[3dem] Using NVLink on RTX cards

Thu Feb 7 16:47:19 PST 2019

Hi Amedee,

NVLINK can provide more GPU memory. I am not aware of any cryo-EM tools which make significant use of shared GPU memory or use NCCL (https://developer.nvidia.com/nccl). Please let me know if you have ideas for applications which would benefit and any efforts underway to implement.

Thank you.

-Jon

Jonathan Lefman
Developer Relations Manager - Healthcare and Life Sciences
NVIDIA<http://www.nvidia.com/>

From: 3dem <3dem-bounces at ncmir.ucsd.edu> On Behalf Of Amedee des Georges
Sent: Wednesday, February 6, 2019 4:52 PM
To: 3dem at ncmir.ucsd.edu
Subject: [3dem] Using NVLink on RTX cards

Following the question on the Titan RTX, I see that we can add an NVLink between two cards to potentially double the available memory.
I am sure many would be interested to know if our beloved cryo-EM programs can take advantage of this natively or if it is not so simple.

Best,
--
Amedee des Georges, Ph.D.
Assistant Professor, Structural Biology Initiative, CUNY Advanced Science Research Center
Assistant professor of Chemistry & Biochemistry, City College of New York
amedee.desgeorges at asrc.cuny.edu<mailto:amedee.desgeorges at asrc.cuny.edu> - http://asrc.cuny.edu  -  212-413-3232

Message: 1
Date: Wed, 6 Feb 2019 19:02:10 +0000
From: Jonathan Lefman <jlefman at nvidia.com<mailto:jlefman at nvidia.com>>
To: Saikat Chowdhury <saikatbioinfo at gmail.com<mailto:saikatbioinfo at gmail.com>>
Cc: "3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>" <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>,
"CCPEM at jiscmail.ac.uk<mailto:CCPEM at jiscmail.ac.uk>" <CCPEM at jiscmail.ac.uk<mailto:CCPEM at jiscmail.ac.uk>>
Subject: Re: [3dem] [ccpem] Titan RTX Vs RTX2080Ti

Hi Saikat,

Would you please let me know which application / functional component of cryo-EM data processing? I will do my best to provide guidance where I am able.

Thank you.

-Jon

Jonathan Lefman
Developer Relations Manager - Healthcare and Life Sciences
NVIDIA<http://www.nvidia.com/>

From: 3dem <3dem-bounces at ncmir.ucsd.edu<mailto:3dem-bounces at ncmir.ucsd.edu>> On Behalf Of Saikat Chowdhury
Sent: Tuesday, February 5, 2019 9:43 PM
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
Cc: CCPEM at jiscmail.ac.uk<mailto:CCPEM at jiscmail.ac.uk>
Subject: Re: [3dem] [ccpem] Titan RTX Vs RTX2080Ti

Hi cryo-EM community members,

I would like to know if anyone is using or benchmarked the Titan RTX card for cryo-EM data processing?

Is it worth the price of the card (almost twice the price of the RTX 2080Ti)?

Thanks,
-Saikat

-SAIKAT CHOWDHURY, Ph.D
Assistant Professor
Dept. of Biochemistry and Cell Biology
Stony Brook University
CMM 144
Stony Brook, NY 11794-5115
(Joint appointment - Brookhaven National Laboratory)

On Wed, Dec 5, 2018 at 1:56 PM Min, Xiaoshan <xmin at amgen.com<mailto:xmin at amgen.com><mailto:xmin at amgen.com>> wrote:
Dear Community,

A couple weeks ago there were a couple of  helpful discussions on the comparison between different GPUs.  I am wondering if people can provide some insight into the newly announced Titan RTX https://www.nvidia.com/en-us/titan/titan-rtx/   The 24GB memory seems to be particularly appealing.

Thanks,

Xiaoshan

Xiaoshan Min | Principal Scientist
Amgen Inc.
Department of Molecular Engineering
1120 Veterans Blvd | South San Francisco, CA
Ph. 6502442412 | xmin at amgen.com<mailto:xmin at amgen.com><mailto:xmin at amgen.com>

Message: 2
Date: Wed, 6 Feb 2019 14:06:09 -0500
From: Saikat Chowdhury <saikatbioinfo at gmail.com<mailto:saikatbioinfo at gmail.com>>
To: Jonathan Lefman <jlefman at nvidia.com<mailto:jlefman at nvidia.com>>
Cc: "3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>" <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>,
"CCPEM at jiscmail.ac.uk<mailto:CCPEM at jiscmail.ac.uk>" <CCPEM at jiscmail.ac.uk<mailto:CCPEM at jiscmail.ac.uk>>
Subject: Re: [3dem] [ccpem] Titan RTX Vs RTX2080Ti

Dear Jonathan,

I am referring to the standard cryo-EM data processing packages like
Relion-3-beta, Cryosparc 2, IMOD to name a few.

Thanks,
-Saikat

On Wed, Feb 6, 2019 at 2:02 PM Jonathan Lefman <jlefman at nvidia.com<mailto:jlefman at nvidia.com>> wrote:

*From:* 3dem <3dem-bounces at ncmir.ucsd.edu<mailto:3dem-bounces at ncmir.ucsd.edu>> *On Behalf Of *Saikat Chowdhury
*Sent:* Tuesday, February 5, 2019 9:43 PM
*To:* 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
*Cc:* CCPEM at jiscmail.ac.uk<mailto:CCPEM at jiscmail.ac.uk>
*Subject:* Re: [3dem] [ccpem] Titan RTX Vs RTX2080Ti

Hi cryo-EM community members,

I would like to know if anyone is using or benchmarked the Titan RTX card
for cryo-EM data processing?

Is it worth the price of the card (almost twice the price of the RTX
2080Ti)?

Thanks,

-Saikat

*-SAIKAT CHOWDHURY, Ph.D*

Assistant Professor

Dept. of Biochemistry and Cell Biology

Stony Brook University

CMM 144

Stony Brook, NY 11794-5115

(Joint appointment - Brookhaven National Laboratory)

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