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retsof
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Re: Length of this project

that's true. Normally the software will only run on one core. There may be some special treatment with multiple operating systems or multiple users on an X2 system, but it are not for the timid.

I bought an AMD64 4000+ single core machine to tear up the workunits. It's 2.4 GHz and the time is comparable to the Pentium 4 3.2 GHz. I'm doing about 4-5 workunits/day, somewhat less than the number of Rosettas that I did before.
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[Edit 2 times, last edit by retsof at Nov 24, 2005 11:45:39 PM]
[Nov 24, 2005 11:41:37 PM]   Link   Report threatening or abusive post: please login first  Go to top 
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Re: Length of this project

whocrazy,

If you run Ubuntu Linux, kernel linux-image-amd64-k8-smp version 2.6.12.16.1, that will run both cores. That is the SMP kernel and will spawn 2 instances of rosetta. One for each core. Just keep your eye out for the SMP package. The good people who support the WCG Linux client were thoughful enough to include SMP! If you are running Windows, someone else will have to help you.

I'm sure there are other distributions of Linux that will support SMP but Ubuntu is the only one I know off the top of my head.


dreplogle
[Nov 25, 2005 12:55:06 AM]   Link   Report threatening or abusive post: please login first  Go to top 
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Re: Length of this project

So, if I were to buy a amd 939 X2 3800
put windows xp sp2 on it, and run the fah project, How long exactly would each work unit take?
Remember, on my p4 3.2ghz machine, it takes roughly 5hr 37 min
[Nov 25, 2005 2:36:03 AM]   Link   Report threatening or abusive post: please login first  Go to top 
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Re: Length of this project

Hello whocrazy,
At this stage ithat is indeterminate. We still have not seen AutoDock run on a Linux compile and associated math libraries. And there are likely to be some version updates which might change the memory footprint and perhaps the runtime.

For that matter, AutoDock 4.0 is getting its first big workout on this project. Looking over the results, Dr. Morris might make some changes. It's in the nature of research that everything is subject to change to follow up on the results being discovered.

mycrofth
[Nov 25, 2005 3:46:56 AM]   Link   Report threatening or abusive post: please login first  Go to top 
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Re: Length of this project

it would take around 1oo minutes, amd rules:)
[Nov 25, 2005 3:52:50 AM]   Link   Report threatening or abusive post: please login first  Go to top 
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Re: Length of this project

ah, so it does work.. Thanks... ps: is these 100 minute work units you've seen running under windows xp sp2 or linux?
I dont use linux, only xp sp2. Still trying to clarify and get a straight answer on this.
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Re: Length of this project

Hello whocrazy,
I think that mariduru was being facetious. I was just looking over a comparison benchmark test comparing Intel's 64 bit code against that of the Athlon 64 earlier today. AMD looks pretty good, but I could not think of any rule of thumb that would have let me predict all of the differences.

So with that understood, I'll try to come up with a ballpark figure. AMD rates their chip at 3800 compared against an Intel 3.2 Ghz chip (3200). So the difference is 3800 - 3200 = 600. Call it a 1/6 difference. If Intel runs a work unit in 5 hours and 37 minutes (337 minutes) then a core of the AMD chip should run the job in [337/6 is about 56 so. . .] 337 - 56 = 281 minutes. So with 2 cores, each running a BOINC Windows work unit, I will guess at 140 minutes so overall throughput is one work unit per 2 hours and 20 minutes rather than 5 hours and 37 minutes.

This probably overstates the AMD advantage a little. But it is reasonable to assume that you can cut 3 hours off the job (remember that I am averaging throughput for 2 cores here). Just remember to double up on memory. (1 GB minimum)

mycrofth
[Nov 26, 2005 1:06:16 AM]   Link   Report threatening or abusive post: please login first  Go to top 
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Re: Length of this project

I'm not using boinc to run the fah project, I'm using the world comunity grid agent.
[Nov 26, 2005 3:52:05 AM]   Link   Report threatening or abusive post: please login first  Go to top 
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Re: Length of this project

Good choice, whocrazy.

Right now we are running UD.exe on Windows, a single-threaded distributed computer agent which is well tested and reliable. We are implementing BOINC for Linux. It is a new distributed computer program that is rapidly changing (and has numerous bugs). But in time we will be running it on Windows as well for all our projects. Right now we have some people running the Human Proteome Folding Project on Windows on BOINC. BOINC can take advantage of multi-processor or multi-core systems.

My guess is that in a few months everyone with multiple processors will switch over to BOINC to take full advantage of their computer power. But right now, running BOINC can be a bit of an adventure. Like my father driving Model A Fords down red clay roads before the highways were paved.

Ummm. . . No, that's a poor analogy. BOINC is already much more stable than that. It is just that I have been spoiled, so I notice even minor glitches.

Even after years, these are still the early days of distributed computing.
mycrofth
[Nov 26, 2005 7:49:45 AM]   Link   Report threatening or abusive post: please login first  Go to top 
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