Posts by James Thompson

1) Message boards : RALPH@home bug list : minirosetta 2.06 (Message 5109)
Posted 1 Apr 2010 by James Thompson
Post:
I've updated minirosetta to 2.06 to introduce some new code for CASP9. Please post about any problems with 2.06 here.
2) Message boards : RALPH@home bug list : Bug Reports for Minirosetta v1.36 (Message 4238)
Posted 5 Oct 2008 by James Thompson
Post:
Please post issues/bugs relating to minirosetta version 1.36 here. Version 1.35 has fixes for access violations, super-long workunit run times and communication problems with the BOINC manager.

3) Message boards : RALPH@home bug list : bug in t042_1_NMRREF_ (Message 4237)
Posted 5 Oct 2008 by James Thompson
Post:
The error in my last 2 wu :
t042_1_NMRREF_1_t015_1_S_00001_0000163IGNORE_THE_REST_040000_5067_2_1
t042_1_NMRREF_1_t015_1_S_00001_0000163IGNORE_THE_REST_040000_5068_18_1
....
if seem to be :

ERROR: Unable to open file: worksramanminirosetta_databasechemical/residue_type_sets/fa_standard/residue_types.txt

ERROR:: Exit from: ....srccorechemicalResidueTypeSet.cc line: 86

---> a file name can't have / in remplace it by , this explain why the file can't be open ... Verifiy all source file, just in case the same error appear somewhere else.


This is a problem with the person who submitted those workunits to Ralph. They have been appropriately disciplined, and will not likely do this again.
4) Message boards : RALPH@home bug list : Bug Reports for Minirosetta version 1.35 (Message 4236)
Posted 5 Oct 2008 by James Thompson
Post:
So if you encounter such a job, please post to this thread so we can properly adjust the parameters of the job to reduce the run times.


...any progress on getting the tasks to automagically report back to you with the runtime for each model? Seems to be a key piece of data that has been neglected in the past. We've been seeing occaisional 4-6 hour models for quite some time and have always assumed they were within the normal range.


We do get that information from our workunits, but it can take a while for that data to come back, especially if the workunits take a long time to make a single decoy. To get a good estimate on the actual amount of time required to make a single decoy, we also need a lot of data because different people have very different computational power available for R@H.

We're doing an update today with more finely tuned parameters for job runtimes, so hopefully this won't be an issue soon. We're also reverting to an older version of the BOINC API that should eliminate at least some of the access violation errors, the BOINC API for v1.35 had some errors.

More soon. Thanks for your input!
5) Message boards : RALPH@home bug list : Bug Reports for Minirosetta version 1.35 (Message 4221)
Posted 27 Sep 2008 by James Thompson
Post:
Please post issues/bugs relating to minirosetta version 1.35 here. Version 1.35 is an attempt to fix several issues from the 1.34 release, including bugs in hydrogen bonding and long run times for certain workunits.

The super-long run times are occasionally a problem with the jobs that we send out to you. So if you encounter such a job, please post to this thread so we can properly adjust the parameters of the job to reduce the run times.
6) Message boards : RALPH@home bug list : Bug Reports for Minirosetta version 1.34 (Message 4193)
Posted 7 Sep 2008 by James Thompson
Post:
Please post issues/bugs relating to minirosetta version 1.34 here. Version 1.34 is an attempt to fix several issues from the 1.33 release.
7) Message boards : RALPH@home bug list : Bug Reports for Minirosetta version 1.33 (Message 4192)
Posted 7 Sep 2008 by James Thompson
Post:
Both of the errors noted above are the fault of application version 1.33, we're very sorry for that. I'm releasing version, 1.34 right now and it should them both. Cheers!
8) Message boards : RALPH@home bug list : Bug Reports for Minirosetta version 1.33 (Message 4189)
Posted 5 Sep 2008 by James Thompson
Post:
We've discovered a tricky little bug that appears in runs of our application that process more than one structure per workunit. We're working on a fix, expect another release sometime tomorrow.

Thanks!

James
9) Message boards : RALPH@home bug list : Bug Reports for Minirosetta version 1.33 (Message 4187)
Posted 4 Sep 2008 by James Thompson
Post:


33 tasks arrived tonight and all failed on 'Computation error' after 3 seconds running.

All are james_abinito units with 't' prefix


Sorry about that, I sent out a batch with options for minirosetta version 1.32 rather than version 1.33. The offending workunits have been removed from the queue, and I'm sending out a new test set now.
10) Message boards : RALPH@home bug list : Bug Reports for Minirosetta version 1.33 (Message 4185)
Posted 4 Sep 2008 by James Thompson
Post:
Please post issues/bugs relating to minirosetta version 1.33 here. Version 1.33 contains several scientific updates, and also addresses a problem related to workunits expiring more freqently following minirosetta application restarts.
11) Message boards : RALPH@home bug list : minirosetta v1.23 bug thread (Message 4042)
Posted 20 May 2008 by James Thompson
Post:
We're releasing version 1.23 of minirosetta today. Post bugs related to minirosetta v1.23 here.

12) Message boards : RALPH@home bug list : minirosetta v1.20 bug thread (Message 4016)
Posted 10 May 2008 by James Thompson
Post:
We have released a new version of minirosetta. Please report bugs related to v1.20 here.

13) Message boards : RALPH@home bug list : minirosetta v1.18 bug thread (Message 3980)
Posted 3 May 2008 by James Thompson
Post:
Post bugs related to minirosetta v1.18 here!
14) Message boards : RALPH@home bug list : minirosetta v1.16 bug thread (Message 3977)
Posted 1 May 2008 by James Thompson
Post:
Apologies for that, I mistakenly signed the app with the incorrect key which causes download errors. We're doing another update to v1.17 later today, and so check around for that thread later.

Cheers,

James
15) Message boards : RALPH@home bug list : minirosetta v1.16 bug thread (Message 3975)
Posted 1 May 2008 by James Thompson
Post:
Please report bugs related to minirosetta v1.16 here.
16) Message boards : RALPH@home bug list : minirosetta 1.14 bug thread (Message 3955)
Posted 22 Apr 2008 by James Thompson
Post:
Thanks for the quick replies. We've found the latest problem, expect a new release in a couple of hours once the compilation and tests are finished.

Cheers,

James






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