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Bug #2597

closed

CL2D crashes

Added by Reginald McNulty almost 11 years ago. Updated almost 11 years ago.

Status:
Won't Fix or Won't Do
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Start date:
12/04/2013
Due date:
% Done:

0%

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

Description

I've run CL2D with 13,938 particles and requesting 300 references. Below is the last few lines of the log file before crashing:

Xmipp: /opt/applications/openmpi/1.4.3/gnu/bin/mpirun -np 64 /opt/applications/xmipp/2.4/gnu/bin/xmipp_mpi_class_averages -i /ami/data15/appion/13oct11a/align/cl2d7/partlist.sel -codes 300 -ite
r 15 -o /ami/data15/appion/13oct11a/align/cl2d7/part13dec02p00 -fast -useCorrelation -classicalMultiref -alignImages
=>> PBS: job killed: node 2 (node0656) requested job terminate, 'EOF' (code 1099) - received SISTER_EOF attempting to communicate with sister MOM's

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 #1

Updated by Gabriel Lander almost 11 years ago

  • Status changed from New to Won't Fix or Won't Do

This is not an appion error, this is a garibaldi issue. What likely happened is that another user's job that was running on node 0656 crashed the node. Nothing can be done to remedy this at our end. Try using more processors per node.

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