I was successful in getting the bps_python egg to load finally. However, there is an issue that remains. When I submit a job it is sent to the local runner and not to pbs. Where should I start looking to change this work? Thanks, Iry On 7/10/12 12:00 PM, "galaxy-dev-request@lists.bx.psu.edu" <galaxy-dev-request@lists.bx.psu.edu> wrote:

Message: 3 Date: Mon, 9 Jul 2012 17:24:25 +0000 From: Iry Witham <Iry.Witham@jax.org> To: "Dorset, Daniel C" <daniel.dorset@Vanderbilt.Edu> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] galaxy-dev Digest, Vol 73, Issue 10 Message-ID: <CC207DDE.8F49%iry.witham@jax.org> Content-Type: text/plain; charset="us-ascii"

Hi Daniel,

I did use -e previously. The ?e was a typo in my post. I ran it again and it tries, but fails to generate the file(s) as shown:

:galaxy@jaxgalaxydev01:/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist> LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python fetch_one(): Trying to fetch: http://eggs.g2.bx.psu.edu/pbs_python/pbs_python-4.1.0.tar.gz fetch_one(): Fetched to:

/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/archives/pbs _ python-4.1.0.tar.gz unpack_source(): Unpacked to:

/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/build/py2.6- l inux-x86_64-ucs4/pbs_python copy_build_script(): Using build script /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/scripts/pbs_ p ython.py run_scramble_script(): Beginning build run_scramble_script(): Executing in /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/build/py2.6- l inux-x86_64-ucs4/pbs_python: /usr/bin/python scramble.py

-------------------------------------------------------------------------- - This script requires setuptools version 0.6c11 to run (even to display help). I will attempt to download it for you (from http://pypi.python.org/packages/2.6/s/setuptools/), but you may need to enable firewall access for this script first. I will start the download in 8 seconds.

(Note: if this machine does not have network access, please obtain the file

http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.e g g

and place it in this directory before rerunning this script.) -------------------------------------------------------------------------- - Downloading http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.e g g checking for pbs-config... /usr/local/lib//../bin/pbs-config Found torque version: 2.5.8 checking for python... /usr/bin/python checking for python version... 2.6 checking for python platform... linux2 checking for python script directory... ${prefix}/lib64/python2.6/site-packages checking for python extension module directory... ${exec_prefix}/lib64/python2.6/site-packages configure: creating ./config.status config.status: creating Makefile config.status: creating setup.py scramble(): Patching setup.py running egg_info creating src/pbs_python.egg-info writing src/pbs_python.egg-info/PKG-INFO writing top-level names to src/pbs_python.egg-info/top_level.txt writing dependency_links to src/pbs_python.egg-info/dependency_links.txt writing manifest file 'src/pbs_python.egg-info/SOURCES.txt' reading manifest file 'src/pbs_python.egg-info/SOURCES.txt' writing manifest file 'src/pbs_python.egg-info/SOURCES.txt' running bdist_egg installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib.linux-x86_64-2.6 copying src/pbs.py -> build/lib.linux-x86_64-2.6 copying src/PBSQuery.py -> build/lib.linux-x86_64-2.6 running build_ext building '_pbs' extension creating build/temp.linux-x86_64-2.6 creating build/temp.linux-x86_64-2.6/src gcc -pthread -fno-strict-aliasing -DNDEBUG -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -fwrapv -fPIC -DTORQUE_2_4 -I/usr/include/python2.6 -c src/pbs_wrap.c -o build/temp.linux-x86_64-2.6/src/pbs_wrap.o gcc -pthread -shared build/temp.linux-x86_64-2.6/src/pbs_wrap.o -L/usr/local/lib -L/usr/lib64 -ltorque -lpython2.6 -o build/lib.linux-x86_64-2.6/_pbs.so creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg copying build/lib.linux-x86_64-2.6/PBSQuery.py -> build/bdist.linux-x86_64/egg copying build/lib.linux-x86_64-2.6/pbs.py -> build/bdist.linux-x86_64/egg copying build/lib.linux-x86_64-2.6/_pbs.so -> build/bdist.linux-x86_64/egg byte-compiling build/bdist.linux-x86_64/egg/PBSQuery.py to PBSQuery.pyc byte-compiling build/bdist.linux-x86_64/egg/pbs.py to pbs.pyc creating stub loader for _pbs.so byte-compiling build/bdist.linux-x86_64/egg/_pbs.py to _pbs.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying src/pbs_python.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying src/pbs_python.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying src/pbs_python.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying src/pbs_python.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt zip_safe flag not set; analyzing archive contents... creating dist creating 'dist/pbs_python-4.1.0-py2.6-linux-x86_64.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/lib/galaxy/eggs/scramble.py" , line 60, in scramble raise ScrambleFailure( self, "%s(): Egg build for %s did not appear to fail, but no egg found to copy from expected path:\n %s" % ( sys._getframe().f_code.co_name, self.name, new_egg ) ) galaxy.eggs.scramble.ScrambleFailure: scramble(): Egg build for pbs_python did not appear to fail, but no egg found to copy from expected path:

