Posts by Mike Tyka

21) Message boards : Number crunching : Minirosetta 1.95/1.96 (Message 62996) Posted 21 Aug 2009 by Mike Tyka Post: Please post your bug reports here! This release has mainly internal, scientific bugfixes.
22) Message boards : Number crunching : Minirosetta 1.86 (Message 62473) Posted 26 Jul 2009 by Mike Tyka Post: THis update includes bugfixes in the disulfide part of the code. NOTE: THere has been a problem uploading this to the server (something went wrong with signing the app), we are currently trying to resolve this - sorry for the outage, we'll try and have this fixed ASAP. Mike
23) Message boards : Number crunching : Rosetta Application Version Release Log (Message 62470) Posted 26 Jul 2009 by Mike Tyka Post: 1.86 is out.
24) Message boards : Number crunching : Minirosetta 1.82/1.88 (Message 62226) Posted 14 Jul 2009 by Mike Tyka Post: Ok, 1.82 is out. This one has - Support for Disulfides. New Science! - Bug fixes for homology modelling with constraints - SOme bugfixes in the watchdog Mike
25) Message boards : Number crunching : Problems with Minirosetta 1.80 (Message 62225) Posted 14 Jul 2009 by Mike Tyka Post: 1.82 is up.
26) Message boards : Number crunching : Problems with Minirosetta 1.76 (Message 61805) Posted 17 Jun 2009 by Mike Tyka Post: Which jobs are failing for you ? The lb_thread_all_multi can all be cancelled, sure. Let us know if anything else is consistently dying. M
27) Message boards : Number crunching : Problems with Minirosetta 1.75 (Message 61769) Posted 15 Jun 2009 by Mike Tyka Post: Hi FalconFly - I don't see the validation problems you're reporting over on RALPH. Could you join over there for a little while, otherwise I cannot actually see the log files your machine is producing. M
28) Message boards : Number crunching : All tasks beginning with lb* have computation error (Message 61714) Posted 12 Jun 2009 by Mike Tyka Post: Yes this was a rotten batch. I don't know how this got through RALPH, the person submitting these jobs has been notified. Sorry about the errors. The lastest WUs seem to be running smoothly though! Thanks for crunching ! Mike
29) Message boards : Number crunching : Problems with Minirosetta 1.75 (Message 61691) Posted 11 Jun 2009 by Mike Tyka Post: Sorry - they were off by mistake. They should be back up now. My bad.
30) Message boards : Number crunching : Rosetta Application Version Release Log (Message 61666) Posted 11 Jun 2009 by Mike Tyka Post: Rosetta 1.75 is out - update your firewalls. Cheers, Mike
31) Message boards : Number crunching : Problems with Minirosetta 1.75 (Message 61665) Posted 11 Jun 2009 by Mike Tyka Post: This one includes a number of new features allowing us to analyse larger amounts of data for homolog modelling and has new features for Docking, and, as always, bugfixes and (hopefully) improved stability. Please post issues here! Mike
32) Message boards : Number crunching : Rosetta Application Version Release Log (Message 61416) Posted 27 May 2009 by Mike Tyka Post: 1.71 is up !
