Posts by rechenknecht123

1) Message boards : Number crunching : Problems with Rosetta version 5.59 (Message 39656) Posted 20 Apr 2007 by rechenknecht123 Post: Looks like rechenknecht123's task in question is this one. It looks like the task was restarted 5 times without reaching a checkpoint and so it was ended. This is part of Rosetta watching out for you. They figure if you've begun the same task 5 times without making any progress, then the task is not well suited for your machine and so it ends it and reports it in. Looks like you never completed the first model and so no output file was produced. So the question becomes, what would cause me to restart a task many times without making progress. Any time a task is removed from memory, it must restart. So, if you do not keep tasks in memory while preempted, then any preemption will cause a restart. Preemption could be from other BOINC tasks taking their share of CPU time, or if you configure BOINC (see General Preferences) to not run while computer is in use, and to not remain in memory while preempted, then each time someone sits down to the computer, the task is removed from memory and must be restarted. This is why the message in the results page suggests "Keep application in memory while preempted." Also, any time the computer is powered off, or BOINC is exited (not just closed, but exited), the task must restart. Once a model is completed, that progress is saved, and would be reflected in your CPU time reported. There may also be checkpoints within a model for some tasks. In short, your machine began the task, and ended it again before allowing it to run long enough to reach the end of a model, or reach a checkpoint. Rhiju: any idea why the task shows it built 30 nstructs in those 3 seconds? hi Rhiju in my opinion "problem boinc-5.8.17 the recalc`s of rosetta." tonight a had made the security patch 4-2007 for mac osx 10.49. shit happend and i had made a hart reset with power off. after this the patch runs again with rejuornaling the 8 harddrives. no problems with rosetta 599. runs fine at 0:34:05h and 34% ready cal. est time 00:02h:34sec. at this WU Fr 20 Apr 10:57:28 2007\|\|Starting BOINC client version 5.8.15 for powerpc-apple-darwin Fr 20 Apr 10:57:28 2007\|\|log flags: task, file_xfer, sched_ops Fr 20 Apr 10:57:28 2007\|\|Libraries: libcurl/7.15.5 OpenSSL/0.9.7l zlib/1.2.3 Fr 20 Apr 10:57:28 2007\|\|Data directory: /Library/Application Support/BOINC Data Fr 20 Apr 10:57:29 2007\|\|Processor: 1 Power Macintosh Power Macintosh [Power Macintosh Model PowerBook3,2] [AltiVec] Fr 20 Apr 10:57:29 2007\|\|Memory: 768.00 MB physical, 501.27 MB virtual Fr 20 Apr 10:57:29 2007\|\|Disk: 56.12 GB total, 251.27 MB free Fr 20 Apr 10:57:30 2007\|rosetta@home\|URL: http://boinc.bakerlab.org/rosetta/; Computer ID: 337257; location: (none); project prefs: default Fr 20 Apr 10:57:30 2007\|boincsimap\|URL: http://boinc.bio.wzw.tum.de/boincsimap/; Computer ID: 39400; location: (none); project prefs: default Fr 20 Apr 10:57:30 2007\|SETI@home\|URL: http://setiathome.berkeley.edu/; Computer ID: 3113647; location: home; project prefs: default Fr 20 Apr 10:57:30 2007\|\|General prefs: from rosetta@home (last modified 2007-04-09 12:16:42) Fr 20 Apr 10:57:30 2007\|\|Host location: none Fr 20 Apr 10:57:30 2007\|\|General prefs: using your defaults Fr 20 Apr 10:57:32 2007\|rosetta@home\|Restarting task CNTRL_ABRELAX_SAVE_ALL_OUT_-2chf_-_filters_1615_96931_0 using rosetta version 559 Fr 20 Apr 13:40:30 2007\|\|Suspending computation - user request Fr 20 Apr 14:21:54 2007\|\|Resuming computation best wishes rechenknecht 123
