Posts by Rollo

1) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (4) (Message 55505) Posted 3 Sep 2008 by Rollo Post: Can you make a similar comparison for CASP8 as POEM did here?
2) Message boards : Number crunching : Newbie-trying-to-get-the-hang-of-it (Message 23546) Posted 19 Aug 2006 by Rollo Post: Hey again! What, if anything, did I do wrong when setting up my laptop? Pls adv. stderr out <core_client_version>5.4.11</core_client_version> <message> Incorrect function. (0x1) - exit code 1 (0x1) </message> <stderr_txt> # random seed: 1660561 # cpu_run_time_pref: 21600 # cpu_run_time_pref: 7200 ERROR:: Exit at: .dock_structure.cc line:401 Nothing. error messages with 'xxx.cc line: yy' indicate a problem with the rosetta software. It is either a problem with the type of workunit or the rosetta program itself.
3) Message boards : Number crunching : Thread Delete: Why I am pulling my machines out. (Message 23516) Posted 19 Aug 2006 by Rollo Post: The one big disadvantage with external forum software is, that in case of trouble with rosetta, there is no easy way to have a look at the erorrs, because the nick are not linked to the boinc database.
4) Message boards : Number crunching : "Predictor of the Day" question... (Message 22232) Posted 11 Aug 2006 by Rollo Post: On a slightly off topic but related point, does anyone know what happened to the scatterplots showing people their results compared to other results for each protein? I miss those. These plots need the RMSD value (as x axis). To determine the RMSD value the native structure is needed, which is not released (yet) for the CASP7 proteins.
5) Message boards : Number crunching : targets 290 to 295 (Message 18795) Posted 16 Jun 2006 by Rollo Post: Targets 290 to 295 are published in the protein database according to the CASP7 website. Is it possible now to do create the top predictions for these proteins? If so, it would be interesting to know how low the best RMSD is.
6) Message boards : Number crunching : Report Problems with Rosetta Version 5.16 II (Message 17350) Posted 30 May 2006 by Rollo Post: I am crunching on 21970571 right now. It stops after reaching 1.210% at time step 2833. If I stop boinc and let it restart from the last checkpoint (here: from the beginning), it stops at same step 2833 in model 1. For me this seems reproducible. Any suggestions, what I can do to produce a reasonable error report, except abort the workunit or wait for the watchdog? I'd wait at least an hour. In theory the watchdog should terminate it after an hour. This is a good opportunity to see if it really works as it should. In any case let it run a few hours and if it really keeps stuck at step 2833 abort and you get all the credits for the time crunched. The watchdog killed the workunit. I have made a backup, so I can rerun it, if that is of any interest.
7) Message boards : Number crunching : Report Problems with Rosetta Version 5.16 II (Message 17317) Posted 29 May 2006 by Rollo Post: I am crunching on 21970571 right now. It stops after reaching 1.210% at time step 2833. If I stop boinc and let it restart from the last checkpoint (here: from the beginning), it stops at same step 2833 in model 1. For me this seems reproducible. Any suggestions, what I can do to produce a reasonable error report, except abort the workunit or wait for the watchdog?
8) Message boards : Number crunching : Report Problems with Rosetta Version 5.16 I (Message 16629) Posted 19 May 2006 by Rollo Post: Wow, that's totally weird. I've never seen that on my Mac. Does the text ever return to normal? Here, I just caught one on Ralph. These two snaps were taken within 10 seconds of each other: The words get stretched out lower and longer to the point that it just becomes a straight line. No. Not until the next model is processed.
9) Message boards : Rosetta@home Science : Comments/questions on Rosetta@home journal (Message 16252) Posted 14 May 2006 by Rollo Post: Today (Friday) we have closed accepting server predictions for the first target, T0283. What should be done with T0283 WUs that are still on our machines? Also. should the deadlines for the CASP7 WUs be just a bit ealier than the real deadlines. Back to the T0283. One of them I still got running has a deadline of May 27. But if the CASP deadline was May 12, will those results be of any benefit? Do Rosetta belong to the group 'server prediction' or 'human expert prediction'? If the latter, than it should be called 'human expert prediction (computer assisted)'.
