Re: [chimerax-users] 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 <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@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 <image003.jpg>
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 [cid:image002.jpg@01D71038.31AE79D0] From: Tom Goddard <goddard@sonic.net> Sent: Wednesday, March 3, 2021 12:33 PM To: Andrea Fera <andrea.fera@revealgc.com> Cc: ChimeraX Users Help <chimerax-users@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@revealgc.com<mailto:andrea.fera@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 <image003.jpg>
Hi Andrea, I saw from your bug report that your "out of memory" error is from the OpenGL graphics trying to create an OpenGL texture of about 20 Gbytes for a 10 Gbyte tiff image stack (graphics is twice as large to handle brightness and transparency in image style). https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4316 <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4316> Your graphics driver is Mesa, software rendering. I don't know what controls how big a 3D texture the Mesa driver will allow. The machine has 1.5 Tbytes memory so it has plenty. I suspect the driver simply won't allow a single large 3D texture, probably limited to 8 Gbytes. By switching ChimeraX to use multiple 2D textures it may be able to render. To use 2D texture rendering for volume model #1 use ChimeraX command volume #1 projectionMode 2d-z documentation here https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsolid <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsolid> Tom
On Mar 3, 2021, at 11:19 AM, Andrea Fera <andrea.fera@revealgc.com> wrote:
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 <image002.jpg>
From: Tom Goddard <goddard@sonic.net> Sent: Wednesday, March 3, 2021 12:33 PM To: Andrea Fera <andrea.fera@revealgc.com> Cc: ChimeraX Users Help <chimerax-users@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 <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@revealgc.com <mailto:andrea.fera@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 <image003.jpg>
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participants (2)
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Andrea Fera -
Tom Goddard