[3dem] Problem with Relion multi-body refinement

[Eric Hanssen]

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 | Office: +61 3 83442449 | Microscope: +61 3 83442509 
Web: 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
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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> 3dem at ncmir.ucsd.edu
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>


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