JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for CCPEM Archives


CCPEM Archives

CCPEM Archives


CCPEM@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

CCPEM Home

CCPEM Home

CCPEM  January 2019

CCPEM January 2019

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: CtfRefine errors

From:

Takanori Nakane <[log in to unmask]>

Reply-To:

Takanori Nakane <[log in to unmask]>

Date:

Thu, 10 Jan 2019 13:50:01 -0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (140 lines)

Hi,

I found a problem in the MPI version of CtfRefine (and several others)
that error messages are not correctly displayed. The latest commit
fixes this problem.

Best regards,

Takanori Nakane

> Dear Takanori,
>
> Thanks for the tip, I will try to find the culprit.
>
> Perhaps it may be possible in future to modify code such that error
> message lists problematic file?
>
> Thanks,
>
> Leo
>
> Prof. Leonid Sazanov
> IST Austria
> Am Campus 1
> A-3400 Klosterneuburg
> Austria
>
> Phone: +43 2243 9000 3026
> E-mail: [log in to unmask]
>
> On 09/01/19 13:43, Takanori Nakane wrote:
>> Hi,
>>
>> Probably one of your MRCS files is truncated; for example,
>> your STAR file points to the 200-th image in the stack, but the
>> MRCS file contains only 190.
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>>> Dear Sjors,
>>>
>>> As I mentioned, error messages looked a bit different each time, so I
>>> did not post them initially.
>>>
>>> Now I noticed that all of them eventually trace back to the same line
>>> in
>>> code, related to MRC file read/write:
>>>
>>> in: /localhome/schloegl/src/relion-3.0-beta/src/rwMRC.h, line 191
>>> terminate called after throwing an instance of 'RelionError'
>>>
>>> This is the example command:
>>>
>>> `which relion_ctf_refine` --i Refine3D/job184/run_data.star --f
>>> PostProcess/job196/postprocess.star --m1
>>> Refine3D/job184/run_half1_class001_unfil.mrc --m2
>>> Refine3D/job184/run_half2_class001_unfil.mrc --mask
>>> MaskCreate/job156/mask_156.mrc --o CtfRefine/job226/ --kmin_defocus 30
>>> --fit_defocus --range 2000 --fit_beamtilt --kmin_tilt 30
>>> --only_do_unfinished? --j 8
>>>
>>> With this set of particles (~30K, ~3.8 A resolution) CtfRefine always
>>> fails, but with another set from the same micrographs (170K, 3.9 A
>>> resolution) the same type of command works.
>>>
>>> I double checked that all files are in place and there are no issues
>>> with permissions, so I am not sure why MRC file read/writing fails.
>>>
>>> Thanks,
>>>
>>> Leo
>>>
>>> Prof. Leonid Sazanov
>>> IST Austria
>>> Am Campus 1
>>> A-3400 Klosterneuburg
>>> Austria
>>>
>>> Phone: +43 2243 9000 3026
>>> E-mail: [log in to unmask]
>>>
>>> On 07/01/19 09:04, Sjors Scheres wrote:
>>>> Dear Leo,
>>>>
>>>> I'm afraid this message does not provide a good starting point for a
>>>> follow-up investigation on our side.  The below is not only for you,
>>>> but
>>>> also for the community.
>>>>
>>>> When reporting errors, it is very useful for us to:
>>>> 1) know the exact command line arguments
>>>> 2) know the exact error
>>>> 3) know when that error occurs and when not
>>>> 4) (most useful) have a small test case you could share with us that
>>>> quickly and reproducibly leads to the error.
>>>>
>>>> In such cases we can relatively quickly find the error. Otherwise, it
>>>> may
>>>> take a long time...
>>>>
>>>> HTH,
>>>> Sjors
>>>>
>>>>
>>>>> Hi, recently using Relion3 build from 04 Dec with CtfRefine I
>>>>> constantly
>>>>> get cryptic errors which are different depending on whether I use
>>>>> several
>>>>> mpi and several threads or one mpi and several threads or even if
>>>>> just
>>>>> 1
>>>>> mpi and 1 thread. Larger set of particles from the same set of images
>>>>> works fine, so that is really puzzling.
>>>>> Any info on what may help highly appreciated.
>>>>> Thanks!
>>>>>
>>>>> ########################################################################
>>>>>
>>>>> To unsubscribe from the CCPEM list, click the following link:
>>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
>>>>>
>>> ########################################################################
>>>
>>> To unsubscribe from the CCPEM list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
>>>
>>
>
> ########################################################################
>
> To unsubscribe from the CCPEM list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
>

########################################################################

To unsubscribe from the CCPEM list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager