Posts by Ethan

1) Message boards : Rosetta@home Science : Rosetta@Home Myspace Group (Message 48249) Posted 1 Nov 2007 by Ethan Post: You're fine, the image is publicly available via http://boinc.bakerlab.org/rosetta/rah_misc.php Cheers, -Ethan
2) Message boards : Rosetta@home Science : R@H in Nature (Message 47795) Posted 16 Oct 2007 by Ethan Post: http://www.nature.com/news/2007/071016/full/449765a.html
3) Message boards : Number crunching : Using University Computers (Message 46645) Posted 19 Sep 2007 by Ethan Post: It sounds like the sysadmin was using his imaging software as an excuse to not have to deal with installing Boinc (which I can understand, it's tough managing a lot of computers and installing another program can be a pain). Generally though, software like deepfreeze and I'm guessing Rdist (haven't used it) can be configured to ignore certain directories.
4) Message boards : Number crunching : Time for a new PC (Message 46135) Posted 13 Sep 2007 by Ethan Post: I'm liking Dell's new Vostro PCs. I've bought several for our department and they're working well. It looks like the really cheap deal is gone (core 2 1.6ghz, 1gb, 120, 19" lcd for 379). They now have a core 2 1.8ghz, 1gb, 160, 19" lcd for 499. Considering you can probably get 150 to 200 on ebay for the monitor (if you don't need it), you're looking at a pretty cheap machine that comes with a 1 year in home warranty.
5) Message boards : Number crunching : Using University Computers (Message 45946) Posted 10 Sep 2007 by Ethan Post: Very true about the other Uni project thing. You could run all the other Uni computers as a single user (U of X) and that user would be recognized in journal articles if anything significant was found on those machines. If you got high enough in the rankings you could also make statements like 'U of X was one of the largest contributors to a Gates Foundation and Howard Hugues project researching bad disease A and B'. Finally, while R@H is part of the UW, Rosetta is used by research groups around the world (for free if academic). Part of what R@H does is improve the Rosetta code, so helping this project could very well impact scientists at your university.
6) Message boards : Number crunching : Using University Computers (Message 45943) Posted 10 Sep 2007 by Ethan Post: Perhaps this will help. The central computing department on campus operates many thousands of machines and recently deployed R@H. I've found it's easier to convice folks to copy what others are doing rather than starting from scratch. http://www.washington.edu/nebula/boinc.html
7) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (3) (Message 45850) Posted 9 Sep 2007 by Ethan Post: Here's a direct link to the journal article mentioned in DB's latest journal post: http://www.pnas.org/cgi/reprint/0703836104v1.pdf
8) Message boards : Number crunching : Could GPU's mean the end of DC as we know it? (Message 42625) Posted 25 Jun 2007 by Ethan Post: I doubt additional CPU power will go unused anytime soon :) Current calculations are designed to be as 'simple' as possible in order to run in a decent amount of time. In many cases assumptions have to be made or the calculation would be millions or billions of times larger. An example from my college days. . We simulated the interactions between stars researching galaxy formation. Since each star gravitationally interacted with every other star, there were ~N^2 calculations where N is the number of stars in the simulation. I think we were able to get away with several thousand and get results in a couple days, but real galaxies have hundreds of billions of stars (100,000,000 calculations per unit of time vs ~10^20). What your time slices are have an impact as well, do you calculate forces on objects over a minute, day, year, century at a time? When galaxies take many millions of years to form the time slice is yet another simplification that needs to be made. The same is true of things that happen very quickly only in reverse. With the exception of looking for primes or star dust in gel, I can't think of any other DC projects that work with without making trade-offs on the accuracy of the results in order to get results in a reasonable amount of time. That’s why the help of everyone participating in R@H is so useful, it allows the project to get better results in a shorter period of time.
9) Message boards : Number crunching : PENDING work units (Message 42087) Posted 12 Jun 2007 by Ethan Post: Thanks to those who posted here who first noticed it!
10) Message boards : Number crunching : Disabel the +/- rating on the boards. (Message 42050) Posted 11 Jun 2007 by Ethan Post: I had noticed this as well. If you go to your account from the main R@H page, then pick 'message board settings', you can change the number of negative ratings it takes for posts to be filtered. For some reason mine was set at -1 so I had a lot of posts hidden. . but it hasn't been a problem since I changed it to -10.
11) Message boards : Number crunching : Automated installer (Message 41917) Posted 7 Jun 2007 by Ethan Post: is it wise to run under the system account, or should i set it to run in a limited user sandbox account? If so, anyone know what permissions BOINC needs and whether I can set these from a batch file? We ran it as a service as the local admin. . watch out if you schedule that pw change, you have to remember to change the log on credentials for the service :)
12) Message boards : Number crunching : Automated installer (Message 41866) Posted 5 Jun 2007 by Ethan Post: Howdy, Here's how we deploy the client to our department's computers: http://www.thelazyslug.com/boinc.htm Post here if you have any problems.
