Posts by James

1) Message boards : RALPH@home bug list : minirosetta v1.43 bug thread (Message 4370) Posted 1 Dec 2008 by James Post: This is a minor update to v1.42 which was posted earlier last week, and contains the following fixes: - Excessive memory usage and long running jobs - jobs submitted with minirosetta v1.43 shouldn't have the same problems with memory and runtimes as earlier versions. - Validator errors - there was a small bug in v1.42 that resulted in results being called invalid by the BOINC server. This is now fixed. - Check point errors and restarting jobs - we have finer-grained checkpointing in our full-atom refinement mode, which means that there should be fewer errors and less wasted time. - NANs in hbonding: we have a more aggressive fix that tests for the NaN condition and continues more gracefully. This has been a tricky bug to track down, but we think that this is a big step forward. Please post bugs to this thread, and thank you very much for your patience. Cheers, James
2) Message boards : RALPH@home bug list : Ralph v1.42 (Message 4365) Posted 27 Nov 2008 by James Post: feet1st: I've solicited information from the developers in our lab about what went into our update of Ralph v1.42, and I'll let some of the other project developers speak for themselves. Here are two update messages from our protein interface design team: - "We've revised the way that filters for protein-interface design runs are executed and reported in minirosetta 1.42. This will mean shorter run times for the Rosetta @ Home participants with more meaningful output for us." - "On the design front, we've made an effort to significantly reduce the memory overhead associated with design, so users with less RAM should be able to run these tasks without it bringing their system to a halt. However, design calculations are by nature very memory-intensive. Therefore, we have also restricted all design WUs to machines that allocate no less than 512MB for Rosetta @ Home." Here's a list of updates from our structure prediction team: "Constraints: Can now specify multiple constraints. Can now specify seperate constraints for centroid/fullatom Silent files now in AbrelaxApplication (FoldCST) Relax: A bunch of previously hardcoded parameters in Relax are now parameters. Native constraints to keep natives from drifting away. Start structure constraints with Loop Selection to restrain homology modelling cores from drifting too far. BugFix in Gaussian Constraints. Added a Pose Recombiner Mode that allows proteins to be spliced together. Job Distribution: Added a shuffle mode which allows us to run the large scale relax benchmark without destroying the BOINC database by flooding it with millions of command lines." Conan - those loop boundary errors were input errors by the person who submitted those workunits. The validate errors are the result of a new format added that's not yet supported by the BOINC server, and we'll have to update our server code to deal with it over the weekend. That slow workunit bug looks like something that we fixed several months ago, we've alerted the person who submitted those jobs and he's looking into them. Thanks for crunching, and from those of us in America - Happy Thanksgiving! Cheers, James
3) Message boards : RALPH@home bug list : Ralph v1.42 (Message 4357) Posted 25 Nov 2008 by James Post: I've just updated Ralph to minirosetta to version 1.42. Please post about bugs/issues here. Cheers, James
4) Message boards : RALPH@home bug list : minirosetta v1.41 bug thread (Message 4343) Posted 16 Nov 2008 by James Post: I've just updated minirosetta to version 1.41. Please post about bugs/issues here.
5) Message boards : RALPH@home bug list : Bug Reports for Minirosetta version 1.34 (Message 4198) Posted 10 Sep 2008 by James Post: Based on these tests, we've identified an issue with on of our protocols taking an unacceptable amount of time to produce a single model, especially for larger proteins. In the next release of the minirosetta application, we're going to put an upper limit on the number of cycles that this protocol can execute so that your workunit time limits aren't exceeded in the future. Thanks for crunching! I'm going to try and write up something tomorrow about the new scientific improvements we're testing with this latest version of minirosetta.
6) Message boards : RALPH@home bug list : Bug Reports for Minirosetta version 1.34 (Message 4197) Posted 10 Sep 2008 by James Post: Based on these test, we've identified an issue with on of our protocols taking an unacceptable amount of time to produce a single model, especially for larger proteins. In the next release of the minirosetta application, we're going to put an upper limit on the number of cycles that this protocol can execute so that your workunit time limits aren't exceeded in the future. Thanks for crunching! I'm going to try and write up something tomorrow about the new scientific improvements we're testing with this latest version of minirosetta.
