Posts by nnneal

1) Message boards : News : Rosetta's role in fighting coronavirus (Message 94124)
Posted 10 Apr 2020 by nnneal
Post:
Dear all,

I‘ve got a question popping up in the back of my head, and I hope, you won‘t get me wrong.
...


I can't imagine on what authority the president could commandeer the results of research done by a public university that's affiliated with the state of Washington. The governor of Washington is Jay Inslee, and he is a great guy.

Neal
2) Message boards : News : Help in the fight against COVID-19! (Message 93864)
Posted 8 Apr 2020 by nnneal
Post:
I suppose by default I am doing it, just install Rosseta and that is (?)


Most if not all of the Rosetta tasks I get lately are covid19-related. So if you are receiving credit then you are contributing to covid19.

Neal
3) Message boards : News : Outage notice (Message 93639)
Posted 6 Apr 2020 by nnneal
Post:
I finally have work units from Rosetta! Yeah!


I do too.
4) Message boards : Number crunching : What are your tips for new Rosetta@home users? (Message 92998)
Posted 2 Apr 2020 by nnneal
Post:
James Lee and Peter Hucker -- Thanks for the tips.
5) Message boards : Number crunching : What are your tips for new Rosetta@home users? (Message 92991)
Posted 1 Apr 2020 by nnneal
Post:
Next, for your buffers.... Set your primary buffer to ".21" and your second to 0(zero). This allows boinc to always go thru its sequence of resource share to get your next WU. DO NOT BUFFER FOR DAYS - ONLY BUFFER FOR HOURS! This is IMPORTANT, for when a project first starts up after a lag in WUs, it does not have to do such a flood of requests, and as a project goes thru a series of WUs for collection, there are not days of WUs that have to be waited on. If you use the optimal number of .21, BOINC will take care of everything. A smaller number will give you a wait period, and a larger number is not healthy for the project.


Are these the buffers that you're talking about? Which one is primary and which is secondary?
6) Message boards : News : Rosetta's role in fighting coronavirus (Message 92675)
Posted 30 Mar 2020 by nnneal
Post:
I was wondering when they would hit the wall. The growth has been phenomenal. They were doing 150,000 GigaFLOPS before the virus hit, and 570,318 GigaFLOPS now.
Maybe they are adding more capacity and had to take the servers down?


This seems like as good a time as any to build out more capacity.
7) Message boards : News : Rosetta's role in fighting coronavirus (Message 92418)
Posted 27 Mar 2020 by nnneal
Post:

Have to ask as a noob, though - what is the max ideal turnaround time for a slow PC? The laptops I'm running WUs on can take 10-12 hours per WU - and I can abort the Rosetta queue so I'm not slowing the research down.


I think they are all supposed to take around 8 hours (of cpu time) no matter how fast or slow the machine. They must be scaling the wus based on benchmarks.
8) Message boards : Rosetta@home Science : BOINC@TACC would love to offer computational resources (Message 92235)
Posted 24 Mar 2020 by nnneal
Post:
I don't know who would be the best contact person, but there is contact info for David Baker here: https://www.bakerlab.org/index.php/contact/
9) Message boards : News : Rosetta's role in fighting coronavirus (Message 92234)
Posted 24 Mar 2020 by nnneal
Post:
We are currently trying are best considering what is happening around here with COVID-19. We are in Seattle, which is among the worst hit regions. Some are working in the lab related to COVID-19 and supporting staff even at risk of exposure, for example, the IPD core production group has been busy making COVID-19 proteins, an antibody known to bind, and the human ACE2 receptor target for research groups around the world. Relating to this project, we are trying to update Rosetta to the latest source so we can start running protein interface design jobs to design binders to COVID-19. This has already been done at a smaller scale on our local computing resources and we have some hopeful candidates that are already being worked on within the web lab. The hope is to have many more candidates as that increases the chance of having a legitimate binder with the potential to develop and optimize for a therapeutic.

ALL COVID-19 related jobs that come out of our lab are named with the COVID-19 tag. Jobs from other institutions running through our structure prediction service, Robetta, may or may not be labeled, which is at the discretion of the individual researchers which we have no control over.

Thank you everyone for your contributions!


Thanks for taking the time to post. Is the science benefitting from an influx of new contributors?
10) Message boards : Number crunching : What are the screensaver graphics showing me? (Message 92212)
Posted 24 Mar 2020 by nnneal
Post:
Could someone either point me in the right direction (links?) or explain what we are looking at in the "Graphics" tab. Such as Accepted Energy, RMSD, The little dots which are yellow, red and what Low Energy and Native are. I've searched, but have found no answers. Thanks in advance.