13) Message boards : Number crunching : why isnt there any "pending credit" at all? (Message 40928) Posted 14 May 2007 by Ethan Post: It's very easy for the project to tell if a result is legitimate, so there's no reason for a quorum.
14) Message boards : Number crunching : NO WORK (Message 40831) Posted 12 May 2007 by Ethan Post: The server status page has shown the number of WU's available going up the last two updates: http://boinc.bakerlab.org/rah_status.php
15) Message boards : Number crunching : NO WORK (Message 40826) Posted 12 May 2007 by Ethan Post: Thanks for the heads up! As of this post it's 0800 in Seattle, so it may be a couple hours to take care of it.
16) Message boards : Number crunching : Why do I receive much less credit than my client claims? (Message 40661) Posted 10 May 2007 by Ethan Post: 2 computers with the same specifications should take the same amount of time to perform a certain number of calculations and therefore should claim and receive the same amount of credits. This it true for ALL projects that offer clients for different platforms, except for Rosetta@Home. In all other projects the differences in credits/time are in a range of ±10% between comparable computers, even for different architectures and operating systems. However, in Rosetta@Home the differences are bigger than 100% between Windows-based systems and MacOS X machines with PowerPC processors Morning Martin, I don't think this is quite right, architecture and OS differences do play a big role. A 486 overclocked to 2ghz isn't going to be within 10% of a 2ghz Core 2 (neglect the whole 486 melting soon after being upped to 2ghz). Similarly, PPC cpus are an older design. . new chips have more processing units within each core, faster access to memory, better branch prediction, etc. Similar differences exist between operating systems (although the differences aren't as significant).
17) Message boards : Number crunching : Why do I receive much less credit than my client claims? (Message 40628) Posted 10 May 2007 by Ethan Post: Here's info I sent out answering the same question a couple weeks ago: There are several calculations going on to determine 'credit'. Boinc itself has a benchmark that determines how many calculations a given computer can do per second. When you first install Boinc it will benchmark your system doing a bunch of integer adds (like 1+1) and floating point divides (1.324 / 6.22222). . . very simple calculations that don't depend on the amount of memory or disk speed of your computer. Boinc calculates the number of credits you 'claim' based on these benchmarks. If (and I'm making numbers up since I don't know the exact equation) a computer that has an integer benchmark of 1000 works for an hour, Boinc would claim 10 credits. A computer that had a benchmark of 2000 would claim 20 credits for the same hour since Boinc has determined it does twice the amount of calculations. The kink in the Boinc credit system is that it doesn't accurately calculate how fast a given computer is at running the Rosetta science application (which is huge compared to simple addition or division). The Boinc benchmark doesn't accurately reflect how much data users are actually sending back. The project team decided to create a new benchmark that would grant credits based on how much data users actually returned to the project. The easiest way to do this was to start with the Boinc credit 'claim'. R@H runs many different work units at once, you can see this when you look at the work units in the Boinc Manager. For each, a running average of the Boinc credit claim is kept per simulation (a work unit will do as many simulations as it can within the timeframe you specified). This average is used to determine how many credits a user gets at the time they return their results. The credits given are 'credit granted', what Boinc claims is 'credit claimed'. The per-simulation credit value is allowed to change as results come in to more accurately determine the number of credits that should be granted. This change is relatively small over time however, the 10th person to return a simulation is going to get a value close to the 10,000th. Now we get rid of the Boinc benchmark, the only thing that matters is how fast a computer can complete a simulation. . . it will get the same number of credits regardless of how long it takes. With all other things being equal, a 2ghz machine will take twice as long (and get 1/2 the credits/hour) as a 4ghz machine (same cpu, just changing frequency) Clock speed isn't the only thing that determines how fast a given calculation takes. Lack of RAM will obviously slow things down, as will a slower or fragmented hard drive. Architecture differences also come into play (the amount of cache a cpu has for example). In the end, the amount of credits you receive is the sum of all these variables. If your machine is always getting less than the 'credit claimed', it's because of the Boinc benchmark not taking the type of work Rosetta is doing into account for your system.
18) Message boards : Rosetta@home Science : Can I predict the 3D structure of my own protein sequence (Message 40166) Posted 1 May 2007 by Ethan Post: Certian types of folks can get a copy of Rosetta. Here's a link to more information: http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/Rosetta/
19) Message boards : Number crunching : TFlops (Message 39897) Posted 26 Apr 2007 by Ethan Post: Good news about R@H potentially being on the xbox 360 http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1262&nowrap=true#39896
20) Message boards : Number crunching : Account deletion - Not possible, so... read this (Message 39580) Posted 18 Apr 2007 by Ethan Post: We're evaluating what it would take to delete users from the system (generally if people decide to stop participating they just stop returning results). What are the concerns that led to these requests? Thanks!

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