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Hi Takanori,
<div>Yes it does thanks. No crash so far. I re run three of the one crashing and they behave perfectly.</div>
<div>Cheers</div>
<div>Eric</div>
<div><br>
<br>
<div id="AppleMailSignature" dir="ltr">Assoc. Prof Eric Hanssen
<div><b style="font-size: 13pt; background-color: rgba(255, 255, 255, 0);">Head - Advanced Microscopy Facility</b></div>
<div><b style="font-size: 13pt; background-color: rgba(255, 255, 255, 0);">Honorary Principal Fellow – Department of Biochemistry and Molecular Biology</b></div>
<div><b style="font-size: 13pt; background-color: rgba(255, 255, 255, 0);"><br>
</b></div>
<div><b style="background-color: rgba(255, 255, 255, 0);">President Australian Microscopy and Microanalysis Society</b></div>
<div><span style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;"><br>
</span></div>
<div><span style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;">Bio21 Molecular Science and Biotechnology Institute - </span><span style="font-size: 13pt; background-color: rgba(255, 255, 255, 0);">30 Flemington Road - The University of Melbourne
- Victoria 3010 - Australia</span></div>
<div><span style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;">email:</span><span style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;"> </span><a href="mailto:ehanssen@unimelb.edu.au" style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;">ehanssen@unimelb.edu.au</a><span style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;"> </span><span style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;">|
Office: +61 3 83442449 | Microscope: +61 3 83442509</span><span style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;"> </span></div>
<div><span style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;">Web:</span><span style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;"> </span><a href="http://www.microscopy.unimelb.edu.au/" style="background-color: rgba(255, 255, 255, 0); font-size: 13pt;">www.microscopy.unimelb.edu.au</a></div>
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On 15 Mar 2019, at 19:17, Takanori Nakane <<a href="mailto:tnakane@mrc-lmb.cam.ac.uk">tnakane@mrc-lmb.cam.ac.uk</a>> wrote:<br>
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<div dir="ltr"><span>Hi,</span><br>
<span></span><br>
<span>Does "Combine iterations through disc?: Yes" help?</span><br>
<span></span><br>
<span>Best regards,</span><br>
<span></span><br>
<span>Takanori Nakane</span><br>
<span></span><br>
<span>On 2019/03/15 5:49, Eric Hanssen wrote:</span><br>
<blockquote type="cite"><span>HI Takanori,</span><br>
</blockquote>
<blockquote type="cite"><span>The sampling was 0.9375 for most and a couple at half of that 0.46875</span><br>
</blockquote>
<blockquote type="cite"><span>Regards</span><br>
</blockquote>
<blockquote type="cite"><span>Eric</span><br>
</blockquote>
<blockquote type="cite"><span>-----------------</span><br>
</blockquote>
<blockquote type="cite"><span>Assoc. Prof Eric Hanssen</span><br>
</blockquote>
<blockquote type="cite"><span>Head - Advanced Microscopy Facility</span><br>
</blockquote>
<blockquote type="cite"><span>Honorary Principal Fellow - Department of Biochemistry and Molecular Biology</span><br>
</blockquote>
<blockquote type="cite"><span>President Australian Microscopy and Microanalysis Society</span><br>
</blockquote>
<blockquote type="cite"><span>Bio21 Molecular Science and Biotechnology Institute</span><br>
</blockquote>
<blockquote type="cite"><span>30 Flemington Road - The University of Melbourne - Victoria 3010 - Australia</span><br>
</blockquote>
<blockquote type="cite"><span>email: <a href="mailto:ehanssen@unimelb.edu.au">ehanssen@unimelb.edu.au</a> | Office: +61 3 83442449 | Microscope: +61 3 83442509</span><br>
</blockquote>
<blockquote type="cite"><span>Web: <a href="http://www.microscopy.unimelb.edu.au">
www.microscopy.unimelb.edu.au</a></span><br>
</blockquote>
<blockquote type="cite"><span> -----Original Message-----</span><br>
</blockquote>
<blockquote type="cite"><span>From: Takanori Nakane [<a href="mailto:tnakane@mrc-lmb.cam.ac.uk">mailto:tnakane@mrc-lmb.cam.ac.uk</a>]</span><br>
</blockquote>
<blockquote type="cite"><span>Sent: Friday, 15 March 2019 4:07 PM</span><br>
</blockquote>
<blockquote type="cite"><span>To: Eric Hanssen; De Biasio, Alfredo (Dr.)</span><br>
</blockquote>
<blockquote type="cite"><span>Cc: <a href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a></span><br>
</blockquote>
<blockquote type="cite"><span>Subject: Re: [3dem] Problem with Relion multi-body refinement</span><br>
</blockquote>
<blockquote type="cite"><span>Hi,</span><br>
</blockquote>
<blockquote type="cite"><span>What is the angular sampling at the crashing iteration?</span><br>
</blockquote>
<blockquote type="cite"><span>Best regards,</span><br>
</blockquote>
<blockquote type="cite"><span>Takanori Nakane</span><br>
</blockquote>
