|
|
Dear all,
An error has occured between two command lines within one of our
pipeline components, cf. attached file. We have no error message.
Moreover this error does not occur each time we submit our pipeline.
Does it exist a log file for such an error in order to understand this
kind of error ?
Thanks in advance for your answers.
Kind regards,
------------------------------------------------------------------------------
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Laure - There are a few places to look here. First, there is a log file in the same directory of your pipeline.xml called pipeline.xml.log and another one catching all the standard output called pipeline.xml.run.out.
Is this pipeline running jobs on a grid? If so, each of those 'groups' listed corresponds to a job scheduled on your grid, and there are output files for each of them in case your job failed. The path to these is defined by the workflow_run_dir setting you have in your ergatis.ini. For me, that's "/usr/local/scratch/workflow". You can go to that directory and you'll find one folder per pipeline ID. Within that you'll find all the output and error files for each job submission, including those listed in the graphic above.
Joshua 2012/1/17 Laure Devlamynck <[hidden email]>
Dear all,
An error has occured between two command lines within one of our pipeline components, cf. attached file. We have no error message. Moreover this error does not occur each time we submit our pipeline.
Does it exist a log file for such an error in order to understand this kind of error ?
Thanks in advance for your answers.
Kind regards,
------------------------------------------------------------------------------
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Joshua,
Thank you for your help.
We have found the output and error files. Unfortunately these files
do not help us to understand why the pipeline have failed.
kind regards,
Laure
Le 18/01/2012 16:50, Joshua Orvis a écrit :
Laure -
There are a few places to look here. First, there is a log file
in the same directory of your pipeline.xml called pipeline.xml.log
and another one catching all the standard output called
pipeline.xml.run.out.
Is this pipeline running jobs on a grid? If so, each of those
'groups' listed corresponds to a job scheduled on your grid, and
there are output files for each of them in case your job failed.
The path to these is defined by the workflow_run_dir setting you
have in your ergatis.ini. For me, that's
"/usr/local/scratch/workflow". You can go to that directory and
you'll find one folder per pipeline ID. Within that you'll find
all the output and error files for each job submission, including
those listed in the graphic above.
Joshua
2012/1/17 Laure Devlamynck <[hidden email]>
Dear all,
An error has occured between two command lines within one of
our pipeline components, cf. attached file. We have no error
message. Moreover this error does not occur each time we
submit our pipeline.
Does it exist a log file for such an error in order to
understand this kind of error ?
Thanks in advance for your answers.
Kind regards,
------------------------------------------------------------------------------
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Laure,
Are you running the pipeline over SGE? If so you might be able to get SGE
job info from 'show group info' and look to see if something is failing in
SGE.
If the directory set in 'workflow_run_dir' from ergatis.ini didn't provide
any clues, you can also check the working directory for the job:
'CWD' from workflow/server-conf/sge_mockserver.conf
Cheers,
Chris
On Fri, 20 Jan 2012, Laure Devlamynck wrote:
> Joshua,
>
> Thank you for your help.
> We have found the output and error files. Unfortunately these files do not
> help us to understand why the pipeline have failed.
>
> kind regards,
> Laure
>
>
> Le 18/01/2012 16:50, Joshua Orvis a écrit :
>> Laure -
>>
>> There are a few places to look here. First, there is a log file in the
>> same directory of your pipeline.xml called pipeline.xml.log and another
>> one catching all the standard output called pipeline.xml.run.out.
>>
>> Is this pipeline running jobs on a grid? If so, each of those 'groups'
>> listed corresponds to a job scheduled on your grid, and there are output
>> files for each of them in case your job failed. The path to these is
>> defined by the workflow_run_dir setting you have in your ergatis.ini. For
>> me, that's "/usr/local/scratch/workflow". You can go to that directory
>> and you'll find one folder per pipeline ID. Within that you'll find all
>> the output and error files for each job submission, including those listed
>> in the graphic above.
