Unfettered use of GPUGrid

Message boards : Number crunching : Unfettered use of GPUGrid

Author	Message
Betting Slip Send message Joined: 5 Jan 09 Posts: 670 Credit: 2,498,095,550 RAC: 0 Level Scientific publications	Message 42998 - Posted: 14 Mar 2016 \| 10:33:14 UTC
	Gerard, has having unfettered use of GPUGrid helped your research?
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Gerard Send message Joined: 26 Mar 14 Posts: 101 Credit: 0 RAC: 0 Level Scientific publications	Message 42999 - Posted: 14 Mar 2016 \| 11:40:29 UTC - in response to Message 42998. Last modified: 14 Mar 2016 \| 12:18:23 UTC
	Hi Betting Slip, I am sorry I don't update you as much as I would want, but there's several reasons for this: mainly being in charge of updating GPUGRID while pursuing my PhD is too much work sometimes, secondarily some of the results cannot made public until published. Your contribution to GPUGRID has helped a lot. The protocol developed in our lab (http://pubs.acs.org/doi/abs/10.1021/ct400919u) seems to work for a subset of molecules by which no binding pose was previously known. We are trying to improve inhibitors exploiting the knowledge generated. However, all these results are still theoretical and a second experimental phase, that we are currently undergoing, will be necessary before results can be made public. Alternatively, for the past months I have been testing an old protocol (umbrella sampling) that seems to work like charm to get a quick idea about the binding affinity of ligands. It is a very extense work, highly applicational and with real impact in biomedicine. It is not a mere proof of concept, we are really pushing the edges of knowdledge here, but slowly and patiently. I hope this gave you a little insight (sorry to be succint) of the trascendence of your contribution. :)
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Betting Slip Send message Joined: 5 Jan 09 Posts: 670 Credit: 2,498,095,550 RAC: 0 Level Scientific publications	Message 43000 - Posted: 14 Mar 2016 \| 12:40:36 UTC - in response to Message 42999.
	Thank you very much Gerard for taking time out to give all participants of this project your update. I'm particularly pleased your work is not just "proof of concept" Thanks Richard
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[CSF] Thomas H.V. DUPONT Send message Joined: 20 Jul 14 Posts: 732 Credit: 126,845,366 RAC: 190,805 Level Scientific publications	Message 43001 - Posted: 14 Mar 2016 \| 14:36:07 UTC - in response to Message 42999.
	+1 :) Thanks Gerard! Really appreciated! ____________ [CSF] Thomas H.V. Dupont Founder of the team CRUNCHERS SANS FRONTIERES 2.0 www.crunchersansfrontieres
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Jim1348 Send message Joined: 28 Jul 12 Posts: 819 Credit: 1,591,285,971 RAC: 0 Level Scientific publications	Message 43003 - Posted: 14 Mar 2016 \| 14:52:34 UTC
	Great stuff. I keep one card on GPUGrid all the time, and will add more when the work increases. You can't do projects just to provide us work, it is important that you do something worthwhile. But it looks like the added capacity has helped you somewhat, which is very nice.
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Vagelis Giannadakis Send message Joined: 5 May 13 Posts: 187 Credit: 349,254,454 RAC: 0 Level Scientific publications	Message 43011 - Posted: 15 Mar 2016 \| 10:28:17 UTC
	Thank you Gerard for this information! I'm very happy to know we are contributing to some actual, real knowledge-expanding research here! ____________
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Retvari Zoltan Send message Joined: 20 Jan 09 Posts: 2343 Credit: 16,206,655,749 RAC: 261,147 Level Scientific publications	Message 43013 - Posted: 15 Mar 2016 \| 10:33:12 UTC - in response to Message 42999.
	Thumbs up!
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Skyler Baker Send message Joined: 19 Feb 16 Posts: 19 Credit: 140,656,383 RAC: 0 Level Scientific publications	Message 43105 - Posted: 29 Mar 2016 \| 14:27:57 UTC - in response to Message 43013.
	Thumbs up! Hey you're that guy I'm chasing on project completion time :D you must have that stupid card LN2 cooled
