Posts by bruce boytler

1) Message boards : Rosetta@home Science : will the data be used for animal testing? (Message 65442)
Posted 2 Mar 2010 by Profile bruce boytler
if i run rosetta at home,will the resulting data be used in experiments that use animals?

the reason i ask is that i don't want to be reponsible for the deaths of thousands of innocent animals.

The rosseta@home project is all about computational biochemistry. They are trying to predict a protien structure from a gene sequence. Its all math and computer science. There are no animals involved. That I have ever seen over the years.
2) Message boards : Number crunching : System Restarts Win 7 Intel i7 (Message 65156)
Posted 30 Jan 2010 by Profile bruce boytler
My core I7 with 3gigs of ram and up to date vista. Running 24/7 365 days a year. Did 920,000 points from jan 26 2009 through december 5 2009.
Rosseta was the only project on the computer the entire time.

Hi bruce:)
I just bought all parts today for my new built: cpu=i7 860, mb=msi p55-gd65 intel 1156, ram=kingston 4gb 1600mhz dual hyperx, hsf=zalman cnps10x qiet cpu cooler, psu=coolmax 700watx and video card= oem radeon 4650 ati ddr2 1gb.
This will keep me busy assembling it tommorow. I am very excited and nervous.
This for my Rosetta@home wu. Question: Do you think this will run as an 8 core processor while running rosetta? I hope it will, because I read from anandtech review that it can run as a virtual 8 core machine. I will reuse my old dual core box, dvd-rw and old hdds.Cost me $838. I am crossing my fingers. I am not that savvy. I always rely on forum information.
Need your comment please. Thanks a lot, joseps.

Both Windows Vista and BOINC see the I7 as an 8 core machine. BOINC will run 8 R@H Work Units at a time and generally completes in 3.5 hours. I dont overclock and I use an I7 920.

The only things I did were to make sure BOINC was set to run 8 processors and that Hyperthreading was turned on. I also run only rossetta at home on this computer.
3) Message boards : Rosetta@home Science : Q about the native shape (Message 64931)
Posted 12 Jan 2010 by Profile bruce boytler
The better a program can predict a protien shape. The better it will be at finding say a molecule that can dock to a cancer protien thus keeping the protien from growing.

In other words, it will design better drugs.
4) Message boards : Cafe Rosetta : Happy Christmas!!! (Message 64897)
Posted 10 Jan 2010 by Profile bruce boytler
Looks like your christmas was very merry!
5) Message boards : Number crunching : System Restarts Win 7 Intel i7 (Message 64896)
Posted 10 Jan 2010 by Profile bruce boytler
My core I7 with 3gigs of ram and up to date vista. Running 24/7 365 days a year. Did 920,000 points from jan 26 2009 through december 5 2009.
Rosseta was the only project on the computer the entire time.
6) Message boards : Number crunching : When will cuda support be ready ? (Message 64833)
Posted 6 Jan 2010 by Profile bruce boytler
AQUA@HOME had a GPU client and they found it very limited and not worth the effort. The CPU actually turned out to do the work many times faster.

And the guy at DWAVE was a professional programer.
7) Message boards : Number crunching : new version of BOINC + CUDA support (Message 63815)
Posted 25 Oct 2009 by Profile bruce boytler
The main problem with GPU (and this was stated by the rosetta@home people) is that the rosetta app would run to slow on the GPU.
I was personaly intriguged by this so I looked into it. The only thing I can see is that GPU is really bad at Monte Carlo simulations. This is due to its lack of branching ability.
8) Message boards : Number crunching : Finally, I made it to the 1 mil club (Message 63015)
Posted 22 Aug 2009 by Profile bruce boytler
Welcome to the club! Hope to see many more join. We need to really get the Flops up as high as possible!!!!!!!!!!!!!! With that comes the folding.
9) Message boards : Number crunching : CPU usage (Message 62077)
Posted 3 Jul 2009 by Profile bruce boytler
This is concerning Rosetta on my laptop, running Vista. When any other projects are running, my CPU usage is in the 95-100% range. Recently, when Rosetta is running the CPU usage drops dramatically - yesterday it was down to 45-50%, and today it's under 10%. All my preferences are set to use 100% of processors. Any ideas why Rosetta is only using 10% instead of 100%?

