Hello John, About the handle ID, that was my understanding too: I was supposed to find a section in the galaxy.ini file (that should be galaxy:tool_handlers). However, that section doesn’t exist so I just insert the server name. If I should create it, what does it look like?
Now, pbs_python 4.4.0 doesn’t work with torque 5.0.1. I’m unable to scramble it successfully (check out attachment). I also found someone with the same problem: https://oss.trac.surfsara.nl/pbs_python/ticket/47 I am not comfortable changing files in TORQUE. I’m satisfied with 4.3.5 for now but if you see a problem in the near future, please feel free to tell me. I’m curious about your input on this. Once again, thank you so much! Cordialement / Regards, Edgar Fernandez De : John Chilton [mailto:jmchil...@gmail.com] Envoyé : December-03-14 9:53 AM À : Fernandez Edgar Cc : galaxy-...@bx.psu.edu Objet : Re: [galaxy-dev] galaxy with torque 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> (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<mailto: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<mailto: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] Envoyé : December-02-14 11:49 AM À : Fernandez Edgar Cc : John Chilton; galaxy-...@bx.psu.edu<mailto: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<mailto: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<mailto: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> [mailto:remy...@gmail.com<mailto:remy...@gmail.com>] Envoyé : December-02-14 6:34 AM À : Fernandez Edgar; John Chilton Cc : galaxy-...@bx.psu.edu<mailto: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<mailto:edgar.fernan...@umontreal.ca>> Pour : "John Chilton" <jmchil...@gmail.com<mailto:jmchil...@gmail.com>> Cc : "galaxy-...@bx.psu.edu<mailto:galaxy-...@bx.psu.edu>" <galaxy-...@bx.psu.edu<mailto: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] Envoyé : November-25-14 12:07 PM À : Fernandez Edgar Cc : galaxy-...@bx.psu.edu<mailto: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<mailto: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<tel: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" > in your mail client. To manage your subscriptions to this and other > Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy@gavroche galaxy-dist]$ LIBTORQUE_DIR=/usr/local/torque/lib/libtorque.so python scripts/scramble.py -e pbs_python fetch_one(): Trying to fetch: http://eggs.galaxyproject.org/pbs_python/pbs_python-4.4.0.tar.gz fetch_one(): Fetched to: /home/galaxy/galaxy-dist/scripts/scramble/archives/pbs_python-4.4.0.tar.gz unpack_source(): Unpacked to: /home/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs4/pbs_python copy_build_script(): Using build script /home/galaxy/galaxy-dist/scripts/scramble/scripts/pbs_python.py run_scramble_script(): Beginning build run_scramble_script(): Executing in /home/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs4/pbs_python: /usr/bin/python scramble.py checking for pbs-config... /usr/local/torque/bin/pbs-config Found torque version: 5.0.1 checking for python... /usr/bin/python checking for python version... 2.6 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/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: WARNING: 'Makefile.in' seems to ignore the --datarootdir setting 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 creating build/temp.linux-x86_64-2.6/src/C++ g++ -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -I/usr/local/torque/include/ -fPIC -DTORQUE_4 -I/usr/include/python2.6 -c src/C++/pbs_wrap.cxx -o build/temp.linux-x86_64-2.6/src/C++/pbs_wrap.o In file included from src/C++/pbs_ifl.h:90, from src/C++/pbs_wrap.cxx:2978: /usr/local/torque/include/u_hash_map_structs.h:82:25: error: container.hpp: No such file or directory In file included from src/C++/pbs_wrap.cxx:2978: src/C++/pbs_ifl.h:91:22: error: u_memmgr.h: No such file or directory In file included from src/C++/pbs_ifl.h:90, from src/C++/pbs_wrap.cxx:2978: /usr/local/torque/include/u_hash_map_structs.h:105: error: string in namespace std does not name a type /usr/local/torque/include/u_hash_map_structs.h:106: error: string in namespace std does not name a type /usr/local/torque/include/u_hash_map_structs.h: In constructor job_data::job_data(const char*, const char*, int, int): /usr/local/torque/include/u_hash_map_structs.h:115: error: name was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:116: error: value was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h: At global scope: /usr/local/torque/include/u_hash_map_structs.h:120: error: container has not been declared /usr/local/torque/include/u_hash_map_structs.h:120: error: expected initializer before < token /usr/local/torque/include/u_hash_map_structs.h:121: error: job_data_container has not been declared /usr/local/torque/include/u_hash_map_structs.h:121: error: expected initializer before job_data_iterator /usr/local/torque/include/u_hash_map_structs.h:123: error: job_data_container was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:123: error: head was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:123: error: expected primary-expression before const /usr/local/torque/include/u_hash_map_structs.h:123: error: expected primary-expression before const /usr/local/torque/include/u_hash_map_structs.h:123: error: expected primary-expression before int /usr/local/torque/include/u_hash_map_structs.h:123: error: expected primary-expression before int /usr/local/torque/include/u_hash_map_structs.h:123: error: initializer expression list treated as compound expression /usr/local/torque/include/u_hash_map_structs.h:125: error: variable or field hash_add_or_exit declared void /usr/local/torque/include/u_hash_map_structs.h:125: error: job_data_container was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:125: error: head was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:125: error: expected primary-expression before const /usr/local/torque/include/u_hash_map_structs.h:125: error: expected primary-expression before const /usr/local/torque/include/u_hash_map_structs.h:125: error: expected primary-expression before int /usr/local/torque/include/u_hash_map_structs.h:127: error: job_data_container was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:127: error: head was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:127: error: expected primary-expression before const /usr/local/torque/include/u_hash_map_structs.h:127: error: initializer expression list treated as compound expression /usr/local/torque/include/u_hash_map_structs.h:129: error: job_data_container was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:129: error: head was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:131: error: job_data_container was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:131: error: head was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:131: error: expected primary-expression before const /usr/local/torque/include/u_hash_map_structs.h:131: error: expected primary-expression before * token /usr/local/torque/include/u_hash_map_structs.h:131: error: env_var was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:131: error: initializer expression list treated as compound expression /usr/local/torque/include/u_hash_map_structs.h:133: error: job_data_container was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:133: error: head was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:135: error: job_data_container was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:135: error: head was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:137: error: job_data_container was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:137: error: dest was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:137: error: job_data_container was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:137: error: src was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:137: error: expected primary-expression before int /usr/local/torque/include/u_hash_map_structs.h:137: error: initializer expression list treated as compound expression /usr/local/torque/include/u_hash_map_structs.h:139: error: job_data_container was not declared in this scope /usr/local/torque/include/u_hash_map_structs.h:139: error: src was not declared in this scope In file included from src/C++/pbs_wrap.cxx:2978: src/C++/pbs_ifl.h:658: error: memmgr has not been declared src/C++/pbs_wrap.cxx: In function PyObject* _wrap_pbs_submit_hash(PyObject*, PyObject*): src/C++/pbs_wrap.cxx:7178: error: memmgr was not declared in this scope src/C++/pbs_wrap.cxx:7178: error: arg2 was not declared in this scope src/C++/pbs_wrap.cxx:7178: error: expected primary-expression before ) token src/C++/pbs_wrap.cxx:7178: error: expected ; before numeric constant src/C++/pbs_wrap.cxx:7228: error: expected primary-expression before ) token error: command 'g++' failed with exit status 1 Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 57, in scramble self.run_scramble_script() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 206, in run_scramble_script raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) ) galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for pbs_python 4.4.0
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