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Retvari Zoltan Send message Joined: 20 Jan 09 Posts: 2343 Credit: 16,206,655,749 RAC: 261,147 Level Scientific publications	Message 43108 - Posted: 29 Mar 2016 \| 15:10:08 UTC - in response to Message 43105. Last modified: 29 Mar 2016 \| 15:10:31 UTC
	Thumbs up! Hey you're that guy I'm chasing on project completion time :D you must have that stupid card LN2 cooled No, LN2 cooling for a 24/7 system is a complete economical nonsense. Perhaps some refrigerated water cooling could worth it. All of my GPUs are standard air cooled ones. They are the fastest because of the lack of the infamous WDDM overhead in my systems, as I am using Windows XP x64 for crunching. That's it.
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Skyler Baker Send message Joined: 19 Feb 16 Posts: 19 Credit: 140,656,383 RAC: 0 Level Scientific publications	Message 43109 - Posted: 29 Mar 2016 \| 16:31:21 UTC - in response to Message 43108.
	Thumbs up! Hey you're that guy I'm chasing on project completion time :D you must have that stupid card LN2 cooled No, LN2 cooling for a 24/7 system is a complete economical nonsense. Perhaps some refrigerated water cooling could worth it. All of my GPUs are standard air cooled ones. They are the fastest because of the lack of the infamous WDDM overhead in my systems, as I am using Windows XP x64 for crunching. That's it. I was joking about the LN2, I did figure they were probably heavily over clocked,interesting about the WDDM overhead. Wonder if there is any solution besides going to XP
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Jim1348 Send message Joined: 28 Jul 12 Posts: 819 Credit: 1,591,285,971 RAC: 0 Level Scientific publications	Message 43111 - Posted: 29 Mar 2016 \| 21:15:05 UTC - in response to Message 43108.
	No, LN2 cooling for a 24/7 system is a complete economical nonsense. Perhaps some refrigerated water cooling could worth it. All of my GPUs are standard air cooled ones. They are the fastest because of the lack of the infamous WDDM overhead in my systems, as I am using Windows XP x64 for crunching. That's it. I am sure you are right about the LN2. And I tried WinXP (32-bit) for a while, with good results. But the cards (probably GTX 660 as I recall) were a little less stable on WinXP than on Win7, and so I had to reduce the clocks a bit to eliminate the "unstable machine" notices. On the other hand, on Win7, I could overclock some, though I usually avoid it. So my impression is that at the stability limit, you can get about the same results with Win7 as on WinXP, you just go about it differently. But I have not tried extensive tests, and have not used WinXP 64-bit at all.
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skgiven Volunteer moderator Volunteer tester Send message Joined: 23 Apr 09 Posts: 3968 Credit: 1,995,359,260 RAC: 0 Level Scientific publications	Message 43119 - Posted: 30 Mar 2016 \| 18:57:31 UTC - in response to Message 43111.
	Wonder if there is any solution besides going to XP It's called Linux (x64). ____________ FAQ's HOW TO: - Opt out of Beta Tests - Ask for Help
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skgiven Volunteer moderator Volunteer tester Send message Joined: 23 Apr 09 Posts: 3968 Credit: 1,995,359,260 RAC: 0 Level Scientific publications	Message 43120 - Posted: 30 Mar 2016 \| 19:02:04 UTC - in response to Message 43111. Last modified: 30 Mar 2016 \| 19:02:16 UTC
	So my impression is that at the stability limit, you can get about the same results with Win7 as on WinXP, you just go about it differently. But I have not tried extensive tests, and have not used WinXP 64-bit at all. The bottom line is that WinXP and Linux allow you to get tasks done quicker. The fact that the card is used more/runs hotter is a result of not having the WDDM overhead. A better cooling strategy covers that. With high end/enthusiast cards the WDDM overhead is probably higher. ____________ FAQ's HOW TO: - Opt out of Beta Tests - Ask for Help
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Skyler Baker Send message Joined: 19 Feb 16 Posts: 19 Credit: 140,656,383 RAC: 0 Level Scientific publications	Message 43121 - Posted: 30 Mar 2016 \| 22:17:33 UTC
	Disabling hyperthreading also seemed to increase gpu usage
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Message boards : Number crunching : Unfettered use of GPUGrid

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