Posts by halfmeg

1) Message boards : Number crunching : Report stuck & aborted WU here please (Message 10500) Posted 6 Feb 2006 by halfmeg Post: While not specifically a stuck or aborted WU, this one has died 10 times with "Client error" & once delayed on a system from 3 - 31 January (lapsed due date). Original create date of 21 Dec 2005 - DEFAULT_1n0u_218_656 . http://boinc.bakerlab.org/rosetta/workunit.php?wuid=3840471 stderr - Incorrect function. (0x1) - exit code 1 (0x1)
2) Message boards : Number crunching : WU Started then switch to new computer no results posted (Message 9227) Posted 17 Jan 2006 by halfmeg Post: Hi folks, I have 3 computers here. One is kind of old 500Mhz, the other two both over 2Ghz. I allowed work on the slow system and a WU ( http://boinc.bakerlab.org/rosetta/result.php?resultid=7035493 ) arrived which was somewhat different than the normal WU I have seen. It incremented in 2.5% chunks instead of 10% and would have run over 40 hours if I had left it in place. I suspended it, thinking I wouldn't get any more work, but another WU downloaded ( http://boinc.bakerlab.org/rosetta/result.php?resultid=7145133 ). I suspended the project and then the 2nd WU. I then transfered the entire BOINC directory to one of the faster computer and allowed them to process on it overnight. They both completed successfully. The 1st one is still odd, in excess of 30 red result dots in the graph before it finished. The 2nd computer uploaded the results but nothing on my results page changed ( shows outcome unknow still ). Thinking perhaps the computer that downloaded the WU has to report them I had already transfered the entire BIONIC directory back to the slow computer before the upload. It also successfully reported them back to the server, but still no change in my results page. Although out of the ordinary, should this have worked ( downloading to one, processing on another, and uploading by either )? I don't care much about the credit, but don't like the idea that orphaned WUs ( status unknown to servers but known to be lost, destroyed, botched, ______ ) have to wait almost a month before being rescheduled for processing. Can a reset be placed on our results page to free the orphaned WUs back into the pool? Oh yeah, what kind of WU has 30+ end results or whatever you call them? Phil
3) Message boards : Number crunching : Newbie needs 2 WUs reset (Message 8435) Posted 5 Jan 2006 by halfmeg Post: Hi folks, I had given my system a break over the holidays and upon selecting "Allow New Work" the message section of BIONC initially stated something like "No Work Available" ( I might be wrong here but didn't get any work units ). The thing looked like it paused for 3 minutes and tried again with same result. After a while I recieved a message about not enough disk space but that seemed odd as I have 7G free preferences set to 100% if needed. I noticed another message similiar to "Communcation and Work halted due to User Active". Believe this was after a WU had 'started downloading' but froze while downloading. Looking around I found one of my general preferences ( Do work while computer is in use?) set to NO. I changed it to YES and still nothing seemed to be happening. After much fooling about with "Suspending", "Updating", "Detaching" & "Attaching to a Project" on the BOINC projects window section, I downloaded all the ROSETTA files and 1 WU which completed today. My results page still shows 2 more WUs "In Progress" which is doubtful at best. I think they are missing in action due to all the stuff going on with my tinkering. Please advise on resolution for removing them and requeueing them for processing. boinc.bakerlab.org/rosetta/workunit.php?wuid=4601012 boinc.bakerlab.org/rosetta/workunit.php?wuid=4602059 Phil
4) Message boards : Rosetta@home Science : Graphics (Message 6600) Posted 17 Dec 2005 by halfmeg Post: I see now that the results are from Nov 15th not Dec 15th, so there wouldn't be any blue "*" for WU completed here ( member since three days ago). I have perused the boards a little more and posed a supposition on directed random selection ( You asked for feedback thread ). The science of folding is unfamiliar to me as my path took me down the inorganic route. Chaperones ( in another thread ) seem to provide a kind of scaffolding for building the protein until the end pieces are in place then, similiar to the space shuttle gantries detaching and setting the shuttle free, protein folding ( relaxing ) begins to take place. Thanks again, Phil
