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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/