<blockquote type="cite"><span>On 2019/03/15 0:28, Eric Hanssen wrote:</span><br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Hi Takanori,</span><br>
</blockquote>
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<blockquote type="cite">
<blockquote type="cite"><span>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.</span><br>
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<blockquote type="cite"><span>Box size 344, 2 or 3 bodies, 4 GTX1080 with 12GB</span><br>
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<blockquote type="cite"><span> 3: MPI_ERR_TRUNCATE: message truncated</span><br>
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<blockquote type="cite"><span> 3: MPI_ERR_TRUNCATE: message truncated</span><br>
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<blockquote type="cite"><span>in: /home/bio21em1/relion/src/mpi.cpp, line 307</span><br>
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<blockquote type="cite"><span>terminate called after throwing an instance of 'RelionError'</span><br>
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<blockquote type="cite">
<blockquote type="cite"><span>[odin:202188] *** Process received signal ***</span><br>
</blockquote>
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<blockquote type="cite"><span>[odin:202188] Signal: Aborted (6)</span><br>
</blockquote>
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<blockquote type="cite"><span>[odin:202188] Signal code: (-6)</span><br>
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<blockquote type="cite"><span>[odin:202188] [ 0] /lib64/libpthread.so.0[0x375c60f7e0]</span><br>
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<blockquote type="cite"><span>[odin:202188] [ 1] /lib64/libc.so.6(gsignal+0x35)[0x375be32495]</span><br>
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<blockquote type="cite"><span>[odin:202188] [ 2] /lib64/libc.so.6(abort+0x175)[0x375be33c75]</span><br>
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<blockquote type="cite"><span>[odin:202188] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d)[0x3762abea7d]</span><br>
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<blockquote type="cite"><span>[odin:202188] [ 4] /usr/lib64/libstdc++.so.6[0x3762abcbd6]</span><br>
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<blockquote type="cite"><span>[odin:202188] [ 5] /usr/lib64/libstdc++.so.6[0x3762abcc03]</span><br>
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<blockquote type="cite"><span>[odin:202188] [ 6] /usr/lib64/libstdc++.so.6[0x3762abcd22]</span><br>
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<blockquote type="cite"><span>[odin:202188] [ 7] /usr/local/bin/relion_refine_mpi(_ZN7MpiNode16report_MPI_ERROREi+0x102)[0x48b052]</span><br>
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<blockquote type="cite"><span>[odin:202188] *** End of error message ***</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
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<blockquote type="cite">
<blockquote type="cite"><span>Regards</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Eric</span><br>
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<blockquote type="cite">
<blockquote type="cite"><span>-----------------</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Assoc. Prof Eric Hanssen</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Head - Advanced Microscopy Facility</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Honorary Principal Fellow - Department of Biochemistry and Molecular Biology</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>President Australian Microscopy and Microanalysis Society</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Bio21 Molecular Science and Biotechnology Institute</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>30 Flemington Road - The University of Melbourne - Victoria 3010 - Australia</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>email: <a href="mailto:ehanssen@unimelb.edu.au">ehanssen@unimelb.edu.au</a> | Office: +61 3 83442449 | Microscope: +61 3 83442509</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Web: <a href="http://www.microscopy.unimelb.edu.au">
www.microscopy.unimelb.edu.au</a></span><br>
</blockquote>
</blockquote>
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<blockquote type="cite"><span> </span><br>
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<blockquote type="cite">
<blockquote type="cite"><span>-----Original Message-----</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>From: 3dem [<a href="mailto:3dem-bounces@ncmir.ucsd.edu">mailto:3dem-bounces@ncmir.ucsd.edu</a>] On Behalf Of Takanori Nakane</span><br>
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<blockquote type="cite"><span>Sent: Friday, 15 March 2019 1:05 AM</span><br>
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<blockquote type="cite">
<blockquote type="cite"><span>To: De Biasio, Alfredo (Dr.)</span><br>
