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apCluster not running during OptiMod run #2771

Closed leginonbot closed 7 months ago

leginonbot commented 7 months ago

Author Name: Dipali Sashital (Dipali Sashital) Original Redmine Issue: 2771, https://emg.nysbc.org/redmine/issues/2771 Original Date: 2014-05-12

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 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

leginonbot commented 7 months ago

Original Redmine Comment Author Name: Sargis Dallakyan (@dallakyan) Original Date: 2014-05-12T16:57:44Z

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:

1. pdsh -w node[01-16] 
pdsh>  yum install   glibc-2.12-1.132.el6.i686 -y

Please try again.

leginonbot commented 7 months ago

Original Redmine Comment Author Name: Dipali Sashital (Dipali Sashital) Original Date: 2014-05-12T17:23:42Z

Thanks Sargis, it is working now.

Best, Dipa

leginonbot commented 7 months ago

Original Redmine Comment Author Name: Dipali Sashital (Dipali Sashital) Original Date: 2014-05-12T17:24:31Z

Thanks Sargis, it is working now.

Best, Dipa