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Bug #4665

open

2d

Added by Zhening Zhang almost 8 years ago. Updated almost 8 years ago.

Status:
New
Priority:
High
Assignee:
-
Category:
-
Target version:
-
Start date:
12/14/2016
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.2
Show in known bugs:
No
Workaround:

Description

I could not run Xmipp 2 Clustering 2D Alignment. The directory is /gpfs/appion/zzhang/16nov25e/align/cl2d12.
Here is the output:

RuntimeError: module compiled against API version 6 but this version of numpy is 4
... Time stamp: 16dec14o46
... Function name: runXmippCL2D
... Appion directory: /opt/myamisnap/lib
... Processing hostname: node09
... Using split database
[0;32mConnected to database: 'nyap_141'
... Committing data to database
... Getting stack data for stackid=249
Old stack info: [0;36m'tst_tmp'
... Run directory: /gpfs/appion/zzhang/16nov25e/align/cl2d12
!!! WARNING: directory '/gpfs/appion/zzhang/16nov25e/align/cl2d12' already
exists.
... Writing function log to: runXmippCL2D.log
... Uploading ScriptData....
... Found 92 processors on this machine
... Running Appion version 'trunk'
... Getting stack data for stackid=249
Old stack info: [0;36m'tst_tmp'
... Stack 249 pixel size: 1.097
... querying one stack particle from stackid=249 on Wed Dec 14 14:46:36 2016
... creating timestamp
48804 of 244024

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 #1

Updated by Kelsey Jordan almost 8 years ago

Similar issue. My cl2d jobs are stuck in the queue on guppy, but other jobs run fine.

The session is for user, Chris Goulbourne. Session ID is 16dec16c.

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 #2

Updated by Sargis Dallakyan almost 8 years ago

For /gpfs/appion/zzhang/16nov25e/align/cl2d12, I see:

[root@SEMC-head cl2d12]# tail cl2d12.appionsub.job.o119068
Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.
=>> PBS: job killed: mem job total 16896100 kb exceeded limit 16777216 kb
Terminated

Zhening can change the default Memory from 16 to 200 for SEMC-head cluster to see if that works.

For Chris Goulbourne, I see:

[root@guppy ~]# qstat -f 713511.guppy
...
    Resource_List.neednodes = 2:ppn=8
...
    comment = Not Running: Not enough of the right type of nodes are available

Chris can change Proc/Node to 4 from 8 to see if that works.

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