Posts by Hoelder1in
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1)
Message boards :
Rosetta@home Science :
DISCUSSION of Rosetta@home Journal (3)
(Message 52035)
Posted 20 Mar 2008 by  Hoelder1in
Post: Here is another link describing the enzyme related work that has just been published in Nature (see David Baker's post in the Rosetta@home journal): Howard Hughes Medical Institute Reserach News (March 20): Building Enzymes from Scratch The article specifically mentions the help from the 190,000 member Rosetta@home community! PS: See also Designer Enzymes created by chemists at UCLA, U.of Washington (UCLA press release) |
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Message boards :
Rosetta@home Science :
DISCUSSION of Rosetta@home Journal (3)
(Message 51903)
Posted 12 Mar 2008 by Hoelder1in
Post: Technology Review article on Baker lab research: Enzymes built from scratch Check out the above Technology Review article discribing the recent successes of the Baker lab with engineering novel enzymes that has just been published in the journal Science (see David Baker's post in the Rosetta@home journal) - in my previous post I had erroneously assumed that this new research would be published in Nature (sorry for the misinformation). |
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3)
Message boards :
Rosetta@home Science :
DISCUSSION of Rosetta@home Journal (3)
(Message 51421)
Posted 16 Feb 2008 by Hoelder1in
Post: Here is a link to the Nature News article discussing the enzyme engineering breakthrough which David Baker mentioned in his recent post in the Rosetta@home Journal (the online version of the actual Nature journal article will only be available by subscription). Also, the publications page on the Baker lab Web site has been updated to include the full(?) list of their 2007 research papers (follow the links to read the abstracts of the journal papers). It is amazing how the Baker lab team manages to produce a string of high profile papers and breakthroughs with the help of our donated Rosetta@home compute cycles. Keep on crunching! -H. :-) |
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Message boards :
Number crunching :
Report problems with Rosetta version 5.36
(Message 30906)
Posted 10 Nov 2006 by Hoelder1in
Post: <core_client_version>5.4.11</core_client_version> 46421301 <core_client_version>5.4.9</core_client_version> <message> Maximum disk usage exceeded </message> <stderr_txt> Graphics are disabled due to configuration... # random seed: 3277006 # cpu_run_time_pref: 28800 SIGSEGV: segmentation violation ...another "disk space exceeded" error and it's the same WU type as the one Conan reported (my first error in ages, btw ;-). |
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Message boards :
Rosetta@home Science :
Interesting results
(Message 30750)
Posted 7 Nov 2006 by Hoelder1in
Post: Clicking though the new results plots and from what can be learned from the WU names I get the impression that a lot of interesting things are going on with the current round of WUs, though this is of course all just guess work. I wonder whether any of this would be suitable for some slightly more detailed explanations, perhaps in David Baker's Rosetta@home journal, than we have been given so far. Another, lets call it a dream, I was having lately would be some kind of 'experts´ corner', somewhere on the website, with more in depth material for those with some background or interest in science to dig their teeth in. I was thinking in terms of something like a repository of powerpoint presentations from internal seminars, students papers/thesis, conference presentations or posters (those that are not already linked in the publications section on the Baker Lab website), etc. And perhaps it would even be useful for the Baker Lab team members to have these things handy on the Web. Also, I understand that some kind of licence agreement is required to get access to the Rosetta source code, but perhaps part of the software documentation could be placed freely on the Web ? Or, another idea, are there perhaps some internal log files to keep track of all those different WUs that could be made available ? I guess it needs to be understood that the Baker Lab team members would not have the time to answer all sorts of specific questions related to this material but I am guessing there must be lots of Rosetta@home participants out there who could learn a lot from this kind of material. Well, I thought I just mention this - of course I am not sure this is really feasible and could be done without investing too much time... -H. ;-) |
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6)
Message boards :
Number crunching :
Report problems with Rosetta version 5.36
(Message 30747)
Posted 7 Nov 2006 by Hoelder1in
Post: Are your team members running with BOINC screensaver enabled?I haven't yet had enough feedback from the team to say for sure whether all of this is a screensaver issue - but it definitely is a possibility (I believe the errors first appeared in version 5.32 which updated the graphics) . Thanks for pointing this out. |
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Message boards :
Number crunching :
Report problems with Rosetta version 5.36
(Message 30676)
Posted 6 Nov 2006 by Hoelder1in