2) Message boards : Number crunching : Problems with Rosetta version 5.59 (Message 39568) Posted 18 Apr 2007 by rechenknecht123 Post: Mi 18 Apr 13:55:15 2007\|\|Host location: none Mi 18 Apr 13:55:15 2007\|\|General prefs: using your defaults Mi 18 Apr 13:55:15 2007\|rosetta@home\|Task s029__BOINC_SYMM_FOLD_AND_DOCK_RELAX-s029_-truncate_hom001__1638_96906_0 is 0.66 days overdue. Mi 18 Apr 13:55:15 2007\|rosetta@home\|You may not get credit for it. Consider aborting it. Mi 18 Apr 13:55:15 2007\|\|Running CPU benchmarks Mi 18 Apr 14:00:18 2007\|\|[error] CPU benchmarks timed out, using default values Mi 18 Apr 14:00:21 2007\|\|[error] Process 540 not found Mi 18 Apr 14:00:21 2007\|rosetta@home\|Restarting task s029__BOINC_SYMM_FOLD_AND_DOCK_RELAX-s029_-truncate_hom001__1638_96906_0 using rosetta version 559 Mi 18 Apr 14:00:21 2007\|\|Running CPU benchmarks Mi 18 Apr 14:00:21 2007\|\|Suspending computation - running CPU benchmarks Mi 18 Apr 14:01:26 2007\|\|Benchmark results: Mi 18 Apr 14:01:26 2007\|\| Number of CPUs: 1 Mi 18 Apr 14:01:26 2007\|\| 267 floating point MIPS (Whetstone) per CPU Mi 18 Apr 14:01:26 2007\|\| 603 integer MIPS (Dhrystone) per CPU Mi 18 Apr 14:01:29 2007\|\|Resuming computation Mi 18 Apr 14:01:56 2007\|rosetta@home\|Computation for task s029__BOINC_SYMM_FOLD_AND_DOCK_RELAX-s029_-truncate_hom001__1638_96906_0 finished Mi 18 Apr 14:01:56 2007\|rosetta@home\|Output file s029__BOINC_SYMM_FOLD_AND_DOCK_RELAX-s029_-truncate_hom001__1638_96906_0_0 for task s029__BOINC_SYMM_FOLD_AND_DOCK_RELAX-s029_-truncate_hom001__1638_96906_0 absent Mi 18 Apr 14:02:00 2007\|rosetta@home\|Deferring communication for 1 min 0 sec Mi 18 Apr 14:02:00 2007\|rosetta@home\|Reason: Unrecoverable error for result s029__BOINC_SYMM_FOLD_AND_DOCK_RELAX-s029_-truncate_hom001__1638_96906_0 (<file_xfer_error> <file_name>s029__BOINC_SYMM_FOLD_AND_DOCK_RELAX-s029_-truncate_hom001__1638_96906_0_0</file_name> <error_code>-161</error_code></file_xfer_error>) abort crunch what happend ? powerbook g4 400 ppc 7410/ mac os x 10.39- bonic man 5.8.17. greets rechenknecht
3) Message boards : Cafe Rosetta : distributed computing story in C&EN (Message 39309) Posted 12 Apr 2007 by rechenknecht123 Post: this is the link. http://pubs.acs.org/isubscribe/journals/cen/85/i14/html/8514sci2.html Elisabeth can you get en offical post of the story because its only for members of cen thanks rechenknecht123 Thanks very much everyone, for your very helpful responses! The story will appear in the April 2 issue of C&EN. pubs.acs.org/cen best, Elizabeth Wilson
4) Message boards : Number crunching : sony will sell grid computing on ps3 fur comcial use Financial times 10/04 /2007 (Message 39263) Posted 11 Apr 2007 by rechenknecht123 Post: http://www.ft.com/cms/s/1238b9f2-e799-11db-8098-000b5df10621.html ony in talks on commercial use for PS3 By Mariko Sanchanta in Tokyo Published: April 10 2007 20:34 \| Last updated: April 10 2007 20:34 Sony PlayStation 3 users may soon be asked to share the supercomputer power of their video game consoles with companies that lack their own technology to run complex research projects, the Financial Times was told. Sony Computer Entertainment is in discussions with a number of companies about possible commercial applications for the PlayStation 3. This comes in the wake of its non-profit partnership with Stanford University in March that harnesses the spare computing capacity of registered PS3s for the analysis of protein cells. However, because this would be a commercial proposition that would benefit profit-making organisations, Sony is studying whether it would need to offer incentives, such as free products, to persuade PS3 owners to participate. PS3s run on the revolutionary Cell processor – co-designed by Sony, IBM and Toshiba – and they can be linked with tens of thousands of other idle PS3s via the internet to run a single analytical programme. A network of just 10,000 PS3s would have as much power as a 200,000-strong network of personal computers. Masa Chatani, chief technology officer at Sony Computer Entertainment, said in an interview with the FT on Tuesday that the company had received numerous inquiries regarding this “distributed computing” model. Under Stanford University’s Folding@Home programme, which