Appion

How did you run this job? If you used qsub command, please try using qsub -V.

-V Declares that all environment variables in the qsub command’s environment are to be exported to the batch job.

I helped Ryan Hoffman yesterday who was getting similar error message (error while loading shared libraries: libmpi.so.0: cannot open shared object file: No such file or directory). qsub -V solved it for him.

I tried to test cl2d.(/ami/data00/appion/zz07jul25b/align/cl2d25) Did not get so far:

/opt/myamisnap/lib/pyami/tifffile.py:903: UserWarning: Failed to import _tifffile.decodepackbits
  warnings.warn("Failed to import %s" % module_function)
/opt/myamisnap/lib/pyami/tifffile.py:903: UserWarning: Failed to import _tifffile.decodelzw
  warnings.warn("Failed to import %s" % module_function)
 ... Time stamp: 12aug21l18
 ... Function name: runXmippCL2D
 ... Appion directory: /opt/myamisnap/lib
 ... Using split database
^[[32mConnected to database: 'ap303'^[[0m
 ... Committing data to database
 ... Getting stack data for stackid=88
Old stack info: ^[[36m'test  ... 361 eman centered substack id 87'^[[0m

Traceback (most recent call last):
  File "/opt/myamisnap/bin/runXmippCL2D.py", line 623, in <module>
    cl2d = CL2D()
  File "/opt/myamisnap/lib/appionlib/appionScript.py", line 81, in __init__
    self.checkConflicts()
  File "/opt/myamisnap/bin/runXmippCL2D.py", line 94, in checkConflicts
    apDisplay.printError("There is no MPI installed")
  File "/opt/myamisnap/lib/appionlib/apDisplay.py", line 57, in printError
    raise Exception, colorString("\n *** FATAL ERROR ***\n"+text+"\n\a","red")
Exception: ^[[31m
 *** FATAL ERROR ***
There is no MPI installed
^G^[[0m
 ... Running on host: guppy-29

I am getting a bit further than that with cl2d, but I'm still getting the error that it cannot create average.mrc after making the initial aligned stack. I am also still getting the libmpi errors when running maxlike, even when running with qsub -V.

New cl2d logfile is /ami/data00/appion/12aug09a/align/cl2d2/cl2d2.appionsub2.log

New maxlike logfile is /ami/data00/appion/12aug09a/align/maxlike6/maxlike6.appionsub2.log

Everyone, if you have a .appion.cfg file in your guppy home directory (ls -a to see hidden files), you must add a -V option to the AdditionalHeaders field:

ProcessingHostType=Torque

Shell=/bin/csh

ScriptPrefix=

ExecCommand=/usr/local/bin/qsub

StatusCommand=/usr/local/bin/qstat

AdditionalHeaders= -m e, -j oe, -V

PreExecuteLines=

By doing this, you will be able to launch jobs from the website that use MPI.

CL2D works on Garibaldi for me, and it does not output the following error like guppy does:

/opt/myamisnap/lib/pyami/tifffile.py:903: UserWarning: Failed to import _tifffile.decodepackbits
  warnings.warn("Failed to import %s" % module_function)
/opt/myamisnap/lib/pyami/tifffile.py:903: UserWarning: Failed to import _tifffile.decodelzw
  warnings.warn("Failed to import %s" % module_function)

This is right at the start of the output file in /ami/data00/appion/zz07jul25b/align/cl2d28.
Do we need to install this tifffile stuff?

Sargis, I have updated everyone's .appion.cfg file in guppy /home dir.
Now I just need you to figure out where the template is for this file for when a new user is added, if there is one, so that can be changed as well.

If we intend to only use the global copy of .appion.cfg, we need to figure out how to make that scenario work on a cluster, because currently it does not.

Also, please assign to Dipali to test and close out only if it works for her.