7) Message boards : RALPH@home bug list : minirosetta v1.26 bug thread (Message 4075) Posted 27 May 2008 by James Post: We're releasing version 1.26 of minirosetta that will hopefully fix the errors in the previous version: - improper reading of the psipred_ss2 file - problems serializing the Pose resulting in a long list of "Error writing" messages. Post bugs/issues here.
8) Message boards : RALPH@home bug list : minirosetta v1.25 bug thread (Message 4061) Posted 24 May 2008 by James Post: Please post bugs related to minirosetta v1.25 here. This version includes fixes to some of the errors identified with the v1.24 application, along with some new protocols that we're trying in CASP8.
9) Message boards : RALPH@home bug list : minirosetta v1.22 bug thread (Message 4035) Posted 19 May 2008 by James Post: We've made several updates to the minirosetta application since v1.20, and it looks like we have the memory bug fixed. The error was actually in the version of Visual Studio C++ that we were using, one of the C++ standard libraries had a memory leak that caused problems with our program. We've since updated Visual Studio, and the bug seems fixed in all of our local tests over the weekend. Post bugs related to minirosetta v1.22 here!
10) Message boards : RALPH@home bug list : minirosetta 1.19 bug thread (Message 3991) Posted 5 May 2008 by James Post: Post bugs related to minirosetta v1.19 here!
11) Message boards : RALPH@home bug list : minirosetta v1.18 bug thread (Message 3990) Posted 5 May 2008 by James Post: Validate error for a successfully completed result This WU <core_client_version>5.10.45</core_client_version> <![CDATA[ <stderr_txt> # cpu_run_time_pref: 21600 ====================================================== DONE :: 1 starting structures 21044.2 cpu seconds This process generated 17 decoys from 17 attempts ====================================================== BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down... called boinc_finish </stderr_txt> ]]> Validate state Invalid The validation errors are related to some new protocols and file formats that we're using in the CASP8 experiment (starting in several hours!). We've sorted more of them out on the BOINC validation server, and we're doing another update right now.
12) Message boards : RALPH@home bug list : minirosetta 1.15 bug thread (Message 3959) Posted 23 Apr 2008 by James Post: Please report bugs related to minirosetta v1.15 here.
13) Message boards : RALPH@home bug list : minirosetta 1.14 bug thread (Message 3946) Posted 22 Apr 2008 by James Post: The application minirosetta v1.14 is released as of now. Post bugs and questions here please.
14) Message boards : RALPH@home bug list : minirosetta 1.13 bug thread (Message 3945) Posted 22 Apr 2008 by James Post: The problems with excessive memory usage have been addressed, and the developer responsible for the bug has been appropriately disciplined. After fixing the memory usage bug, we have released minirosetta v1.14. The problems with the 1vie workunits should be fixed in this release as well. Thank you all for your help. I'm now moving over to the minirosetta v1.14 thread! Cheers, James Thompson
15) Message boards : RALPH@home bug list : minirosetta 1.13 bug thread (Message 3921) Posted 18 Apr 2008 by James Post: Thanks, the Minirosetta 1.13 has successfully run on my Linux-box (Ubuntu 7.10 x86) and ended valid. Thanks again for your efforts. Path7. Hi Path7, I was very excited to get your workunit back. You're totally correct, this application seems to be running properly on Linux machines. Thanks for your help!
16) Message boards : RALPH@home bug list : minirosetta 1.13 bug thread (Message 3918) Posted 17 Apr 2008 by James Post: Version 1.13 of minirosetta is released, please post bugs in this thread. After talking with the BOINC developers, we have a brand-new version of the BOINC API and a new version of the minirosetta application for everyone to try. I'm especially hopeful that the problems on the Linux platform will be fixed, our local tests on Linux have completed successfully. It's critical for CASP8 that we have minirosetta up and running, so thank you all for your help and comments.
17) Message boards : RALPH@home bug list : minirosetta 1.12 bug thread (Message 3908) Posted 15 Apr 2008 by James Post: The new version (v1.12) is now released. Post bugs here!
18) Message boards : RALPH@home bug list : minirosetta 1.12 bug thread (Message 3903) Posted 15 Apr 2008 by James Post: We're releasing minirosetta version 1.12 which will hopefully fix the recent problems with running on BOINC clients running. Please bear with us as we get ready for CASP8, and thank you all for your help! Report problems with the application in this thread. Cheers, James Thompson
19) Message boards : RALPH@home bug list : Bug reports for 5.95 (Message 3807) Posted 28 Feb 2008 by James Post: Update to 5.94! Please report any weirdness!