Post: Clicking through my team-mates' computer pages it turned out that a quarter of the computers (6 of 24) are showing errors more or less on a regular basis. Below I linked to the "results for computer" pages with two or more errors. These errors fall into two groups: about half are access violations (exit code 0xc0000005) and the other half are "validate errors" giving the message "Rosetta score is stuck or going too long. Watchdog is ending the run!" While some of the errors occured with version 5.34, it doesn't look like the error rate declined with the most recent app. version 5.36. I included the type of error (AV for access violation and S for "stuck or going too long") and also whether the errors occured in the most recent version with the links: 298712 (AV, S), 287935 (5.36, AV, S), 282932 (5.36, AV), 301240 (5.36, AV), 287942 (AV, S), 289776 (5.36, S) I am a bit concerned that this relatively high error rate will discourage people from crunching. So, I guess it would be good if these problems were being looked into. Thanks, -H. |
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Message boards :
Number crunching :
1000+ new hosts in past two days & question
(Message 29557)
Posted 18 Oct 2006 by Hoelder1in
Post: also, as pointed out, we can't send out many of the design calculations, as they require too much memory (we have to consider all 20 amino acids at all positions in the protein in some cases which involves a lot of precomputation of large interaction tables)I am sure there would be those who would install whatever memory is required to perform those large calculations on their computers... -H. |
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Message boards :
Number crunching :
CPU Upgrade Suggestions Anyone?
(Message 29522)
Posted 17 Oct 2006 by Hoelder1in
Post: I have a socket 939, so I could upgrade to a A64 x2 (dual core) and crunch maybe 2-3 times faster (depending on clock speed), but I figure that I better wait a few months for quad cores to be more affordable and crunch 9-12 times faster... I'll catch up on those few months of slower work quite quickly and have more MIPS/$ that way. Yay for Moore's Law :)I am delighted to hear that. This will be a welcome boost for our team... -H. :-)) |
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10)
Message boards :
Rosetta@home Science :
Energy vs rmsd plots
(Message 28998)
Posted 7 Oct 2006 by Hoelder1in
Post: I think I fixed it. Let me know if anyone is still having this problem. It was an issue with the text data returned from the report server.Yes, it's ok now on firefox - thanks, -H. |
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11)
Message boards :
Rosetta@home Science :
Energy vs rmsd plots
(Message 28991)
Posted 6 Oct 2006 by Hoelder1in
Post: You can now view energy vs rmsd plots for active work units. To view your results, click on the "Results" link under "Returning participants" on the home page. To view results from the top users, hosts, and teams, click on the "Rank" numbers on the respective leader lists. The data gets updated daily.WOW, great - thanks to all who worked on this ! However, there seem to be "%00"s interspersed between all the characters of the BatchID and SubBatchName string and I need to remove them manually for the query to work: http://boinc.bakerlab.org/rosetta/rah_results.php?BatchID=%001%002%005%002%00& SubBatchName=%001%00u%00t%00g%00_%00_%00B%00O%00I%00N%00C%00_%00F%00I%00L%00T%00E%00R %00S%00_%00A%00B%00R%00E%00L%00A%00X%00_%00S%00A%00V%00E%00_%00A%00L%00L%00_%00 O%00U%00T%00_%00f%00r%00a%00g%00s%008%003%00_%00&UserID=2080 EDIT: line breaks added |
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Message boards :
Number crunching :
Math for Farmers
(Message 28849)
Posted 3 Oct 2006 by Hoelder1in
Post: Core2 Duo e6700: 213 watts...just checked the power comsumption of my Core 2 Duo E6700: my watt-meter claims that it uses just 135 Watts (while crunching Rosetta with monitor turned off) - it is certainly not a 'gaming setup' but otherwise fully equipped system (one HD, DVD-Rom, streamer, 'non-gaming' graphics card, 300 W power supply). |
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13)
Message boards :
Rosetta@home Science :
Two U.S. scientists win Nobel for 'gene silencing'
(Message 28845)
Posted 3 Oct 2006 by Hoelder1in
Post: "...a potential road to new treatments for diseases from AIDS to blindness and cancer."...I guess "solving the protein folding problem" would also be worthy of a Nobel prize - and we might one day all have our tiny little share in that prize - at least this is something to dream about (it is late at night over here) - and something I haven't yet seen on any of the "reasons why I crunch for Rosetta" pages. And now lets all imagine DB wearing a tailcoat as he approaches the Swedish King... ok, time to get some more sleep. ;-) |
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Message boards :
Rosetta@home Science :
Quantum Leap in Protein Folding
(Message 28149)
Posted 22 Sep 2006 by Hoelder1in
Post: Here is a link to the full text of a relatively current paper by the same author, titled "Dominant pathways in protein folding", so presumably it is about the same method as the paper in question:I'm curious if the scientists (or anyone else) here have any thoughts about this article: http://arxiv.org/pdf/q-bio/0510045 |
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Message boards :
Number crunching :
credit/hour how much is possible??
