It is most likely due to the cluster configuration, since on our non-cluster production machine doesn't have this behaviour. Cheers, J Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 05/17/2013 10:16 AM, Joachim Jacob | VIB | wrote:

Hi all,

I have fired up an cloud instance of Galaxy, 2 persistent nodes, scalable up to 10. I have updated the code to the latest stable, after issues with not being able to select multiple input for workflows (more background: http://dev.list.galaxyproject.org/selecting-multiple-inputs-for-workflows-no...)

Running a workflow on multiple inputs (#=58) gives me - after a very long page loading - this error:

************************************************

Internal Server Error

Galaxy was unable to sucessfully complete your request

URL: http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb...

Module galaxy.web.framework.middleware.error:*149* in |__call__| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>app_iter *=* self*.*application*(*environ*,* sr_checker*)*| Module paste.recursive:*84* in |__call__| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*return* self*.*application*(*environ*,* start_response*)*| Module paste.httpexceptions:*633* in |__call__| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*return* self*.*application*(*environ*,* start_response*)*| Module galaxy.web.framework.base:*128* in |__call__| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*return* self*.*handle_request*(* environ*,* start_response *)*| Module galaxy.web.framework.base:*184* in |handle_request| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>body *=* method*(* trans*,* ****kwargs *)*| Module galaxy.webapps.galaxy.controllers.workflow:*1443* in |run| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>job*,* out_data *=* tool*.*execute*(* trans*,* step*.*state*.*inputs*,* history*=*target_history*)*| Module galaxy.tools:*2342* in |execute| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*return* self*.*tool_action*.*execute*(* self*,* trans*,* incoming*=*incoming*,* set_output_hid*=*set_output_hid*,* history*=*history*,* ****kwargs *)*| Module galaxy.tools.actions:*397* in |execute| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>job*.*add_input_dataset*(* name*,* dataset *)*| Module galaxy.model:*247* in |add_input_dataset| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*input_datasets*.*append*(* JobToInputDatasetAssociation*(* name*,* dataset *)* *)*| Module ?:*4* in |__init__| Module sqlalchemy.orm.state:*82* in |initialize_instance| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*return* manager*.*events*.*original_init*(****mixed*[**1**:**]**,* ****kwargs*)*| Module galaxy.model:*450* in |__init__| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*dataset *=* dataset| Module sqlalchemy.orm.attributes:*150* in |__set__| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*impl*.*set*(*instance_state*(*instance*)**,* instance_dict*(*instance*)**,* value*,* None*)*| Module sqlalchemy.orm.attributes:*590* in |set| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>value *=* self*.*fire_replace_event*(*state*,* dict_*,* value*,* old*,* initiator*)*| Module sqlalchemy.orm.attributes:*610* in |fire_replace_event| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>value *=* ext*.*set*(*state*,* value*,* previous*,* initiator *or* self*)*| Module sqlalchemy.orm.unitofwork:*69* in |set| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>sess*.*add*(*newvalue*)*|

Module sqlalchemy.orm.session:*1091* in |add| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*_save_or_update_state*(*state*)*|

Module sqlalchemy.orm.session:*1100* in |_save_or_update_state| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*_save_or_update_impl*(*state*)*|

Module sqlalchemy.orm.session:*1267* in |_save_or_update_impl| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*_update_impl*(*state*)*|

Module sqlalchemy.orm.session:*1259* in |_update_impl| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*_attach*(*state*)*|

Module sqlalchemy.orm.session:*1286* in |_attach| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*(*mapperutil*.*state_str*(*state*)**,* state*.*key*)*| *InvalidRequestError: Can't attach instance <HistoryDatasetAssociation at 0x8591c50>; another instance with key (<class 'galaxy.model.HistoryDatasetAssociation'>, (200,)) is already present in this session.* extra data <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#extra_data>

full traceback <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#full_traceback>

text version <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#text_version>

This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. ************************************************

After clicking history refresh, the workflow is actually in progress! It completes EXCEPT for the last dataset, which stays gray. Clicking on rerun on this last dataset, gives me the error:

************************************************

Internal Server Error

Galaxy was unable to sucessfully complete your request

URL: http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca...

Module galaxy.web.framework.middleware.error:*149* in |__call__| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>app_iter *=* self*.*application*(*environ*,* sr_checker*)*| Module paste.recursive:*84* in |__call__| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>*return* self*.*application*(*environ*,* start_response*)*| Module paste.httpexceptions:*633* in |__call__| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>*return* self*.*application*(*environ*,* start_response*)*| Module galaxy.web.framework.base:*128* in |__call__| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>*return* self*.*handle_request*(* environ*,* start_response *)*| Module galaxy.web.framework.base:*184* in |handle_request| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>body *=* method*(* trans*,* ****kwargs *)*| Module galaxy.webapps.galaxy.controllers.tool_runner:*142* in |rerun| |>> <http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>*raise* Exception*(*"Failed to get job information for dataset hid %d" *%* data*.*hid*)*| *Exception: Failed to get job information for dataset hid 112* extra data <http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#extra_data>

full traceback <http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#full_traceback>

text version <http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#text_version>

This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. ********************************************************

I have to manually rerun the last job with the corresponding workflow.

Thanks, Joachim