Neue Rosetta/Minirosetta-Version

G

Gast09072017f

Guest
naja für platz 1 reicht das nicht :P
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EDIT :
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neue minirosetta wu version

The minirosetta application has been updated to version 1.15. This version introduces an improved method for modeling larger RNA molecules
 
neue minirosetta version

The minirosetta application has been updated to version 1.19. This version introduces several bugfixes for our CASP8 abinitio and template-based modeling protocols. We'll be testing small batches of workunits this evening and tomorrow morning

hier die google übersetzung

Die minirosetta Anwendung wurde aktualisiert auf Version 1,19. Diese Version enthält einige Bugfixes für unsere CASP8 abinitio und Template-basierte Modellierung von Protokollen. Wir werden Tests Kleinserien von workunits heute Abend und morgen Vormittag
 
und die minirosetta version wurde gleich mal geupdatet

nun in der version 1.24 vorhanden

The minirosetta application has been updated to version 1.24. This version contains a fix for a memory leak that was causing tasks with long run times to fail

es wurde ein speicherleck behoben was bei langen laufzeiten zu problemen führen konnte

was mich freut unser output ist wieder stark gestiegen wenn er mal länger anhalten würde könnten wir das intel team mal einhollen ^^
 
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glückwunsch :D im team sind wir garnicht soviele :X

der bot nervt ...


und wieder eine neue minirosetta version jetzt die version 1.25

hier das changelog

The minirosetta application has been updated to version 1.25. This version contains a fix for a file formatting problem that was causing certain jobs running abinitio folding to fail.

hier die googleübersetzung

Die minirosetta Anwendung wurde aktualisiert auf Version 1,25. Diese Version enthält eine Korrektur für einen Datei-Formatierung Problem wurde verursacht, dass bestimmte Arbeiten ausgeführt abinitio Faltung zum Scheitern verurteilt.
hoffe das kommt so hin :)
 
eine neue minirosetta version 1.28

The minirosetta application has been updated to version 1.28. This version contains a fix for the graphics application and jumping and loop modeling protocols.

laut google übersetzung wurde was in der grafik gefixt und beim Springen und Loop-Modeling-Protokolle.
 
und auch die Rosetta beta version bekommt mal ein update auf die version 5.98

The rosetta application has been updated to version 5.98. This version includes a bug fix for the stalled client issue.

es wurde das problem behoben das der client einfach stehen blieb, ich selber hatte ein paar solcher wu´s auf meinem quad
 
so eine neue minirosetta version 1.32 ist raus

Version 1.32 of minirosetta is now released. This version includes various updates to the graphics application. Minirosetta graphics now look like rosetta++ graphics. Additionally, a linux graphics application is now available.

The minirosetta database is now being packaged and distributed with the application to deal with backwards compatibility.

Please keep in mind that the graphics frame rate may be reduced due to the extra overhead of shared data between the worker application and the graphics application. To increase the frame rate at the cost of cpu cycles, you can set the "Percentage of CPU time used for graphics" R@h project preference to a higher value than the default.

Also keep in mind that there may still be issues with the linux graphics application.

minitrosetta 1.32 ist nun veröffentlicht. Diese Version beinhaltet verschiedene Updates der grafischen Anwendung. Minirosetta Grafiken schauen nun aus wie rosetta++ Grafiken. Zusätzlich ist nun eine grafische Linux Anwendung vorhanden.

Die minirosetta Datenbank wird nun mit der Anwendung gepackt und verteilt wegen der abwärts Kompatibilität.

Bitte beachten dass die Grafische frame Rate reduziert sein könnte wegen dem extra Overhead von verteilten Daten zwischen der Arbeits Anwendung und der Grafischen Anwendung. Um die Frame Rate auf Kosten der CPU Cycles zu erhöhen, kann man die "Percentage of CPU time used for graphics" erhöhen in der R@h Projekt Einstellung.

Beachtet auch dass es immer noch zu Problemen mit der grafischen Linux Anwendung kommen kann.
 
