Please keep all replies on-list so that everyone can contribute.
Someone more knowledgeable about systems than me suggests that lsof(8) and/or /proc/<galaxy server pid>/fd should yield some clues as to what file is being written to.
Good luck, J.
On Mar 25, 2013, at 10:01 AM, Joachim Jacob | VIB | wrote:
Hi,
About the exporting of history, which fails:
the preparation seems to work fine: meaning: choosing 'Export this history' in the History menu leads to a URL that reports initially that the export is still in progress.
when the export is finished, and I click the download link, the root partition fills and the browser displays "Error reading from remote server". A folder ccpp-2013-03-25-14:51:15-27045.new is created in the directory /var/spool/abrt, which fills the root partition.
The handler reports in its log: """ galaxy.jobs DEBUG 2013-03-25 14:38:33,322 (8318) Working directory for job is: /mnt/galaxydb/job_working_directory/008/8318 galaxy.jobs.handler DEBUG 2013-03-25 14:38:33,322 dispatching job 8318 to local runner galaxy.jobs.handler INFO 2013-03-25 14:38:33,368 (8318) Job dispatched galaxy.jobs.runners.local DEBUG 2013-03-25 14:38:33,432 Local runner: starting job 8318 galaxy.jobs.runners.local DEBUG 2013-03-25 14:38:33,572 executing: python /home/galaxy/galaxy-dist/lib/galaxy/tools/imp_exp/export_history.py -G /mnt/galaxytemp/tmpHAEokb/tmpQM6g_R /mnt/galaxytemp/tmpHAEokb/tmpeg7bYF /mnt/galaxytemp/tmpHAEokb/tmpPXJ245 /mnt/galaxydb/files/013/dataset_13993.dat galaxy.jobs.runners.local DEBUG 2013-03-25 14:41:29,420 execution finished: python /home/galaxy/galaxy-dist/lib/galaxy/tools/imp_exp/export_history.py -G /mnt/galaxytemp/tmpHAEokb/tmpQM6g_R /mnt/galaxytemp/tmpHAEokb/tmpeg7bYF /mnt/galaxytemp/tmpHAEokb/tmpPXJ245 /mnt/galaxydb/files/013/dataset_13993.dat galaxy.jobs DEBUG 2013-03-25 14:41:29,476 Tool did not define exit code or stdio handling; checking stderr for success galaxy.tools DEBUG 2013-03-25 14:41:29,530 Error opening galaxy.json file: [Errno 2] No such file or directory: '/mnt/galaxydb/job_working_directory/008/8318/galaxy.json' galaxy.jobs DEBUG 2013-03-25 14:41:29,555 job 8318 ended """
The system reports: """ Mar 25 14:51:26 galaxy abrt[16805]: Write error: No space left on device Mar 25 14:51:27 galaxy abrt[16805]: Error writing '/var/spool/abrt/ccpp-2013-03-25-14:51:15-27045.new/coredump' """
Thanks, Joachim
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
On Tue 19 Mar 2013 11:22:27 PM CET, Jeremy Goecks wrote:
I'm unable to reproduce this behavior using a clean version of galaxy-dist. The code (export_history.py) doesn't create any temporary files and appears to write directly to the output file, so it seems unlikely that Galaxy is writing anything to the root directory.
Can you provide the name of any file that Galaxy appears to be writing to outside of <galaxy-home>? What about watching the job output file/export file to see if that's increasingly in size and causing the out-of-space error?
Best, J.
On Mar 19, 2013, at 10:56 AM, Joachim Jacob | VIB | wrote:
Hi all,
Exporting histories fails on our server: " Reason: *Error reading from remote server".
*When looking at the logs and the system: tail /var/log/messages Mar 19 15:52:47 galaxy abrt[25605]: Write error: No space left on device Mar 19 15:52:49 galaxy abrt[25605]: Error writing '/var/spool/abrt/ccpp-2013-03-19-15:52:37-13394.new/coredump'
So I watched my system when I repeated the export, and saw that Galaxy fills up the root directory (/), instead of any temporary directory.
Somebody has an idea where to adjust this setting, so the export function uses any temporary directory?
Thanks, Joachim
-- Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
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