Posts by David E K

21) Message boards : Number crunching : Rosetta 4.03 (Message 87398) Posted 27 Sep 2017 by David E K Post: It's historical. R@h first started with a "rosetta" app which was the early fortran to C++ port of the Rosetta software package. The fortran like C++ code base was then ported to a better organized, multi-library, object oriented C++ software package which current Rosetta is still based on. This package was called "minirosetta" to distinguish it from the old fortran like Rosetta package. The 4.03 version has a different name mainly because "rosetta_scripts" xml based protocols are not backwards compatible with minirosetta jobs, giving us a reason to go back to the actual "rosetta" name. So the naming went from rosetta to minirosetta and back to rosetta.
22) Message boards : Number crunching : Rosetta 4.03 (Message 87395) Posted 27 Sep 2017 by David E K Post: Eventually it will replace minirosetta. Our public structure prediction server, Robetta, and in house pipelines are not yet compatible with the new version.
23) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 87379) Posted 25 Sep 2017 by David E K Post: Good to hear.
24) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 87377) Posted 25 Sep 2017 by David E K Post: Are you still seeing upload issues?
25) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 87376) Posted 25 Sep 2017 by David E K Post: Hmmm, looks like something weird was/is going on with our filesystem. I had to create/touch the file upload handler log file for one of our web servers. I'll talk to our sys admin about this to see what might have caused this.
26) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 87375) Posted 25 Sep 2017 by David E K Post: Oh, I'm sorry, this is likely another issue. I'll take a look.
27) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 87372) Posted 25 Sep 2017 by David E K Post: Some daemons crashed unexpectedly sometime this weekend. They are back up and running now. May have been a network glitch. Seems ok so far.
28) Message boards : Number crunching : Rosetta 4.03 (Message 87330) Posted 20 Sep 2017 by David E K Post: I just announced it to the lab so I'd expect some production jobs soon.
29) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 87327) Posted 19 Sep 2017 by David E K Post: This is a different issue that is probably specific to your computer/boinc client.
30) Message boards : Number crunching : Rosetta 4.03 (Message 87278) Posted 13 Sep 2017 by David E K Post: I'll have to look into the possible consequences/negative impacts of enabling this feature. We'd prefer not to enable any bias though.
31) Message boards : Number crunching : Rosetta 4.03 (Message 87270) Posted 12 Sep 2017 by David E K Post: Yes, I'm running some tests before an official release.
32) Message boards : Number crunching : Upload errors. (Message 87226) Posted 6 Sep 2017 by David E K Post: "Which leads to the long history of project struggles." We've been up since late June with the new server front and back ends without any significant issues (knock on wood). This has been the first significant issue since and may or may not have been related to network and power instability here at the UW recently. The file locking logic in the upload handler started to fail for the majority of upload requests. We rebooted the web servers and filesystem but that didn't fix the issue. We had to modify the source code to comment out the file locking logic and rebuild the upload handler. This appears to have fixed the issue. The file locking logic is not necessary for our system and things appear to be back to normal. On a positive note, I think our project has a long history of success including research from our lab being runner-up to Science magazine's breakthrough of 2016 for protein design, success in using co-evolution sequence data from meta-genomes to determine new protein structures at a cost significantly less than structural genomics initiatives, and designing/modeling small cyclic peptides with non-canonical amino acids (much of which was modeled on mobile android devices), and more.
33) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 87221) Posted 6 Sep 2017 by David E K Post: I think we've resolved this issue. Please let us know if it persists. The file locking logic in the upload handler was failing. We don't know what caused this; rebooting the filesystem didn't help. But rebuilding the upload handler after commenting out the locking logic did appear to fix the issue.
34) Message boards : Number crunching : Minirosetta android 3.83 (Message 87040) Posted 11 Aug 2017 by David E K Post: Just read this thread. Sorry. I'll alert the researcher.
35) Message boards : Number crunching : Group Foundership (Message 86864) Posted 26 Jul 2017 by David E K Post: These are great suggestions. I would post them on the BOINC development group threads from the BOINC web site.
36) Message boards : Number crunching : Server update/upgrade (Message 86863) Posted 26 Jul 2017 by David E K Post: Foldit has it's own code repository. The Rosetta core components are not updated as frequently as UI/game related features because I think it is a large task to merge the code. The Rosetta Commons repository maintains the main source/scientific code. It is constantly being developed by the commons developers/scientists who are from institutions from all over the world (and the contributor base is growing). When we update the R@h app, we use the latest commons code. I'm still waiting for our graphics app to be debugged but an update should hopefully come soon. A lot has changed including increased use of C++11 from the commons developers, some of which is not yet supported by Visual C++ and has to be ported, also new dependencies, and a migration away from Boost (related to increased C++11 use). Also, the "rosetta scripts" protocols will not be backwards compatible due to new XML format rules so the next app version will be a new app named "rosetta" which is appropriate :)
37) Message boards : Number crunching : Larger Memory Models (Message 86862) Posted 26 Jul 2017 by David E K Post: On the list of things to do. great idea. I'll remind/alert the lab about the memory issues. thanks.
38) Message boards : Number crunching : Larger Memory Models (Message 86836) Posted 21 Jul 2017 by David E K Post: This is my fault. I was asked by someone in the lab to increase the length limit on Robetta, our publicly available structure prediction server, so I did but since realized the memory issue. I've reverted the length limit until we can figure out a good approach to handle them. Sorry. There may still be some jobs left over. These are medically relevant targets.
39) Message boards : Number crunching : Server update/upgrade (Message 86805) Posted 12 Jul 2017 by David E K Post: I've been out for the past 2 weeks on a vacation without any network access for the last 5 days last week. The researcher has also been out of the lab from conferences and workshops and will be back in communication soon.
40) Message boards : Number crunching : Server update/upgrade (Message 86778) Posted 1 Jul 2017 by David E K Post: We've been waiting for a while for a researcher to fix his protocol for the graphics app. Just waiting on him for the update.

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