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World Community Grid Forums
Category: Completed Research
Forum: Human Proteome Folding
Thread: Is there a change in HPF ? |
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Thread Status: Active Total posts in this thread: 8
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
My WU need much more time to finish as usual. One of my computers is at 65 % and is crunching since 11 hours. Normaly a WU is finished after 8 hours.
Best wishes Marco |
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retsof
Former Community Advisor USA Joined: Jul 31, 2005 Post Count: 6824 Status: Offline Project Badges: 
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Comparing anything depends on the speed of your computer.
----------------------------------------Times for HPF are all over the place. They all do not run in the same amount of time. Yours sounds within reason. A Pentium III/500 here usually takes 4 days per HPF workunit. Sometimes it runs one in 12 hours. Last year a Pentium II/400 here took 13 days to run the longest workunit. Fast AMD computers here can finish a HPF workunit in 2-4 hours. The long running workunit will receive more points and more run time credit when it is sent in.
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----------------------------------------Work+GPU i7 8700 12threads School i7 4770 8threads Default+GPU Ryzen 7 3700X 16threads Ryzen 7 3800X 16 threads Ryzen 9 3900X 24threads Home i7 3540M 4threads50% [Edit 4 times, last edit by retsof at Jan 5, 2006 4:45:38 PM] |
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Viktors
Former World Community Grid Tech Joined: Sep 20, 2004 Post Count: 653 Status: Offline Project Badges: 
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The work units are not fixed in their run time. They vary somewhat unpredictably based on the difficulty in folding the particular protein. We use a heuristic to get the average work unit run time to be about 10 hours for an average machine. So slower machines will on the average take longer and faster ones less time. But even so, the times can vary considerably for individual work units.
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retsof
Former Community Advisor USA Joined: Jul 31, 2005 Post Count: 6824 Status: Offline Project Badges:
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I am seeing some extremely long run times. Here is the last one that came in early today from my slowest machine:
----------------------------------------Pentium III/500 MHz, processor score 50 02/14/2006 0:008:08:43:21 3,303 1 8 days, 8 hours, 43 minutes, 21 seconds (over 200 hours) 3,303 points 1 result The next workunit is 3% complete after 10 hours. It has been rebooted a few times this week....the processing is normal and other things rarely run on it.
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----------------------------------------Work+GPU i7 8700 12threads School i7 4770 8threads Default+GPU Ryzen 7 3700X 16threads Ryzen 7 3800X 16 threads Ryzen 9 3900X 24threads Home i7 3540M 4threads50% [Edit 2 times, last edit by retsof at Feb 14, 2006 2:58:47 PM] |
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retsof
Former Community Advisor USA Joined: Jul 31, 2005 Post Count: 6824 Status: Offline Project Badges:
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Is the timeout barrier still set to two weeks?
----------------------------------------My UDMonitor on that machine has 4 cache slots. Most previous workunits ran from 1 day to 4 days, but the current batch seems to be a nasty plant. Still Aradopsis?
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----------------------------------------Work+GPU i7 8700 12threads School i7 4770 8threads Default+GPU Ryzen 7 3700X 16threads Ryzen 7 3800X 16 threads Ryzen 9 3900X 24threads Home i7 3540M 4threads50% [Edit 3 times, last edit by retsof at Feb 14, 2006 2:54:05 PM] |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
The latest status update from Dr. Bonneau at http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=5626 says that we have crunched 90 genomes! Back when he was talking about Arabidopsis, he said we had crunched 80 genomes.
The recent update says that we are crunching through Swiss-Prot. It is a database of annotated proteins set up back in 1986 (in Zurich then, now I believe it is hosted in the United Kingdom) when scientists had to do proteins one at a time rather than a genome at a time. So these are proteins somebody considered important. If our predicted structure for one of these proteins is very similar to anything we have crunched in our 90 genomes, then the annotated information probably applies to our protein as well. It's one way to avoid reinventing the wheel! mycrofth |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Hi mycrofth,
I just would like to ask for clarification on your response. Do you mean that by crunching the Swiss-Prot database we are actually able to identify the role of the proteins we have crunched earlier?. Or are we just checking for the accuracy of our predictions. Thanks a lot. |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Hello thom217,
The curators of the Swiss-Prot database have included all the information that anyone has been able to develop on their proteins. But a lot of them do not have structures determined for them. When we predict a structure (which we hope is nearly correct) then that means that proteins with similar structures probably behave much the same way. It's just another way to try to extend our knowledge. Similar proteins (probably) behave in similar ways. |
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