/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/build/py2.6- l inux-x86_64-ucs4/pbs_python/dist/pbs_python-4.1.0-py2.6-linux-x86_64-ucs4. e gg"

Iry

On 7/7/12 3:10 PM, "Dorset, Daniel C" <daniel.dorset@Vanderbilt.Edu> wrote:

...

________________________________________ From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of galaxy-dev-request@lists.bx.psu.edu [galaxy-dev-request@lists.bx.psu.edu] Sent: Saturday, July 07, 2012 11:00 AM To: galaxy-dev@lists.bx.psu.edu Subject: galaxy-dev Digest, Vol 73, Issue 10

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Today's Topics:

1. pbs_python issues (Iry Witham) 2. Which css file does welcome.html use? (Dorset, Daniel C) 3. Re: Which css file does welcome.html use? (Jeremy Goecks)

Hi Ira,

I'm in charge of a Galaxy instance that's also deployed on a PBS Cluster, and I went through this process a couple of months ago. If I remember correctly, when you run your Python script, you're supposed to run it with "-e" not "?e" Assuming that you are pointing to the correct directory, it looks like everything else about your command is correct.

Have you tried that?

----------------------------------------------------------------------

Message: 1 Date: Fri, 6 Jul 2012 16:32:14 +0000 From: Iry Witham <Iry.Witham@jax.org> To: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Subject: [galaxy-dev] pbs_python issues Message-ID: <CC1C8B4D.8EAD%iry.witham@jax.org> Content-Type: text/plain; charset="windows-1252"

I am having an issue with pbs_python loading, but not submitting jobs to the cluster.

The first issue is that when I ran 'LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py ?e pbs_python' it failed to generate the pbs_python egg in the /galaxy-dist/eggs/ directory.

Secondly I copied the pbs_python-4.1.0-py2.6-linux-x86_64-ucs4.egg from my production galaxy server and restarted my test server. It appears to start, but when I attempt to run anything it uses the local runner and fails. The runner0.log shows the pbsjobrunner is loaded is below:

galaxy.jobs.handler DEBUG 2012-07-06 10:08:45,681 Loaded job runner: galaxy.jobs.runners.pbs:PBSJobRunner galaxy.jobs.handler INFO 2012-07-06 10:08:45,682 job handler stop queue started galaxy.jobs.manager INFO 2012-07-06 10:08:45,687 job manager queue started galaxy.jobs.manager INFO 2012-07-06 10:08:45,688 job manager stop queue started galaxy.jobs.handler INFO 2012-07-06 10:08:45,692 job handler queue started

I can't seem to get past this point since I upgraded. Can someone point me in the right direction?

Thanks, Iry

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