33) Message boards : Number crunching : Problems with Minirosetta Version 1.67 (Message 61163) Posted 13 May 2009 by Mike Tyka Post: http://boinc.bakerlab.org/rosetta/result.php?resultid=250780868 iRp40_S_3d85_ip40_1zzo.pdb.gz_00000010_fa_dock.xml_score12_pert38_DOCK_11891_476_1 "The validator error has been found: Our data format was changed and the validator was not updated. We're doing that now. " More details please? Lol - sure if you want the gory details, here they are :) Here's the content of one of our result files: SEQUENCE: IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQKNKTFLRCEAKNYSGRFTCWWL TTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRNKEYEYSVECQEDSACPAAEESLPIEVMVDAVHKLKYEQYTSSFFIRDIIKPDPPKNLQLKPLQVEVSWEYPDTWSTPHSYFSLTFCVQVQGKD RVFTDKTSATVICRKNASISVRAQDRYYSSSWSEWASVPCAHPLENAWTFWFDNPQGKSRQRDWGSTIHPIHTFSTVEDFWGLYNNIHNPSKLNVGADFHCFKNKIEPKWEDPISANGGKWTISCGRGKS DTFWLHTLLAMIGEQFDFGDEICGAVVSVRQKQERVAIWTKNAANEAAQISIGKQWKEFLDYKDSIGFIVHEDAKRSDKGPKNRYTV SCORE: score fa_atr fa_rep fa_sol hack_elec hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss _dst dslf_cs_ang dslf_ss_dih dslf_ca_dih fa_dun ref rms description REMARK BINARY_SILENTFILE SCORE: -575.033 -705.385 16.172 295.133 -5.204 -24.046 -60.222 -11.093 -8.141 -11 .137 -8.813 -2.536 -2.322 19.600 -67.040 6.010 S_S_3d85_ip40_2idv.pdb.gz_00000009.pdb.gz_00000001 FOLD_TREE EDGE 1 117 -1 EDGE 117 290 -1 EDGE 117 405 1 EDGE 405 291 -1 EDGE 405 467 -1 S_S_3d85_ip40_2idv.pdb.gz_00000009.pd b.gz_00000001 RT 0.635059 0.770564 -0.0541478 -0.64237 0.565739 0.51701 0.429023 -0.293549 0.854265 -20.5199 35.9508 31.0298 S_S_3d85_ip40_2id v.pdb.gz_00000009.pdb.gz_00000001 ANNOTATED_SEQUENCE: I[ILE_p:NtermProteinFull]WELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKE DGIWSTDILKDQKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRNKEYEYSVECQEDSACPAAEESLPIEVMVDAVHKLKYEQYTSSFFIRDIIKPDPPKNLQL KPLQVEVSWEYPDTWSTPHSYFSLTFCVQVQGKDRVFTDKTSATVICRKNASISVRAQDRYYSSSWSEWASVPC[CYS_p:CtermProteinFull]A[ALA_p:NtermProteinFull]HPLENAW TFWFDNPQGKSRQRDWGSTIH[HIS_D]PIHTFSTVEDFWGLYNNIHNPSKLNVGADFHCFKNKIEPKWEDPISANGGKWTISCGRGKSDTFWLHTLLAMIGEQFDFGDEICGAVVSVRQKQERVAIWTK NAANEAAQISIGKQWKEFLDYKDSIGFIVH[HIS_D]EDAKRSDKGPKNRYTV[VAL_p:CtermProteinFull] S_S_3d85_ip40_2idv.pdb.gz_00000009.pdb.gz_00000001 CHAIN_ENDINGS 290 S_S_3d85_ip40_2idv.pdb.gz_00000009.pdb.gz_00000001 LWOksBxKHvH0xLCoQ5QbqBJbn1HUO0GoQR2+oB13P8HErc8nQ++JqBZkt+HEv0rnQO0irBZQg8HkSMQoQ99TpBVNeAI0KHXoQf/UtBZ5wCIUMIMoQEYVqBBr8CIUgVhoQD IduB1lIwHUqmEoQk8gsB5SJnHUh4CoQ+/6sBJ6YvHEho0nQUo3oBdqiwHEfMKoQ+TtsBpFZ3HkQgVoQlYQoBNcdDIEEYSoQjs9nBBBW6H057YoQueEuBFYFFIU14SoQKxA vBFYFBI0GvHoQGZLsB9SXFIkR2GoQy2poBtdeEIk++loQNeZrBtz3/HEAAmoQDCsrB5lOGIUKcfoQ S_S_3d85_ip40_2idv.pdb.gz_00000009.pdb.gz_00000001 LBWZmBBrc+HkWk/nQ++5kBx0tCIEW5wnQqGviBFYlFIUep9nQ8nKiBtyBEIUy2HoQ46xjB9na/HEZ7cnQVj3hBd8S2HkoFhnQKxgiBhU4rH0gAlnQ2O/dB9S32HEsyhnQt dOgB557lHEAAonQOJGcBZQgsHUGEmnQRLSaBdSM/H0IbfnQwfqWBhrHqHE+TnnQQ14UBVO08HU6mgnQhrHTBRgVyH04lknQcSclBFXP7H0NJGoQXsPmBVTtFI02GqnQIwq iBlsdCI0GvSnQXPalBtz37HEsyTnQfUokBNy2pH00NlnQXPKgBlBBeHkrHrnQZ7cbBdnvDIEFucnQyLdVBhU4hHkmZqnQFDCSBlupBIUjXenQpw1OBJFuwHEShlnQ S_S_ 3d85_ip40_2idv.pdb.gz_00000009.pdb.gz_00000001 LZ7shB9RBKIk8S1nQFDifBx0NNIECsAoQgqxZBRK8LIkSM8nQT3EYBd9oMI025pnQiBRgBRhLTIESh9nQBr8cB5k4WI03PFoQWOUeBB/pcI0bSDoQamZhBB/JeIU5QFoQT iBbBlsdfIk789nQnvPiBhVOLIUxgmnQlB8fBh9YMIUzNJoQzhWiBZ78TIkqxAoQam5fB125TIUxgsnQcSsYBlYQWIULyDoQuz3dB1h2VIkQgNoQ S_S_3d85_ip40_2idv .pdb.gz_00000009.pdb.gz_00000001 LgVuWBxJRKIkSMGoQ67HRB1h2II0yhEoQZ78NBZ78NIE7RDoQrcILB9TtOI0Jx2nQKc9OBpvfFIkR2NoQc9IJBNepDI0fqMoQx1jIBVMIAIULyCoQPKcHBd9oAIUhrWoQM