That handle id seems wrong... at least it is not what I am used to. It
needs to match a server section specified in your galaxay ini file -
usually this is a simple string like handler0 or something.

It looks like the specific error is :

/home/galaxy/galaxy-dist/eggs/pbs_python-4.3.5-py2.6-linux-x86_64-ucs4.egg/_pbs.so:
undefined symbol: log_record

I am not sure what causes this - some subtle incompatibility.

So the pbs_python 4.4.0 egg is available on eggs.galaxyproject.org (
http://eggs.galaxyproject.org/pbs_python/pbs_python-4.4.0.tar.gz) - I think
it may be needed for newer torque versions - do you want to update the
version specified in eggs.ini, delete the old egg, and rescramble the egg
with 4.4.0?

-John

P.S. Since you are setting up a new server I would strongly suggest using
postgres instead of MySQL - but the previous comment about it not needing
to be accessed on the compute servers is correct.


On Tue, Dec 2, 2014 at 3:10 PM, Fernandez Edgar <
edgar.fernan...@umontreal.ca> wrote:

>  Hello again,
>
>
>
> I’m very close in making pbs_python work but I’m hitting a new wall.
>
> So I’ve created the file config/job_conf.xml which looks like this
>
> <?xml version="1.0"?>
>
> <job_conf>
>
>     <plugins>
>
>         <plugin id="pbs" type="runner"
> load="galaxy.jobs.runners.pbs:PBSJobRunner"/>
>
>     </plugins>
>
>     <handlers default="*gavroche.esi.umontreal.ca
> <http://gavroche.esi.umontreal.ca>*">
>
>         <handler id="*gavroche.esi.umontreal.ca
> <http://gavroche.esi.umontreal.ca>*" tags="pbs"/>
>
>     </handlers>
>
>     <destinations default="pbs_default">
>
>         <destination id="pbs_default" runner="pbs" tags="mycluster"/>
>
>         <destination id="pbs_longjobs" runner="pbs"
> tags="mycluster,longjobs">
>
>             <param id="Resource_List">walltime=72:00:00</param>
>
>         </destination>
>
>     </destinations>
>
> </job_conf>
>
> *gavroche.esi.umontreal.ca <http://gavroche.esi.umontreal.ca>* is my
> torque server.
>
> I know that in your documentation it doesn’t say to put in a handlers tag
> but galaxy doesn’t parse the xml without it.
>
>
>
> Now, once I try to start galaxy, I get the error you see in the file
> *paster.log* attached to this email.
>
> Can anyone help please?
>
>
>
> Cordialement / Regards,
>
> Edgar Fernandez
>
>
>
> *De :* Fernandez Edgar
> *Envoyé :* December-02-14 1:33 PM
> *À :* 'Rémy Dernat'
> *Cc :* John Chilton; galaxy-...@bx.psu.edu
> *Objet :* RE: Re : [galaxy-dev] galaxy with torque
>
>
>
> Thank you for that correction.
>
>
>
> Just a small FYI (maybe it will be useful to update the wiki)…
>
>
>
> I had to export three variables to make the scramble possible:
>
>
>
> export PBS_PYTHON_INCLUDEDIR=/usr/local/torque/include/
>
> export PBSCONFIG=/usr/local/torque/bin/pbs-config
>
> export LIBTORQUE_DIR=/usr/local/torque/lib/libtorque.so
>
> python scripts/scramble.py -e pbs_python
>
>
>
> Cordialement / Regards,
>
> Edgar Fernandez
>
>
>
> *De :* Rémy Dernat [mailto:remy...@gmail.com <remy...@gmail.com>]
> *Envoyé :* December-02-14 11:49 AM
> *À :* Fernandez Edgar
> *Cc :* John Chilton; galaxy-...@bx.psu.edu
> *Objet :* Re: Re : [galaxy-dev] galaxy with torque
>
>
>
> Sorry for answer 7. There is no benefit to do that. Once the egg is done,
> there is nothing to do from here, except if you change your python
> version... If that variable is empty, that is normal, because it is not an
> environment variable, it is just used by the following python command:
>
> LIBTORQUE_DIR=/path/to/libtorque python scripts/scramble.py -e pbs_python
>
>
>
> 2014-12-02 16:27 GMT+01:00 Rémy Dernat <remy...@gmail.com>:
>
> Hi Edgar,
>
>
>
> You are right. It is very annoying...
>
>
>
> So, to answer your questions:
>
