Posts by JDHalter

1) Message boards : Rosetta@home Science : Research News (Message 54425) Posted 10 Jul 2008 by JDHalter Post: The below site & free download softwre is a very interesting breakthrough if it applies to protein folding, design & docking...??? They claim: "is a molecular modeling tool targeting pharmaceutical, biotechnology, and chemical researchers", based on Grand Unified Theory of Classical Physics (GUT-CP) "GUT-CP yields exact, closed form solutions to molecular structures. All the major functional groups involved in most organic molecules have been solved with CP. By using these functional groups as building blocks, or independent units, a potentially infinite number of organic molecules can be solved. Instantaneous Results Millsian software can visualize the exact 3D structure, calculate the total bond energy and the heat of formation of almost any organic molecule in real time without resorting to complex computational algorithms or supercomputers." Millsian_Software
2) Message boards : Number crunching : Report stuck & aborted WU here please - II (Message 13671) Posted 13 Apr 2006 by JDHalter Post: Here's another 1% hang...again at 1.04%...on a 3rd machine. http://boinc.bakerlab.org/rosetta/result.php?resultid=17036887
3) Message boards : Number crunching : Report stuck & aborted WU here please - II (Message 13653) Posted 13 Apr 2006 by JDHalter Post: I had 2 or 3 1% hangs today...this one was for one machine, and hung at 1.04% for somewhere between 18-22 hrs...(can't remember which one this machine was...), I aborted the other ones, but didn't note the % complete before...sorry. http://www.boinc.bakerlab.org/rosetta/result.php?resultid=17018657 Here's a second wu that had the 1% hang error (don't know what %), but here's the result link to it: http://www.boinc.bakerlab.org/rosetta/result.php?resultid=17014563 There may be a few more, as I've got another 2 machines that haven't checked in for 12+ hrs...usually they've been checking in every 4-6. If I get some time, I'll get their result links too. Hope it helps, JDHalter
4) Message boards : Rosetta@home Science : new possible funding source for advancing Rosetta... (Message 10635) Posted 10 Feb 2006 by JDHalter Post: If they are already funded by DARPA, that would explain why the goals of the protein design appear to match so closely...good 'nuf! JDHalter
5) Message boards : Rosetta@home Science : new possible funding source for advancing Rosetta... (Message 10604) Posted 9 Feb 2006 by JDHalter Post: While searching DARPA's website today for business opportunities (for my company), I stumbled upon an interesting possible funding source for Rosetta et al...DARPA! The weblink below describes what DARPA's goals are (similar to Rosetta's protein design goals), and the program manager's contact info if the Rosetta development team (Dr. Baker et al) has interest in following up on it. http://www.darpa.mil/dso/thrust/biosci/pdp.htm JDHalter Rosetta@Home - Team XPC
6) Message boards : Rosetta@home Science : Pilotohalcon (Message 10503) Posted 6 Feb 2006 by JDHalter Post: How do we communicate witht he team in our stats? Thanks It looks as if your Rosetta team, "U.S. Army," does not have their own message forums for communication. One possible way to try to start communication is to click on the names of fellow team members, and see if any of them have posted messages in the message boards (one of the last items listed in the personal information section that appears when you click on someones username)...if there is anyone that usually posts on the message boards, you may be able to get there attention by posting a reply/comment to their message posts... or...I would suggest creating a post in the 'Cafe' (general chat area) message boards for any/all "U.S. Army" team members to reply, and that way you can get their attention (if they even visit the message boards), and figure out how you all plan to keep in touch...starting your own team communication post in the 'cafe' could be a possibility... Besides that, I don't know how to help you (maybe the team captain has the ability to write an email message to all team members...I don't know what rights a captain has though. The boards are currently set-up with limitations, for safety/spam reasons, so that there is no way to email, or obtain the email address of your team or any person through these message boards as a user...again, maybe the team captain can, as they may have more options available to them. Good luck, JDHalter Rosetta Team - XPC