studies how protein cells assemble, PS3 users can join the network by clicking on an icon on the screen. Stanford automatically sends packets of data out to these machines – which have to remain switched on when they are idle – to analyse and collect, tabulate and visualise the results. “This kind of computing model could be used in a commercial application,” Mr Chatani said. “For example, a start-up or a pharmaceutical company that lacks a super-computer could utilise this kind of infrastructure. We are discussing various options with companies and exploring commercial applications.” He added: “If there is a big problem to be solved, each computer is responsible for processing a small chunk of information, then by analysing it all together a big conclusion can be made. At any single moment, there are 11,000-12,000 PS3 users participating in Folding@Home. The number of contributors is far greater than we had anticipated.” A commercial endeavour would be a more difficult strategically, Mr Chatani admitted, because users would be loathe to let companies use the power of their PS3 Cell processors for free. One scenario, he said, would be for a company to offer each of its PS3 users incentives such as free products, or points, in exchange for their participation in distributed computing. Copyright The Financial Times Limited 2007 in german http://www.heise.de/newsticker/meldung/88087
5) Message boards : Number crunching : WU run times out of whack (Message 39232) Posted 10 Apr 2007 by rechenknecht123 Post: lost 4 WU- times as en error of my mac os x 10.3.9 installation ppc g4 400MHZ . wu estimatet time ca. 4-5h , real chruching time 13h cpu time - 1 day in liftime- 3 checkponit nesccery at my opinion at 25%,50%,75% ready of work. so it is not so userfriendly. lost 2 seti WU as time overdue of the SETI-WUs. grettings rechenknecht My main consideration for wanting short runtimes in this project is the lack of checkpointing within a model. I don't want to have a machine go off and lose 2, 3, 4 hours of work. This is one focal point of the Rosetta release that is presently under development. More frequent checkpoints will allow BOINC more flexibility in rotating amongst projects as well, as I believe the new BOINC version has a strong preference to only switch when a task reaches a checkpoint. This will help debt remain near zero as well, another advantage. The next release is only a few weeks away. But until then, if you set your cache size down lower for a short time, then ratchet your WU runtime preference up to even the 3 hour default (or higher), then once DCF adjusts and predicts new tasks will take about 3hrs (or the new runtime preference), then set cache as desired... then you'll be quite happy with the accuracy of the completion times and the cache size. Setting the runtime preference higher will not risk loseing any work that is not already being lost. So there's really nothing to lose in trying a longer runtime.
6) Message boards : Number crunching : Problems with Rosetta version 5.59 (Message 39188) Posted 9 Apr 2007 by rechenknecht123 Post: Might a Boinc problem. this WU. Mo 9 Apr 11:02:32 2007\|rosetta@home\|Resuming task s029__BOINC_SYMM_FOLD_AND_DOCK_RELAX-s029_-truncate_hom014__1638_298_1 using rosetta version 559 Running up til 6:24:20h running time at 97,455% ready. resttime 0:09:21h in step 1. modell 69969 then stop the All WUs( seti, simap, r@h) in Bonic- all runs fine. wenn i press start to continue the single WU. but as i close boinc over the Quit- button in the Menue this happends. rechenknecht Just a minor problem observed (may not be RAH's problem): I'm currently crunching 1fkaA_BOINC_ZEROWATSONCRICK_RNA_ABINITIO-1fkaA-chunk006__1659_76_1. I changed my RAH preferences (resource share) while another project was running. A new WU downloaded from RAH. When BOINC switched back to my first RAH WU, the Progress % reset to zero. (Thankfully) CPU Time did not change, but the To Completion time grew to almost double (to 03:58:45) what it was before switching projects/changing prefs/downloading new WU. Like I say, the CPU Time did not change, so there was no loss of work. I realise it could be a BOINC issue as much as RAH, but I thought I'd share this anyway. Prime Lemur
