Hi Dave,
You could window your particles more generously (to include more
delocalised signal and to reduce interpolation problems with pad1), and
then use --pad 1 (instead of --pad 2). This would save a lot of GPU memory.
HTH,
Sjors
david lawson (JIC) wrote:
>
> 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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--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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