Q: Please could you help me to solve the “mystery” with refine2d.py command? Problem is from time to time is running properly and finished with all output files for defined number of iterations.
But more frequently finishes after initial startnrclasses calculation of 10 classes and then stops with the error message segmentation fault. Even after rebooting the machine I am getting this error. I am sure there is no problem with memory issue or dataset size and fact that sometime is working and sometime not getting me crazy.
my command is: refine2d.py start.hed --iter=8 -I 30
we have EMAN1.8 and python 2.4
A: Are you using actual 1.8, or a more recent snapshot version ? If you are using 1.8, please update to a nightly snapshot. Due to EMAN2 development, we haven't had a new EMAN1 release for over a year, and quite a lot of minor fixes have been made. Very little EMAN1 development is occurring now, so the snapshots are generally very stable. If this doesn't fix the problem please report back, and we'll help you debug it. --steve
Q: Steve, thank you for very fast response. I am sorry, our Linux administrator is not here but what I recall we have installed nightly snapshot of EMAN. Actually what I have found we have this nightly snapshot: EMAN 1.8 ($Date: 2008/01/22 05:13:25 $).
Again, after calculating classes.nr. output files, the refine2d.py script stops with "Segmentation fault" error.
PS: Meanwhile I have restarted the machine few times without any effect. --bohus
A: It's very unlikely to be something specific with the machine. That version is old enough it might still be worth updating to something a bit newer, but it may well not stop the problem. We need to isolate which program called by refine2d.py is causing the issue. Could you copy the full screen output from a run of the program when it crashes ? Also, can you do:
iminfo (refine2d input file) all stat >test
and email 'test' as well ?
Q: Here is the 'test' file as well as the screen shot (report.jpg) you asked for (plus emanlog file). I hope it will be useful.
Q: Anybody at home???? Did you check the attached files? What's the king's decision?