JobManager object has no attribute dispatcher
Hi all, Does anyone know what might have introduced this problem running galaxy-dist when using the task splitting functionality? I'm using the latest code from the default branch, changeset: 7027:f6e790d94282 galaxy.jobs.manager DEBUG 2012-04-17 13:55:03,610 (4) Job assigned to handler 'main' 127.0.0.1 - - [17/Apr/2012:13:55:06 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://127.0.0.1:8081/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.18) Gecko/20110622 CentOS/3.6-1.el5.centos Firefox/3.6.18" galaxy.jobs DEBUG 2012-04-17 13:55:08,710 (4) Working directory for job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/4 galaxy.jobs.handler DEBUG 2012-04-17 13:55:08,711 dispatching job 4 to tasks runner galaxy.jobs.handler INFO 2012-04-17 13:55:08,845 (4) Job dispatched galaxy.datatypes.sequence DEBUG 2012-04-17 13:55:09,470 Split /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat into 4 parts... galaxy.datatypes.sequence DEBUG 2012-04-17 13:55:09,470 Attemping to split FASTA file /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat into chunks of 1 sequences galaxy.datatypes.sequence DEBUG 2012-04-17 13:55:09,471 Writing /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat part to /mnt/galaxy/galaxy-central/database/job_working_directory/000/4/task_0/dataset_2.dat galaxy.datatypes.sequence DEBUG 2012-04-17 13:55:09,472 Writing /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat part to /mnt/galaxy/galaxy-central/database/job_working_directory/000/4/task_1/dataset_2.dat galaxy.jobs.splitters.multi DEBUG 2012-04-17 13:55:09,472 do_split created 2 parts galaxy.jobs DEBUG 2012-04-17 13:55:09,506 (4) Working directory for job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/4 galaxy.jobs.runners.tasks ERROR 2012-04-17 13:55:09,784 failure running job 4 Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/tasks.py", line 86, in run_job self.app.job_manager.dispatcher.put(tw) AttributeError: 'JobManager' object has no attribute 'dispatcher' Thanks, Peter
On Apr 17, 2012, at 9:04 AM, Peter Cock wrote:
Hi all,
Does anyone know what might have introduced this problem running galaxy-dist when using the task splitting functionality? I'm using the latest code from the default branch, changeset: 7027:f6e790d94282
Hi Peter, This was resolved in changeset 5c93ac32ace1. Thanks for reporting it. --nate
galaxy.jobs.manager DEBUG 2012-04-17 13:55:03,610 (4) Job assigned to handler 'main' 127.0.0.1 - - [17/Apr/2012:13:55:06 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://127.0.0.1:8081/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.18) Gecko/20110622 CentOS/3.6-1.el5.centos Firefox/3.6.18" galaxy.jobs DEBUG 2012-04-17 13:55:08,710 (4) Working directory for job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/4 galaxy.jobs.handler DEBUG 2012-04-17 13:55:08,711 dispatching job 4 to tasks runner galaxy.jobs.handler INFO 2012-04-17 13:55:08,845 (4) Job dispatched galaxy.datatypes.sequence DEBUG 2012-04-17 13:55:09,470 Split /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat into 4 parts... galaxy.datatypes.sequence DEBUG 2012-04-17 13:55:09,470 Attemping to split FASTA file /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat into chunks of 1 sequences galaxy.datatypes.sequence DEBUG 2012-04-17 13:55:09,471 Writing /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat part to /mnt/galaxy/galaxy-central/database/job_working_directory/000/4/task_0/dataset_2.dat galaxy.datatypes.sequence DEBUG 2012-04-17 13:55:09,472 Writing /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat part to /mnt/galaxy/galaxy-central/database/job_working_directory/000/4/task_1/dataset_2.dat galaxy.jobs.splitters.multi DEBUG 2012-04-17 13:55:09,472 do_split created 2 parts galaxy.jobs DEBUG 2012-04-17 13:55:09,506 (4) Working directory for job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/4 galaxy.jobs.runners.tasks ERROR 2012-04-17 13:55:09,784 failure running job 4 Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/tasks.py", line 86, in run_job self.app.job_manager.dispatcher.put(tw) AttributeError: 'JobManager' object has no attribute 'dispatcher'
Thanks,
Peter ___________________________________________________________ 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:
On Thu, Apr 19, 2012 at 2:53 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Apr 17, 2012, at 9:04 AM, Peter Cock wrote:
Hi all,
Does anyone know what might have introduced this problem running galaxy-dist when using the task splitting functionality? I'm using the latest code from the default branch, changeset: 7027:f6e790d94282
Hi Peter,
This was resolved in changeset 5c93ac32ace1. Thanks for reporting it.
--nate
Are you sure? I've just updated to the tip and the same problem persists. Also looking at that commit it isn't obvious how is might be linked to this issue: https://bitbucket.org/galaxy/galaxy-central/changeset/5c93ac32ace1 Thanks, Peter
On Apr 19, 2012, at 10:44 AM, Peter Cock wrote:
On Thu, Apr 19, 2012 at 2:53 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Apr 17, 2012, at 9:04 AM, Peter Cock wrote:
Hi all,
Does anyone know what might have introduced this problem running galaxy-dist when using the task splitting functionality? I'm using the latest code from the default branch, changeset: 7027:f6e790d94282
Hi Peter,
This was resolved in changeset 5c93ac32ace1. Thanks for reporting it.
--nate
Are you sure? I've just updated to the tip and the same problem persists. Also looking at that commit it isn't obvious how is might be linked to this issue: https://bitbucket.org/galaxy/galaxy-central/changeset/5c93ac32ace1
You're right, that's what I get for reading hastily. Fix coming shortly...
Thanks,
Peter
On Apr 19, 2012, at 11:12 AM, Nate Coraor wrote:
On Apr 19, 2012, at 10:44 AM, Peter Cock wrote:
On Thu, Apr 19, 2012 at 2:53 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Apr 17, 2012, at 9:04 AM, Peter Cock wrote:
Hi all,
Does anyone know what might have introduced this problem running galaxy-dist when using the task splitting functionality? I'm using the latest code from the default branch, changeset: 7027:f6e790d94282
Hi Peter,
This was resolved in changeset 5c93ac32ace1. Thanks for reporting it.
--nate
Are you sure? I've just updated to the tip and the same problem persists. Also looking at that commit it isn't obvious how is might be linked to this issue: https://bitbucket.org/galaxy/galaxy-central/changeset/5c93ac32ace1
You're right, that's what I get for reading hastily. Fix coming shortly...
Not quite "shortly", but it's been committed as 476ce0b78713. Sorry for the wait. --nate
Thanks,
Peter
___________________________________________________________ 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:
participants (2)
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Nate Coraor -
Peter Cock