7) Message boards : Number crunching : Problems with Rosetta version 5.59 (Message 39187) Posted 9 Apr 2007 by rechenknecht123 Post: Might a Boinc problem. this WU. Mo 9 Apr 11:02:32 2007\|rosetta@home\|Resuming task s029__BOINC_SYMM_FOLD_AND_DOCK_RELAX-s029_-truncate_hom014__1638_298_1 using rosetta version 559 Running up til 6:24:20h running time at 97,455% ready. resttime 0:09:21h in step 1. modell 69969 then stop the All WUs( seti, simap, r@h) in Bonic- all runs fine. wenn i press start to continue the single WU. but as i close boinc over the Quit- button in the Menue this happends. rechenknecht Just a minor problem observed (may not be RAH's problem): I'm currently crunching 1fkaA_BOINC_ZEROWATSONCRICK_RNA_ABINITIO-1fkaA-chunk006__1659_76_1. I changed my RAH preferences (resource share) while another project was running. A new WU downloaded from RAH. When BOINC switched back to my first RAH WU, the Progress % reset to zero. (Thankfully) CPU Time did not change, but the To Completion time grew to almost double (to 03:58:45) what it was before switching projects/changing prefs/downloading new WU. Like I say, the CPU Time did not change, so there was no loss of work. I realise it could be a BOINC issue as much as RAH, but I thought I'd share this anyway. Prime Lemur
8) Message boards : Number crunching : Problems with Rosetta version 5.59 (Message 39186) Posted 9 Apr 2007 by rechenknecht123 Post: Hallo anders n, this is a other WU- on my other disk partition. it Runs under MAc os 10.49 in the Boinc container 5.8.15 . at 97,415% ready cpu time 6:17:00h time til ready 00:09:54h stands there for 10 min. Grafic kontrol is ok- stage symetric relax stands at model 1. step 69969 acceptet energy: - 311,4855 Now Mo 9 Apr 11:02:32 2007\|rosetta@home\|Resuming task s029__BOINC_SYMM_FOLD_AND_DOCK_RELAX-s029_-truncate_hom014__1638_298_1 using rosetta version 559 Hi Rhiju, and anders n, this WU Mo 9 Apr 00:02:04 2007\|rosetta@home\|Restarting task s029__BOINC_SYMM_FOLD_AND_DOCK_RELAX-s029_-truncate_hom001__1638_96906_0 using rosetta version 559 hangs now in the 13h. at 98,745 % no checkpoint wrote, now i runs from Zero 0 %, 3104:34:17h to run the 5 run at Easter. what now kill for ever or run a 6 time. rechenknecht Hi there I tried to calculate how long a model should take on your MAC. It should take 3,5-5,5 H with that kind of Wu. If you decide to let it run check the grafics sometimes so the steps are counting up. Anders n
9) Message boards : Number crunching : Problems with Rosetta version 5.59 (Message 39180) Posted 8 Apr 2007 by rechenknecht123 Post: Hi Rhiju, and anders n, this WU Mo 9 Apr 00:02:04 2007\|rosetta@home\|Restarting task s029__BOINC_SYMM_FOLD_AND_DOCK_RELAX-s029_-truncate_hom001__1638_96906_0 using rosetta version 559 hangs now in the 13h. at 98,745 % no checkpoint wrote, now i runs from Zero 0 %, 3104:34:17h to run the 5 run at Easter. what now kill for ever or run a 6 time. rechenknecht Hi greg_be ... I think the behavior is OK. Please leave it running! Fixing the scale on the graph of the energy is definitely on the "TO DO" list. This seems to be stuck when it is in ab initio stage. As far as I can tell the strand is stuck, its on model 24 step 11,000 and counting higher. But the RMSD is stuck on 13.xx with xx being the variable numbers. The accepted energy is not really stuck, but does not register on the graph. It appears stuck at the top. The progress keeps counting in BOINC manager though, so it's not stuck in a endless loop according to it. I will let it run its course as it is now 6 hrs into the process. I have one more WU of the same type to run still. Is this normal?
