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2d #4665

Open leginonbot opened 6 months ago

leginonbot commented 6 months ago

Author Name: Zhening Zhang (Zhening Zhang) Original Redmine Issue: 4665, https://emg.nysbc.org/redmine/issues/4665 Original Date: 2016-12-14

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 Connected to database: 'nyap_141' ... Committing data to database ... Getting stack data for stackid=249 Old stack info: '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: '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

leginonbot commented 6 months ago

Original Redmine Comment Author Name: Kelsey Jordan (Kelsey Jordan) Original Date: 2016-12-20T21:46:32Z

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.

leginonbot commented 6 months ago

Original Redmine Comment Author Name: Sargis Dallakyan (@dallakyan) Original Date: 2016-12-21T02:04:21Z

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.