Hello All!

We're ready for a new update. I want to say thank all of you who have helped over the last months to find and fix errors in minirosetta. A particular thank you goes to those who have donated their time over on RALPH and helped with their active feedback - we managed to find a number of difficult and rare bugs and put some new features into minirosetta that should help conserve computer time. Read about it here: http://ralph.bakerlab.org/forum_thread.php?id=431
and here http://ralph.bakerlab.org/forum_thread.php?id=432
I should add that work over there will continue,but now supplemented with information from Rosetta@HOME.

This update is highly focused on bugfixing and stability issues - we have virtually no new science in it, but: We will hopefully now be able to run the science projects that have been in the pipeline waiting for BOINC - we're expecting quite a bit of work to go out very soon indeed. See Dr. Baker's journal for more details.


Features/Fixes:
1.54 Release CHANGELOG

• Faster loop closing in FoldCST/Abinitio (affects cc_* cc2_* cs_* WUs), should help with overrunning WUs.
  
  
• Bug fix concerning intermittent crashes in relax benchmark jobs (_rlbd_) jobs - caused by buggy input file reader.
  
  
• Bug fix for a potential instability in handling text files (affects all types of WUs).
  
  
• Bug fix in checkpointing machinery, states were not being correctly restored, probably contributing to long runtimes. (affects cc_* cc2_* cs_* WUs)
  
  
• Increased the density of checkpoints to lose less time on restarts and address the weired "backjumping" of the time reported in this thread. This will still happen, but the jumps should be much smaller (basically maximally as long as the time between checkpoints.)
  
  
• Added checkpointing to Loopclosing part of FoldCST. (affects cc_* cc2_* cs_* WUs)
  
  
• Added checkpointing to Looprelax.
  
  
• The Watchdog has been checked and improved, now returning information on the aborted jobs to help us figure out how the remaining long running models come about. The watchdog will now abort if the runtime exceeds your preferred runtime + 4 hours. In other words the WUs should not overrun for more than around 4 hours. If they do please let us know !!
  
  
• Added a limit ont he number of decoys per WU: 99. The WU will end gracefully after that and give full credit. This should address issues with excessive upload problems.
  
  
• Fixed a bug in the BOINC API concerned with unzipping the input data. (I will let the BOINC guys know about this)
  
  
• Fixed a strange problem in the options system leading to early crashes on some systems.
  
  
• Two nasty instabilities fixed deep in the FoldConstraints/abinitio protocol (cc_* tasks and other homology modelling tasks)
  
  
• Generally implemented much better error reporting - many many potential problems will now show up a meaningful error messages and not random segmentation faults.
  
  

NOTE: This new version contains a lot of debug output still. YOu will see that the stderr fills up with stuff - that is ok . It does not slow down the program nor cause much extra upload - but it tells us a lot about where things can go wrong still.


Despite all these fixes there are, i'm sure, many problems left. Most of them occur extremely rarely now though or are highly specific to particular machines. Thus we have decided to move the current version over from RALPH to Rosetta@HOME and give it a go on a much larger scale. Our effords to keep the failure rate down will continue and your time donations over on RALPH as well as error reports are still highly appreciated.

Please let us know how things work out there. Particularily i'd like to know about

• Stuck workunits
  
• Overrunning workunits (WUs should now, due to the new watchdog, never run more than 4 hours longer than the preferred user time)
  
• Problems with checkpointing.
  
• Any other strange behaviour.
  

Happy crunching - I'm very excited to see how this new version will pan out.

Mike