>>
>> Joshua
>>
>>
>>
>> 2012/1/17 Laure Devlamynck < [hidden email]
>> <mailto: [hidden email]>>
>>
>> Dear all,
>>
>> An error has occured between two command lines within one of our
>> pipeline components, cf. attached file. We have no error message.
>> Moreover this error does not occur each time we submit our pipeline.
>> Does it exist a log file for such an error in order to understand
>> this kind of error ?
>>
>> Thanks in advance for your answers.
>>
>> Kind regards,
>>
>> ------------------------------------------------------------------------------
>> Keep Your Developer Skills Current with LearnDevNow!
>> The most comprehensive online learning library for Microsoft
>> developers
>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3,
>> MVC3,
>> Metro Style Apps, more. Free future releases when you subscribe now!
>> http://p.sf.net/sfu/learndevnow-d2d>> _______________________________________________
>> Ergatis-users mailing list
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>> <mailto: [hidden email]>
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users>>
>>
>
> ------------------------------------------------------------------------------
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Chris,
Thank you for your help.
Yes we are running the pipeline over SGE. The SGE job info from
'show group info' does not help to understand what happened (grid id
= 0 and there is no workflow event log). See below an example of
'show group info' we get for a group 'failed' :
In the working directory, for the job, we have one subdirectory per
group of the component. Contents of the subdirectories are described
below :
- Contents of subdirectories corresponding to a group 'complete' :
total 64
-rw-rw-rw- 1 ng6 NG6 530 Jan 17 11:22 event.log
-rw-r--r-- 1 ng6 NG6 5 Jan 17 11:19 pid.log
-rwxr-xr-x 1 ng6 NG6 7577 Jan 17 11:17 sge_job.sh
-rw-r--r-- 1 ng6 NG6 52 Jan 17 11:18 sge_submit.out
- Contents of subdirectories corresponding to a group 'failed' :
total 16
-rw-r--r-- 1 ng6 NG6 0 Jan 17 11:17 event.log
-rw-r--r-- 1 ng6 NG6 7577 Jan 17 11:17 sge_job.sh
We also observed that all subdirectories corresponding to a group
'complete' have the permissions 'drwxrwxrwx', whereas those
corresponding to a group 'failed' have permissions 'drwxr-xr-x'.
Kind regards,
Laure
Le 20/01/2012 18:48, Chris Hemmerich a écrit :
Laure,
Are you running the pipeline over SGE? If so you might be able to
get SGE job info from 'show group info' and look to see if
something is failing in SGE.
If the directory set in 'workflow_run_dir' from ergatis.ini didn't
provide any clues, you can also check the working directory for
the job:
'CWD' from workflow/server-conf/sge_mockserver.conf
Cheers,
Chris
On Fri, 20 Jan 2012, Laure Devlamynck wrote:
Joshua,
Thank you for your help.
We have found the output and error files. Unfortunately these
files do not help us to understand why the pipeline have failed.
kind regards,
Laure
Le 18/01/2012 16:50, Joshua Orvis a écrit :
Laure -
There are a few places to look here. First, there is a log
file in the
same directory of your pipeline.xml called pipeline.xml.log
and another
one catching all the standard output called
pipeline.xml.run.out.
Is this pipeline running jobs on a grid? If so, each of
those 'groups'
listed corresponds to a job scheduled on your grid, and there
are output
files for each of them in case your job failed. The path to
these is
defined by the workflow_run_dir setting you have in your
ergatis.ini. For
me, that's "/usr/local/scratch/workflow". You can go to that
directory
and you'll find one folder per pipeline ID. Within that
you'll find all
the output and error files for each job submission, including
those listed
in the graphic above.
Joshua
2012/1/17 Laure Devlamynck
<[hidden email]
[hidden email]>
Dear all,
An error has occured between two command lines within one
of our
pipeline components, cf. attached file. We have no error
message.
Moreover this error does not occur each time we submit
our pipeline.
Does it exist a log file for such an error in order to
understand
this kind of error ?
Thanks in advance for your answers.