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neue minirosetta version 1.39

The minirosetta application has been updated to version 1.39. In this version, we added two important applications to minirosetta, docking and protein folding with explicit zinc metal ion. New features have been added to the graphic to show chain colors for a multi-chain protein complex and display metal ions by sphere.
 
neue minirosetta version 1.40

The minirosetta application has been updated to version 1.40. This version contains improved protein-protein docking along with small-molecule ligands and the capabilities to do design, where the surface amino-acid residues are allowed to mutate during the simulation. Messages on the scientific aspects will be posted on the message board.
 
so minirosetta gibt es nun in der version 1.45

This update includes fixes to long runtimes for 'relax' jobs, validation errors, check point recovery issues, and numerical instability in hydrogen-bond scoring.

We think we might have fixed the preemption problem so please keep an eye out for this. The "can't acquire lockfile" issue might also be related. If you are having lockfile problems, please make sure there are no other boinc applications running in the same slot. If necessary, turn off the client and make sure all boinc apps are not running, and then restart the client.

die kurze google übersetzung

Dieses Update enthält Updates zu lange Laufzeiten für "Entspannung" Arbeitsplätze, Validierung Fehler, Check Point Erholung Fragen, und numerische Instabilität in Wasserstoff-Bond-Scoring.
 
seit 15.12 gibt es die minirosetta version 1.47 welche viele kleine und ein großen bug behoben hat

hier ein auszug aus dem thread

Amongst a bunch of minor things, one major bug that was fixed was causing jobs ro rash when they enetered full-atom stage ut had a fullatom energy > 0. Which usually occurs rarely, which would explain the random errors seen with the cs_vanilla jobs. The bug was due to a wrongly initialized varaible.
This bug was also causing the majority of the ccc_1_8_* jobs to fail on RALPH (we didnt move these over to BOINC of course, sicne we noticed the bug there).
THe reason those failed more frequently was that they have constraints built in and those cause the energy to be offset to higher values increasing the frequency of the problem to more like 70%.

Looking at the RALPH results i think most of the easily reproducable errors i think we've fixed. I recently ran close to 10000 WUs on our local compute cluster resulting in.. well.. 0 errors. This is wherei t gets tricky really, if stuff is only failing on other plattforms or due to machine dependent issues or *god knows what*. I will propose that the lab aquire a small farm of windows machiens to do extensive bug testing& hunting on to get a grip one these errors.. but believe us, these are difficult grounds.

Thanks for bearing with us,

Mike
 
so es gibt eine neue minirosetta version 1.54 hier das englische changelog *falls wer es übersetzen möchte kann das gerne tun und wird hier gerne gesehen :)

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
 
es gibt eine neue Minirosetta version 1.64

We've got a new minirosetta version, with some infrastructure changes and a new protocol for using experimental data from NMR.

google übersetzung

Wir haben eine neue Version minirosetta, mit einigen Änderungen der Infrastruktur und ein neues Protokoll für die Verwendung von experimentellen Daten ausm NMR.
 
die minirosetta version 1.67 ist raus hier das changelog

Version 1.67 has a nifty new threading mode built in. And corrects some of the validator problems people have reported in prior releases.
 
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die minirosetta version 1.75 ist draussen

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.
 
nach ein paar versions sprünge *durch den ein oder anderen bug verursacht* ist nun die Rosetta Mini 1.90 raus hier das kleine changelog

This version should solve the slowing down, and instant quitting problems.

New protocol added for predictions of changes in protein stability by mutations.
 
neue Rosetta Mini version 1.91 ist raus

A number of users are still getting signature verification errors with the database file so we've updated the minirosetta application to version 1.91 with a new database filename. 1.91 is a copy of 1.90 with the only difference being a new name for the database file to ensure that every host updates the signature

es ist praktisch die gleiche version wie 1.90 mit dem einzigen Unterschied, ein neuen Namen für die Datenbank-Datei.
 
so Minirosetta ist nun bei der Version 2.00 angekommen das changelog ist aber nicht sehr groß

minirosetta 2.00 is now up.
The energy function optimization we've been working on for the last few month are now in.
This version also fixes some stability issues brought in by 1.98.
 
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