Re: [scipion-users] Out of memory with "Show classification in Scipion"

[Grigory S. <sha...@gm...>]

Hi Pablo,

Since this is one of the biggest bottlenecks now, I'd suggest a default of
8Gb. I haven't seen machines used for data processing with 4Gb RAM in years.

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...


On Sun, Jan 24, 2021 at 7:35 PM <pc...@cn...> wrote:

> Nice Juha.  Default value is 2GB...should we increase the default value?
>
> Will at least 4GB be better?
>
> El 24 ene. 2021 12:13, "Huiskonen, Juha T" <juh...@he...>
> escribió:
>
> Found the answer:
>
>
>
> I added JAVA_MAX_MEMORY = 15 in my scipion.conf
>
>
>
> And now it works.
>
>
>
> *From: *"Huiskonen, Juha T" <juh...@he...>
> *Date: *Sunday 24. January 2021 at 11.23
> *To: *"sci...@li..." <
> sci...@li...>
> *Subject: *Out of memory with "Show classification in Scipion"
>
>
>
> Hi all,
>
>
>
> I have classified 3.8M particles to 4 classes.  Next I would like to
> create a new SetOfParticles with particles from 2 classes.  Normally I do
> this by clicking “Analyse Results”, "Show classification in Scipion" and
> saving particles from manually selected classes.  In the current case, I
> run out of memory (the maximum for interactive jobs is 15 Gb on the HPC
> cluster I am using) when I click  “Show classification in Scipion”.
>
>
>
> Is there any other way making a subset of particles after 3D
> classification than to visualize the classes?
>
>
>
> Best wishes,
>
> Juha
>
>
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