Thanks in advance...

This is an interesting problem that I have experianced from time to time on my
I7 windows vista machine running 6.6.36 BOINC. This machine has 3 gigs of memory and runs 8 rossetta mini 1.80 workunits at a time. Yes, it is running hyperthreaded.

It will for what appears to be no reason at all throttle down the CPU from 90 to 50 percent usage. Acording to Task Manager. Causing the exact same problem you have on 4 of 8 threads.
This machine will normally do 8 workunits in 3 hours. When this problem occurs 4 wu take anywhere fron 12 to 50 hours.

What I have to do to correct this problem is to go to the ADVANCED dropdown menu in boinc manager. Click on Run CPU Benchmarks.

Run CPU Benchmarks shuts down the wu computations, runs the benchmarks then restarts the 8 workunits at 100 percent cpu usage according to TASK Manager.
The eight wu's then complete in 3 hours.

I have another I7 which just started running rosseta having this problem on a daily basis. This machine is the exact same setup as the older machine except it has 6 gigs of ddr3 memory.
10) Message boards : Cafe Rosetta : Personal Milestones (Message 61875)
Posted 21 Jun 2009 by Profile bruce boytler
Guess I passed the million point mark. Just hope that the baker lab was able to benefit from any science the 1000,000 points might have produced.
11) Message boards : Number crunching : Fetching no GPU work (Message 61782)
Posted 16 Jun 2009 by Profile bruce boytler
Will 6.6.36 BOINC manager enable a CUDA enabled device to work on Rosetta @Home.
I hope so. Because the head of BOINC came out in a statement a while back (6 months ago) that to reach an exoflop would require GPU type devices. I dont think Rosseta will ever get enough computing power untill an exoflop is reached.
12) Message boards : Number crunching : Play Station 3 for rosetta@home? (Message 60593)
Posted 10 Apr 2009 by Profile bruce boytler
Tell me who tried computing with CELL processor which is in Play Station 3. Is it tested by you or not. Some experiences on this way?
I want fix PS3 to computer with normal linux. I'm interested how it will work.
I'm looking forward your answer.

I currently have a PS3 doing molecular dynamics simulations. I have been doing this for Stanford University Pande Group. They have a DEV Kit. You can contact them through the Folding@Home website.
13) Message boards : Number crunching : difference between robetta and crunchers (Message 59944)
Posted 3 Mar 2009 by Profile bruce boytler
I have one more question, that I asked on another thread unreplied:
how can you optimize Rosetta for supercomputers on BOINC, which by definition doesn't permit "p2p" communications? In other words, on a supercomputer you can define "interactions" between software threads running on different processors, on your BOINC client you can't. I'm sure these "interactions" could help really a lot your algoritm, but you're unable to test it on BOINC platform unless using local SMP client. Am I right? Are you planning on distributing a SMP client? Or it isn't so important at this point of the development?


Cenit....You are trying to compare apples to oranges with your question.
Using SMP in a multi-core computer would indeed solve a workunit very fast. Much faster than applying a single core to a workunit. SMP is actually the prefered method of crunching a workunit at folding@home. It is thier belif that using muliple cores on just one workunit is more efficent than applying say 4 workunits to 4 cores.

BOINC does not use SMP. BOINC is the middleware that runs rosseta@home. It will apply say the 4 cores to 4 workunits. Rosseta@home has nothing to do with how the proccessors crunch the workunit.
14) Message boards : Rosetta@home Science : R@H in Nature (Message 47828)
Posted 18 Oct 2007 by Profile bruce boytler
How does this form of Rosetta relate to what Rosetta@home is doing?
15) Message boards : Cafe Rosetta : Last one to post here wins! #2 (Message 47635)
Posted 12 Oct 2007 by Profile bruce boytler
yada, yada, yada,...................
16) Message boards : Number crunching : How to get a million credits? (Message 44882)
Posted 11 Aug 2007 by Profile bruce boytler
Run a Athlon dual 3800+ an honest 24/7 for nearly two years and you will be close to 400,000 if that helps. Mine has never been turned off.
17) Message boards : Rosetta@home Science : Help me explain the science behind Rosetta@home! (Message 42311)
Posted 19 Jun 2007 by Profile bruce boytler
First you should explain things on a 8th or 9th Grade level. The jargon is really irritating. Most of the participants are not Biochemists. So the minute jargon is used most of your audience gets quickly lost.

