2012 at 10:05 AM, Mariette <jma...@to... 
> <mailto:jma...@to...>> wrote:
>
>
>     Hi again,
>
>     so I made a component with just a env as execution, and the paths
>     are not right !
>     What are the steps after the execution of the script ?
>
>     Jerome
>
>
>
>
>
>
>     Le 02/05/2012 16:48, Mariette a écrit :
>>
>>     Hi everyone,
>>
>>     I'm still facing the same probleme ... I moved on by making a sed
>>     to all ergatis scripts to add the right PERL5LIB path, but this
>>     is just a patch! I need to do the same with the
>>     LD_LIBRARY_PATH and the PATH variables ... but it's working with
>>     non of them!
>>
>>     The script produced (pipeline.*.run.sh) is correctly written
>>     down, and the execution with an echo right after display the
>>     right path !
>>
>>     What we changed is the full cluster, so we are running the open
>>     sge version and no longer the sun sge.
>>
>>     any idea on debugging ?
>>     thanks,
>>
>>     Jerome
>>
>>
>>
>>
>>
>>
>>     Le 20/04/2012 17:08, Joshua Orvis a écrit :
>>>     Jérôme -
>>>
>>>     The script looks right, and that was going to be my next
>>>     question.  Yes, Ergatis writes that shell script and then
>>>     executes it, and within that script RunWorkflow is called.  Has
>>>     anything else changed in your SGE configuration?  You could
>>>     replace the RunWorkflow line in the script with your own qsub
>>>     test that just prints out the environment once it's placed on a
>>>     node.  This would allow you to see if it's within the SGE job
>>>     submission that your job is being lost.  Out of curiosity, do
>>>     you have the 'submit_pipelines_as_jobs' option turned on in the
>>>     ergatis.ini file?
>>>
>>>     Joshua
>>>
>>>
>>>
>>>     2012/4/20 Mariette <jma...@to...
>>>     <mailto:jma...@to...>>
>>>
>>>
>>>         Joshua,
>>>
>>>         there is something I'm missing. I did modified the
>>>         Pipeline.pm so the PERL5LIB is settled. When I take a look
>>>         at the pipeline.XXX.run.sh <http://pipeline.XXX.run.sh>
>>>         script written down,
>>>         the variable is correctly set ! Is this script used to
>>>         process the workflow ?
>>>
>>>         Jérôme
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>         Le 19/04/2012 10:16, Mariette a écrit :
>>>>
>>>>         Joshua,
>>>>         the file is in attachement. The error returned is:
>>>>
>>>>         Can't locate Config/IniFiles.pm in @INC (@INC contains:
>>>>         /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5//x86_64-linux-thread-multi
>>>>         /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5/
>>>>         /usr/local/lib64/perl5 /usr/local/share/perl5
>>>>         /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl
>>>>         /usr/lib64/perl5/5.10.0 /usr/lib64/perl5 /usr/share/perl5 .
>>>>         /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/5.8.8/x86_64-linux-thread-multi
>>>>         /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/5.8.8) at
>>>>         /usr/local/bioinfo/src/ergatisng6/v2r17b2/bin/replace_template_keys.pl
>>>>         <http://replace_template_keys.pl> line 17
>>>>
>>>>         Paths I provided to Pipeline.pm are not in @INC.
>>>>
>>>>         thanks for your time!
>>>>         Jérôme
>>>>
>>>>
>>>>         Le 13/04/2012 20:32, Joshua Orvis a écrit :
>>>>>         Jerome -
>>>>>
>>>>>         Do you mind sending me your modified Pipeline.pm file?  I
>>>>>         don't see any changes here that would cause the ENV
>>>>>         changes you make in the _setup_environment() method of
>>>>>         Pipeline.pm to not make it to the execution of the
>>>>>         create_template_keys.pl <http://create_template_keys.pl>
>>>>>         script.  I'd like to test it locally.
>>>>>
>>>>>         Joshua
>>>>>
>>>>>
>>>>>         On Fri, Apr 13, 2012 at 1:14 PM, Joshua Orvis
>>>>>         <jo...@gm... <mailto:jo...@gm...>> wrote:
>>>>>
>>>>>             Jérôme -
>>>>>
>>>>>             I'm taking a look at this.
>>>>>
>>>>>             Joshua
>>>>>
>>>>>             On Fri, Apr 13, 2012 at 10:24 AM, Mariette
>>>>>             <jma...@to...
>>>>>             <mailto:jma...@to...>> wrote:
>>>>>
>>>>>                 Hi everyone,
>>>>>
>>>>>                 the environment we are running ergatis on is a bit
>>>>>                 tricky. The perl libs
>>>>>                 are not located on the usual perl path.
>>>>>                 usually when I have this kind of trouble with
>>>>>                 ergatis, I set the path
