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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 almost 14 years ago. Updated about 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:

0%

Estimated time:
Affected Version:
Appion/Leginon 2.0.1
Show in known bugs:
No
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 runNew07/19/2010

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Related to Appion - Bug #534: Jobs show as qeued instead of runningClosed05/21/2010

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Related to Appion - Bug #612: Stack creation states complete though still runningAssigned06/03/2010

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Related to Appion - Bug #1087: Difficult to tell when a Guppy job is queued, running or stalled/dead. ClosedAmber Herold12/14/2010

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 #1

Updated by Neil Voss almost 14 years ago

  • Assignee changed from Neil Voss to Christopher Irving

I dunno on this one.

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 #2

Updated by Neil Voss almost 14 years ago

  • Project changed from Appion to 20
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 #3

Updated by Christopher Irving almost 14 years ago

  • Project changed from 20 to Appion
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 #4

Updated by Christopher Irving almost 14 years ago

  • Assignee deleted (Christopher Irving)

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

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 #5

Updated by Anna-Clare Milazzo over 13 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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 #6

Updated by Amber Herold over 13 years ago

  • Status changed from New to Assigned
  • Assignee set to Amber Herold
  • Priority changed from Normal to High
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 #7

Updated by Amber Herold over 13 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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 #8

Updated by Anna-Clare Milazzo over 13 years ago

  • Workaround updated (diff)

Here's the workaround

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 #9

Updated by Amber Herold over 13 years ago

  • Target version set to Appion/Leginon 2.1.0
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 #10

Updated by Eric Hou over 13 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 over 13 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 over 13 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 over 13 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 about 10 years ago

  • Status changed from In Test to Closed
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