Posts by l_mckeon

21) Message boards : Number crunching : minirosetta 2.05 (Message 65184) Posted 3 Feb 2010 by l_mckeon Post: I aborted lr15clus_opt_.1ptq.1ptq.IGNORE_THE_REST.c.3.21.pdb.pdb.JOB_17471_3_0 after 50 minutes. Stuck on model 1, step 0, with funny looking graphics. I no longer have the patience to see how these turn out.
22) Message boards : Number crunching : minirosetta 2.05 (Message 65147) Posted 30 Jan 2010 by l_mckeon Post: "This app update includes a fix for checkpointing. Please report issues and bugs here!" I had a task yesterday that restarted from model one when the computer was switched off then on again. The task had been saving checkpoints. The upload was >200kB and the task ended a few minutes after restarting. I don't know the task number but I'm fairly sure it was an lr5 task.
23) Message boards : Number crunching : lr8_combine_smooth_torsion_it00 - All Errors? (Message 64332) Posted 2 Dec 2009 by l_mckeon Post: Here's another problem with the rama...redo tasks. The tasks started from scratch when computer was switched off then restarted. More than 5 hours X 3 cores wasted. The tasks terminated shortly after restart. lr5_combine_smooth_torsion_it00_redo_rama08_A_rlbd_1c7k_SAVE_ALL_OUT_IGNORE_THE_REST_DECOY_16279_992_0_0 was one of the culprits. BTW, the tasks had been saving checkpoints according to the slots directory.
24) Message boards : Number crunching : Latest WUs don't set check points. (Message 63223) Posted 9 Sep 2009 by l_mckeon Post: 4HTC.bound.mppk.min.pdb_dock_score12_ddg.xml_yfsong_14675_4426_0 1AHW.bound.mppk.min.pdb_dock_score12_ddg.xml_yfsong_14675_4425_0 The above WUs had run times of about 1:35 hours without setting any check points. They terminated after 99 models complete and uploaded OK (21MB total - ouch!) .
25) Message boards : Number crunching : Problems with Minirosetta Version 1.67 (Message 61252) Posted 18 May 2009 by l_mckeon Post: I have aborted three WUs from the following batch: pp_lr6_A_score12_rlbd_1fkj_IGNORE_THE_REST_DECOY_12373_149_0 using minirosetta version 167. When I go into the graphics these pp_lr6 WUs show you on model 21 (or whatever) but with 0 steps, 0 accepted energy and no graphics.
26) Message boards : Rosetta@home Science : Herpes Simplex Virus? (Message 61145) Posted 12 May 2009 by l_mckeon Post: Nothing to do with Rosetta, but I believe the Australian team that invented the preventative vaccine for genital herpes is now working on a curative version for those who are already infected. Of course, expect it to take years at a minimum. Oops, my error. They are working on the Human Papilloma Virus (warts), not herpes.
27) Message boards : Rosetta@home Science : Herpes Simplex Virus? (Message 61116) Posted 11 May 2009 by l_mckeon Post: HSV1 and HSV2 I want to know if Rosetta really researching on these viruses??? If yes, then what level or stage we are now? How many years before a cure will be found? Nothing to do with Rosetta, but I believe the Australian team that invented the preventative vaccine for genital herpes is now working on a curative version for those who are already infected. Of course, expect it to take years at a minimum.
