Posts by Zydor

1) Message boards : Number crunching : Pentathlon Rosetta Newb? Read On :) (Message 70309) Posted 10 May 2011 by Zydor Post: Hope I've not committed another faux par ... :) Learning from yesterday, I made sure the cache was run dry after a good overnight/morning session of 3 hour Models, then set the machine to my "work" preference where I had set it for 12 hours - aim being to load up 3-4 days worth of 12hr preference models for six cores on a 1090T. Down came the models. So far so good. They then proceeded to error out one by one within 30 seconds to 3 mins of download ..... all of them. I guess I did something wrong, but cant fathom what - I ran it dry, changed to the 12hr preference, waited 10/15 seconds then started the download. Changed nothing else from the previous 12/15 hr successful trial crunching session. Enlightenment greatfully received ... I dont want to set off another download batch and trash those. I managed to catch the last third or so and abort transfer to stop models trashing. EDIT: Set cache this end to zero to limit and trashing, until find out whats happening. Downloaded one with preference set to Work (12hr), trashed within 2 mins. Going to set it back to default preference, see what happens. Regards Zy
2) Message boards : Number crunching : Pentathlon Rosetta Newb? Read On :) (Message 70306) Posted 10 May 2011 by Zydor Post: First off - yup me also a Pentathlon Rosetta Newb. I came in Monday night to have a quiet spin round, get the feel of Rosetta, try some short WUs {more of that later } ..... and promptly hit the buffers in time honoured newb fashion :) Mod.Sense very kindly picked me up, pointed out a few home truths, and got me on the right track. It was suggested I start a thread for Pentathlon Rosetta Newbs on Q&A best practice etc. So here we are. Scratched the head a little, and thought, yup a central place to quickly get advice would be neat for us Pentathlon Visitors. So here it is ... To start it I thought I would briefly relate the advice I was given, and pointed at, that would immediately affect an enquiring Pentathlete who's sole aim in life is get up and running for their Team with minimum hassle:) - Select WU size in Preferences, select 3 hours or above, smaller size will cause issues, not worth it for us, summary of issue: ... expectations of what a 1hr work unit is are not realistic for R@h..... when you do that, some of the other nice things such as accurate progress %, and consistently completing within such a limited timeframe go out the door. Each task must complete at least one model. For some tasks you will see a model every 5 minutes or so, for others, it can take several hours. So, not all tasks are going to complete within your one hour target, and that is normal and to be expected. - It would seem that BOINC gets more confused than it usually does if frequent changes are made to WU length, the advice is apparently settle on a size of 3-4 hours or above, and stick with it. - Progress Percent not advancing? A: Rosetta recomputes the progress percent at the end of each model. The model number is shown in the graphic. As long as the "steps" are continuing to progress, it is working. Once it completes the model it is working on, it will recompute the progress. At that point the progress % will be determine by looking at the time it took to complete the first model, as compared to your WU runtime preference. If your WU runtime preference is low (<4hrs) you will frequently see the progress % jump from 1.xx to 100%, or into the 50% range. Basically, each different protein takes a different time to crunch a model. Some proteins will crunch for several hours to complete a single model. Others will crunch a model every 5 or 10 minutes. It is the nature of the science being done with Rosetta. BOINC and Rosetta have measures in place that will abort work units that aren't running properly. So, in general, unless you see some specific advice to the contrary, you should NOT abort work units (WUs). {sic: no prizes for guessing what I did ...} - "To completion" time is going UP! A: This is normal. The time gets revised when the progress % is recomputed at the end of each model. So at the end of a model the time to completion will drop. Then during the crunching of the next model it will increase again. - I'm familiar with SETI and BOINC already, but what should I know about Rosetta? See this link: That'll do .... I think ..... and will get most up and running, any more becomes a War and Peace novel for Pentathelon Visitors, not what the thread is for. Questions to the local experts - and that decidedly is not me! - by posting on the thread. Local Experts, any susinct hints of best practice for the Pentathletes would doubtless be greatly received, and may result in some Rosetta converts. Your words of wisdom are sought after :) Regards Zy
3) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 70305) Posted 10 May 2011 by Zydor Post: Re Thread - Okie Doke, will do Regards Zy
4) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 70303) Posted 9 May 2011 by Zydor Post: Spoke too soon :) Another for you, from the laptop - it has had a total attatch/detatch and clean out, so this one started on a pristine clean default setup, no tweeks or o/c - but some more detail this time as I was trying to watch out for it. Task ID 421414504 finished in normal time. Task ID 421414503 had started at exactly the same time as the one that finished, except it had only completed 20% by the time the one above finished. It also was using (and still is) 270Mb of memory. That figure has slowly risen all the time it has run, not fast, but has steadily risen (and still rises at a rate of about 0.5Mb per minute - no wild fluctuation (barring the odd 100Kb or so), just steady inexorable rise. Memory Leak? Blasee phrase, but not impossible. The one that went through ok (421414504) was using 63Mb of memory when it finished. The replacement task that has started, began using 43Mb of memory, to early to say if thats a bad one as well. Good luck on the hunt .... fingers crossed you nail it tomorrow with the Pentathelon coming up. EDIT: Just seen your post above ... its not pentathelon related as such, when that starts, the longer the WU the better for me - less messing around. The short ones selected was only because the option was there and wanted to do some quick ones to check all was well before the event start's tommorow night, my not being used to Rosetta. Point noted, I will change it to default 3hours for now. I can start a thread re pentathelon if it helps you, but I'm not knowledgeable enough yet on Rosetta to comment or set it up properly. I'll give it a whirl if you want me to ... ?? Regards Zy
5) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 70300) Posted 9 May 2011 by Zydor Post: Quick note to close the loop on my posts above. I've ended up having to do an detatch/attatch (after aborting held WUs) on my machines. Sorry about the aborts, but felt I had no choice. On restarts, the problem has disappeared, and at present at least, all appears to be progressing normaly now. Yet to complete one since detatch etc, but all three machine appear to be behaving now. No idea the reason, strange it hit all three machines. No hang over from other worries elsewhere as far as I know as things have been stable in my recent travels around BOINC. Anyway .... for what its worth, detatch etc resolved my problems, absolutely no idea why though :) Regards Zy
6) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 70297) Posted 9 May 2011 by Zydor Post: Could someone take a peek at the list for my laptop? I'm not new to BOINC, but am a total newb at Rosetta, so I will at present miss the obvious until my feet are under the table. (running a few WUs to get used to Rosetta ready for the penthalon in a day or so) http://boinc.bakerlab.org/rosetta/results.php?hostid=1441160&offset=20 I made a post two up re slow ones, but I'm wondering if its a bad batch. Running two from same date time batch, and they are slow as well (18-19% done circa 2hrs45min for 1 hour WUs). Two running at present are Task IDs: 421246725 and 421246743 . I am starting to wonder if they are 1hr WUs, maybe there are longer ones in that batch, there were 1hr ones I did previously in the same batch, so its a bit strange. Ignore the laptop preference as set at present, it was set for 1hr when that batch was downloaded. Regards Zy
7) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 70294) Posted 9 May 2011 by Zydor Post: Couple of possible problem WUs for you - they are 1 hour WUs, ran for around 25-30 mins, and failed to progress beyond 2-3% completion. Other 1hr ones had a consistent completion percentage roughly in line with time done so far, so I aborted both. http://boinc.bakerlab.org/rosetta/result.php?resultid=421246729 http://boinc.bakerlab.org/rosetta/result.php?resultid=421246619 Regards Zy