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<blockquote type="cite">
<blockquote type="cite"><span>Cc: <a href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a></span><br>
</blockquote>
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<blockquote type="cite">
<blockquote type="cite"><span>Subject: Re: [3dem] Problem with Relion multi-body refinement</span><br>
</blockquote>
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<blockquote type="cite">
<blockquote type="cite"><span></span><br>
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<blockquote type="cite"><span>Hi,</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
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<blockquote type="cite">
<blockquote type="cite"><span>We recently fixed a bug in multi-body refinement.</span><br>
</blockquote>
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<blockquote type="cite">
<blockquote type="cite"><span>Could you please try the latest version (3.0.2) on our GitHub?</span><br>
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<blockquote type="cite"><span></span><br>
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<blockquote type="cite"><span>Best regards,</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Takanori Nakane</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
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<blockquote type="cite"><span>Dear all,</span><br>
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<blockquote type="cite"><span>I am running Multi-Body Refinement on a two-body complex and I get the</span><br>
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<blockquote type="cite"><span>following error message after the 8th iteration:</span><br>
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<blockquote type="cite"><span> 3: Message truncated</span><br>
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<blockquote type="cite"><span> 3: Message truncated, error stack:</span><br>
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<blockquote type="cite"><span>PMPI_Wait(219).....: MPI_Wait(request=0x7ffea6199c88,</span><br>
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<blockquote type="cite"><span>status=0x7ffea6199d10) failed</span><br>
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<blockquote type="cite"><span>MPIR_Wait_impl(100): fail failed</span><br>
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<blockquote type="cite"><span>do_cts(649)........: Message truncated; 409319840 bytes received but</span><br>
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<blockquote type="cite"><span>buffer size is 409172384</span><br>
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<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><span>srun: error: compute5: task 3: Segmentation fault (core dumped)</span><br>
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<blockquote type="cite"><span></span><br>
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<blockquote type="cite"><span>If I continue the job from the 8th iteration, it gets to completion but</span><br>
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<blockquote type="cite"><span>the final maps of the 2 bodies have completely different masks from the</span><br>
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<blockquote type="cite"><span>initial (correct) masks and are highly anisotropic.</span><br>
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<blockquote type="cite"><span>Could you, please, help?</span><br>
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<blockquote type="cite"><span>Thank you,</span><br>
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<blockquote type="cite"><span>Alfredo De Biasio</span><br>
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<blockquote type="cite"><span>LISCB, Leicester</span><br>
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<blockquote type="cite"><span>_______________________________________________</span><br>
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<blockquote type="cite"><span>3dem mailing list</span><br>
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<blockquote type="cite"><span><a href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a></span><br>
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<blockquote type="cite"><span><a href="https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem">https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem</a></span><br>
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<blockquote type="cite"><span>3dem mailing list</span><br>
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<blockquote type="cite"><span><a href="https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem">https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem</a></span><br>
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