Hi Sjors,
Thanks for the tip. Since we have 500 Ang diameter particles (~470 pixels), should we be thinking about boxes of 780 pixels or more? The data were collected at 300 kV with a maximum defocus of -2.5 micron, and we are aiming for ~3 Ang resolution.
Thanks again,
Dave
-------------------------------
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]
-----Original Message-----
From: Sjors Scheres <[log in to unmask]>
Sent: 11 March 2019 15:57
To: david lawson (JIC) <[log in to unmask]>; [log in to unmask]
Subject: Re: [ccpem] Refine3D jobs crashing and occasionally causing server to become unresponsive
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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