Posts by Feet1st

1) Message boards : Number crunching : Rosetta 4.1+ and 4.2+ (Message 96077)
Posted 4 May 2020 by Profile Feet1st
Post:
BOINC hung up and, when I rebooted my computer, it seems to have cancelled all of the WUs it had, and downloaded a new batch of v4.20 junior halfroids.

I now have a 1GB minirosetta_database directory in each of my 4 slot directories, along with a file called minirosetta_database.zip.is_extracted

The project directory has a 1GB database_357d5d93529_n_methyl directory. along with the .zip, a .zip.is_bad and a .zip.is_extracted.

The application shown is Rosetta 4.20 (not mini).

The creation dates in the slots are from when I rebooted. The creation dates on the project directory are from the 2nd when I got v4.20.

I was expecting all v4.20 tasks to use the directory under the project rather than within the slot.
2) Message boards : Number crunching : Rosetta 4.1+ and 4.2+ (Message 95894)
Posted 3 May 2020 by Profile Feet1st
Post:
The task list shows the application for all is Rosetta 4.20 on my host.

Is there a symbolic link in each slots directory back to the project expanded DB?

Each slot seems to have a file called "minirosetta_database.zip.is_extracted"
3) Message boards : Number crunching : Rosetta 4.1+ and 4.2+ (Message 95878)
Posted 2 May 2020 by Profile Feet1st
Post:
I now seem to have several slots with the 960MB folder called "minirosetta_database", I also have in the projects directory a 960MB folder called "database_357d5d93529_n_methyl". I have only Rosetta and Ralph v4.20 work onboard at this point. I was expecting to no longer see the large folder in the slots directory. But they seem to have different names?
4) Message boards : Number crunching : How does BOINC adjust initial runtime estimate? (Message 95144)
Posted 22 Apr 2020 by Profile Feet1st
Post:
Finally now new work units for v4.15 are showing 33.5hr estimates, much better! That took it about a week to figure out!
5) Message boards : Number crunching : How does BOINC adjust initial runtime estimate? (Message 95102)
Posted 22 Apr 2020 by Profile Feet1st
Post:
The only one I have, that has not already started, was requested this morning. Several days after upping to 36hrs.
6) Message boards : Number crunching : How does BOINC adjust initial runtime estimate? (Message 95096)
Posted 22 Apr 2020 by Profile Feet1st
Post:
My system has requested (and received) new work about every 12 hours for the last many days with the 36hr runtime setting.
7) Message boards : Number crunching : How does BOINC adjust initial runtime estimate? (Message 95091)
Posted 22 Apr 2020 by Profile Feet1st
Post:
Yes. And I understand that a few have to crunch that way. But I've done that, and BOINC Manager still shows a new, unstarted WU with a 7.5H runtime expected.
8) Message boards : Number crunching : How does BOINC adjust initial runtime estimate? (Message 95088)
Posted 22 Apr 2020 by Profile Feet1st
Post:
I've completed and reported a number of tasks with Rosetta (not "mini") v4.15 the new 36hour runtime, but BOINC Manager still shows unstarted WUs with an estimated runtime of 7H27M.

I've been keeping very small cache of work, because experience tells me that if I set things to try to keep a 24 hour cache of work, that I'll get way too much for the three day deadlines.

When should I expect BOINC Manager to start predicting a new WU will take 36hrs?
9) Message boards : Number crunching : Large proteins (Message 94953)
Posted 19 Apr 2020 by Profile Feet1st
Post:
If you are also crunching small memory tasks, such as WCG, what loss of credit exists?
10) Questions and Answers : Wish list : PowerPC 64 version (Message 94928)
Posted 19 Apr 2020 by Profile Feet1st
Post:
Just for some perspective, my phone benchmarked about double those numbers.

Rosetta is not open-source, so recompile is not possible.
11) Message boards : Number crunching : Tells us your thoughts on granting credit for large protein, long-running tasks (Message 94922)
Posted 19 Apr 2020 by Profile Feet1st
Post:
It will depend on the checkpointing. If these long models need a continuous span of 5 hours to complete, then a fair amount of work will be lost on machines that are not running 24/7.

It will also depend on the % of time where more than 1 GB of memory is required to run it.

I don't watch credits much. I'll just add some WCG to the mix (which are usually low memory WUs), and let the BOINC Manager worry about what to dispatch when.
12) Message boards : Number crunching : R@h Supported ARM Platforms for Portable Devices (Message 94471)
Posted 14 Apr 2020 by Profile Feet1st
Post:
When I reinstall, it does not ask about an install location. No prompts at all.
13) Message boards : Number crunching : R@h Supported ARM Platforms for Portable Devices (Message 94398)
Posted 13 Apr 2020 by Profile Feet1st
Post:
BOINC seems to be running from the main storage of my phone rather than my much larger micro SD. Is there a way to move it?
14) Message boards : Rosetta@home Science : Interesting starting point for attacking Coronavirus (Message 94290)
Posted 13 Apr 2020 by Profile Feet1st
Post:
Is it possible to make synthetic COVID-19 antibodies? Why search for compounds that bind to receptors, and hope they neutralize the virus, when you already know that the antibodies have the desired effect?

Another thought that I had was, would it be possible to bind something to another area of the virus, that invokes an immune response. For example, bind something to the virus cell that looks like small pox or the measles? The immune system already knows what to do with cells like that. Perhaps there are easier binding sites than the spikes that help it to invade healthy cells.
15) Message boards : Cafe Rosetta : Losing WU progress (Message 93682)
Posted 6 Apr 2020 by Profile Feet1st
Post:
Can you give a link to the task?
16) Message boards : Cafe Rosetta : Parkinson's Disease (Message 78304)
Posted 14 Jun 2015 by Profile Feet1st
Post:
Computer modeling showed that alpha-synuclein can bind to the cell membrane at four main sites, or zones. Of the four, only one is significant.
http://www.isgtw.org/feature/shape-shifting-proteins-play-key-role-parkinsons-disease
17) Message boards : Rosetta@home Science : How Rosetta works, an explanation your cat will follow (Message 77739)
Posted 19 Dec 2014 by Profile Feet1st
Post:
Thought this thread was worth reviving so new crunchers see the explanation.
18) Message boards : Cafe Rosetta : Foldit news (Message 77590)
Posted 19 Oct 2014 by Profile Feet1st
Post:
The entire video is very interesting. Foldit is referenced about 13.5 min in. The crowdsource was about to solve in days what scientists had puzzled over (is that a pun?) for years.

http://www.ted.com/talks/regina_dugan_from_mach_20_glider_to_humming_bird_drone?language=en
19) Message boards : Cafe Rosetta : Personal Milestones (Message 71949)
Posted 31 Dec 2011 by Profile Feet1st
Post:
Wow! What timing!! ONE MILLION Rosetta@home credits right on year-end! 6 years and one day from when I joined the effort.

Thanks to all that make this collaboration of crowd-sourcing and public participation in science possible. May the new year bring faster CPUs, lower power consumption, and a population of users that value the good of the project over any perceived potential risks to their computer.
20) Message boards : Rosetta@home Science : Rosetta@home home game - Fold.it (Message 71573)
Posted 6 Nov 2011 by Profile Feet1st
Post:
The lesson of gamification, and Foldit, is that previously insurmountable problems can be shattered simply by offering the right tools and making the quest for a solution fun.


http://www.digitalmanufacturingreport.com/dmr/2011-11-02/you_gotta_know_when_to_fold_%E2%80%98em.html


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