Kind regards,
------------------------------------------------------------------------------
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Microsoft
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HTML5, CSS3,
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There are a few things that come to my mind. The first is that the qsub failed for the job. Because if qsub succeeded then it runs the prolog script which writes to event.log. Also, sge_submit.out would be there.
Is your pipeline.xml.og or equivalent file non-zero? If so can you search for this string "Submission Failure"
in that file. I have a feeling that the submission failed for some reason and we need to track that down.
Chris,
Thank you for your help.
Yes we are running the pipeline over SGE. The SGE job info from 'show group info' does not help to understand what happened (grid id = 0 and there is no workflow event log). See below an example of 'show group info' we get for a group 'failed' :
In the working directory, for the job, we have one subdirectory per group of the component. Contents of the subdirectories are described below :
- Contents of subdirectories corresponding to a group 'complete' :
total 64
-rw-rw-rw- 1 ng6 NG6 530 Jan 17 11:22 event.log
-rw-r--r-- 1 ng6 NG6 5 Jan 17 11:19 pid.log
-rwxr-xr-x 1 ng6 NG6 7577 Jan 17 11:17 sge_job.sh
-rw-r--r-- 1 ng6 NG6 52 Jan 17 11:18 sge_submit.out
- Contents of subdirectories corresponding to a group 'failed' :
total 16
-rw-r--r-- 1 ng6 NG6 0 Jan 17 11:17 event.log
-rw-r--r-- 1 ng6 NG6 7577 Jan 17 11:17 sge_job.sh
We also observed that all subdirectories corresponding to a group 'complete' have the permissions 'drwxrwxrwx', whereas those corresponding to a group 'failed' have permissions 'drwxr-xr-x'.
Kind regards,
Laure
Le 20/01/2012 18:48, Chris Hemmerich a écrit :
Laure,
Are you running the pipeline over SGE? If so you might be able to get SGE job info from 'show group info' and look to see if something is failing in SGE.
If the directory set in 'workflow_run_dir' from ergatis.ini didn't provide any clues, you can also check the working directory for the job:
'CWD' from workflow/server-conf/sge_mockserver.conf
Cheers,
Chris
On Fri, 20 Jan 2012, Laure Devlamynck wrote:
Joshua,
Thank you for your help.
We have found the output and error files. Unfortunately these files do not help us to understand why the pipeline have failed.
kind regards,
Laure
Le 18/01/2012 16:50, Joshua Orvis a écrit :
Laure -
There are a few places to look here. First, there is a log file in the
same directory of your pipeline.xml called pipeline.xml.log and another
one catching all the standard output called pipeline.xml.run.out.
Is this pipeline running jobs on a grid? If so, each of those 'groups'
listed corresponds to a job scheduled on your grid, and there are output
files for each of them in case your job failed. The path to these is
defined by the workflow_run_dir setting you have in your ergatis.ini. For
me, that's "/usr/local/scratch/workflow". You can go to that directory
and you'll find one folder per pipeline ID. Within that you'll find all
the output and error files for each job submission, including those listed
in the graphic above.
Joshua
2012/1/17 Laure Devlamynck <[hidden email]
[hidden email]>
Dear all,
An error has occured between two command lines within one of our
pipeline components, cf. attached file. We have no error message.
Moreover this error does not occur each time we submit our pipeline.
Does it exist a log file for such an error in order to understand
this kind of error ?
Thanks in advance for your answers.
Kind regards,
------------------------------------------------------------------------------
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Anup,
You are right, the submission failed for each group 'failed'. Below
the 'Submission Failure' in the pipeline.xml.log. There is a
'Submission Failure' for each group 'failed'.
We have rerun the sge_job.sh for a group 'failed' without any
problem.