(Message 26779)
Posted 14 Sep 2006 by Hoelder1in
Post: Has anyone but me looked at the histogram shape for their nodes ? C2D E6700 @ 2.66 GHz c/h per core (64 eight hour WUs) -------------------------------------------------- 15 ** 16 ***** 17 ***** 18 **** 19 ****** 20 ************ 21 *** 22 ***** 23 **** 24 *********** 25 ***** 26 27 28 * 29 30 * I'd expect the histogram of completion times of individual decoys to be sort of multi-peaked (because some trajectories are terminated early when the algorithm decides that the energy isn't low enough). The credit/hour are averages over many decoys of different WU types, so the shapes of the credit/hour histograms are probably hard to predict... |
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Message boards :
Number crunching :
credit/hour how much is possible??
(Message 26736)
Posted 14 Sep 2006 by Hoelder1in
Post: Core 2 Duo E6700 @ 2.8 GHz: 23.75 c/h per core (47.5 c/h total) - got mine last weekend :-)I turned out the numbers I posted close to the beginning of this thread were somewhat on the high side (due to poor statisitics and my initial enthusiasm when I had the chip for just a couple of days ;-). I now have data from 60 eight hour WUs and the updated numbers should be accurate to about 2%: Core 2 Duo E6700 @ 2.66 GHz: 21.4 c/h per core (42.8 c/h total, 8.0 c/h per core per GHz) I now run it at stock clock speed and the OS is Linux. Oh, and I am still using DDR1 memory (ram:fsb ratio is 2/3), so this may have some negative impact. |
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Message boards :
Number crunching :
Putting a Bell on the Cat
(Message 26213)
Posted 6 Sep 2006 by Hoelder1in
Post: Just found this:So why is it that Germans seem to want to show off their non-existant Latin skills ?? - myself included, mea culpa (I hope at least this is right ;-). |
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18)
Message boards :
Number crunching :
Putting a Bell on the Cat
(Message 26198)
Posted 6 Sep 2006 by Hoelder1in
Post: Hm, just checked the list of countries contributing to Rosetta. There is unfortunately no one from the Vatican - they'd probably be able to help. ;-) Now about "I moderate...", dusting off my Latin dictionary and grammer, it seems "to moderate" is "moderi" in Latin, and "I moderate" would be "moderor" (it is one of those verbs with passive form but active meaning). So my non-expert vote would be "Moderor ergo sum"... ;-)Well, at least get the Latin right. That should be "Moderato ergo sum." Now write 100 times, "Romanes Eunt Domus" :-) |
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Message boards :
Number crunching :
credit/hour how much is possible??
(Message 25580)
Posted 30 Aug 2006 by Hoelder1in
Post: Are you running yours at the Stock Rated Speed or have you Overclocked itIt is only 5 % overclocked (to 2.8 GHz) - the board I am using is not designed for overclocking and I want it to be rock-bottom stable. I'm still playing with the BIOS settings to squeeze some more speed out of it... ;-) |
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20)
Message boards :
Number crunching :
credit/hour how much is possible??
(Message 25555)
Posted 30 Aug 2006 by Hoelder1in
Post: Core 2 Duo E6700 @ 2.8 GHz: 23.75 c/h per core (47.5 c/h total) - got mine last weekend :-) Intel P4 3.2 GHz HT: 7.5 c/h per thread (15 c/h total) Intel P3 1.0GHz 256 kB cache, 384 MB ram: 3.75 c/h |
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