Posts by Jeff Gilchrist

21) Message boards : Number crunching : Project encountered internal error: shared memory (Message 29297) Posted 13 Oct 2006 by Jeff Gilchrist Post: Looks like the project WAS down... Yes, but they think it is "back up" according to this on the website: Outage Resolved: The project is back online. The power upgrades have been completed.
22) Message boards : Number crunching : Project encountered internal error: shared memory (Message 29291) Posted 13 Oct 2006 by Jeff Gilchrist Post: Same here. I can upload results, but cannot "report" them. I cannot download any new work units either. "Message from server: Project encountered internal error: shared memory" Project is down
23) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (2) (Message 21161) Posted 25 Jul 2006 by Jeff Gilchrist Post: Not sure if this will be useful to your research but might find it interesting anyways: http://www.nytimes.com/2006/07/25/science/25dna.html?ex=1311480000&en=34d8e6ced8d42f47&ei=5089&partner=rssyahoo&emc=rss "Researchers believe they have found a second code in DNA in addition to the genetic code. The genetic code specifies all the proteins that a cell makes. The second code, superimposed on the first, sets the placement of the nucleosomes, miniature protein spools around which the DNA is looped. The spools both protect and control access to the DNA itself."
24) Message boards : Rosetta@home Science : Comments/questions on Rosetta@home journal (Message 16500) Posted 18 May 2006 by Jeff Gilchrist Post: Just wondering if you could comment more on how you were able to reduce the memory requirements by over 2x? What kind of tricks did you use to accomplish this?
25) Message boards : Number crunching : Information on Ver 4.97 errors (Message 13390) Posted 10 Apr 2006 by Jeff Gilchrist Post: The DC project that I was involved in during CASP 5 and CASP 6 has been shut down since Oct 2004 while they work on improved energy scoring functions. Which one is that, distributed folding? I'm not sure if they are ever coming back...
26) Message boards : Rosetta@home Science : How can we bring more users to the Rosetta project? (Message 12451) Posted 21 Mar 2006 by Jeff Gilchrist Post: I'm trying to do my part. I just sent an e-mail to the well known (in Canada) science radio program Quirks and Quarks giving them info about the project and asking if they were interested in doing a story. I also gave them David's e-mail and phone # so don't be surprised if you do get a call from Canada. ;-) http://www.cbc.ca/quirks/
27) Message boards : Number crunching : No Work (Message 11722) Posted 6 Mar 2006 by Jeff Gilchrist Post: Its now listed as "0" queued which would explain why I am not getting any work. All my boxes are empty so hopefully there will be something soon...
28) Message boards : Number crunching : Work Unit Compression discussion (Message 10411) Posted 3 Feb 2006 by Jeff Gilchrist Post: I'm assuming it's the Rosetta core that handles the .gz input files and not the BOINC client, so switching from GZIP to using BZIP2 (http://www.bzip.org/) seems would save a lot of space for tranferring data. A bzip2 library is available as free open source and works very similarly to the gzip library that Rosetta would be currently using. Taking a few files my client is current working on: aa1ogw_09_05.400_v1_3.gz is 3657522 bytes bb1bm8_09_05.200_v1_3.gz is 2425482 bytes bb1iibA09_05.200_v1_3.gz is 2492662 bytes The same files compressed with bzip2 are: aa1ogw_09_05.400_v1_3.bz2 is 2224708 bytes bb1bm8_09_05.200_v1_3.bz2 is 1481306 bytes bb1iibA09_05.200_v1_3.bz2 is 1488119 bytes So you can see it would make a big difference in bandwidth to switch over to using bzip2 to compress the data files from gzip. Jeff.
29) Message boards : Number crunching : @ Dave Baker (Deadlines causes EDF) (Message 10265) Posted 31 Jan 2006 by Jeff Gilchrist Post: The deadlines should be set to suit the project scientists only. Rosetta are not doing this for us, we are providing resources for them. If the workload is unsuitable for a machine's circumstances, then that machine is unsuited to the project. I'm sorry if that sounds callous or harsh but it is unfortunately the truth. Yes, and if the scientists want resources from people, it is in their best interest to accomodate the users as best they can. If there is an easy solution for Rosetta to allow some longer deadline workunits then that will allow more people to participate and stop others from leaving. If there is no solution then so be it, but it's worth at least looking into. You will notice that nobody is "demanding" the WUs have longer deadlines, people are politely asking if it is possible.
30) Message boards : Rosetta@home Science : New Update From David Baker (Message 10220) Posted 30 Jan 2006 by Jeff Gilchrist Post: Yes thanks, that will be very useful.
31) Message boards : Number crunching : @ Dave Baker (Deadlines causes EDF) (Message 10219) Posted 30 Jan 2006 by Jeff Gilchrist Post: I would let such machines work only on projects with deadlines of 14 days or more. Set the ressource share for Rosetta higer on the other computers. If the Rosetta team needs the data back earlier, than seldom connected computers can't help. Has nothing to do with "penalize". I only wish to donate my CPU time to Rosetta, I do not run any other BOINC projects and thus cannot modify my resource share. I'm not saying that all WUs need a 2 week deadline, but David Baker suggesting having a queue with some work that can be returned in 2+ weeks would be very helpful for those of us with slower machines or non-permanent Internet connections. I just wanted to point out that there are some people out there that can't handle very short deadlines.
32) Message boards : Number crunching : @ Dave Baker (Deadlines causes EDF) (Message 10187) Posted 29 Jan 2006 by Jeff Gilchrist Post: TDF isn't the only problem. BOINC will let uses queue work for 10 days, some of us have machines not connected to the net very often. This is causing me some problems. I have some machines that are not frequently connected to the Internet so I have my cache set to queue 10 days of work and I sometimes can only connect once a week to upload. I am now not able to fill up my cache because I cannot complete the work in time for the deadline. Could you reconsider this and possibly select 2 weeks instead of 1 so that you still get your work back reasonably fast but you dont penalize some people?
33) Message boards : Number crunching : Shorter WU deadlines (Message 10061) Posted 27 Jan 2006 by Jeff Gilchrist Post: Sorry for the lack of warning! we switched to one week for just the reason you point out--we want to analyze the results and be able to draw conclusions as soon as possible! This is causing me some problems. I have some machines that are not frequently connected to the Internet so I have my cache set to queue 10 days of work and I sometimes can only connect once a week to upload. I am now not able to fill up my cache because I cannot complete the work in time for the deadline. Could you reconsider this and possibly select 2 weeks instead of 1 so that you still get your work back reasonably fast but you dont penalize some people?

Previous 20