ZeroDivisionError: integer division or modulo by zero

[christopher.j...@gmail.com]

Hello Dr. Ludtke,

I've searched through the archives to find a solution for this error message, but it doesn't return anything useful. I'm analyzing tilt-series in the SPT workflow. Ultimately, for particle picking, I want to use your new CNN particle picker, and to do that I'll need  to open the "Box Training References" job under the "Segmentation" tab of the SPT workflow. I'm able to pick 'good' particles, however, after making a new group for the bad particles using the "Options" panel, I get the following error after laying down the first box to highlight  a bad region, after which all EMAN2 windows close.

e2projectmanager.py

NOT Writing notes, ppid=-2

{0: '01_good', 1: '01_bad', 2: 'bad2'}

Traceback (most recent call last):

  File "/programs/x86_64-linux/eman2/2.31/bin/e2spt_boxer.py", line 956, in xy_down

    self.update_box(self.xydown[0])

  File "/programs/x86_64-linux/eman2/2.31/bin/e2spt_boxer.py", line 892, in update_box

    self.boxesviewer.set_selected((n,),True)

  File "/programs/x86_64-linux/eman2/2.31/lib/python2.7/site-packages/eman2_gui/emimagemx.py", line 1524, in set_selected

    t %= len(self.data)

Best,

Christopher J. Brenjamin

ZeroDivisionError: integer division or modulo by zero

[Steve Ludtke]

Hi,

we need to see the full output of e2version.py from the same computer to be able to help...

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[C Ben]

Thanks I have that output here:

[cben@tjlab_em1 ~]$ e2version.py
EMAN 2.31 final (GITHUB: 2019-09-30 10:41 - commit: 194df95 )
Your EMAN2 is running on: Linux-3.10.0-957.12.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core 3.10.0-957.12.1.el7.x86_64
Your Python version is: 2.7.14

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[Steve Ludtke]

Hi Chris(?),

none of us recall running into this specific problem back when we were working with EMAN2.31. My best guess is that the trigger for this is probably some very subtle form of user error. To be clear, there isn't anything you can do which _should_ trigger this sort of crash, I'm just suspecting that you are doing something subtly different which we never noticed, triggering a bug we never noticed.

Our current recommendation to people doing anything in the EMAN2 subtomogram averaging pipeline right now is to use a current 'continuous build' version of EMAN2 rather than the release from last year, as this pipeline has been undergoing major development efforts this year. Results are better, bugs are fewer, things run faster, just better all around. We were supposed to have a new release about 6 months ago, but have continued to have coordination delays. The continuous builds are quite stable at the moment, and I use it myself every day. Almost all of what is happening now are new features rather than bugfixes. The plan is that this will be the final release version before we undergo a very major version change. 

Anyway, it should be very easy to install the snapshot version in your own account with no special permissions, and that's what we would suggest. If there is a reason this is impossible we can get into more details and try to figure out what is going wrong with 2.31, but in that case we will need a very precise sequence of operations you perform leading up to the crash, at the level of "I run this program, then push this button, then this button ...".

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CALc8r_3G9pymFBFBRSPv7Ag2ds8p6cEOB7XBG-ohbCrzAKtWWw%40mail.gmail.com.

[christopher.j...@gmail.com]

Thank you. I believe the problem is solved now. 

Just for the archives, I went though and documented each step of the Tomo workflow from the beginning. There are two things here. Firstly, I started a new project under a different directory, and went through each step carefully  in this order:  importing, generate the tomogram, CTF correction, preprocessing, and training box references. I'm able to pick good and bad particles without the software crashing.

Basically, I can't recreate the error either doing that. However (and secondly), going back into the old project directory, still after trying to pick the bad particles the software crashes. The only difference here is that I didn't do the preprocessing step, but that's an optional step and I don't think this should cause the software to crash by skipping it. Maybe there's still something else there I'm missing. 

This issue is now solved though. I'll definitely do as recommended and work from the continuous build version instead. 

Best,

Christopher J. Benjamin

[Steve Ludtke]

Hi Chris,

I'm glad the problem went away! Since there is no further development on EMAN2.31, there isn't much reason for us to go back and try to sort out exactly what is wrong with the folder that's still 'broken'.

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/6cbe6afc-889c-4e4a-b494-55594d5f69can%40googlegroups.com.