28) Message boards : Number crunching : Problems with Minirosetta v1.54 (Message 60657) Posted 15 Apr 2009 by l_mckeon Post: The following two tasks had shorter run times than usual (about 1:30 hrs and 1:50 hrs from memory) and their uploads totalled around 16MB. rest3d85_ip40_1t4w.patchdock.6.pdb_0002_fa_dock.xml_score12_pert38_DOCK_10797_354_0_0 rest3d85_ip40_1t4w.patchdock.6.pdb_0002_fa_dock.xml_score12_pert38_DOCK_10797_354_0_0
29) Message boards : Number crunching : Intel i7 CPU (Message 58552) Posted 6 Jan 2009 by l_mckeon Post: The Intel I7s are undoubtedly great processors and the coming thing, but I think they are a poor value choice at the current prices. Come back in 6 months and look at them then. The latest issue of Australian PC User magazine has a number of articles on upgrades. Did you know that a 45nm. Intel E5200 (about US $84.00) can be overclocked to 4 GHz? In PC User's tests an OC'ed I7 920 (3.6GHz) was about 20% faster than the 4GHz E5200. But the I7 retails for about US $570 for the chip alone. Add to that the extra costs of expensive mother boards and DDR3 memory and I don't think the I7 currently makes sense. LM
30) Message boards : Number crunching : Minirosetta v1.34 bug thread (Message 56092) Posted 29 Sep 2008 by l_mckeon Post: Here's a weird one. I've had a couple of tasks that refuse to suspend, both hombench tasks on 1.34. I manually suspend the task (and BOINC reports Task Suspended) or the task is "Waiting to Run" and the task continues to run. I've only got a dual core processor but I have three tasks running at once, two Rosetta tasks plus one World Community grid. Task Manager reports all three tasks having 33 per cent of CPU cycles. The tasks complete and upload normally.
31) Message boards : Number crunching : Tasks end prematurely. (Message 55513) Posted 3 Sep 2008 by l_mckeon Post: I'll get a new batch of Rosetta tasks and watch things more closely. Task 187847619 ended after 1:50 hours after computer and task restarted. Predicted run time was about 2:50 hours (from memory) which is normal for me. From watching the graphic before shut down, the task was at least on its tenth model (maybe eleventh). In the results it says the task completed one decoy (which I guess equals models?). Rosetta didn't used to do this; I think its a bug.
32) Message boards : Number crunching : Tasks end prematurely. (Message 55371) Posted 29 Aug 2008 by l_mckeon Post: Thanks for the info on checkpoints. I've always been scared of poking about the BOINC files but I think I'd like to try this. Give me a week or so, to search through several forums for everything that could go wrong and then to build up my courage to try it anyway:) Snags When BOINC tasks save a checkpoint they have to put the data somewhere, and I believe it's the SLOTS sub-directories/folders. They are called are called Slots/0, Slots/1, etc depending on the number of current tasks and projects in memory. You can see it clearly on the World Community Grid project on rice; it updates every couple of minutes and so does the corresponding slots directory. These directories are deleted when all tasks are finished and uploaded. I'll get a new batch of Rosetta tasks and watch things more closely.
33) Message boards : Number crunching : Tasks end prematurely. (Message 55332) Posted 27 Aug 2008 by l_mckeon Post: ... and another one -- 26/08/2008 3:44:31 PM\|rosetta@home\|Restarting task abinitio_only62_A_256bA_4438_6378_0 using minirosetta version 132 26/08/2008 3:45:01 PM\|rosetta@home\|Computation for task abinitio_only62_A_256bA_4438_6378_0 finished after 2 hours and 7 minutes of run time, when 2 hours 40 minutes was predicted. What are you[r] actual run time settings either in BOINC manager or on the Rosetta account page? 4 hours or what? predicted run times are not always accurate and can vary widely from way under the preferred run time in your settings to up to 30 minutes or less under those settings, if the program feels it can not run another model/decoy in the time you gave it run. In my prefs. Target CPU run time is "Not Selected". My tasks typically run between 2:30 and 3:00 hours. Both Rosetta and I have been doing this long enough to know what to expect. I believe this is NEW behaviour.