>>>>>                 within the Pipeline.pm file. However it doesn't
>>>>>                 work with the new version.
>>>>>
>>>>>                 The script crashing is the create_template_keys,
>>>>>                 when I add the correct
>>>>>                 lib path to this wrapper line:
>>>>>                 export
>>>>>                 PERL5LIB=/usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5/:/path/....
>>>>>
>>>>>                 it does work! I would have guessed the Pipeline.pm
>>>>>                 was adding what I
>>>>>                 wanted bu this one is not called in the
>>>>>                 create_template_keys.pl
>>>>>                 <http://create_template_keys.pl> script ...
>>>>>
>>>>>                 How can I manage to fix this problem, without
>>>>>                 adding to all the wrapper
>>>>>                 my path ?
>>>>>                 thanks,
>>>>>
>>>>>                 Jérôme
>>>>>
>>>>>
>>>>>                 ------------------------------------------------------------------------------
>>>>>                 For Developers, A Lot Can Happen In A Second.
>>>>>                 Boundary is the first to Know...and Tell You.
>>>>>                 Monitor Your Applications in Ultra-Fine
>>>>>                 Resolution. Try it FREE!
>>>>>                 http://p.sf.net/sfu/Boundary-d2dvs2
>>>>>                 _______________________________________________
>>>>>                 Ergatis-users mailing list
>>>>>                 Erg...@li...
>>>>>                 <mailto:Erg...@li...>
>>>>>                 https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>         ------------------------------------------------------------------------------
>>>>>         For Developers, A Lot Can Happen In A Second.
>>>>>         Boundary is the first to Know...and Tell You.
>>>>>         Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>>>>         http://p.sf.net/sfu/Boundary-d2dvs2
>>>>>
>>>>>
>>>>>         _______________________________________________
>>>>>         Ergatis-users mailing list
>>>>>         Erg...@li...  <mailto:Erg...@li...>
>>>>>         https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>
>>>>
>>>>
>>>>         ------------------------------------------------------------------------------
>>>>         For Developers, A Lot Can Happen In A Second.
>>>>         Boundary is the first to Know...and Tell You.
>>>>         Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>>>         http://p.sf.net/sfu/Boundary-d2dvs2
>>>>
>>>>
>>>>         _______________________________________________
>>>>         Ergatis-users mailing list
>>>>         Erg...@li...  <mailto:Erg...@li...>
>>>>         https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>
>>>
>>>         ------------------------------------------------------------------------------
>>>         For Developers, A Lot Can Happen In A Second.
>>>         Boundary is the first to Know...and Tell You.
>>>         Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>>         http://p.sf.net/sfu/Boundary-d2dvs2
>>>         _______________________________________________
>>>         Ergatis-users mailing list
>>>         Erg...@li...
>>>         <mailto:Erg...@li...>
>>>         https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>
>>>
>>>
>>>
>>>     ------------------------------------------------------------------------------
>>>     For Developers, A Lot Can Happen In A Second.
>>>     Boundary is the first to Know...and Tell You.
>>>     Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>>     http://p.sf.net/sfu/Boundary-d2dvs2
>>>
>>>
>>>     _______________________________________________
>>>     Ergatis-users mailing list
>>>     Erg...@li...  <mailto:Erg...@li...>
>>>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>
>>
>>
>>     ------------------------------------------------------------------------------
>>     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
>>     Erg...@li...  <mailto:Erg...@li...>
>>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>
>
>     ------------------------------------------------------------------------------
>     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
>     Erg...@li...
>     <mailto:Erg...@li...>
>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>
>
>
>
> ------------------------------------------------------------------------------
> 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
> Erg...@li...
> https://lists.sourceforge.net/lists/listinfo/ergatis-users

