Hi Stephan, I will just quickly answer to your last question. Because, I’m not sure to understand the first part of your message or take the time to :P
i am hoping i am overlooking something :-). is there a way to define job resource defaults on a per-tool basis?
Perhaps, I didn’t understand your message at all: In your tool wrapper, you can use "\${GALAXY_SLOTS:-8}" to dynamically set the ressource according to the setting in the job_conf.xml. Here by default, the job will take 8 CPU (personally, I find that it’s a trap when the administrator/me miss this default value, I prefer to set the default value to 1) <tool id="my_amazing_wrapper" name="My Amazing" > <command> my_amazing_tool -query "$query" […] -num_threads "\${GALAXY_SLOTS:-8}" […] </command> In your job_conf.xml, you can set per tool a destination. Thus, you can specify the number of CPU/Slot, the memory needed, the queue, the nodes ... <destinations default="sge_default"> <destination id="thread4-men_free10" runner="sge"> <param id="nativeSpecification">-V -w n -q galaxy.q -R y -pe thread 4 -l mem_free=10G </param> </destination> </destinations> <tools> <tool id="my_amazing_wrapper" destination="thread4-men_free10"/> </tools> I hope it will help you Cheers Gildas ----------------------------------------------------------------- Gildas Le Corguillé - Bioinformatician/Bioanalyste Plateform ABiMS (Analyses and Bioinformatics for Marine Science) http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/> Member of the Workflow4Metabolomics project http://workflow4metabolomics.org <http://workflow4metabolomics.org/> Station Biologique de Roscoff - UPMC/CNRS - FR2424 Place Georges Teissier 29680 Roscoff FRANCE tel: +33 2 98 29 23 81 ------------------------------------------------------------------
Le 12 mars 2016 à 10:36, Stephan Oepen <oe@ifi.uio.no> a écrit :
dear colleagues,
at the university of oslo, we develop a galaxy-based portal for natural language processing (LAP: Language Analysis Portal). jobs are submitted to a compute cluster via DRMAA and SLURM. current development is against the galaxy release of march 2015.
i am wondering about fine-grained control of job resources. our goal is that most users need not look past the ‘Use default job resource parameters’ toggle in the job configuration dialogue.
as i understand it, i think we can populate the ‘nativeSpecification’ parameter in ‘job_conf.xml’ with SLURM-specific command-line options to set defaults, for example the project, maximum run-time, number of cores, memory per core, and such. i assume these defaults will be combined with and overwritten by ‘custom’ job resource parameters, in case any are specified in the job configuration dialogue?
i tried to track the flow of information from ‘lib/galaxy/jobs/runners/drmaa.py’ via ‘scripts/drmaa_external_runner.py’ into the drmaa-python egg, but i could not easily work out where the merging of ‘nativeSpecification’ and custom resource parameters happens; presumably at about the same time as an actual job script file is created, for submission to SLURM? could someone point me in the right direction here?
—more importantly, maybe: we would like to establish per-tool resource defaults. for example, some of our tools require substantially more memory per core than others. i cannot easily find a way of associating resource default with individual tools. i looked at the tool configuration syntax, ‘job_conf.xml.sample_advanced’, and ‘job_resource_params_conf.xml.sample’, as well as at the following documentation pages:
https://wiki.galaxyproject.org/Admin/Config/Jobs https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
i am hoping i am overlooking something :-). is there a way to define job resource defaults on a per-tool basis?
with warmest thanks in advance, oe ___________________________________________________________ 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/
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