dTYB989JIkZmNoQx+uQBVEiGI0eY6nQmupRBtHFCIE7RNoQ2jiPB5OfHIUxgVoQhArGBR2OHIkEDMoQjXaEBxfq9HkBBCoQ+TtJBpFZCIUHa3nQEtILBJaR5HU3kDoQzMT DBxfq+H0P1VoQKxAKBh/U6HEsyXoQ46xHBxJRDIU6mdoQ S_S_3d85_ip40_2idv.pdb.gz_00000009.pdb.gz_00000001 LtIbOB55bRIk8SLoQXktLBJxgWI0eULoQR2OPBR2OaIUIwRoQCBWTBFDiYIEAAWoQOJGGBpZGWIEqGQoQ789FBhUYUIEsyboQ9oQABpvfTI0cofoQepb6A13vYIUKcgoQ6 mEvAlX6XIU6mjoQgqxQBxLdQIkWkRoQ0rULBBN/XIEaJDoQ03PEBFDCaI0eUPoQ3k4DBx0NTI0bSLoQR2OIBhArQI04lcoQCB2HBpvfXI04lgoQFue8AdR2QIk++ZoQBWZ ABNJmRIUNenoQ3kY+ANIQbIUjXmoQIFu6AZktaIE/pYoQueUrA5OfbI0jCkoQamZrA14lVIUJGeoQCsyuANJGWIktzqoQ S_S_3d85_ip40_2idv.pdb.gz_00000009.p db.gz_00000001 THere's a line there starting with CHAIN ENDINGS - that was added b one of our developers. We didn't realize and so the validator was not updated, hence rejecting these results that contained that new line. It should be fixed now.
34) Message boards : Number crunching : Problems with Minirosetta Version 1.67 (Message 61137) Posted 12 May 2009 by Mike Tyka Post: The validator error has been found: Our data format was changed and the validator was not updated. We're doing that now.
35) Message boards : Number crunching : screensaver bug..? (Message 61134) Posted 12 May 2009 by Mike Tyka Post: Thanks! This issue will be fixed in the next release. It seems to only affect jobs with _seq_ in the name, and we're not sending out any more jobs out like that right now. M
36) Message boards : Number crunching : Rosetta Application Version Release Log (Message 61055) Posted 8 May 2009 by Mike Tyka Post: 1.67 is up !
37) Message boards : Number crunching : Rosetta Application Version Release Log (Message 61013) Posted 5 May 2009 by Mike Tyka Post: THe application has been updated to 1.65. This contains a small number of bugfixes, but mainly new science, particularily folding with sparse experimental data (In particular residual dipolar couplings http://en.wikipedia.org/wiki/Residual_dipolar_coupling )
38) Message boards : Number crunching : Problems with Minirosetta Version 1.64/1.65 (Message 60955) Posted 2 May 2009 by Mike Tyka Post: 1.65 was released. This is a high-priority patch that should fix a problem with the uploads.
39) Message boards : Number crunching : Problems with Minirosetta Version 1.64/1.65 (Message 60954) Posted 2 May 2009 by Mike Tyka Post: It seems that I'm using Mini 1.65 instead of 1.64 for the current work unit, but I just wanted to say that I tried reapplying the day-of-week network-availability overrides in BOINC advanced preferences to see if the work unit would freeze as it did in 1.54, and it appears to be working fine. Thanks ^_^ Yes that's one of the fixes in this version :-D excellent !
40) Message boards : Number crunching : Checkpointing under Rosetta Mini (Message 60658) Posted 15 Apr 2009 by Mike Tyka Post: Points about checkpointing. a) THe Checkpoint interval affects the flush-to-disk of checkpoints. THese can be multiple files! The log (as far as i understand) should reflect the flushing. b) Rosetta tries not to flush to disk more than the setting but will sometimes flush more frequently to prevent excessive memory buildup. c) when rosetta actuall finishes a decoy it will write to disk. This is completely unaffected by checkpointing and cannot be affected by user settings. Which jobs are miss behaving on your machine ? Mike

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