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,
On Fri, Apr 13, 2012 at 10:24 AM, Mariette <[hidden email]> 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,
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 <[hidden email]> wrote:
Jérôme -
I'm taking a look at this.
Joshua
On Fri, Apr 13, 2012 at 10:24 AM, Mariette <[hidden email]> 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,
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
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
script. I'd like to test it locally.
Joshua
On Fri, Apr 13, 2012 at 1:14 PM, Joshua
Orvis <[hidden email]>
wrote:
Jérôme -
I'm
taking a look at this.
Joshua
On Fri, Apr 13, 2012 at 10:24
AM, Mariette <[hidden email]>
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,
------------------------------------------------------------------------------
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
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 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
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
script. I'd like to test it locally.
Joshua
On Fri, Apr 13, 2012 at 1:14 PM,
Joshua Orvis <[hidden email]>
wrote:
Jérôme
-
I'm
taking a look at this.
Joshua
On Fri, Apr 13, 2012 at
10:24 AM, Mariette <[hidden email]>
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,
------------------------------------------------------------------------------
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
------------------------------------------------------------------------------
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
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?
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 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
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
script. I'd like to test it locally.
Joshua
On Fri, Apr 13, 2012 at 1:14 PM,
Joshua Orvis <[hidden email]>
wrote:
Jérôme
-
I'm
taking a look at this.
Joshua
On Fri, Apr 13, 2012 at
10:24 AM, Mariette <[hidden email]>
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,
------------------------------------------------------------------------------
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
------------------------------------------------------------------------------
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
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?
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
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 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
script. I'd like to test it locally.
Joshua
On Fri, Apr 13, 2012 at
1:14 PM, Joshua Orvis <[hidden email]>
wrote:
Jérôme
-
I'm taking a look at
this.
Joshua
On Fri, Apr
13, 2012 at 10:24 AM, Mariette <[hidden email]>
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,
------------------------------------------------------------------------------
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
------------------------------------------------------------------------------
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
------------------------------------------------------------------------------
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
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________
Ergatis-users mailing list
[hidden email] https://lists.sourceforge.net/lists/listinfo/ergatis-users
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?
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
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
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
script. I'd like to test it locally.
Joshua
On Fri, Apr 13, 2012
at 1:14 PM, Joshua Orvis <[hidden email]>
wrote:
Jérôme
-
I'm taking a look at
this.
Joshua
On Fri, Apr
13, 2012 at 10:24 AM, Mariette <[hidden email]>
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,
------------------------------------------------------------------------------
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
------------------------------------------------------------------------------
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
------------------------------------------------------------------------------
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
------------------------------------------------------------------------------
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/
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________
Ergatis-users mailing list
[hidden email] https://lists.sourceforge.net/lists/listinfo/ergatis-users
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 <[hidden email]> 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?
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
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
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
script. I'd like to test it locally.
Joshua
On Fri, Apr 13, 2012
at 1:14 PM, Joshua Orvis <[hidden email]>
wrote:
Jérôme
-
I'm taking a look at
this.
Joshua
On Fri, Apr
13, 2012 at 10:24 AM, Mariette <[hidden email]>
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,
------------------------------------------------------------------------------
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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 <[hidden email]>
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?
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
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
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
script. I'd like to test it
locally.
Joshua
On Fri,
Apr 13, 2012 at 1:14 PM,
Joshua Orvis <[hidden email]>
wrote:
Jérôme
-
I'm
taking a look at this.
Joshua
On
Fri, Apr 13, 2012 at
10:24 AM, Mariette <[hidden email]>
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,
------------------------------------------------------------------------------
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------------------------------------------------------------------------------
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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 <[hidden email]>
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?
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
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
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
script. I'd like to test it
locally.
Joshua
On
Fri, Apr 13, 2012 at 1:14
PM, Joshua Orvis <[hidden email]>
wrote:
Jérôme
-
I'm
taking a look at this.
Joshua
On
Fri, Apr 13, 2012
at 10:24 AM,
Mariette <[hidden email]>
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,
------------------------------------------------------------------------------
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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
------------------------------------------------------------------------------
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Boundary is the first to Know...and Tell You.
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------------------------------------------------------------------------------
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------------------------------------------------------------------------------
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will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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will include endpoint security, mobile security and the
latest in malware
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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 <[hidden email]> 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:
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 <[hidden email]>
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?
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
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
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
script. I'd like to test it
locally.
Joshua
On
Fri, Apr 13, 2012 at 1:14
PM, Joshua Orvis <[hidden email]>
wrote:
Jérôme
-
I'm
taking a look at this.
Joshua
On
Fri, Apr 13, 2012
at 10:24 AM,
Mariette <[hidden email]>
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,
------------------------------------------------------------------------------
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will include endpoint security, mobile security and the latest in malware
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will include endpoint security, mobile security and the
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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!
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 <[hidden email]>
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:
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 <[hidden email]>
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?
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
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
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
script. I'd
like to test it
locally.
Joshua
On
Fri, Apr 13,
2012 at 1:14
PM, Joshua
Orvis <[hidden email]>
wrote:
Jérôme -
I'm
taking a look
at this.
Joshua
On
Fri, Apr 13,
2012 at 10:24
AM, Mariette <[hidden email]>
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,
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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!
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 <[hidden email]>
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:
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 <[hidden email]>
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?
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
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
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
script. I'd
like to test
it locally.
Joshua
On
Fri, Apr 13,
2012 at 1:14
PM, Joshua
Orvis <[hidden email]>
wrote:
Jérôme -
I'm
taking a look
at this.
Joshua
On
Fri, Apr 13,
2012 at 10:24
AM, Mariette <[hidden email]>
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,
------------------------------------------------------------------------------
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Boundary is the first to Know...and Tell You.
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------------------------------------------------------------------------------
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Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
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------------------------------------------------------------------------------
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Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
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