On Thu, Mar 22, 2012 at 3:34 PM, Daniel Sobral <dsobral@igc.gulbenkian.pt> wrote:

Hello,

For certain tools, like bwa or blast, there is a non-configurable number of threads to use inside the tool xml. This is inconvenient for certain cluster configurations, where what we want is division of a job into multiple jobs (I guess this is what is intended by the <parallel> tag), and not creation of threads that may wreak havoc in a cluster.

Is there any reason why bwa and blast have --num-threads=8 pre-configured in the xml file?

Because there isn't a way (yet) to set this via the universe_wsgi.ini file. I have asked about this in the past - but can see it is quite complex and often the idea setting is going to be tool specific. Note those setttings hardcoded in the <command> tag control the number of thread in a single job - and I setup my job runners in universe_wsgi.ini to match (e.g. tell SGE I want 8 threads, or an entire machine for this job). Separately to this, in the <parallelism> tag of a tool is a hard coded splitting strategy (if this experimental feature is enabled in your universe_wsgi.ini file) for breaking a job into sub-jobs, which are submitted to the cluster separate. Here again a configuration mechanism could be nice. Peter