10) Message boards : Number crunching : Problems with Rosetta version 5.59 (Message 39160) Posted 8 Apr 2007 by rechenknecht123 Post: I don't know what happend. After 11H there should have been atleast a few models made. Next time you shut down the MAC please check in the grafics how much work it has done on the WU. Then check again when you restart it. I will Do this, but no the Boning Manager 5.8.17 gets " Grey" and no grafic window openens, running time 1:03:12h ready 35,456% rest time 1276:50:15h so i can`t control the checkpoint in the moment. If it happens again please post here again. i will do Remember for now 1 model has to be done before a checkpoint is made. (they are working at more checkpoints in the Wu) Anders n thanks Anders n rechenknecht
11) Message boards : Number crunching : Problems with Rosetta version 5.59 (Message 39158) Posted 8 Apr 2007 by rechenknecht123 Post: Running time 00:24:00 13,327% Time til ready 2281:34:26 Result ID 71817153 Time to complete dropping fast? yes time to complete dropping very fast in my eyes runnning time 00:35:00h complete 19,624% time til ready 1981:05:45h runinning time 00:54:18h complete 30,359% time til ready 1482:56:34h What model did at restart at? now when i click on show grafics the boing manager gets " Grey " and no grafic is shown
12) Message boards : Number crunching : Problems with Rosetta version 5.59 (Message 39156) Posted 8 Apr 2007 by rechenknecht123 Post: 98,547 % running time 11.50h resttime 00:38.45h is that 11H 50 min? yes this was the running time before i restart my powerbook after rosetta was running in the night. after restart all was 0 % and 00:00:00h running time Rest til ready 3012:06:07h
13) Message boards : Number crunching : Problems with Rosetta version 5.59 (Message 39153) Posted 8 Apr 2007 by rechenknecht123 Post: If you look to the right on grafics it looks something like this Model: 5(?) Step: 300245 what model do you have? now Run Model 1 step 23613
14) Message boards : Number crunching : Problems with Rosetta version 5.59 (Message 39152) Posted 8 Apr 2007 by rechenknecht123 Post: Running time 00:24:00 13,327% Time til ready 2281:34:26 Result ID 71817153 Time to complete dropping fast? yes time to complete dropping very fast in my eyes runnning time 00:35:00h complete 19,624% time til ready 1981:05:45h What model did at restart at? So 8 Apr 13:50:13 2007\|\|Starting BOINC client version 5.8.17 for powerpc-apple-darwin So 8 Apr 13:50:13 2007\|\|log flags: task, file_xfer, sched_ops So 8 Apr 13:50:13 2007\|\|Libraries: libcurl/7.15.5 OpenSSL/0.9.7l zlib/1.1.4 So 8 Apr 13:50:13 2007\|\|Data directory: /Library/Application Support/BOINC Data So 8 Apr 13:50:15 2007\|\|Processor: 1 Power Macintosh Power Macintosh [Power Macintosh Model PowerBook3,2] [AltiVec] So 8 Apr 13:50:15 2007\|\|Memory: 768.00 MB physical, 604.07 MB virtual So 8 Apr 13:50:15 2007\|\|Disk: 27.42 GB total, 354.07 MB free So 8 Apr 13:50:16 2007\|rosetta@home\|URL: http://boinc.bakerlab.org/rosetta/; Computer ID: 328691; location: (none); project prefs: default So 8 Apr 13:50:16 2007\|boincsimap\|URL: http://boinc.bio.wzw.tum.de/boincsimap/; Computer ID: 33988; location: (none); project prefs: default So 8 Apr 13:50:16 2007\|Predictor @ Home\|URL: http://predictor.scripps.edu/; Computer ID: 282590; location: (none); project prefs: default So 8 Apr 13:50:16 2007\|\|General prefs: from Predictor @ Home (last modified 2007-02-16 01:17:52) So 8 Apr 13:50:16 2007\|\|Host location: none So 8 Apr 13:50:16 2007\|\|General prefs: using your defaults So 8 Apr 13:50:16 2007\|rosetta@home\|Restarting task s029__BOINC_SYMM_FOLD_AND_DOCK_RELAX-s029_-truncate_hom001__1638_96906_0 using rosetta version 559
15) Message boards : Number crunching : Problems with Rosetta version 5.59 (Message 39150) Posted 8 Apr 2007 by rechenknecht123 Post: If I opens the Grafik the the Left window with " Searching runs" Low energy at -71,xxx now at 00:31:0h 17,166% ready time til ready 2105:44:05h to crunsch mac os 10:39 powerbook g 4/ @400mhz 786 mb ram rechenknecht
16) Message boards : Number crunching : Problems with Rosetta version 5.59 (Message 39148) Posted 8 Apr 2007 by rechenknecht123 Post: Running time 00:24:00 13,327% Time til ready 2281:34:26 Result ID 71817153
17) Message boards : Number crunching : Problems with Rosetta version 5.59 (Message 39146) Posted 8 Apr 2007 by rechenknecht123 Post: The same problem with So 8 Apr 13:50:16 2007\|rosetta@home\|Restarting task s029__BOINC_SYMM_FOLD_AND_DOCK_RELAX-s029_-truncate_hom001__1638_96906_0 using rosetta version 559 Result ID 71817153 end befor restart powerbook mac os 103.9 98,547 % running time 11.50h resttime 00:38.45h what happen there When I started my Powerbook up again, I noticed that the Progress of the same work unit is 0% and the data processing has since restarted. I didn't see any error messages at the time of when I switched my mac back on.[/quote]