10) Message boards : Rosetta@home Science : Comments/questions on Rosetta@home journal (Message 16036) Posted 12 May 2006 by Rollo Post: If I understand Casp correctly, you're only allowed to turn in 5 guesses.. and if using lowest energy, then you'll send in the blue spot, and two models on the left and the two on the right that are just a little higher energy than the blue dot. Since you can't graph the CASP7 results like this (not having the native structure to compare RMSD on), then there's no way to select the higher energy models 1 angstrom to the left of the 5 low energy models? One could use the following approach. Use the lowest energy structure as a reference and calculate the RMSD to that one. Then send only structures as guess 2 to 5, which have at least an RMSD > x compared to the lowest energy structure.
11) Message boards : Number crunching : Report Problems with Rosetta Version 5.13 (Message 16023) Posted 12 May 2006 by Rollo Post: running homo log abrelax homo 002_t283_505_162 . When the progam started i don't get space for RSMD on the display That is because you are modelling a protein from the CASP7 trials. Researchers gave their results for the shape of the proteins to the CASP7 organizers, without publishing it at the moment. Now several groups try to figure the shape f the protein from the amino acid sequence without knowing the shape, which is of course the purpose for which rosetta is made. So withou the original shape no RMSD can be calculated for your models and thus you do not see see it.
12) Message boards : Number crunching : Rosetta keeps preempting (Message 15458) Posted 3 May 2006 by Rollo Post: What about setting no new work for CPDN, so you have only one model running, and than increase the resource share of CPDN to more than 50%, lets say 60%. Since you have only one CPDN model, boinc cannot run that model on both cores simultaneously. So you can run CPDN effectivly at maximum of 50% share. This is lower than your setting of 60%. Therefore CPDN should always run and prevent rosetta from starting on both cores.
13) Message boards : Number crunching : Team Credit (Message 15056) Posted 30 Apr 2006 by Rollo Post: documentational post: Members (with AND without Credit) 2 Total credit 169.44 Recent average credit 53.40 Used for later reference That were exactly the numbers before I quit. (a short but pleasant stay :)
14) Message boards : Number crunching : Team Credit (Message 15047) Posted 29 Apr 2006 by Rollo Post: Rollo, I've attached two AMD64 3700's, one AMD64 2800, and one P4 1.8 to Rosetta, that should start running up the total team score, if you wan't the team that is. I really don't care about the team. I just wanted to help with the test. If you want to do other tests, I'm glad to leave, thrown out (whatever suits you :).
15) Message boards : Number crunching : Team Credit (Message 15040) Posted 29 Apr 2006 by Rollo Post: Now, If I remove Rollo from the team, his credit is supposed to be dropped from the team total, but what if he removes himself?? Any Ideas? We can only test one of the above. It's up to you.
16) Message boards : Number crunching : Team Credit (Message 15018) Posted 29 Apr 2006 by Rollo Post: I joined. I was not in a team before and have morethan 6000 credits. Lets see what happens.
17) Message boards : Rosetta@home Science : rosetta client changelogs? (Message 14265) Posted 21 Apr 2006 by Rollo Post: From where? Did you mean download the app? Or to check the app version? from here
18) Message boards : Number crunching : Does Rosie create new jobs if no 'net connection available? (Message 14118) Posted 19 Apr 2006 by Rollo Post: Rosetta must be able to tell if there is work available as it crunches the work if it is! If there is no work available then it's a case of running the next model of the current job and adding it to the result file. If it's the last job in the queue then it shouldn't be marked for upload as more models will be run on it until there's another job added to the queue. It can then be marked for upload by BOINC, and as BOINC has no idea what's in the result file it'll send it as if it was the result file without the extra models in. Are there any major flaws in my logic? (I don't mind minor flaws...) I am no expert, but I think, that rosetta has no knowledge about the boinc queue. Therefore it can not decide whether it is working on the last model or not...
19) Message boards : Cafe Rosetta : Message encrypter? (Message 13978) Posted 17 Apr 2006 by Rollo Post: Search for rot-13 and you get www.rot13.com. HTH
20) Message boards : Number crunching : Result was reported too late to validate ???????????? (Message 11890) Posted 11 Mar 2006 by Rollo Post: How can you use a quorum in a system, in which each user can set a different run time for the _same_ work unit. A quorum simply make no sense at all.

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