In case this is useful to someone else…
looks like this was some really huge upoad jobs that caused a DOS.
Maybe the pubic instance has some config in place to avoid blowing up in this
situation.
While watching the logs during startup i see the memory usage of handler0 go
from about 200M to about 4G
right after the simple json module conflict warning. it seems to stop
increasing right after it prints the cloudlaunch line.
Soon thereafter it jumps to 7G of RAM at which point it starts swapping.
Then I see a huge number of lines like this (fills my terminal buffer)
galaxy.jobs DEBUG 2014-11-24 21:16:02,205 (159978) Persisting job destination
(destination id: gridengine)
galaxy.jobs.handler INFO 2014-11-24 21:16:02,315 (159978) Job dispatched
galaxy.jobs DEBUG 2014-11-24 21:16:02,337 (159979) Working directory for job
is: /mnt/galaxy/data/galaxy/job_working_directory/000/159/
159979
galaxy.jobs.handler DEBUG 2014-11-24 21:16:02,352 (159979) Dispatching to
gridengine runner
galaxy.tools.deps DEBUG 2014-11-24 21:17:05,076 Building dependency shell
command for dependency 'samtools'
galaxy.tools.deps WARNING 2014-11-24 21:17:05,088 Failed to resolve dependency
on 'samtools', ignoring
galaxy.jobs DEBUG 2014-11-24 21:17:29,869 (159979) Persisting job destination
(destination id: gridengine)
galaxy.jobs.handler INFO 2014-11-24 21:17:30,177 (159979) Job dispatched
galaxy.jobs.runners DEBUG 2014-11-24 21:22:24,137 (159978) command is: python
/mnt/galaxy/data/galaxy/galaxy-dist/tools/data_source/upload.py
/mnt/galaxy/data/galaxy/galaxy-dist /mnt/galaxy/data/galaxy/tmp/tmpVdupFJ
/mnt/galaxy/data/galaxy/tmp/tmpLHXyqa
219868:/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/dataset_219868_files:/mnt/galaxy/data/galaxy/user-data/000/219/dataset_219868.dat
219869:/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/dataset_219869_files:/mnt/galaxy/data/galaxy/user-data/000/219/dataset_219869.dat
219870:/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/dataset_219870_files:/mnt/galaxy/data/galaxy/user-data/000/219/dataset_219870.dat
219871:/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/dataset_219871_files:/mnt/galaxy/data/galaxy/user-data/000/219/dataset_219871.dat
219872:/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/dataset_219872_files:/mnt/galaxy/data/galaxy/user-data/000/219/dataset_219872.dat
219873:/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/dataset_219873_files:/mnt/galaxy/data/galaxy/user-data/000/219/dataset_219873.dat
219874:/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/dataset_219874_files:/mnt/galaxy/data/galaxy/user-data/000/219/dataset_219874.dat
219875:/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/dataset_219875_files:/mnt/galaxy/data/galaxy/user-data/000/219/dataset_219875.dat
219876:/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/dataset_219876_files:/mnt/galaxy/data/galaxy/user-data/000/219/dataset_219876.dat
…
thousands and thousands of lines later...
978/metadata_results_LibraryDatasetDatasetAssociation_27280_rGPnso,,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_override_LibraryDatasetDatasetAssociation_27280_xFpkLn
/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_in_LibraryDatasetDatasetAssociation_27282_EjpcbG,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_kwds_LibraryDatasetDatasetAssociation_27282_wVaFjB,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_out_LibraryDatasetDatasetAssociation_27282_OeHNUy,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_results_LibraryDatasetDatasetAssociation_27282_G1Q9PY,,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_override_LibraryDatasetDatasetAssociation_27282_17V4t6
/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_in_LibraryDatasetDatasetAssociation_27290_Y5X8Ih,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_kwds_LibraryDatasetDatasetAssociation_27290_8E55GA,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_out_LibraryDatasetDatasetAssociation_27290_W11KQm,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_results_LibraryDatasetDatasetAssociation_27290_65u8Ja,,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_override_LibraryDatasetDatasetAssociation_27290_3jbsMb
/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_in_LibraryDatasetDatasetAssociation_27296_DmijyX,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_kwds_LibraryDatasetDatasetAssociation_27296_u1ihbO,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_out_LibraryDatasetDatasetAssociation_27296_MYIvvx,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_results_LibraryDatasetDatasetAssociation_27296_eLwrTR,,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_override_LibraryDatasetDatasetAssociation_27296_UpVqz7
/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_in_LibraryDatasetDatasetAssociation_27321_gSfC2s,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_kwds_LibraryDatasetDatasetAssociation_27321_ienD2I,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_out_LibraryDatasetDatasetAssociation_27321_hUnFKv,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_results_LibraryDatasetDatasetAssociation_27321_zWIzcm,,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_override_LibraryDatasetDatasetAssociation_27321_4KvsAs
/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_in_LibraryDatasetDatasetAssociation_27270_5oWQ0p,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_kwds_LibraryDatasetDatasetAssociation_27270_Rv3rwJ,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_out_LibraryDatasetDatasetAssociation_27270_VyM6CA,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_results_LibraryDatasetDatasetAssociation_27270_3nmQ_S,,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_override_LibraryDatasetDatasetAssociation_27270_ZCTSSJ
/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_in_LibraryDatasetDatasetAssociation_27317_YBjGjl,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_kwds_LibraryDatasetDatasetAssociation_27317_xC8TCo,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_out_LibraryDatasetDatasetAssociation_27317_ygYy0B,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_results_LibraryDatasetDatasetAssociation_27317_WJO3MW,,/mnt/galaxy/data/galaxy/job_working_directory/000/159/159978/metadata_override_LibraryDatasetDatasetAssociation_27317_8MY55s;
sh -c "exit $return_code"
Whaaaa…..
brad
galaxy.web.framework.base DEBUG 2014-11-24 21:15:17,288 Enabling 'workflow'
controller, class: WorkflowController
/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/__init__.py:63: UserWarning:
Module simplejson was already imported from
/mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/simplejson/__init__.pyc,
but
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg
is being added to sys.path
self.check_version_conflict()
galaxy.web.framework.base DEBUG 2014-11-24 21:15:29,670 Enabling 'cloudlaunch'
controller, class: CloudController
galaxy.web.framework.base DEBUG 2014-11-24 21:15:30,620 Enabling 'data_manager'
controller, class: DataManager
--
Brad Langhorst, Ph.D.
Applications and Product Development Scientist
On Nov 24, 2014, at 8:50 PM, Langhorst, Brad
<langho...@neb.com<mailto:langho...@neb.com>> wrote:
I recently upgraded galaxy to the 10/06 unannounced galaxy-dist.
I typically run with 2 web processes and 2 job handlers on a single machine.
It seems that now the job handlers consume all RAM at startup and are killed by
the kernel.
Anybody seen something like this?
Bad job? bug?
I’m considering a downgrade to the previous stable release.
Brad
--
Brad Langhorst, Ph.D.
Applications and Product Development Scientist
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___________________________________________________________
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