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Bug #2771

closed

apCluster not running during OptiMod run

Added by Dipali Sashital over 10 years ago. Updated over 10 years ago.

Status:
Closed
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Start date:
05/12/2014
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 2.1.0
Show in known bugs:
No
Workaround:

Description

Hi all,

I hope all is well with you! I am trying to run OptiMod on Goby, and running into some issues. Firstly, I can't submit a job through the web interface. I don't get an error or anything, just a blank page. This is less of an issue since I can run a job from the terminal.

Once I do start a job, it runs fine until it calls apCluster.exe (Just after the ML3D alignment, I think). I then get the error:

Traceback (most recent call last):
File "/opt/myamisnap/bin/OptiMod.py", line 895, in <module>
ACL.start()
File "/opt/myamisnap/bin/OptiMod.py", line 806, in start
preffile, box, apix)
File "/opt/myamisnap/lib/appionlib/apCommonLines.py", line 871, in run_affinity_propagation
apDisplay.printError("apCluster did not run")
File "/opt/myamisnap/lib/appionlib/apDisplay.py", line 65, in printError
raise Exception, colorString("\n * FATAL ERROR *\n"+text+"\n\a","red")
Exception: * FATAL ERROR *
apCluster did not run

You can see a run where this occurred in /ami/exdata/appion/14apr23b/angrecon/acl2_iter/acl2_iter.appionsub.log

Thanks and please let me know if I can provide more information.
-Dipa

Actions #1

Updated by Sargis Dallakyan over 10 years ago

From log file I see that it was trying to run 32-bit programme on 64-bit OS:

/bin/sh: /opt/myamisnap/bin/apcluster.exe: /lib/ld-linux.so.2: bad ELF interpreter: No such file or directory

I've installed 32-bit support on goby nodes:
# pdsh -w node[01-16] 
pdsh>  yum install   glibc-2.12-1.132.el6.i686 -y

Please try again.

Actions #2

Updated by Dipali Sashital over 10 years ago

Thanks Sargis, it is working now.

Best,
Dipa

Actions #3

Updated by Dipali Sashital over 10 years ago

  • Status changed from New to Closed

Thanks Sargis, it is working now.

Best,
Dipa

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