Have you seen this page yet? https://boinc.bakerlab.org/rosetta/rah/rah_graphics.php

Neal
11) Message boards : News : Designing shape-shifting proteins (Message 92088)
Posted 19 Mar 2020 by nnneal
Post:
Does this study help with the recent coronavirus crisis in any way?


I'm going to take a guess... This kind of research is probably at least a few years away from becoming a treatment that can be offered to patients. So it probably is too late to help in this Coronavirus pandemic, but it might help future ones.
12) Message boards : Number crunching : Is Rosetta still issuing COVID-19 relataed workunits? (Message 91906)
Posted 9 Mar 2020 by nnneal
Post:
Just some recent examples from yesterday March 8th if you're not convinced:

Already Completed:
http://robetta.bakerlab.org/results.php?id=17804
http://robetta.bakerlab.org/results.php?id=17803
http://robetta.bakerlab.org/results.php?id=17801


Still Active:
http://robetta.bakerlab.org/results.php?id=17823

List of all currently active Robetta jobs: http://robetta.bakerlab.org/queue.php?id=&target=&status=active


Are those wus automatically given priority over ones that are less urgent, or how do they finish in a day or two when the deadlines are typically a week?

Thanks
13) Message boards : Cafe Rosetta : What does "low energy mean" ? (Message 91883)
Posted 6 Mar 2020 by nnneal
Post:
It's not clear exactly what you're asking. Rosetta is looking for the best and most natural shape for the protein. The "lowest energy" shape is another way of saying best. In the screensaver, I think the "low energy" frame shows the best shape that your computer has found so far.

Neal
14) Message boards : Rosetta@home Science : CoronaVirus (Message 91831)
Posted 2 Mar 2020 by nnneal
Post:

Seems there isn't these wus


That one was a couple of weeks old already when I posted it.
15) Message boards : Rosetta@home Science : CoronaVirus (Message 91790)
Posted 27 Feb 2020 by nnneal
Post:
The answer is obvious. They don't identify any of their projects.
They want them crunched according to their priority, not ours. It works for me.


It's not exactly a secret. The information is encoded into the task name. Here's a quote from a post on the Number Crunching forum:

These are likely jobs that are modeling the Spike complex (http://new.robetta.org/results.php?id=15652) of 2019-nCoV_S, the corona virus. The genome has been sequenced and there is a mad rush to determine structures for possible drug targets.


Here is one of the task names:

rb_02_08_15652_15556__t000__0_C1_SAVE_ALL_OUT_IGNORE_THE_REST_891233_2882_1
16) Message boards : Number crunching : Can't get new tasks (Message 91586)
Posted 20 Jan 2020 by nnneal
Post:
I agree, a message from the admins would have been a good thing. That would have probably prevented dozens of crunchers having doubts about the own hardware and software setup.

Let's assume they are so busy to to solve the problem, there is no time to inform the users.


You have to use your imagination and imagine what the admins are thinking.
17) Message boards : Number crunching : Can't get new tasks (Message 91560)
Posted 16 Jan 2020 by nnneal
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I have had a hard time getting any new tasks in the last day or so. Help is appreciated!

18) Message boards : Number crunching : I think 6 Million credits is my limit.... (Message 91278)
Posted 16 Oct 2019 by nnneal
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I have been testing the "task scheduler" to auto wake the PC's from sleep mode to the time off day under the bonic daily schedule. No luck yet. Other wise I am wasting 60 watts at idle over 5 systems. My total power over the 5 machines is 210 watts.


I don't think that Task Scheduler can wake the PC. Getting the PC to automatically wake itself at a specified time is going to be difficult.

EDIT:
I tried googling "automatically wake up computer" and I found some hits that look promising.

https://www.howtogeek.com/119028/how-to-make-your-pc-wake-from-sleep-automatically/
19) Message boards : Number crunching : I think 6 Million credits is my limit.... (Message 91267)
Posted 14 Oct 2019 by nnneal
Post:
My system has 48 GBs of RAM. I run around 15.2 GBs. I only run 24 at a time. Looking at the Processes in the task manager, it varies by thread between 213 MBs - 710 MBs ,


Thanks. Have you figured out how many Watts your system consumes when running Rosetta?
20) Message boards : Number crunching : I think 6 Million credits is my limit.... (Message 91257)
Posted 12 Oct 2019 by nnneal
Post:
How much memory does it take to run 32 Rosetta threads?

Neal


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