If this is even possible: Try to explain in a step by step fashion what rosseta is really doing or trying to do. I have been doing this project for 2 years and all this time I thought I was helping develope a program to crack the folding problem (whatever that is). Now I am not sure what is going on.

Most people what to know about PROGRESS. How much better or different is rosseta after 2 years of distributed computing. This would explain alot to many folks.
18) Message boards : Rosetta@home Science : 10 reasons I crunch R@H and you should too (Message 41630)
Posted 30 May 2007 by Profile bruce boytler
My 10 reasons for crunching Rosetta:

1: My belief that major Breakthroughs come through long hard years in the trenches developing programs like Rosetta.

2: My Brother is a Type one Diabetic and just recenctly contracted a Staff infection from a Dialysis Machine and lost the use of his legs plus a four month stay in the Hosipital.

3: My father died of Cancer. When he was in the last stages of the disease all they had to offer was some Hormone, that did not work.

4: I like to see a computer actually doing what a computer was intended to do.

5: The Graphics are Cool.

6: I would like to see the Sequenced Human Genome Morph into an actual Human Protome. So Some real good could start coming from such a huge effort.

7: The Baker Lab needs the help.

8: I like to gain points to better my world BOINC standing.

9: There is no intelligent life beyond Earth so SETI@Home was no longer Cool.

10: Because.....

19) Message boards : Number crunching : Peakstream launches GPGPU for Windows (Message 40103)
Posted 30 Apr 2007 by Profile bruce boytler
Hi All,

Was this an interesting thread! First off the CPU although slow is extremely flexible and accurate, makes few mistakes. So in DC computing it can crunch anything.

The CELLBE is of course very fast compared to the PC CPU. But is less flexible in what it can do. AT F@H the cell can only do explicit solvation calculations whereas the PCCPU can do both explicit and implicit. This is just one example.

The GPU computing is even less flexible than the cell. The GPU runs extremely fast but makes alot of mistakes. The speed is so quick that even with correcting mistakes it is way faster than cellbe. The main problem is that it can only be used for a narrow range of calculation.

The NVIDA GPU was abandoneed at F@H because it does not have the correct shader archecture to render a fold any bettter than a CPU, as does most other GPU's. At this point ATI 19xx series with its 48 shaders has the ability to run a narrow range of folding workunits and very fast.

But what the ATI can do is very, very exciting and really pushing the science forward.

I tried to keep this in laymans terms tough topic to comment on. Hope this helps with any one contemplating using a GPU to crunch.
20) Message boards : Rosetta@home Science : Boinc/Rosetta on the Xbox 360? (Message 39984)
Posted 28 Apr 2007 by Profile bruce boytler
Hello All,

Thought I might add a slightly different spin on this topic.

I have been crunching on folding@home for a few weeks now with a PLAYSTATION 3.
The feeling I am getting is that SONY seems commited to distributed (public) computing and that the folding@home is just going to be one project.

They appear to be wanting to set up something along the line of a World Community Grid. So maybe Baker Lab should look into using the PS 3 network also.

As an owner of both a PS3 and a XBOX360. I can tell you with a high degree of certainty, that the PS3 blows the XBOX360 right out of the water as far as raw computational ability. Cell uses seven cores for heavy number crunching and one POWERPC 64 bit core for housekeeping.

Also PS3 has no hardware issues (as of yet been running 24/7 for 3 weeks now) were as my xbox360 has had issues (mainly) with heat and mainly from Gears of War.

Hope this helps, may ask MR Hey? to find a xbox builder or design with a more reliable hardware config. Really is frustrating to have the box taking a dump right in the middle of Gears.

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