Peter, Thanks for the great information. I see where to tune the "split_size" variable and also the READMEs :)
I'll do so more sleuthing, let the job run and observe. So far it is ~3hr after job launch and still no load on the workers. I think from looking at the /mnt/galaxy/tmp/job_working_directory all of the sub-job directories are prepared. Maybe an issue with the job scheduler/dispatch. Thanks again. David On Tue, May 3, 2016 at 5:11 PM Peter Cock <p.j.a.c...@googlemail.com> wrote: > On Tue, May 3, 2016 at 9:23 PM, David Kovalic <kova...@analome.com> wrote: > > Peter, > > > > We made the modification to the config file, restarted galaxy and things > > seem to be working from the galaxy end. We see sub-job directories being > > created in /mnt/galaxy/tmp/job_working_directory. We think all of the > > required job chunks have been created (i.e. total sequences/1000 sub-job > > directories now with no more being created now) > > > > Now we have what may be a CloudMan question: our working cluster has a > head > > node and 4 workers. The head node is loaded up but the workers are idle. > I > > would have thought jobs should be pushing out to the workers but we don't > > see any load on these machines. > > > > Any advice? Thanks. > > Wait a bit longer? The downside of the job splitting is the extra > disk I/O overhead of splitting the files (here FASTA inputs) and > then merging the output (e.g. BLAST tabular, XML, etc). IIRC, > this happens on the head node only. > > I've not used CloudMan so I have no specific advice here, > other than ask did you confirm that jobs were getting sent to > the worker nodes before turning on use_tasked_jobs = True > in your config/galaxy.ini file? > > > David > > > > PS. what is the path of the file which contains the split_size="1000" > > configuration? > > This is currently defined by the tool wrapper author in the tool > wrapper XML file. Setting up something which will work well > on a broad range of input file sizes is a bit of an art - simply > always dividing the input into 8 chunks does not scale well. > With BLAST+ I found chunks of 1000 queries was a good > balance, while for other tools processing FASTA inputs I > used chunks of 2000 queries. > > I'll link to the latest files on GitHub, but you can browse this on > the Galaxy Tool Shed too - it also ought to show the README > text quite prominently: > > https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus > > In a simple tool, you would see the <parallelism> tag directly > in the wrapper XML file, usually near the top by convention. > e.g. > > > https://github.com/peterjc/pico_galaxy/blob/master/tools/protein_analysis/promoter2.xml > > https://github.com/peterjc/pico_galaxy/blob/master/tools/protein_analysis/tmhmm2.xml > > However, with the BLAST+ wrappers we use macros. So, > using BLASTX as an example, the wrapper is this XML file: > > > https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml > > No sign of the <parallelism> tag directly, but it is pulled in from: > > > https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_plus/ncbi_macros.xml > > This happens via: > > ... > <macros> > ... > <import>ncbi_macros.xml</import> > </macros> > <expand macro="parallelism" /> > ... > > This is a bit more complex, but means avoiding repeating the XML > snippet in almost all the BLAST+ wrapper files. > > Peter >
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