Reply With QuoteI managed to get the Free-DC Distributed Folding homepage online.
Yea!!! We have our own Forum!
Project Homepage
Free-DC Team
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I managed to get the Free-DC Distributed Folding homepage online.
So much good news for one day...glad to have such workoholics around
rm -Rf /
ironbits
Use the right tool for the right job!
how cool is this?
not only does the computer guy post in team forums, but so does the head scientist guy!
this is ripped from the arstechnica DC forum
these guys are better at PR than those stanford dudesFrequency curves...
Hi folks,
This is Christopher Hogue, I'm the scientist in charge of the Distributed Folding project. I sensed a cry for help here...
quote:
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Originally posted by FoBoT:
Quote: "Originally posted by hanser:
I just took a look at that brief benchmark page, and perhaps I'm an idiot, but what exactly is the Y axis measuring? What is "frequency"?"
i don't get it either, perhaps a smart person could splain it to us
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No you aren't an idiot! Good question - benchmarks for systems that take indeterminate amounts of time are hard to show accurately. Everybody wants a simple "number" but the shape of the profiles can be revealing...
So then, the FOLDTRAJ benchmark results are the ones in the figures posted at:
http://bioinfo.mshri.on.ca/yac/speed.html
We did these benchmarks before we bought our cluster.
These are time vs frequency plots for 5000 samples of a protein called myoglobin. The frequency on the Y axis is how often a protien (as a fraction of 1.0) a protein is finished in a particular time (x axis) on each system. A better system has the frequency peak nearer to the left, and a narrower profile. Tall and thin if you like ...
If you look at the bold curve for the 500 MHz Alpha 21264, you can see that the peak is at about 1.3 seconds on the time x-axis and about 0.53 on the frequency y-axis.
This means that it takes 1.3 seconds to finish a structure, for about 53% of the 5000 attempted structures. If you look at where this curve hits the baseline, near 8-10 seconds, this means that a very small fraction of proteins completes in a longer time, but not too unreasonable.
Each protein made takes a slightly different amount of time owing to backtracking, and atomic collisions that ocurr at random. Backtracking usually causes disk I/O to occur, and unusual response times for this will cause the peak to have a broad tail to the right, like the SGI - Irix MIPS R5000 200MHz system. Various combinations of disk speed, cache size and OS buffering settings will cause this tail to broaden or narrow. The integral (area under the curves) is the exactly the same for each curve and represents the sample size.
Proteins that take a long time to complete often are quite compact - and that's a good thing for our science.
If you are interested in generating these curves for your system let us know. It is possible that we can add an option to dump this frequency data out for you from the text client in a form that you can load into a spreadsheet. E-mail Howard at trades@mshri.on.ca and let him know...
Finally, thanks for all your help! Looks like we will hit 100 million structures this weekend.
Christopher Hogue
Senior Scientist, Samuel Lunenfeld Research Institute.
P.S. I'm in Tokyo attending a scientific meeting. Do you think it coincidence that the maid left a folded paper crane on my pillow?
Use the right tool for the right job!
Dang FoBoT ! Thanks for the information.
I have finished fleshing out the homepage. (It's never really done is it?)
Let me know if something needs to be fixed, added or removed please.
I think you should add (or persuade Dyy[Tab] to add) DisFold team into Current Team Rank or whatever is that called - especially because we're number one!
rm -Rf /
Good point Supp!
It has been done
Thanks for the suggestions and bug spray Supp!
I have forwarded it to the STATS God.
I have created a bplog database and have it all ready to go. Now we will have to wait on the my Master to get some time to 'skin' it so it looks perfect before implementing it.
Then I can add some folks that want to post news and information for the Free-DC Distributed Folding Team
I heard ** you need somebody to look after this project and report news on regular basis.
If you're hiring then I'm your man.
rm -Rf /
That's a deal Supp! Now all I need to do is catch my Master's attention
Thanks!
Try burning some incense in front of computerOriginally posted by IronBits
...Now all I need to do is catch my Master's attention
Thanks!
rm -Rf /
For those who are interested in this project:
New version has been launched this Monday (02/18)
rm -Rf /
i'm not so sure RAM has much to do with speed on this
i am currently running a benchmark on a Celeron 300Mhz with only 32MB of RAM (66Mhz)
it just passed 500 structures at the 36 minute mark, so if a 300Mhz/32MB boxen (running RedHat 7.1) can do 1000 structures in 1.2 hours, you compare this to some of the other benchmarks posted, say the 1:05 entry for a PII-350Mhz with 256MB also running linux, it would seem the cpu speed is the main linearity point
i think it is confirmed that linux boxen beat winders pc's , at least with the current software, since the development is all done on linux, i guess that isn't a surprise
Use the right tool for the right job!
Let's start three different teams and then have a poll to pick the one we want.
While all the time kicking Ars!!!!!!
Colin Thompson
hehe, you funny T man
Use the right tool for the right job!
Hmm... It seems that I'm going to need another box to stay in the pack with the leaders. Good thing I've got a case coming to put this 1.2 Tbird in
um, good question, i;m a little disorganized at the moment, i have g@h and df and RC5 strewn about here , i'll try to take a countOriginally posted by Darkness Productions
FoBoT??? WTF do you have on this project, GHz-wise? Just curious.
in the mean time
w00t!!!!! for darkness!!! you are #3 in lowest structure!!
a 3.78, very nice!
in the long run, that means more than the number of useless carp/structures a person has run
i look at it kinda like the lottery, anybody can win!
Use the right tool for the right job!
ok, looks like about 8.3Ghz right now
but last weekend, i had about 8Ghz more doing df, i moved that to g@h, and about 1.8Ghz is doing f@h
i just got ten new boxen in today, 5 1Ghz p3's and 5 1.1Ghz celery's
but i was only supposed to get the celeries, so i'll see how many days it takes my boss/ the supply department to notice the extra p3's they accidently sent me
ps. all but a couple of Ghz of this is at work, in a test lab, i have 3 pc at home doing df right now, 750 duron, 1Ghz duron and celery 733
Use the right tool for the right job!
Jebus Christus man!!!! All but 1.5GHz of my production is at home... So about 5GHz. And thanks. I just noticed myself that I had something that low
I added my three accounts to the Free-DC team tonight.
Maybe I can get this embarassing user name changed now...
Angus (not@ars anymore)
Careful what you ask for around here
Welcome aboard !
Welcome to the team Angus... Just one more person that FoBoT and myself have to look out for.
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