Index  | Recent Threads  | Unanswered Threads  | Who's Active  | Guidelines  | Search
 

Quick Go »
No member browsing this thread
Thread Status: Active
Total posts in this thread: 27
Posts: 27   Pages: 3   [ Previous Page | 1 2 3 ]
[ Jump to Last Post ]
Post new Thread
Author
Previous Thread This topic has been viewed 7282 times and has 26 replies Next Thread
Jim1348
Veteran Cruncher
USA
Joined: Jul 13, 2009
Post Count: 1066
Status: Offline
Project Badges:
Reply to this Post  Reply with Quote 
Re: Suggestions for Future Organisms to Fold

According to the Rosetta@home scientists, the software isn't suitable for GPU's

OK, I hadn't seen that mentioned here yet. Another area that would seem ripe for GPUs is climate research, but they say on Climateprediction.net that is not suitable either. I guess we will have to wait for a new generation of software entirely.
[Mar 14, 2013 9:18:04 PM]   Link   Report threatening or abusive post: please login first  Go to top 
Former Member
Cruncher
Joined: May 22, 2018
Post Count: 0
Status: Offline
Reply to this Post  Reply with Quote 
Re: Suggestions for Future Organisms to Fold

Ha ha, and there I was reading of 9GB models being run at one project. Don't know of a GPU that has this, or the bandwidth to exchange all that data back to RAM and storage, but those with 32GB system ram were commenting that their octo showed jobs being frozen "waiting for memory" when trying to run more than 3 of those [they have not discovered <max_concurrent> yet.] Think multi-threading would be the better solution, to not have devices end up in RAM cram.
[Mar 15, 2013 9:11:27 AM]   Link   Report threatening or abusive post: please login first  Go to top 
Former Member
Cruncher
Joined: May 22, 2018
Post Count: 0
Status: Offline
Reply to this Post  Reply with Quote 
Re: Suggestions for Future Organisms to Fold

Yeah, I looked at the Vina code a bit and found that the current step relied on the results from the previous step.. which is incremental/sequential and best suited for a single thread (If I'm reading that code correctly). The algorthm itself would most likely need to change in order to take advantage of GPU "data parallelism".
[May 8, 2013 1:12:56 PM]   Link   Report threatening or abusive post: please login first  Go to top 
rilian
Veteran Cruncher
Ukraine - we rule!
Joined: Jun 17, 2007
Post Count: 1460
Status: Offline
Project Badges:
Reply to this Post  Reply with Quote 
Re: Suggestions for Future Organisms to Fold

I'm in favor of having research on ageing.

+100500 :)
----------------------------------------
[May 8, 2013 5:33:28 PM]   Link   Report threatening or abusive post: please login first  Go to top 
Falconet
Master Cruncher
Portugal
Joined: Mar 9, 2009
Post Count: 3297
Status: Offline
Project Badges:
Reply to this Post  Reply with Quote 
Re: Suggestions for Future Organisms to Fold

Yeah, I looked at the Vina code a bit and found that the current step relied on the results from the previous step.. which is incremental/sequential and best suited for a single thread (If I'm reading that code correctly). The algorthm itself would most likely need to change in order to take advantage of GPU "data parallelism".



VINA is used in DSFL, SN2S and GFAM. Rosetta is the one used in HPF2
----------------------------------------


- AMD Ryzen 5 1600AF 6C/12T 3.2 GHz - 85W
- AMD Ryzen 5 2500U 4C/8T 2.0 GHz - 28W
- AMD Ryzen 7 7730U 8C/16T 3.0 GHz
[May 8, 2013 5:44:05 PM]   Link   Report threatening or abusive post: please login first  Go to top 
ngmwcg
Cruncher
Joined: Jan 2, 2010
Post Count: 18
Status: Offline
Project Badges:
Reply to this Post  Reply with Quote 
Re: Suggestions for Future Organisms to Fold

dpenfoldbrown I couldn't agree with you more that it is more useful to dedicate limited resources to tasks that can achieve broad benefit rather than targeting specific diseases or issues.

With that said, I want to double down on my suggestions for the Mole Rat and Jelly fish as those should produce broadly interesting and hopefully useful data not only for aging but other considerations as well. I also thinking aging is a pretty broad area to study as it is the root cause or factor in the many if not the majority of health issues.

In general, it is the role of government, big companies, NGO's and big high risk funding to produce tools and data that will ultimately make it easy and inexpensive for startups and small companies to develop biological tests, treatments, drugs, etc... This is what happened in the computing space. Once big money was spent to develop low cost PCs and development software, the web and app movements took off.

Thanks,

-NGM
[May 18, 2013 7:18:39 AM]   Link   Report threatening or abusive post: please login first  Go to top 
Falconet
Master Cruncher
Portugal
Joined: Mar 9, 2009
Post Count: 3297
Status: Offline
Project Badges:
Reply to this Post  Reply with Quote 
Re: Suggestions for Future Organisms to Fold

dpenfoldbrown I couldn't agree with you more that it is more useful to dedicate limited resources to tasks that can achieve broad benefit rather than targeting specific diseases or issues.

With that said, I want to double down on my suggestions for the Mole Rat and Jelly fish as those should produce broadly interesting and hopefully useful data not only for aging but other considerations as well. I also thinking aging is a pretty broad area to study as it is the root cause or factor in the many if not the majority of health issues.

In general, it is the role of government, big companies, NGO's and big high risk funding to produce tools and data that will ultimately make it easy and inexpensive for startups and small companies to develop biological tests, treatments, drugs, etc... This is what happened in the computing space. Once big money was spent to develop low cost PCs and development software, the web and app movements took off.

Thanks,

-NGM



The project is ending soon...
----------------------------------------


- AMD Ryzen 5 1600AF 6C/12T 3.2 GHz - 85W
- AMD Ryzen 5 2500U 4C/8T 2.0 GHz - 28W
- AMD Ryzen 7 7730U 8C/16T 3.0 GHz
[May 18, 2013 10:21:13 AM]   Link   Report threatening or abusive post: please login first  Go to top 
Posts: 27   Pages: 3   [ Previous Page | 1 2 3 ]
[ Jump to Last Post ]
Post new Thread