Thank you,
Laure
DEBUG 11:17:53:773 [Thread: HTC ID: 7239862 runner] SGERunner
run:350 Error submitting job to the Grid Submission Failure
WARN 11:17:53:802 [Thread: HTC ID: 7239862 runner] SGERunner
run:372 SGE Runner error Submission Failure
java.lang.Exception: Submission Failure
DEBUG 11:17:54:329 [Thread: HTC ID: 7239863 runner] SGERunner
run:350 Error submitting job to the Grid Submission Failure
WARN 11:17:54:330 [Thread: HTC ID: 7239863 runner] SGERunner
run:372 SGE Runner error Submission Failure
java.lang.Exception: Submission Failure
DEBUG 11:17:54:875 [Thread: HTC ID: 7239864 runner] SGERunner
run:350 Error submitting job to the Grid Submission Failure
WARN 11:17:54:875 [Thread: HTC ID: 7239864 runner] SGERunner
run:372 SGE Runner error Submission Failure
java.lang.Exception: Submission Failure
DEBUG 11:17:55:317 [Thread: HTC ID: 7239865 runner] SGERunner
run:350 Error submitting job to the Grid Submission Failure
WARN 11:17:55:318 [Thread: HTC ID: 7239865 runner] SGERunner
run:372 SGE Runner error Submission Failure
java.lang.Exception: Submission Failure
DEBUG 11:17:55:964 [Thread: HTC ID: 7239866 runner] SGERunner
run:350 Error submitting job to the Grid Submission Failure
WARN 11:17:55:964 [Thread: HTC ID: 7239866 runner] SGERunner
run:372 SGE Runner error Submission Failure
java.lang.Exception: Submission Failure
DEBUG 11:17:56:340 [Thread: HTC ID: 7239867 runner] SGERunner
run:350 Error submitting job to the Grid Submission Failure
WARN 11:17:56:340 [Thread: HTC ID: 7239867 runner] SGERunner
run:372 SGE Runner error Submission Failure
java.lang.Exception: Submission Failure
DEBUG 11:17:56:617 [Thread: HTC ID: 7239868 runner] SGERunner
run:350 Error submitting job to the Grid Submission Failure
WARN 11:17:56:617 [Thread: HTC ID: 7239868 runner] SGERunner
run:372 SGE Runner error Submission Failure
java.lang.Exception: Submission Failure
DEBUG 11:17:56:950 [Thread: HTC ID: 7239869 runner] SGERunner
run:350 Error submitting job to the Grid Submission Failure
WARN 11:17:56:950 [Thread: HTC ID: 7239869 runner] SGERunner
run:372 SGE Runner error Submission Failure
java.lang.Exception: Submission Failure
DEBUG 11:17:57:163 [Thread: HTC ID: 7239870 runner] SGERunner
run:350 Error submitting job to the Grid Submission Failure
WARN 11:17:57:163 [Thread: HTC ID: 7239870 runner] SGERunner
run:372 SGE Runner error Submission Failure
java.lang.Exception: Submission Failure
DEBUG 11:17:57:627 [Thread: HTC ID: 7239871 runner] SGERunner
run:350 Error submitting job to the Grid Submission Failure
WARN 11:17:57:628 [Thread: HTC ID: 7239871 runner] SGERunner
run:372 SGE Runner error Submission Failure
java.lang.Exception: Submission Failure
DEBUG 11:17:57:839 [Thread: HTC ID: 7239872 runner] SGERunner
run:350 Error submitting job to the Grid Submission Failure
WARN 11:17:57:839 [Thread: HTC ID: 7239872 runner] SGERunner
run:372 SGE Runner error Submission Failure
java.lang.Exception: Submission Failure
DEBUG 11:17:58:355 [Thread: HTC ID: 7239873 runner] SGERunner
run:350 Error submitting job to the Grid Submission Failure
WARN 11:17:58:356 [Thread: HTC ID: 7239873 runner] SGERunner
run:372 SGE Runner error Submission Failure
java.lang.Exception: Submission Failure
DEBUG 11:17:58:740 [Thread: HTC ID: 7239874 runner] SGERunner
run:350 Error submitting job to the Grid Submission Failure
WARN 11:17:58:741 [Thread: HTC ID: 7239874 runner] SGERunner
run:372 SGE Runner error Submission Failure
java.lang.Exception: Submission Failure
DEBUG 11:17:58:960 [Thread: HTC ID: 7239875 runner] SGERunner
run:350 Error submitting job to the Grid Submission Failure
WARN 11:17:58:960 [Thread: HTC ID: 7239875 runner] SGERunner
run:372 SGE Runner error Submission Failure
java.lang.Exception: Submission Failure
Le 24/01/2012 21:18, Mahurkar, Anup a écrit :
There are a few things that
come to my mind. The first is that the qsub failed for the job.
