Project

General

Profile

Actions
Copy link

Bug #4052

open

Xmipp projection matching refinement does not work

Added by Christoph Wigge over 8 years ago. Updated over 8 years ago.

Status:
In Test
Priority:
High
Assignee:
Christoph Wigge
Category:
Image Processing
Target version:
-
Start date:
03/21/2016
Due date:
% Done:

0%

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

Description

When running xmipp the prepare stack functions seems to work and then the run finishes but when I would like to upload the results it complains with following error

.. Time stamp: 16mar21p00
... Function name: uploadXmippRefine
... Appion directory: /opt/myamisnap/lib
... Processing hostname: guppy-18
... Using split database
Connected to database: 'nyap_20'
... Committing data to database
!!! WARNING: recon dir already exist, no need to unpack
... Getting stack data for stackid=122
Old stack info: 'xmipp stack combine ... combined stack ids 121,119,118,117'

!!! WARNING: timestamp could not be found from the jobdata
uploading refinement results for Xmipp reconstruction routine
... Getting stack data for stackid=122
Old stack info: 'xmipp stack combine ... combined stack ids 121,119,118,117'

... Mapping 49673 stack particle IDs
... Mapped 49673 stack particle IDs in 358.39 msec
... Run directory: /gpfs/appion/cwigge/15dec11c/recon/xmipp_recon3
!!! WARNING: directory '/gpfs/appion/cwigge/15dec11c/recon/xmipp_recon3' already
exists.
... Writing function log to: uploadXmippRefine.log
... Uploading ScriptData....
... Found 1 processors on this machine
... Running Appion version 'myami-3.2'
... Xmipp ran 1 iterations
Traceback (most recent call last):
File "/opt/myamisnap/bin/uploadXmippRefine.py", line 490, in
upload3D.start()
File "/opt/myamisnap/bin/uploadXmippRefine.py", line 441, in start
uploadIterations = self.verifyUploadIterations(lastiter)
File "/opt/myamisnap/lib/appionlib/reconUploader.py", line 322, in verifyUploadIterations
"--uploadIterations=1,2,3,4,5,6,7,8" % (self.package, lastiter, self.runparams['numiter']))
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 ***
    Xmipp job did not go to completion. The last completed iteration is 1, out of 10 specified. Please s
    ... terations=1,2,3,4,5,6,7,8
Actions
Copy link
 #1

Updated by Sargis Dallakyan over 8 years ago

  • Status changed from New to In Test
  • Assignee changed from Sargis Dallakyan to Christoph Wigge

I've looked at the code that prints this error. It's taking NumberofIterations=10 from xmipp_protocol_projmatch.py while the last completed iteration is 1. I was able to run this by setting "Upload only iteration" to 1 in Upload Recon page. I've also looked at the logs before this step and it seems that it run 1 iteration out of 10 because it run out of memory:

[root@SEMC-head xmipp_recon3]# tail xmipp_recon3.appionsub.job.o34845
 Size of mpi jobs 10

Reducing the number of MPI workers from 15 to 6
   1/   1 sec. ..................................................----------

Processing time: 2.93304 secs.
Transfers time: 1.99805 secs.
=>> PBS: job killed: mem job total 5710476 kb exceeded limit 4194304 kb
Terminated

You can run this again on SEMC cluster and request more memory to see if that works.

Actions
Copy link

Also available in: Atom PDF