7) Message boards : Number crunching : Report stuck & aborted WU here please (Message 10285) Posted 31 Jan 2006 by JDHalter Post: It appears that the 1% bug was found on at least three seperate 2reb work units!... Assuming that the issue is somewhere between Rosetta & BOINC (as previous data from Dr. Kim proved that Rosetta completed a BOINC failed work unit command & seed without failing when run independant from BOINC), there is something that appears to be unique in the reb work units that initiates the 1% bug... I aborted a second 2reb work unit on a different machine that had been stuck on 1% for 9+hrs, but I forgot to get its stdout.txt file before aborting it, so I didn't post it here. ...that makes 2 2reb work units that failed w/ 1% bug from me, and 1 2reb work unit from Marie Lucie that failed w/ 1% bug... Three scenerios could account for this...1) there is a problem with the 2reb work unit files generated by Bakerlab...2) there is a problem that arrises when compressing/uncompressing the 2reb work units (something not found when tested at Bakerlab, as they don't have to compress/uncompress the reb files)...or 3) something unique is in the 2reb work unit commands (that is not in other work unit commands that don't fail) that initiates the 1% error. JDHalter
8) Message boards : Number crunching : Report stuck & aborted WU here please (Message 10225) Posted 30 Jan 2006 by JDHalter Post: I had a work unit run at 1% for ~ 54 hrs over this past weekend. I aborted the work-unit this morning when I found it. The command and random seed # from the slots directory/stdout.txt file are below. command executed: projects/boinc.bakerlab.org_rosetta/rosetta_4.81_windows_intelx86.exe aa 2reb _ -abrelax -stringent_relax -more_relax_cycles -relax_score_filter -output_chi_silent -vary_omega -rand_envpair_res_wt -rand_SS_wt -farlx -ex1 -ex2 -silent -barcode_from_fragments -new_centroid_packing -barcode_from_fragments_length 30 -ssblocks -barcode_mode 3 -omega_weight 1.0 -jitter_frag -jitter_variation gauss -max_frags 400 -output_silent_gz -paths frags400.txt -filter1 -90 -filter2 -115 -nstruct 10 # ===================================== # random seed: 500481 # ===================================== I'm running Win2k w/ Boinc set-up as a service (no graphics) to run Rosetta only. Hopefully this may help to solve the issue of 1% error...??? JDHalter
9) Message boards : Number crunching : 75GB is not enough free space? (Message 9677) Posted 24 Jan 2006 by JDHalter Post: I believe your issue is not the actual hard drive space on your disk, but the amount of space that is allowed to be used on your hard drive for Rosetta, which is specified by your online account settings. bah HAH! Many thanks, that was indeed the issue! I'm glad I could help. JDHalter XPC & Rosetta Fanatic!
10) Message boards : Number crunching : 75GB is not enough free space? (Message 9457) Posted 20 Jan 2006 by JDHalter Post: I've got R@H running on a number of systems. Trying to load it on another Linux box (Ubuntu) and it responds telling me that I must free 400.6 MB. I don't understand, there's gigs and gigs and gigs of free space on this system.... Fri 20 Jan 2006 10:05:32 AM EST\|rosetta@home\|Message from server: No work sent Fri 20 Jan 2006 10:05:32 AM EST\|rosetta@home\|Message from server: (there was work but you don't have enough disk space allocated) Fri 20 Jan 2006 10:05:32 AM EST\|rosetta@home\|Message from server: No disk space (YOU must free 400.6 MB before BOINC gets space). Review preferences for minimum disk free space allowed. Fri 20 Jan 2006 10:05:32 AM EST\|rosetta@home\|No work from project I believe your issue is not the actual hard drive space on your disk, but the amount of space that is allowed to be used on your hard drive for Rosetta, which is specified by your online account settings. -Go to the Rosetta homepage, then click on the link to 'Your Account' under returning participants heading. -Once logged in, go to edit general preferences, and once there, adjust the settings for the disk and memory usage. -Once you save the settings, open Boinc Manager, and on the 'Projects' tab, click the update button. This will load your saved preferences onto the PC, and this should solve the issue. This has happened to many new users, so don't feel bad. There is a forum topic specifically to help out new Rosetta users to get over these types of issues. The topic is called 'Hints, cheats, and advice for New users', and is the 3rd topic currently in the 'Number Crunching' forum. This should help. If this doesn't solve the issue, I'm sure one of the volunteer moderators, project staff, or another user that has had this same experience will be able to help. JDHalter XPC Team - Rosetta@Home
11) Message boards : Number crunching : Report stuck & aborted WU here please (Message 9350) Posted 19 Jan 2006 by JDHalter Post: I encountered the 1% bug on wu command: command executed: projects/boinc.bakerlab.org_rosetta/rosetta_4.81_windows_intelx86.exe xx 1lou A -output_silent_gz -silent -increase_cycles 10 -nstruct 40 random seed: # random seed: 510621 I aborted the wu, but I did get the stdout.txt file saved before it was aborted...didn't read the instructions properly to test & help out on my own...sorry. Hopefully the info above will help to recreate the issue back at the UWashington Bakerlab...or wherever someone has the proper work unit files. JDHalter XPC - Rosetta@Home