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Science Anyone here familiar with Mr Bayes (Bioinfo)?, Running Mr Bayes on Nvidia GPU

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TS[PF] T.J.
post Mar 11 2012, 08:16 PM, updated 14y ago

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From: Perak
Hi guys~

I'm having some problems running my Mr. Bayes 3.2.1 (a bioinformatics program for the calculation of Bayesian inference) on an Nvidia GPU (rather than CPU). It is said that running analyses using the GPU would be much faster than by using the CPU, but that's not the case for my system lol....
I've searched through the internet and couldn't find much info on how to go about this, hence I'm trying my luck here to see whether there are any bioinfo sifus here who are familiar with this~

Nvidia GPU - GT555m
Nvidia driver version - 295.73

Mr. Bayes 3.2.1 download site: http://mrbayes.sourceforge.net/download.php

I hope someone would be able to help me out, thanks thanks notworthy.gif notworthy.gif
TS[PF] T.J.
post Apr 28 2012, 01:57 AM

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From: Perak
Thanks for the reply bro notworthy.gif
I din't think anyone here would know what I'm asking also haha doh.gif

The one from your link is a different type of Mr Bayes (Mr Bayes GPU), the algorithms there are slightly lesser/ different than the standard one iinm

Anyway I've managed to set up the original Mr. Bayes 3.2.1 to run on the GPU... but weirdly its a whole lot slower than when running on CPU... which is very, very weird doh.gif
TS[PF] T.J.
post Apr 29 2012, 10:50 PM

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From: Perak
QUOTE(herofire86 @ Apr 29 2012, 07:37 PM)
on which platform are you running it on? i guess beagle is still buggy,depending on cards model, been using the mpi version for quite awhile...using 64 cores...pretty much do the job.
anyway . anyway here is a good article to share regarding comparative models http://sysbio.oxfordjournals.org/content/60/5/685
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Running on Windows 7 (64-bit)? hmm.gif
I don't think my GPU is supported... I've tried F@H with my GPU before and its a hell lot faster than my CPU, which is why its quite weird for it to not perform similarly on Mr. Bayes laugh.gif
If GPU works faster and better, that'll affect the choices of laptops/ workstations we choose later on..

And thanks alot for the article notworthy.gif
I'd probably need some time to digest the info there laugh.gif
I'm a little bit outdated in the phylogenetic programs used, especially those pertaining to ML lol
TS[PF] T.J.
post May 1 2012, 12:01 AM

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From: Perak
QUOTE(herofire86 @ Apr 30 2012, 11:19 AM)
owh , tweaking it under windows 7 may have some limitation, to play around with the sourcecode and library, unix/linux based platform have more freedom to do so.
yup , gpu now seems to be still understandardised, ,if only we can work on a universal interpreter, that can act as emulator to every comp that equipped with gpu, not just for specific software or hardware. kinda like javavm,
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Too deep already bro, I don't understand haha~
Are you a programmer? You seemed to know quite a lot haha

I'm just an end-user tongue.gif

 

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