34) Message boards : Number crunching : Tasks end prematurely. (Message 55297) Posted 26 Aug 2008 by l_mckeon Post: Please post links to the tasks in question. Some tasks end before your runtime preference. Some can end after. That would be normal. Is it possible that interrupting the task was coincidence? Did you happen to see the graphic display prior to interrupting it? Was it proceeding normally? Just looking at some of my past results, these look like two examples: Task ID 186604373 Name abinitio_only62_A_1ew4A_4434_7211_0 Workunit 170438591 Task ID 186604330 Name abinitio_homfrag_71_A_1gu3A_4443_2760_0 Workunit 170438511 Everything was proceeding normally. This is a fairly new behaviour. ... and another one -- 26/08/2008 3:44:31 PM\|rosetta@home\|Restarting task abinitio_only62_A_256bA_4438_6378_0 using minirosetta version 132 26/08/2008 3:45:01 PM\|rosetta@home\|Computation for task abinitio_only62_A_256bA_4438_6378_0 finished after 2 hours and 7 minutes of run time, when 2 hours 40 minutes was predicted. Lindsay
35) Message boards : Number crunching : Tasks end prematurely. (Message 55268) Posted 24 Aug 2008 by l_mckeon Post: Please post links to the tasks in question. Some tasks end before your runtime preference. Some can end after. That would be normal. Is it possible that interrupting the task was coincidence? Did you happen to see the graphic display prior to interrupting it? Was it proceeding normally? Just looking at some of my past results, these look like two examples: Task ID 186604373 Name abinitio_only62_A_1ew4A_4434_7211_0 Workunit 170438591 Task ID 186604330 Name abinitio_homfrag_71_A_1gu3A_4443_2760_0 Workunit 170438511 Everything was proceeding normally. This is a fairly new behaviour.
36) Message boards : Number crunching : Tasks end prematurely. (Message 55247) Posted 23 Aug 2008 by l_mckeon Post: I've had a number of tasks recently that will end prematurely if the computer has been switched off, or if the task or Rosetta has been suspended. The task(s) resume, then end and upload within 15 seconds or so. In some cases I've deliberately waited until after a checkpoint before switching off; no difference. The tasks are well short of predicted run times.
37) Message boards : Rosetta@home Science : CAN YOU HELP ROSETTA?? (Message 55246) Posted 23 Aug 2008 by l_mckeon Post: The trouble with those image-based verification systems, is that they involve a lot of quite high-level coding, and at the moment, I couldn't make them. I have made the as ott with seperate verification processes (I wont discuss what exactly - kinda destroys the point of putting them in!). If you trigger any of the validation, I will also (or the webmaster will) get an email telling them (me) that the validation has been triggered. If you're looking for a free anti-bot CAPTCHA system, look up reCAPTCHA. I know nothing about web site creation, but I gather they provide a fairly simple plug-in for web sites.
38) Message boards : Rosetta@home Science : west nile virus (Message 55171) Posted 19 Aug 2008 by l_mckeon Post: http://news.yahoo.com/s/nm/20080806/hl_nm/westnile_genes_dc World Community Grid, another BOINC project, already has a sub-project that's working on treatments for West Nile virus as well as other flaviviruses, including Hepatitis-C. It's "Discovering Dengue Drugs Together".
39) Message boards : Number crunching : Rosetta Checks (Message 54765) Posted 30 Jul 2008 by l_mckeon Post: Hi Robert! Have a look at http://boinc.berkeley.edu/wiki/Client_configuration This is the documentation for the BOINC client configuration file. If you set the <checkpoint_debug> flag to 1 (default is 0), you will at least be able to see when workunits checkpoint. OR just go into the BOINC/SLOTS program folder. You'll find sub-folders called 0, 1, 2, 3 etc, one per current running Work Unit. The last time that each SLOTS sub-folder was modified is the time of the last check point. I'm not sure if that applies when the Boinc manager is switching between WUs from different projects I have an old freeware file manager program called EF Commander that I keep permanently pointed at this location for just this purpose, although of course Windows Explorer will do. Having said that, is it really necessary for the WU to run as just one model with no check points or is that just poor/lazy design?
40) Message boards : Number crunching : One model per WU -- no check points. (Message 54124) Posted 1 Jul 2008 by l_mckeon Post: My latest WU ran all the way as one model with no check points. This means that if I switch my computer off after completing 90% then I lose all that work and have to start again. Not the way to do it!

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