On Wed, Mar 5, 2014 at 3:10 PM, Pete Schmitt <Peter.R.Schmitt@dartmouth.edu> wrote:

Is there any other alternatives to pbs_python for interfacing to a torque scheduler. This method appears to be a dead end.

On 3/4/14, 9:51 AM, Nate Coraor wrote:
Pete,

Is it possible that `python` as the Galaxy user is calling a python other than /opt/python/2.7.6/bin/python (e.g. the system version without the -dev/-devel package installed)? The safest bet for ensuring you're using the right python and that it's not going to have conflicting modules, I'd suggest using a Python virtualenv. This is easy to set up, just make sure you run it with the correct python executable, for example:

% wget https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.11.4.tar.gz
% tar zxf virtualenv-1.11.4.tar.gz
% /opt/python/2.7.6/bin/python ./virtualenv-1.11.4/virtualenv.py galaxyvenv
% . ./galaxyvenv/bin/activate
% cd galaxy-dist
% python ./scripts/fetch_eggs.py
% LIBTORQUE_DIR=/opt/torque/active/lib python scripts/scramble.py -e pbs_python

--nate
On Mon, Mar 3, 2014 at 5:19 PM, Pete Schmitt <Peter.R.Schmitt@dartmouth.edu> wrote:
I uninstalled pbs_python 4.4.0 and reinstalled 4.3.5 as root (not using scramble)

When I try this method as the galaxy user:
LIBTORQUE_DIR=/opt/torque/active/lib python scripts/scramble.py -e pbs_python

I get the following output:

src/pbs_wrap.c:2813: warning: function declaration isn't a prototypegcc -pthread -shared build/temp.linux-x86_64-2.7/src/pbs_wrap.o -L/opt/torque/4.2.7/lib -L. -ltorque -lpython2.7 -o build/lib.linux-x86_64-2.7/_pbs.so -L/opt/torque/4.2.7/lib -ltorque -Wl,-rpath -Wl,/opt/torque/4.2.7/lib/usr/bin/ld: cannot find -lpython2.7

LD_LIBRARY_PATH="/opt/python/2.7.6/lib:/opt/torque/active/lib:/usr/local/lib"

I'm not sure why it can't find the libpython2.7.so file. When I built it as root there is a -L/opt/python/2.7.6/lib in that gcc line.
On 3/3/14, 4:13 PM, Nate Coraor wrote:
Hi Pete,

Your subject says you are unable to build pbs_python using scramble.
Could you provide details on what's not working there?

Galaxy is not going to work with a different version of pbs_python
unless a bit of hacking is done to make it attempt to do so. We test
Galaxy with specific versions of its dependencies, which is why we
control the versions of those dependencies and provide the scramble
script to (hopefully) make it painless to build them yourself, should
it be necessary to do so, as is always the case with pbs_python.

--nate

On Mon, Mar 3, 2014 at 3:57 PM, Pete Schmitt
<Peter.R.Schmitt@dartmouth.edu> wrote:
Following the directions from here:
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS

I'm trying to get pbs_python to work as I'm using torque for scheduling
galaxy jobs.

Note: This is a fresh install of galaxy from galaxy-dist on CentOS 5.10

I have pbs_python 4.4.0 module installed into a source-built version of
python/2.7.6

I get the following error in the output of run.sh:

galaxy.jobs INFO 2014-03-03 15:46:45,485 Handler 'main' will load all
configured runner plugins
Traceback (most recent call last):
  File
"/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/webapps/galaxy/buildapp.py",
line 39, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/app.py", line 130, in
__init__
    self.job_manager = manager.JobManager( self )
  File "/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/jobs/manager.py", line
31, in __init__
    self.job_handler = handler.JobHandler( app )
  File "/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/jobs/handler.py", line
30, in __init__
    self.dispatcher = DefaultJobDispatcher( app )
  File "/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/jobs/handler.py", line
568, in __init__
    self.job_runners = self.app.job_config.get_job_runner_plugins(
self.app.config.server_name )
  File "/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/jobs/__init__.py", line
449, in get_job_runner_plugins
    module = __import__( module_name )
  File "/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/jobs/runners/pbs.py",
line 31, in <module>
    raise Exception( egg_message % str( e ) )
Exception:

The 'pbs' runner depends on 'pbs_python' which is not installed or not
configured properly.  Galaxy's "scramble" system should make this
installation
simple, please follow the instructions found at:

    http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster

Additional errors may follow:
pbs-python==4.3.5

This is the job_conf.xml file:

<?xml version="1.0"?>
<job_conf>
    <plugins>
        <plugin id="pbs" type="runner"
load="galaxy.jobs.runners.pbs:PBSJobRunner"/>
    </plugins>
    <handlers>
        <handler id="dirigo"/>
    </handlers>
    <destinations default="pbs_default">
        <destination id="pbs_default" runner="pbs"/>
                <param
id="Resource_List">walltime=72:00:00,nodes=1:ppn=4</param>
    </destinations>
</job_conf>

I did not use the scramble system to install the pbs_python module.  I
downloaded the latest version
available and installed it from the root account.


--

Pete Schmitt


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--

Pete Schmitt Technical Director: Discovery Cluster NH INBRE Grid Computational Genetics Lab Institute for Quantitative Biomedical Sciences Dartmouth College, HB 6203 L12 Berry/Baker Library Hanover, NH 03755 Phone: 603-646-8109 http://discovery.dartmouth.edu http://columbia.dartmouth.edu/grid http://www.epistasis.org http://iQBS.org
--

Pete Schmitt Technical Director: Discovery Cluster NH INBRE Grid Computational Genetics Lab Institute for Quantitative Biomedical Sciences Dartmouth College, HB 6203 L12 Berry/Baker Library Hanover, NH 03755 Phone: 603-646-8109 http://discovery.dartmouth.edu http://columbia.dartmouth.edu/grid http://www.epistasis.org http://iQBS.org