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 prototype gcc -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 *
