[3dem] Help with 7z issue, likely also with DM/GMS software

Amy Bondy albondy at umich.edu
Wed Feb 6 11:55:38 PST 2019

Hi Aguang,

Sorry for the late response, but here's one other potential fix you could
try that seems to work for us at Michigan after experiencing this same

According to the fix suggested by Gatan, on the K2 computer under the Gatan
folder, I changed the name of the "Log" folder, as a new one was created
when Digital Micrograph crashed at some point previously. If you change the
folder name instead to "~Log", this seems to fix the issue. And then in the
future if you have this problem again, it is likely because another "Log"
folder was created, so you can simply rename the folder again to "~Log01",
"~Log02", etc.

We were originally planning on changing the time on the computer since this
file holding only occurred at midnight, however IT recommended against this
so we came up with this other fix.


On Wed, Feb 6, 2019 at 2:25 PM Daniel Dai <dawaylong at hotmail.com> wrote:

> Thanks a lot for everyone's input.
> We did check Task Scheduler, not any suspicious task exists.
> I'm more leaned to this logging issue of DM/GMS, since I did see similar
> issue on SerialEM in our system.
> And at that time we changed the time to "fix" the issue.
> I'm trying to clean the logging content to see how it works.
> If it doesn't work for us, we'll try changing time to pass midnight (Our
> ITS thinks it could cause other problems).
> Again thanks for the help.
> Best regards,
> Aguang @ UT Austin
> ------------------------------
> *From:* Guenter Resch <lists at nexperion.net>
> *Sent:* Tuesday, February 5, 2019 11:20:36 AM
> *To:* Daniel Dai; 3dem at ncmir.ucsd.edu
> *Subject:* Re: [3dem] Help with 7z issue, likely also with DM/GMS software
> Hi Daniel,
> > We use Leginon to collect data, and once a while we encountered some
> problem with data transfer from K2 camera PC to our data storage.
> > Every time, there are 7z.exe commands running in Task Manager.
> > This problem always happens at midnight (12AM), most of the time, at
> Friday night.
> This sounds like a problem that also exists in SerialEM and that is
> related to the rotation of Digital Micrograph logs. This is the solution
> that Craig Yoshioka posted in 2017:
> "The midnight issue is caused by the DM log directory being too full. If
> you empty it the problem should go away.  I suspect DM is trying to rotate
> and compress the logs at midnight and if it takes too long and there is an
> ongoing exposure it breaks."
> In SerialEM, there is even a WaitForMidnight command to cover this ...
> Hope that helps,
>         Guenter
> --
> Dr. Guenter Resch
> Nexperion e.U. - Solutions for Electron Microscopy - www.nexperion.net
> Ziegelhofstrasse 136/1, 1220 Vienna, Austria - Phone +43 664 94 17 210
> Registered at Commercial Court Vienna, FN 397677w - VAT Reg. ATU67962234
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Amy Bondy, Ph.D.
Cryo-EM Research Specialist
Life Sciences Institute
University of Michigan, Ann Arbor, MI
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