Posts by David E K

1) Message boards : Number crunching : BOINC Android trying to run 4 Rosetta WU when device doesn't have enough RAM. (Message 90497)
Posted 8 Mar 2019 by Profile David E K
Post:
Can you configure R@h to use only 1 cpu for your device and see if that helps?
2) Message boards : Number crunching : Rosetta 4.0+ (Message 90496)
Posted 8 Mar 2019 by Profile David E K
Post:
I'll look into this.
3) Message boards : Number crunching : Rosetta 4.0+ (Message 90473)
Posted 4 Mar 2019 by Profile David E K
Post:
There are a few large proteins that were submitted recently that are error prone. They should clear the queue soon as they complete.
4) Message boards : Number crunching : Rosetta 4.0+ (Message 90448)
Posted 27 Feb 2019 by Profile David E K
Post:
hmm, I'll look into this
5) Message boards : Number crunching : Problems with web site (Message 90447)
Posted 27 Feb 2019 by Profile David E K
Post:
done, thanks for the reminder
6) Message boards : Number crunching : No android tasks? (Message 90430)
Posted 26 Feb 2019 by Profile David E K
Post:
The Rosetta android application was used for this study:

http://science.sciencemag.org/content/358/6369/1461/

There are a number of researchers working on the next android application update related to RNA folding and cyclic-peptide design. Hopefully the app will be updated soon and a new batch of workunits will be available.

If there are no tasks available, there just isn't any work to be done at that moment in time.
7) Message boards : Number crunching : Problems with web site (Message 90429)
Posted 25 Feb 2019 by Profile David E K
Post:
I think both issues have been resolved now. The user of the day should now have at least a RAC of 1. If there are any other issues feel free to contact me directly at dekim at uw dot edu
8) Message boards : Number crunching : Link from tasks page does not show private details when signed on to website. (Message 90427)
Posted 25 Feb 2019 by Profile David E K
Post:
I think I fixed this. If there are other web site related issues please email me directly at dekim at uw dot edu
9) Message boards : Number crunching : Keeping new volunteers (Message 89512)
Posted 10 Sep 2018 by Profile David E K
Post:
That's a good idea. I'll look into this. Thanks.
10) Message boards : Number crunching : Rosetta 4.1+ (Message 88772)
Posted 28 Apr 2018 by Profile David E K
Post:
Hmmm, any other information? Let us know if it persists.
11) Message boards : Number crunching : 3-day deadlines (Message 88015)
Posted 5 Jan 2018 by Profile David E K
Post:
I'll look into this. It's likely due to modelling we are doing for a collaboration with SSGCID. https://www.ssgcid.org/
12) Message boards : Number crunching : Progess going backwards? (Message 88014)
Posted 5 Jan 2018 by Profile David E K
Post:
What work units are having issues? It may be specific to the particular job(s). Maybe a large protein? Or particular score filters that are failing more often than usual for the particular protein. Or maybe boinc checkpointing is not properly implemented for the particular protocol.

The core molecular modeling software is developed, tested, and used by many academic institutions around the world through the Rosetta Commons. Rosetta is freely available to academics including the source code. I would not jump to a conclusion that the issues you mention may also reflect the science.
13) Questions and Answers : Web site : Upload of profile images (Message 88001)
Posted 3 Jan 2018 by Profile David E K
Post:
Thanks for alerting us about this issue. It should be fixed now.
14) Message boards : Number crunching : no new tasks (Message 87998)
Posted 2 Jan 2018 by Profile David E K
Post:
I've just alerted the lab about the empty queue. I'm sure there will be plenty of jobs submitted soon.
15) Message boards : Rosetta@home Science : New article in "Science" journal co-authored by Dr. Baker (Message 87921)
Posted 17 Dec 2017 by Profile David E K
Post:
R@h was used for this research. Most of the computations were from android devices. I'll post a news item on Monday.
16) Message boards : Number crunching : ProtonMail "email address is invalid" (Message 87754)
Posted 26 Nov 2017 by Profile David E K
Post:
It may not be passing the https://www.stopforumspam.com/ filter for some reason.

I couldn't find my username or e-mail address on that list. This e-mail address is less than a month old.


More info about this and other BOINC spam filtering options is posted here:

https://boinc.berkeley.edu/trac/wiki/ProtectionFromSpam


I'm not the one in charge of the Rosetta@home server, so I wouldn't know what BOINC spam filtering options you are using. Perhaps you could take a look and let us know? I'd really like to know if ProtonMail is blacklisted for some reason, or if there's just a whitelist of "trusted" e-mail domains that ProtonMail just never got added to.


I'll look into it further tomorrow when I get into lab. We are using the default BOINC server spam filter which uses stopforumspam.com. No other filter is used. stopfurumspam.com uses your IP address and email to validate. I'm not sure what the repercussions would be if I turn off this validation step but if the result is a bunch of spam, I'd prefer to keep it. One option would be to add your email address to a trusted list on our server and add logic to use the list in the validation routine. I can work on this tomorrow if necessary. Sorry for this inconvenience. We'll get it working for you.
17) Message boards : Number crunching : ProtonMail "email address is invalid" (Message 87745)
Posted 25 Nov 2017 by Profile David E K
Post:
It may not be passing the https://www.stopforumspam.com/ filter for some reason.

More info about this and other BOINC spam filtering options is posted here:

https://boinc.berkeley.edu/trac/wiki/ProtectionFromSpam
18) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 87418)
Posted 29 Sep 2017 by Profile David E K
Post:
There is a lull in jobs being submitted by Baker lab researchers. I sent out an alert that the queue is nearly empty. There should still be Robetta jobs trickling in from the public structure prediction server.
19) Message boards : Number crunching : Rosetta 4.03 (Message 87398)
Posted 27 Sep 2017 by Profile 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.
20) Message boards : Number crunching : Rosetta 4.03 (Message 87395)
Posted 27 Sep 2017 by Profile 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.


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