Hello Joachim, Couple of things to check:
> On Mar 25, 2013, at 10:01 AM, Joachim Jacob | VIB | wrote: > >> Hi, >> >> About the exporting of history, which fails: >> 1. 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. >> >> 2. 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. Something in your export is likely not finishing fine, but crashes instead (either the creation of the archive, or the download). The folder "/var/spool/abrt/ccpp-XXXX" (and especially a file named "coredump") hints that the program crashed. "abrt" is a daemon (at least on Fedora) that monitors crashes and tries to keep all relevant information about the program which crashed (http://docs.fedoraproject.org/en-US/Fedora/13/html/Deployment_Guide/ch-abrt.html). So what might have happened, is that a program (galaxy's export_history.py or other) crashed during your export, and then "abrt" picked-up the pieces (storing a memory dump, for example), and then filled your disk. >> >> 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' >> """ >> One thing to try: if you have galaxy keeping temporary files, try running the "export" command manually: === 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 === Another thing to try: modify "export_history.py", adding debug messages to track progress and whether it finishes or not. And: check the "abrt" program's GUI, perhaps you'll see previous crashes that were stored successfully, providing more information about which program crashed. As a general rule, it's best to keep the "/var" directory on a separate partition for production systems, exactly so that filling it up with junk wouldn't intervene with other programs. Even better, set each sub-directory of "/var" to a dedicated partition, so that filling up "/var/log" or "/var/spool" would not fill up "/var/lib/pgsql" and stop Postgres from working. -gordon ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
