[chimerax-users] How to expand the RAN in ChimeraX?

[Andrea Fera]

Hi Tom,

Thank you for your quick answer.

If the default value is 50% of the physical RAM of the computer, in my case in this server (Lynux) it should be a few hundreds Gb then.
My tomogram is about 8 Gb and therefore it should all fit.

I knew that you had set it up in a great way but since I have had such problems in the past, and my first run of t he rendering failed… I was just checking. Thank you!

Thank you and all best…
Andrea Fera

--
Andrea Fera, PhD
Senior Data Scientist
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From: Tom Goddard <goddard at sonic.net>
Sent: Wednesday, March 3, 2021 12:33 PM
To: Andrea Fera <andrea.fera at revealgc.com>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: How to expand the RAN in ChimeraX?

Hi Andrea,

The volume command dataCacheSize option will do this.  For example for 32 Gbytes of memory cache for volume data use command

                volume dataCacheSize 32000

The default is to set it to half the physical memory of the computer.

https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling

I would not suggest changing it because surface and image rendering typically use an amount memory for the graphics similar to the data size.  The cache is only for the volume data, so with graphics, the current setting can utilize all your memory.  Increasing it can cause data to be paged out to disk with horrible performance.  The above setting is not saved.  If you did want to change it for every ChimeraX session you would use Preferences / Startup / Execute these commands at startup.

                Tom





On Mar 3, 2021, at 9:04 AM, Andrea Fera <andrea.fera at revealgc.com<mailto:andrea.fera at revealgc.com>> wrote:

Dear Mr. Goddard,

This is Andrea. I am not sure that you remember me, but we met in 2013 or so in S. Francisco and Berkeley.

I am a strenuous fan of your software! Especially for volume rendering of cryo-type tomograms.
I do have a tomogram pf a few Gb that I would like to render with your software. I use a Lynux server with LOTS of RAM. How can I increase the RAM allocated by ChimeraX?

Thank you and all best…
Andrea Fera

--
Andrea Fera, PhD
Senior Data Scientist
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