Hi,
Aren't you running out of CPU memory? Try fewer MPI processes.
> it is possible to use the full image resolution and a 512 x
> 512 pixel box and run on the GPU for all but the last cycle
With 'skip padding: yes', you can process up to 1000 px boxes
with 1080 Ti (1 MPI / GPU).
Best regards,
Takanori Nakane
> Hi All,
> We have several datasets collected using a magnified pixel size of 1.065
> Ang/pixel from icosahedral virus particles that have a diameter of ~500
> Ang. By down-sampling to 1.5 Ang/pixel we can use box sizes under 512 x
> 512 pixels and therefore run Refine3D jobs to completion on GPUs.
Initial
> processing elsewhere has yielded reconstructions approaching 3 Ang
> resolution after postprocessing using the full image resolution and a
600
> x 600 pixel box in Refine3D running on CPU only. My feeling is that this
> ought to yield better results than down-sampling. However, when we try
to
> reproduce this on our server, jobs crash on the last iteration and
> sometimes cause the server to hang and require a reboot.
> Our server specs are as follows:
> 2x Intel Xeon CPU Broadwell E5-2680v4 (14-core)
> 256GB ECC DDR4-2400 RAM
> 8x NVIDIA GTX 1080Ti
> 480GB SSD for boot
> 5TB SSD
> 8x 10TB Enterprise SAS HDD
> I am currently trying to optimise parameters using a small subset of the
> dataset comprising only 1814 particles (one class from Class3D). I have
> tried different MPI/thread combinations, pooling different numbers of
> particles and copying particles either to RAM or SSD, amongst other
> things.
> Incidentally, it is possible to use the full image resolution and a 512
x
> 512 pixel box and run on the GPU for all but the last cycle, giving 8.3
> Ang resolution after the Refine3D job and 7.6 Ang resolution after
> postprocessing for this small dataset. However, I'm concerned that this
is
> cropping the particles too closely and I'm losing information.
> Any suggestions as to how I might complete these jobs with a 600 x 600
> pixel box would be most welcome.
> I attach run.out, run.err and note.txt files for a job that was the only
> one running on the server.
> Many thanks in advance,
> Dave Lawson
> -------------------------------
> Dr. David M. Lawson
> Department of Biological Chemistry,
> John Innes Centre,
> Norwich,
> NR4 7UH, UK.
> Tel: +44-(0)1603-450725
> Fax: +44-(0)1603-450018
> Email: [log in to unmask]<mailto:[log in to unmask]>
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