Re: [Ergatis-users] PERL5LIB

From: Joshua O. <jo...@gm...> - 2012-05-02 16:00:13

Jerome -

I think you should take a step back here.  Take Ergatis and Workflow Engine
completely out of this.  What happens if you write a shell script that sets
an ENV variable and then does the equivalent of a qsub to run your script
that prints your environment to a file?  Is the ENV retained?

Joshua

On Wed, May 2, 2012 at 10:05 AM, Mariette <jma...@to...> wrote:

>
> Hi again,
>
> so I made a component with just a env as execution, and the paths are not
> right !
> What are the steps after the execution of the script ?
>
> Jerome
>
>
>
>
>
>
> Le 02/05/2012 16:48, Mariette a écrit :
>
>
> Hi everyone,
>
> I'm still facing the same probleme ... I moved on by making a sed to all
> ergatis scripts to add the right PERL5LIB path, but this is just a patch! I
> need to do the same with the
> LD_LIBRARY_PATH and the PATH variables ... but it's working with non of
> them!
>
> The script produced (pipeline.*.run.sh) is correctly written down, and the
> execution with an echo right after display the right path !
>
> What we changed is the full cluster, so we are running the open sge
> version and no longer the sun sge.
>
> any idea on debugging ?
> thanks,
>
> Jerome
>
>
>
>
>
>
> Le 20/04/2012 17:08, Joshua Orvis a écrit :
>
> Jérôme -
>
>  The script looks right, and that was going to be my next question.  Yes,
> Ergatis writes that shell script and then executes it, and within that
> script RunWorkflow is called.  Has anything else changed in your SGE
> configuration?  You could replace the RunWorkflow line in the script with
> your own qsub test that just prints out the environment once it's placed on
> a node.  This would allow you to see if it's within the SGE job submission
> that your job is being lost.  Out of curiosity, do you have the
> 'submit_pipelines_as_jobs' option turned on in the ergatis.ini file?
>
>  Joshua
>
>
>
> 2012/4/20 Mariette <jma...@to...>
>
>>
>> Joshua,
>>
>> there is something I'm missing. I did modified the Pipeline.pm so the
>> PERL5LIB is settled. When I take a look at the pipeline.XXX.run.shscript written down,
>> the variable is correctly set ! Is this script used to process the
>> workflow ?
>>
>> Jérôme
>>
>>
>>
>>
>>
>>
>>
>> Le 19/04/2012 10:16, Mariette a écrit :
>>
>>
>> Joshua,
>> the file is in attachement. The error returned is:
>>
>> Can't locate Config/IniFiles.pm in @INC (@INC contains:
>> /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5//x86_64-linux-thread-multi
>> /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5/ /usr/local/lib64/perl5
>> /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl
>> /usr/share/perl5/vendor_perl /usr/lib64/perl5/5.10.0 /usr/lib64/perl5
>> /usr/share/perl5 .
>> /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/5.8.8/x86_64-linux-thread-multi
>> /usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/5.8.8) at
>> /usr/local/bioinfo/src/ergatisng6/v2r17b2/bin/replace_template_keys.plline 17
>>
>> Paths I provided to Pipeline.pm are not in @INC.
>>
>> thanks for your time!
>> Jérôme
>>
>>
>> Le 13/04/2012 20:32, Joshua Orvis a écrit :
>>
>> Jerome -
>>
>>  Do you mind sending me your modified Pipeline.pm file?  I don't see any
>> changes here that would cause the ENV changes you make in the
>> _setup_environment() method of Pipeline.pm to not make it to the execution
>> of the create_template_keys.pl script.  I'd like to test it locally.
>>
>>  Joshua
>>
>>
>> On Fri, Apr 13, 2012 at 1:14 PM, Joshua Orvis <jo...@gm...> wrote:
>>
>>> Jérôme -
>>>
>>>  I'm taking a look at this.
>>>
>>>  Joshua
>>>
>>> On Fri, Apr 13, 2012 at 10:24 AM, Mariette <jma...@to...>wrote:
>>>
>>>> Hi everyone,
>>>>
>>>> the environment we are running ergatis on is a bit tricky. The perl libs
>>>> are not located on the usual perl path.
>>>> usually when I have this kind of trouble with ergatis, I set the path
>>>> within the Pipeline.pm file. However it doesn't
>>>> work with the new version.
>>>>
>>>> The script crashing is the create_template_keys, when I add the correct
>>>> lib path to this wrapper line:
>>>> export
>>>> PERL5LIB=/usr/local/bioinfo/src/ergatisng6/v2r17b2/lib/perl5/:/path/....
>>>>
>>>> it does work! I would have guessed the Pipeline.pm was adding what I
>>>> wanted bu this one is not called in the
>>>> create_template_keys.pl script ...
>>>>
>>>> How can I manage to fix this problem, without adding to all the wrapper
>>>> my path ?
>>>> thanks,
>>>>
>>>> Jérôme
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> For Developers, A Lot Can Happen In A Second.
>>>> Boundary is the first to Know...and Tell You.
>>>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>>> http://p.sf.net/sfu/Boundary-d2dvs2
>>>> _______________________________________________
>>>> Ergatis-users mailing list
>>>> Erg...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> For Developers, A Lot Can Happen In A Second.
>> Boundary is the first to Know...and Tell You.
>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!http://p.sf.net/sfu/Boundary-d2dvs2
>>
>>
>>
>> _______________________________________________
>> Ergatis-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> For Developers, A Lot Can Happen In A Second.
>> Boundary is the first to Know...and Tell You.
>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!http://p.sf.net/sfu/Boundary-d2dvs2
>>
>>
>>
>> _______________________________________________
>> Ergatis-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> For Developers, A Lot Can Happen In A Second.
>> Boundary is the first to Know...and Tell You.
>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>> http://p.sf.net/sfu/Boundary-d2dvs2
>> _______________________________________________
>> Ergatis-users mailing list
>> Erg...@li...
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>
>>
>
>
> ------------------------------------------------------------------------------
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!http://p.sf.net/sfu/Boundary-d2dvs2
>
>
>
> _______________________________________________
> Ergatis-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/ergatis-users
>
>
>
>
> ------------------------------------------------------------------------------
> 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 lis...@li...https://lists.sourceforge.net/lists/listinfo/ergatis-users
>
>
>
>
> ------------------------------------------------------------------------------
> 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
> Erg...@li...
> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>
>

14 messages has been excluded from this view by a project administrator.

Flat | Threaded

1 2 3 .. 36 > >> (Page 1 of 36)