Bug #706: Reconstruction jobs on Goby are being listed as "queued" when they are running - Appion - Electron Microscopy Group

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Bug #706

closed

Reconstruction jobs on Goby are being listed as "queued" when they are running

Added by Anna-Clare Milazzo over 14 years ago. Updated over 10 years ago.

Status:

Closed

Priority:

Normal

Assignee:

Amber Herold

Category:

Target version:

Appion/Leginon 2.1.1

Start date:

06/24/2010

Due date:

% Done:

Estimated time:

Affected Version:

Appion/Leginon 2.0.1

Show in known bugs:

Workaround:

type in at the command line on goby /opt/appion/bin/updateAppionDB.py job# R projectid#

Description

Reconstruction jobs on Goby are being listed as "queued" when they are running

Related issues 4 (2 open — 2 closed)

Related to Appion - Bug #747: Appion shows job is queued when job doesn't run

New

07/19/2010

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Related to Appion - Bug #534: Jobs show as qeued instead of running

Closed

05/21/2010

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Related to Appion - Bug #612: Stack creation states complete though still running

Assigned

06/03/2010

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Related to Appion - Bug #1087: Difficult to tell when a Guppy job is queued, running or stalled/dead.

Closed

Amber Herold

12/14/2010

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Issue # Delay: days Cancel

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Updated by Neil Voss over 14 years ago

Assignee changed from Neil Voss to Christopher Irving

I dunno on this one.

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Updated by Neil Voss over 14 years ago

Project changed from Appion to 20

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Updated by Christopher Irving over 14 years ago

Project changed from 20 to Appion

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Updated by Christopher Irving over 14 years ago

Assignee deleted (~~Christopher Irving~~)

This isn't a goby cluster issue, this is a problem with appion.

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Updated by Anna-Clare Milazzo about 14 years ago

The work around is that I manually log into goby and update the database but this is not a fix for other users. I think it is in the job file script for EMAN so I'm not sure why the command is not being executed when the job launches.

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Updated by Amber Herold about 14 years ago

Status changed from New to Assigned
Assignee set to Amber Herold
Priority changed from Normal to High

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Updated by Amber Herold about 14 years ago

Sounds like Anna-Clare has a workaround for herself, but it wont work for users on the outside, so we should fix this sooner rather than later. Perhaps it is the sinedon config file as in #534 ?

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Updated by Anna-Clare Milazzo about 14 years ago

Workaround updated (diff)

Here's the workaround

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Updated by Amber Herold about 14 years ago

Target version set to Appion/Leginon 2.1.0

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#10

Updated by Eric Hou about 14 years ago

Priority changed from High to Normal
Target version changed from Appion/Leginon 2.1.0 to Appion/Leginon Future Version

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#11

Updated by Anna-Clare Milazzo almost 14 years ago

Good session to use on goby:

10jun17n50a - 052010 defocal pairs of doses 15 and 30

Job file after setting up for EMAN reconstruction does not show command
/opt/appion/bin/updateAppionDB.py "job number" R "session number"

so while EMAN is running it is listed as queued instead of running and does not pull back the results of the reconstruction as they are coming in.

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#12

Updated by Amber Herold almost 14 years ago

Target version changed from Appion/Leginon Future Version to Appion/Leginon 2.1.1

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#13

Updated by Amber Herold almost 14 years ago

Status changed from Assigned to In Test

r15197 should fix this and #1087, I'll have Neil review from #1087. After we test it a bit more we can merge to the branch, update Goby and then Anna can try this again...

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#14

Updated by Amber Herold over 10 years ago

Status changed from In Test to Closed

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Bug #706

Reconstruction jobs on Goby are being listed as "queued" when they are running

Updated by Neil Voss over 14 years ago

Updated by Neil Voss over 14 years ago

Updated by Christopher Irving over 14 years ago

Updated by Christopher Irving over 14 years ago

Updated by Anna-Clare Milazzo about 14 years ago

Updated by Amber Herold about 14 years ago

Updated by Amber Herold about 14 years ago

Updated by Anna-Clare Milazzo about 14 years ago

Updated by Amber Herold about 14 years ago

Updated by Eric Hou about 14 years ago

Updated by Anna-Clare Milazzo almost 14 years ago

Updated by Amber Herold almost 14 years ago

Updated by Amber Herold almost 14 years ago

Updated by Amber Herold over 10 years ago