On Thu, Nov 15, 2012 at 10:06 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi all,
Something has changed in the job handling, and in a bad way. On my development machine submitting jobs to the cluster didn't seem to be working anymore (never sent to SGE). I killed Galaxy and restarted: ... (segmentation fault)
Looking into the problem with submitting the jobs, there seems to be a problem with task splitting somehow recursing - the same file is split four times, the filename getting longer and longer: galaxy.jobs DEBUG 2012-11-15 10:08:33,510 (321) Working directory for job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/321 galaxy.jobs.handler DEBUG 2012-11-15 10:08:33,510 dispatching job 321 to tasks runner galaxy.jobs.handler INFO 2012-11-15 10:08:33,714 (321) Job dispatched galaxy.datatypes.sequence DEBUG 2012-11-15 10:08:34,457 Split /mnt/galaxy/galaxy-central/database/files/000/dataset_344.dat into batches of 1000 records... galaxy.datatypes.sequence DEBUG 2012-11-15 10:08:34,457 Attemping to split FASTA file /mnt/galaxy/galaxy-central/database/files/000/dataset_344.dat into chunks of 1000 sequences galaxy.datatypes.sequence DEBUG 2012-11-15 10:08:34,458 Writing /mnt/galaxy/galaxy-central/database/files/000/dataset_344.dat part to /mnt/galaxy/galaxy-central/database/job_working_directory/000/321/task_0/dataset_344.dat galaxy.jobs.splitters.multi DEBUG 2012-11-15 10:08:34,458 do_split created 1 parts galaxy.jobs DEBUG 2012-11-15 10:08:34,558 (321) Working directory for job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/321 galaxy.jobs.handler DEBUG 2012-11-15 10:08:34,558 dispatching task 823, of job 321, to tasks runner 127.0.0.1 - - [15/Nov/2012:10:08:35 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://127.0.0.1:8081/history" "Mozilla/5.0 (X11; Linux x86_64; rv:10.0.8) Gecko/20121012 Firefox/10.0.8" galaxy.datatypes.sequence DEBUG 2012-11-15 10:08:35,458 Split /mnt/galaxy/galaxy-central/database/files/000/dataset_344.dat into batches of 1000 records... galaxy.datatypes.sequence DEBUG 2012-11-15 10:08:35,459 Attemping to split FASTA file /mnt/galaxy/galaxy-central/database/files/000/dataset_344.dat into chunks of 1000 sequences galaxy.datatypes.sequence DEBUG 2012-11-15 10:08:35,459 Writing /mnt/galaxy/galaxy-central/database/files/000/dataset_344.dat part to /mnt/galaxy/galaxy-central/database/job_working_directory/000/321/task_0/task_0/dataset_344.dat galaxy.jobs.splitters.multi DEBUG 2012-11-15 10:08:35,459 do_split created 1 parts galaxy.jobs DEBUG 2012-11-15 10:08:35,541 (321) Working directory for job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/321 galaxy.jobs.handler DEBUG 2012-11-15 10:08:35,542 dispatching task 824, of job 321, to tasks runner galaxy.datatypes.sequence DEBUG 2012-11-15 10:08:36,171 Split /mnt/galaxy/galaxy-central/database/files/000/dataset_344.dat into batches of 1000 records... galaxy.datatypes.sequence DEBUG 2012-11-15 10:08:36,171 Attemping to split FASTA file /mnt/galaxy/galaxy-central/database/files/000/dataset_344.dat into chunks of 1000 sequences galaxy.datatypes.sequence DEBUG 2012-11-15 10:08:36,171 Writing /mnt/galaxy/galaxy-central/database/files/000/dataset_344.dat part to /mnt/galaxy/galaxy-central/database/job_working_directory/000/321/task_0/task_0/task_0/dataset_344.dat galaxy.jobs.splitters.multi DEBUG 2012-11-15 10:08:36,172 do_split created 1 parts galaxy.jobs DEBUG 2012-11-15 10:08:36,232 (321) Working directory for job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/321 galaxy.jobs.handler DEBUG 2012-11-15 10:08:36,232 dispatching task 825, of job 321, to tasks runner galaxy.datatypes.sequence DEBUG 2012-11-15 10:08:36,843 Split /mnt/galaxy/galaxy-central/database/files/000/dataset_344.dat into batches of 1000 records... galaxy.datatypes.sequence DEBUG 2012-11-15 10:08:36,843 Attemping to split FASTA file /mnt/galaxy/galaxy-central/database/files/000/dataset_344.dat into chunks of 1000 sequences galaxy.datatypes.sequence DEBUG 2012-11-15 10:08:36,843 Writing /mnt/galaxy/galaxy-central/database/files/000/dataset_344.dat part to /mnt/galaxy/galaxy-central/database/job_working_directory/000/321/task_0/task_0/task_0/task_0/dataset_344.dat galaxy.jobs.splitters.multi DEBUG 2012-11-15 10:08:36,844 do_split created 1 parts galaxy.jobs DEBUG 2012-11-15 10:08:36,906 (321) Working directory for job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/321 galaxy.jobs.handler DEBUG 2012-11-15 10:08:36,906 dispatching task 826, of job 321, to tasks runner Hmm. Peter