As a follow-up for SGE + TMP variables, I've also encountered problems with settings TEMP,TMP and TMPDIR variables. Tried setting "~/.sge_request" and changing the Galaxy environment variables before starting python - nothing worked - TMPDIR and TMP were always set to "/tmp/all.q.XXXXX" by SGE .
What finally worked is changing the SGE configuration queue, and simply setting the "tmpdir" variable to my desired temp directory. Do that by running: $ sudo qconf -mq all.q and changing the line: tmpdir /tmp to tmpdir /my/temporary/directory/path Problem solved :) No more messing around with TMP,TMPDIR variables in any Galaxy related source files. Hope this helps, -gordon Shantanu Pavgi wrote, On 07/26/2011 05:40 PM: > > On Jul 21, 2011, at 6:24 PM, Shantanu Pavgi wrote: > >> >> We have configured galaxy to work with our SGE cluster using drmaa job >> runner interface. We are using 'unified method' for this install and >> both TEMP environment variable and new_file_path in universe_wsgi.ini file >> have been configured correctly. However, we are seeing some errors where >> local /tmp space on compute nodes is being referenced by the galaxy tools. >> Specifically we saw it mentioned in error messages from following tools: >> * bwa_wrapper and upload tools: 'No space left on device: /tmp...' >> * sam_to_bam tool: 'Error sorting alignments from /tmp/filename..' >> >> Shouldn't it be referencing TEMP environment variable or new_file_path >> configuration value? Is it getting overridden by TMP or TMPDIR variables in >> python wrapper code? Has anyone else experienced similar issue? >> >> > > Further debugging showed that there are two more temporary directory related > environment variables - TMP and TMPDIR which were pointing local /tmp > location on compute nodes. We tried to set these variables in our shell > environment (drmaa URL uses -V to export current shell env) however SGE > overwrote TMP and TMPDIR before actual job execution. The TEMP variable > remained unmodified by SGE scheduler. > > The galaxy tools seemed to be using temporary directory space pointed by TMP > and TMPDIR and hence we saw local /tmp related errors mentioned in my earlier > post. > > We have temporarily fixed this problem by hard coding TEMP, TMP and TMPDIR > values in job template files - > 1. lib/galaxy/jobs/runners/drmaa.py > 2. lib/galaxy/jobs/runners/sge.py > > This will affect all jobs submitted through the galaxy. It will be helpful to > know how it can be handled in the tool wrapper scripts. It seems like it can > be handled in the tool wrapper scripts using directory prefix while creating > the tempfile ( http://docs.python.org/library/tempfile.html ). Any > thoughts/comments? Are there any other SGE users having similar issue? > > Also, there is a similar thread started today regarding usage of temporary > directory location in tool wrapper scripts. It would be helpful to know how > galaxy or tool wrappers are using the temporary directory and ways to > configure it. > > -- > Thanks, > Shantanu. > ___________________________________________________________ > 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/ ___________________________________________________________ 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/