5) Message boards : Rosetta@home Science : Well, you said you wanted feedback ... (Message 6580) Posted 17 Dec 2005 by halfmeg Post: Jack Schonbrun stated on Nov 1 05: > In fact, I hope we can move on from the discussion of random number > generation, and talk about what perhaps is the real issue: whether the > non-randomness that we intentionally introduce to bias our search is doing > what we want. No matter what algorithm is utilized ( perfect or impaired ), unless there has been an analysis of the output of your specific coding ( embedded in rosetta ) to determine randomness, you cannot assume it works as expected. If the non-randomness introduced is something of the sort: RANDOM High energy random point is flexed. SUBSTITUTE A pre-constructed segment array ordered by low-energy 1st is joined at the random point. REPEAT SUBSTITUTE for x segments Lowest energy results of previous step are keep. DO RANDOM until no high energy segments remain. This type of thing will not look like a random sampling but should favor the lower energy portion of the graph. The completeness of a universe of low energy segments for substitution could inhibit the 'final' threshold levels from being plotted. This might account for a "walled off" target level. Phil - then again I might have misunderstood the method of directing the search
6) Message boards : Rosetta@home Science : Graphics (Message 6552) Posted 17 Dec 2005 by halfmeg Post: A couple more inquiries, please bear with me. I'm like a curious George. > > Multiple Red Dots in results splatter graph. > > Both seem to be explained in posts in this forum, although multiple low > > energy reports back to you seem odd if we are only looking for lowest energy > > state. > This is a good point. It helps us refine our algorithm to see the end point > of every folding run. Alright, just for clarity, each folding run generates a low energy 'red dot' in the local graph on local system. There are generally multiple folding runs per work unit so multiple 'red dots' are expected, just not all visible at the same time due to the shifting of the local splatter graph window to accommodate the range of energy levels. The resulting 'red dots' are sent back to rosetta to be consolidated into the 'results' splatter graph along with other completed WUs. All the 'green points' the local computer has generated in the local splatter graph are discarded. The link you gave for viewing results: http://boinc.bakerlab.org/rosetta/rah_results.php shows several different graphs, none of which specifically match the work unit name ( we have only 1 WU returned to rosetta ) completed so far. Within the graphs themselves there seems to be no blue "*" ( designates point found by the WU completed here ) which would indicate we weren't able to contribute or our run was some type of verifying run for results already obtained (is this done as follows - double checking only on 'red dot' results?). The "RESULTS" link on the "HOME" page takes me to the link above. The "VIEW" link beside "RESULTS" on the "YOUR ACCOUNT" page under the "Account statistics" heading gives details on the WU status. It would be nice to have something in this table which would link us to the splatter graph for the particular WU. Looking at the detail for my WU there is an entry: max # of error/total/success results 10, 20, 10 What does this tell us? We never like to see a number > 0 in an error field. Although not related to graphics ( don't mean to hijack this thread ), does rosetta fold proteins in isolation, restraints are the ones imposed by segments repelling or attracting each other, or are there such things as catalysts in the mix which might enable lower energy folds to take place without the catalysts becoming part of the protein? Is this thinking too far out of the box? Noticing a lot of void area in the result splatter graphs prompted this idea. Phil
7) Message boards : Rosetta@home Science : Graphics (Message 6511) Posted 17 Dec 2005 by halfmeg Post: Newbie observations and a question or two. Folding Image migrates/exceeds display box (Searching, Accepted, Lowest) boundaries. Multiple Red Dots in results splatter graph. Both seem to be explained in posts in this forum, although multiple low energy reports back to you seem odd if we are only looking for lowest energy state. Where can we ( or is it possible to ) view the splatter graph for work units we have completed and sent back to rosetta@home? Is any information retained on our local systems which we can review completed work units and the results? Are larger work units allocated to more capable processor platforms or are work units generally similiar in size? ( ie 3+GHz systems get larger work units while 1.5Ghz and below are sent smaller work units ) To overcome color impairements, perhaps a crosshatch or dot pattern fill for the segments. Phil - on an old K6-2 500MHZ