Because if qsub succeeded then it runs the prolog script which
writes to event.log. Also, sge_submit.out would be there.
Is your pipeline.xml.og or equivalent file non-zero? If so
can you search for this string "Submission Failure" in that file. I have a feeling that the
submission failed for some reason and we need to track that
down.
Chris,
Thank you for your help.
Yes we are running the pipeline over SGE. The SGE job info
from 'show group info' does not help to understand what
happened (grid id = 0 and there is no workflow event log).
See below an example of 'show group info' we get for a group
'failed' :
In the working directory, for the job, we have one
subdirectory per group of the component. Contents of the
subdirectories are described below :
- Contents of subdirectories corresponding to a group
'complete' :
total 64
-rw-rw-rw- 1 ng6 NG6 530 Jan 17 11:22 event.log
-rw-r--r-- 1 ng6 NG6 5 Jan 17 11:19 pid.log
-rwxr-xr-x 1 ng6 NG6 7577 Jan 17 11:17 sge_job.sh
-rw-r--r-- 1 ng6 NG6 52 Jan 17 11:18 sge_submit.out
- Contents of subdirectories corresponding to a group
'failed' :
total 16
-rw-r--r-- 1 ng6 NG6 0 Jan 17 11:17 event.log
-rw-r--r-- 1 ng6 NG6 7577 Jan 17 11:17 sge_job.sh
We also observed that all subdirectories corresponding to a
group 'complete' have the permissions 'drwxrwxrwx', whereas
those corresponding to a group 'failed' have permissions
'drwxr-xr-x'.
Kind regards,
Laure
Le 20/01/2012 18:48, Chris Hemmerich a écrit :
Laure,
Are you running the pipeline over SGE? If so you might be
able to get SGE job info from 'show group info' and look
to see if something is failing in SGE.
If the directory set in 'workflow_run_dir' from
ergatis.ini didn't provide any clues, you can also check
the working directory for the job:
'CWD' from workflow/server-conf/sge_mockserver.conf
Cheers,
Chris
On Fri, 20 Jan 2012, Laure Devlamynck wrote:
Joshua,
Thank you for your help.
We have found the output and error files. Unfortunately
these files do not help us to understand why the
pipeline have failed.
kind regards,
Laure
Le 18/01/2012 16:50, Joshua Orvis a écrit :
Laure -
There are a few places to look here. First, there is
a log file in the
same directory of your pipeline.xml called
pipeline.xml.log and another
one catching all the standard output called
pipeline.xml.run.out.
Is this pipeline running jobs on a grid? If so, each
of those 'groups'
listed corresponds to a job scheduled on your grid,
and there are output
files for each of them in case your job failed. The
path to these is
defined by the workflow_run_dir setting you have in
your ergatis.ini. For
me, that's "/usr/local/scratch/workflow". You can go
to that directory
and you'll find one folder per pipeline ID. Within
that you'll find all
the output and error files for each job submission,
including those listed
in the graphic above.
Joshua
2012/1/17 Laure Devlamynck <[hidden email]
[hidden email]>
Dear all,
An error has occured between two command lines
within one of our
pipeline components, cf. attached file. We have
no error message.
Moreover this error does not occur each time we
submit our pipeline.
Does it exist a log file for such an error in
order to understand
this kind of error ?
Thanks in advance for your answers.
Kind regards,
------------------------------------------------------------------------------
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