In my case, the problem is that the job didn’t run but just stopped (although rounding error seems not harmful).

I am sure that the job really stopped since I checked on PID related to relion and there was nothing.

Here’s CPU usage; 1 MPI, 16 thread

This setting was exactly the same with that mentioned in relion 3.0 tutorial.

Of course, when I performed Bayesian polishing with some other data set, there was no problem at all.


A little while ago, curiously enough, I found that this job can be finished normally when CPU usage is set to 1 MPI, 1 thread.


I don’t know this is related to relion compilation in install process or to some hidden bug in software.

Anyway, light CPU usage was helpful to solve this issue.


Thanks to your comments, Nakane and Laura.


Best regards,

Han



Bum Han Ryu

Postdoctoral Researcher
Korea Basic Science Institute (KBSI)
161 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si
Chungcheongbuk-do, Republic of Korea

Office) +82-43-240-5329
Mobile) +82-10-7119-0505


2018. 9. 20. 오후 4:05, Takanori Nakane <[log in to unmask]> 작성:

Hi,

> the warning of rounding error in performing bayesian polishing?

This is probably harmless. See comments from Jasenko (the developer
of Bayesian Polishing) on
https://bitbucket.org/scheres/relion-3.0_beta/issues/16/bogus-warning-messages-about-pixel-size

> No progress after preparing alignment data

Perhaps it is just taking time? Unfortunately, tuning can be very slow.
What is the CPU usage during this?

It is also useful to see if it finishes quickly if you specify only
100 particles for tuning (of course, the result is not useful;
just for testing).

Best regards,

Takanori Nakane

P.S.

Please paste error messages as texts and avoid attaching as
screen shots. Images are large and cannot be searched.

On 2018/09/20 7:47, 류범한 wrote:
Hello, ccpem
Has anybody seen the warning of rounding error in performing bayesian polishing?
It just stopped without any error message like below. (No progress after preparing alignment data)
And the following is the run.err.
I put “—angpix 0.885” into the additional arguments blank in Running Tab, but it did not work.
And everything related to the calculation of angpix (in star file) looked just fine.
N. of MPI procs was set to 1, and N of thread to 16, as mentioned in tutorial. So, it is probably not a MPI issue or something.
How can I progress it further?
Hope somebody suggest a solution to this problem.
Best regards,
Han
Bum Han Ryu
Postdoctoral Researcher
Korea Basic Science Institute (KBSI)
161 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si
Chungcheongbuk-do, Republic of Korea
Office) +82-43-240-5329
Mobile) +82-10-7119-0505
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