[3dem] Problem with Relion multi-body refinement

[Takanori Nakane]

Hi,

Thank you very much for feedback.

We will fix the problem with  "Combine iterations through disc?: No".

Best regards,

Takanori Nakane

On 2019/03/16 10:28, Eric Hanssen wrote:
> 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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