> 1/ First answer of google / wikipedia with DRMAA :
> http://en.wikipedia.org/wiki/DRMAA
>
> It is a pattern to talk with any DRM system (SGE, torque, whatever...)
>
>
>
> 2/ This is a library (python version) for your Torque installation.
>
>
>
> 3/ MySQL access is only needed by your galaxy frontend.
>
>
>
> 4/ Internet access is not required for your compute node (except the
> galaxy one), but it is better if you want to use a package manager on your
> compute nodes, for example...
>
>
>
> 5/ On my part, I use permissions like 760 on galaxy directory. It depends
> on your needs... Some applications might need an access to your galaxy
> installation, but you should split binaries, the galaxy installation and
> your data (datasets, libraries...). But do not forget to share this folders
> by NFS (if needed).
>
>
>
> 6/ Sorry, no idea; but I see no reason for that to become unavailable, if
> your proxy is well configured.
>
>
>
> 7/ You have to put this command line into a file which will be sourced
> like $HOME_GALAXY/.bashrc or your environment file
> ("environment_setup_file" in universe_wsgi.ini or config/galaxy.ini)
>
>
>
> Regards,
> Remy
>
>
>
> 2014-12-02 13:59 GMT+01:00 Fernandez Edgar <edgar.fernan...@umontreal.ca>:
>
> Hi everyone,
>
>
>
> I’m guessing Remy, you click on the send button by mistake on your HTC
> device.
>
> It happens to me ALL the time…
>
>
>
> I wanted to take this opportunity to add some questions to the three
> questions in my previous email.
>
> So here goes:
>
>
>
> 4.       Is it necessary that my torque compute nodes have internet
> access?
>
> Because right now, only my torque server and my galaxy server has internet
> access.
>
> However, communication between the submit node (a.k.a. galaxy server) and
> the torque server is enabled.
>
> Likewise, between the torque server and the compute nodes.
>
> 5.       Furthermore, would I disable any galaxy functionalities if I
> change the permissions on the whole galaxy installation directory like so:
> chmod –R 700 galaxy_install_directory
>
> I have created a user galaxy for running everything that is galaxy.
>
> 6.       I’ve actually installed my galaxy server using a proxy server
> (as described on your web site). Can I still use the Report Tool
> functionalities on galaxy?
>
> 7.       Any instructions on making PBS (running jobs via TORQUE resource
> manager), because I have successfully scrambled the egg pbs_python with the
> command:
>
> LIBTORQUE_DIR=/path/to/libtorque python scripts/scramble.py -e pbs_python.
>
> However, LIBTORQUE_DIR is empty.
>
>
>
> Once again, thank you in advance for all your help!
>
>
>
> Cordialement / Regards,
>
> Edgar Fernandez
>
>
>
> *De :* remy...@gmail.com [mailto:remy...@gmail.com]
> *Envoyé :* December-02-14 6:34 AM
> *À :* Fernandez Edgar; John Chilton
>
>
> *Cc :* galaxy-...@bx.psu.edu
> *Objet :* Re : [galaxy-dev] galaxy with torque
>
>
>
> 1 a drmaa d
>
> Envoyé depuis mon HTC
>
> ----- Reply message -----
> De : "Fernandez Edgar" <edgar.fernan...@umontreal.ca>
> Pour : "John Chilton" <jmchil...@gmail.com>
> Cc : "galaxy-...@bx.psu.edu" <galaxy-...@bx.psu.edu>
> Objet : [galaxy-dev] galaxy with torque
> Date : mer., nov. 26, 2014 19:09
>
>
> Hi John,
>
> First, thank you very much for your prompt answer.
> It's extremely appreciated.
>
> Secondly, I have some other questions: whatever answers you can provide me
> with, will be greatly helpful.
> Please, forgive my beginner level understanding of an DRM system.
>
> 1. Once I compile, make and install the Torque Submit Node code against
> the server running Galaxy, what exactly is the purpose for an DRMAA ?
>
> 2. What is exactly the PBS step describe here:
> https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
