Hello all, I'm wondering if it is sensible to make Galaxy tools automatically use the environment variable $NSLOTS to automatically adjust their number of threads?
Using $NSLOTS works on SGE, but is it generally used on other clusters? The idea here is rather than hard coding the number of threads in a tool or its XML file, which may need to be altered for different local setups, and it can be specified in universe_wsgi.ini under [galaxy:tool_runners] e.g. By default our SGE allocates one slot, so with the following BWA should use one thread: [galaxy:tool_runners] bwa_wrapper = drmaa://-V/ However, if we ask SGE for 8 slots, the tool should use eight threads: [galaxy:tool_runners] bwa_wrapper = drmaa://-V -pe smp 8/ For this to be truly general, we would need a way to set environement variables for local:// runners. However, we can cope with $NSLOTS being undefined with a little magic in the XML definitions. .e.g For the BWA wrapper this is currently hard coded to use 4 threads: <command interpreter="python"> bwa_wrapper.py --threads="4" ... </command> Instead, this could be something like this: <command interpreter="python"> bwa_wrapper.py #if "$NSLOTS"=="": --threads="4" #else: --threads="$NSLOTS" #end if ... </command> Likewise for the BLAST+ wrappers etc. i.e. If the environment variable is set (e.g. via the cluster settings) use that, otherwise keep the current hard coded default. Would this work in principle on other cluster setups? i.e. Is $NSLOTS sufficiently general? It would be messy but the XML if statement could be expanded to handle a second environment variable as well if needs be. Would the Galaxy team accept a pull request implementing this for the BWA and BLAST+ wrappers? Thanks, Peter ___________________________________________________________ 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: http://lists.bx.psu.edu/