Looking more closely at the parse error, it appears that galaxy cannot find the
PBS plugin (pbs_python installed from source):
for plugin in ElementTree.parse(job_conf_xml).find('plugins').findall('plugin'):
As expected, pbs_python can happily detect my PBS installation when I run its
PBSQuery.py script. The source and python installers are noticeably different
upon inspection, unfortunately I still haven’t managed to get the python
installation working yet.
Here is my job_conf.xml:
<plugins>
<plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner"/>
</plugins>
<destinations default="pbs_default">
<destination id="pbs_default" runner="pbs"/>
<destination id="other_cluster" runner="pbs">
<param id="destination">@other.cluster</param>
</destination>
</destinations>
Thanks,
Sandra
From: Sandra Maksimovic <[email protected]>
Sent: Thursday, 29 August 2019 10:08 AM
To: '[email protected]' <[email protected]>
Subject: [galaxy-dev] Re: pbs-python issues
Hi Fred,
For us, PBS (free) is installed to a shared filesystem that is mounted via NFS
to the galaxy server (and via GPFS to the rest of the HPC). The server home
directory is also custom (/opt) but local to the disk on each HPC node
(including galaxy).
I have tested running a simple PBS script from the galaxy node as the galaxy
user and it was able to run successfully. In your case, have you installed PBS
Pro with all default installations paths? It seems to me that the pbs-python
module is happy to be installed with PBS defaults but has trouble with a custom
PBS install. I am having to look into the pbs-python installer script to hunt
down the relevant variables.
Re: parse error – I had configured a basic job_conf.xml to test with galaxy,
but it seems it was too basic. Are you perchance able to provide an example of
your job_conf.xml for reference?
Thanks,
Sandra
From: SAPET, Frederic via galaxy-dev
<[email protected]<mailto:[email protected]>>
Sent: Wednesday, 28 August 2019 5:09 PM
To: Sandra Maksimovic
<[email protected]<mailto:[email protected]>>;
'[email protected]'
<[email protected]<mailto:[email protected]>>
Subject: [galaxy-dev] Re: pbs-python issues
Hi Sandra
We're running a Galaxy with PBS Pro as jobs scheduler.
I never had any problem with pbs-python however.
Here, for us, the PBS client is installed locally (on the VM that hosts Galaxy).
Are you sure that PBS is well installed ? Are you able to launch a simple PBS
script with the galaxy user ?
Maybe the error you see (xml.etree.ElementTree.ParseError ) is because one XML
config file has an issue.
Fred
-----Message d'origine-----
De : Sandra Maksimovic
<[email protected]<mailto:[email protected]<mailto:[email protected]%3cmailto:[email protected]>>>
Envoyé : mercredi 28 août 2019 02:36
À : '[email protected]'
<[email protected]<mailto:[email protected]<mailto:[email protected]%3cmailto:[email protected]>>>
Objet : [galaxy-dev] pbs-python issues
Hi all,
As a galaxy newbie, I'm struggling to get the pbs-python module working on our
galaxy instance. PBS is installed to a custom location on a shared filesystem
mounted via NFS to our galaxy server, however, installing pbs-python using the
git clone / python venv method in the documentation fails because it can't find
PBS and there does not appear to be any way to define it for pbs-python (I
could be wrong?).
...
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector-strong --param=ssp-buffer-size=4
-grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64
-mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DTORQUE_4
-I/usr/include/torque -Isrc/C++ -I/usr/include/python2.7 -c
src/C++/pbs_wrap.cxx -o build/temp.linux-x86_64-2.7/src/C++/pbs_wrap.o
In file included from src/C++/pbs_wrap.cxx:2978:0:
src/C++/pbs_ifl.h:90:32: fatal error: u_hash_map_structs.h: No such file or
directory #include "u_hash_map_structs.h"
^
compilation terminated.
error: command 'gcc' failed with exit status 1
So I went ahead and installed pbs_python from source (which does allow you
define a PBS_PYTHON_INCLUDEDIR environment variable), however, galaxy does not
seem to like this as evidenced by errors during startup. I suspect this has to
do with pbs_python not being installed into the galaxy virtual environment.
galaxy[97486]: Traceback (most recent call last):
galaxy[97486]: File "<string>", line 1, in <module>
galaxy[97486]: File
"/hpc/software/installed/galaxy/19.05/lib/galaxy/dependencies/__init__.py",
line 179, in optional
galaxy[97486]: conditional = ConditionalDependencies(config_file)
galaxy[97486]: File
"/hpc/software/installed/galaxy/19.05/lib/galaxy/dependencies/__init__.py",
line 32, in __init__
galaxy[97486]: self.parse_configs()
galaxy[97486]: File
"/hpc/software/installed/galaxy/19.05/lib/galaxy/dependencies/__init__.py",
line 41, in parse_configs
galaxy[97486]: for plugin in
ElementTree.parse(job_conf_xml).find('plugins').findall('plugin'):
galaxy[97486]: File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1182,
in parse
galaxy[97486]: tree.parse(source, parser)
galaxy[97486]: File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 656,
in parse
galaxy[97486]: parser.feed(data)
galaxy[97486]: File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1642,
in feed
galaxy[97486]: self._raiseerror(v)
galaxy[97486]: File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506,
in _raiseerror
galaxy[97486]: raise err
galaxy[97486]: xml.etree.ElementTree.ParseError: junk after document element:
line 4, column 0
I've attempted reinstalls of the git clone / python venv method with the PBS
environment variable to no avail. I was wondering if someone might have any
ideas about working around this roadblock, or may have encountered a similar
module installation issue in the past?
Also, I was hoping to get some ideas/examples of generic job_conf.xml
definitions for PBS clusters? Things like best practices, caveats, etc. My
understanding is that, unless configured otherwise, galaxy will submit jobs as
the galaxy user and that configuring the server to run jobs as end users
themselves is difficult/risky. Just wondering if you guys might have
opinions/thoughts/recommendations about this?
And finally, what would be a good way to test that galaxy is submitting jobs to
the queue properly? Is there some generic test data/procedure to verify that
the galaxy instance is working as expected?
Thanks,
Sandra Maksimovic
Systems Administrator
Information Technology
Murdoch Children's Research Institute
The Royal Children's Hospital, 50 Flemington Road Parkville, Victoria 3052
Australia
T +61 3 8341 6498
E
[email protected]<mailto:[email protected]<mailto:[email protected]%3cmailto:[email protected]<mailto:[email protected]%3cmailto:[email protected]%3cmailto:[email protected]%3cmailto:[email protected]>>>
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