> galaxy_user@galaxy_server% LIBTORQUE_DIR=/path/to/libtorque python
> scripts/scramble.py -e pbs_python
> What does it do exactly ?
>
> 3. All servers which includes my torque server, torque compute nodes and
> torque submit node (a.k.a galaxy server) have the galaxy user defines and
> its home shared on all of them. This means all of them have access (via
> NFS) of the installation directory of galaxy. But what about the MySQL
> server access. Does the torque server or the compute nodes need access to
> that service?
>
> I hope I'm not sending too many emails/questions...
> Thank you very much!
>
> Cordialement / Regards,
> Edgar Fernandez
>
> -----Message d'origine-----
> De : John Chilton [mailto:jmchil...@gmail.com <jmchil...@gmail.com>]
> Envoyé : November-25-14 12:07 PM
> À : Fernandez Edgar
> Cc : galaxy-...@bx.psu.edu
> Objet : Re: [galaxy-dev] galaxy with torque
>
> I am not sure we have a walkthrough for Torque specifically - but if you
> have Galaxy up and running and you can qsub commands to torque - hopefully
> you have done all of the hard parts.
>
> You will need a DRMAA library for your torque setup -
> https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
> suggests compiling pbs_drmaa and outlines how to set it up. After that you
> just need to add a plugin and default destination to your job_conf.xml file
> - also outlined on that wiki page.
>
> Other good resources to consult if you are scaling up your Galaxy this way
> are:
> https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
> https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay/AdminWalkthrough
>
> Good luck and let us know if you encounter any problems.
>
> -John
>
> On Fri, Nov 21, 2014 at 2:30 PM, Fernandez Edgar <
> edgar.fernan...@umontreal.ca> wrote:
> > Hello all,
> >
> >
> >
> > My name is Edgar Fernandez. I’m a sys. admin. at University of Montreal.
> >
> > I’ve contacted you a while back about installing galaxy and I’ve
> > successfully done it on a redhat 6 server.
> >
> >
> >
> > I see myself in a situation where I need to utilise all my redhat
> > servers (who are identical to the server running the galaxy website).
> >
> >
> >
> > I’ve also successfully installed a server torque with compute notes
> > and clients nodes.
> >
> >
> >
> > What are the last step to make the link between galaxy and torque?
> >
> > Also, once that connection is made, how will galaxy keep track of the
> > jobs sent?
> >
> > I mean who will it know this job that just finished is for this user
> > and not another ?
> >
> >
> >
> > Also, my torque installation is so that my server running galaxy is a
> > submit node and a client node.
> >
> > I hope this is not a problem.
> >
> >
> >
> > Please help!
> >
> >
> >
> > Cordialement / Regards,
> >
> >
> >
> > Edgar Fernandez
> >
> > System Administrator (Linux)
> >
> > Direction Générale des Technologies de l'Information et de la
> > Communication
> >
> > (  Bur. : 1-514-343-6111 poste 16568
> >
> >
> >
> > Université de Montréal
> >
> > PAVILLON ROGER-GAUDRY, bureau X-218
> >
> >
> >
> >
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
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> >   https://lists.galaxyproject.org/
> >
> > To search Galaxy mailing lists use the unified search at:
> >   http://galaxyproject.org/search/mailinglists/
> ___________________________________________________________
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>
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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>
> To search Galaxy mailing lists use the unified search at:
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>
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