[3dem] Problem with Relion multi-body refinement

Eric Hanssen ehanssen at unimelb.edu.au
Sat Mar 16 03:28:38 PDT 2019


Hi Takanori,
Yes it does thanks. No crash so far. I re run three of the one crashing and they behave perfectly.
Cheers
Eric


Assoc. Prof Eric Hanssen
Head - Advanced Microscopy Facility
Honorary Principal Fellow – Department of Biochemistry and Molecular Biology

President Australian Microscopy and Microanalysis Society

Bio21 Molecular Science and Biotechnology Institute - 30 Flemington Road - The University of Melbourne - Victoria 3010 - Australia
email: ehanssen at unimelb.edu.au<mailto:ehanssen at unimelb.edu.au> | Office: +61 3 83442449 | Microscope: +61 3 83442509
Web: www.microscopy.unimelb.edu.au<http://www.microscopy.unimelb.edu.au/>


On 15 Mar 2019, at 19:17, Takanori Nakane <tnakane at mrc-lmb.cam.ac.uk<mailto:tnakane at mrc-lmb.cam.ac.uk>> wrote:

Hi,

Does "Combine iterations through disc?: Yes" help?

Best regards,

Takanori Nakane

On 2019/03/15 5:49, Eric Hanssen wrote:
HI Takanori,
The sampling was 0.9375 for most and a couple at half of that 0.46875
Regards
Eric
-----------------
Assoc. Prof Eric Hanssen
Head - Advanced Microscopy Facility
Honorary Principal Fellow - Department of Biochemistry and Molecular Biology
President Australian Microscopy and Microanalysis Society
Bio21 Molecular Science and Biotechnology Institute
30 Flemington Road - The University of Melbourne - Victoria 3010 - Australia
email: ehanssen at unimelb.edu.au<mailto:ehanssen at unimelb.edu.au> | Office: +61 3 83442449 | Microscope: +61 3 83442509
Web: www.microscopy.unimelb.edu.au<http://www.microscopy.unimelb.edu.au>
   -----Original Message-----
From: Takanori Nakane [mailto:tnakane at mrc-lmb.cam.ac.uk]
Sent: Friday, 15 March 2019 4:07 PM
To: Eric Hanssen; De Biasio, Alfredo (Dr.)
Cc: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] Problem with Relion multi-body refinement
Hi,
What is the angular sampling at the crashing iteration?
Best regards,
Takanori Nakane
On 2019/03/15 0:28, Eric Hanssen wrote:
Hi Takanori,
I have had a similar issue on several datasets. I updated this morning as requested. it is still happening and at the same iteration. I have tried on 3 datasets (same protein and same box size, different particle numbers and resolution) and it is consistent, it keeps happening.
Box size 344, 2 or 3 bodies, 4 GTX1080 with 12GB

   3: MPI_ERR_TRUNCATE: message truncated
   3: MPI_ERR_TRUNCATE: message truncated
in: /home/bio21em1/relion/src/mpi.cpp, line 307
terminate called after throwing an instance of 'RelionError'
[odin:202188] *** Process received signal ***
[odin:202188] Signal: Aborted (6)
[odin:202188] Signal code:  (-6)
[odin:202188] [ 0] /lib64/libpthread.so.0[0x375c60f7e0]
[odin:202188] [ 1] /lib64/libc.so.6(gsignal+0x35)[0x375be32495]
[odin:202188] [ 2] /lib64/libc.so.6(abort+0x175)[0x375be33c75]
[odin:202188] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d)[0x3762abea7d]
[odin:202188] [ 4] /usr/lib64/libstdc++.so.6[0x3762abcbd6]
[odin:202188] [ 5] /usr/lib64/libstdc++.so.6[0x3762abcc03]
[odin:202188] [ 6] /usr/lib64/libstdc++.so.6[0x3762abcd22]
[odin:202188] [ 7] /usr/local/bin/relion_refine_mpi(_ZN7MpiNode16report_MPI_ERROREi+0x102)[0x48b052]
[odin:202188] *** End of error message ***

Regards
Eric


-----------------
Assoc. Prof Eric Hanssen

Head - Advanced Microscopy Facility
Honorary Principal Fellow - Department of Biochemistry and Molecular Biology

President Australian Microscopy and Microanalysis Society

Bio21 Molecular Science and Biotechnology Institute
30 Flemington Road - The University of Melbourne - Victoria 3010 - Australia
email: ehanssen at unimelb.edu.au<mailto:ehanssen at unimelb.edu.au> | Office: +61 3 83442449 | Microscope: +61 3 83442509
Web: www.microscopy.unimelb.edu.au<http://www.microscopy.unimelb.edu.au>





-----Original Message-----
From: 3dem [mailto:3dem-bounces at ncmir.ucsd.edu] On Behalf Of Takanori Nakane
Sent: Friday, 15 March 2019 1:05 AM
To: De Biasio, Alfredo (Dr.)
Cc: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] Problem with Relion multi-body refinement

Hi,

We recently fixed a bug in multi-body refinement.
Could you please try the latest version (3.0.2) on our GitHub?

Best regards,

Takanori Nakane

Dear all,

I am running Multi-Body Refinement on a two-body complex and I get the
following error message after the 8th iteration:

  3: Message truncated
   3: Message truncated, error stack:
PMPI_Wait(219).....: MPI_Wait(request=0x7ffea6199c88,
status=0x7ffea6199d10) failed
MPIR_Wait_impl(100): fail failed
do_cts(649)........: Message truncated; 409319840 bytes received but
buffer size is 409172384
srun: error: compute5: task 3: Segmentation fault (core dumped)

If I continue the job from the 8th iteration, it gets to completion but
the final maps of the 2 bodies have completely different masks from the
initial (correct) masks and are highly anisotropic.

Could you, please, help?

Thank you,

Alfredo De Biasio
LISCB, Leicester



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