SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Reply
 
Thread Tools
Old 05-31-2012, 10:40 AM   #1
cement_head
Senior Member
 
Location: Oxford, Ohio

Join Date: Mar 2012
Posts: 253
Question To TESLA or not to TESLA

Hello,

I'm in the processing of spec'ing a new bioinformatics workstation for a DNA Genomics Core (academic users) and I have a question on the use of TESLA's for bioinformatics.

Most of our user base is non-technical and will not be coding/compiling software. They are end-users of produced software, be it FOSS or commercial (e.g. CLC Genomics Workbench, Newbler).

Is it worth buying a TESLA equipped machine for bioinformatics, or not? We are planning on installing BioLinux 6 (7 when it is ready). If I have interpreted the state-of-affairs right now, GPU enabled software for bioinformatics is not widespread - but is becoming available.

A second question is: Is it difficult to make software use a GPU/TESLA option? Does the CUDA development kit make this easy, or it actually quite labour/coding intensive at the moment?

Any thoughts would be welcome.

Regards,
Andor
cement_head is offline   Reply With Quote
Old 05-31-2012, 06:05 PM   #2
ymc
Senior Member
 
Location: Hong Kong

Join Date: Mar 2010
Posts: 498
Default

For academic beginners, I would recommend trying a GeForce card first, for example, a GTX570, because a Tesla equivalent is about 3x to 5x the price. The development kit is easy to use as long as you know the basics of C and its related development tools in Linux.

When you find the GTX570 is too slow for double precision math or you think it is not stable enough or you need more VRAM, then move on to the Tesla. For now, it would make sense to wait for the Tesla K20 that comes out end of this year.
ymc is offline   Reply With Quote
Old 05-31-2012, 06:16 PM   #3
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,079
Default

If you are buying this machine mainly for end-users then consider omitting high end GPU and using that money to get additional RAM/SSD's. You would get more out of the machine for normal use that way.

You can always buy a GPU later and stick it in the machine if you determine that you must have one (or more) down the road.
GenoMax is offline   Reply With Quote
Old 06-01-2012, 12:33 AM   #4
arvid
Senior Member
 
Location: Berlin

Join Date: Jul 2011
Posts: 156
Default

I'd agree with GenoMax, if you don't know for sure now that a major software you will be running can use the GPU, use the money for more RAM, cores, SSDs or storage instead.
arvid is offline   Reply With Quote
Old 06-01-2012, 08:57 AM   #5
adaptivegenome
Super Moderator
 
Location: US

Join Date: Nov 2009
Posts: 437
Default

We are using at GTX480 for development. It is not pricey but we can still develop and run CUDA applications.
adaptivegenome is offline   Reply With Quote
Reply

Tags
biolinux, gpu, tesla

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:55 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO