News Rosetta's role in fighting coronavirus

[StefanR5R]

(ninja'd by @Orange Kid and @TennesseeTony)

TN grid doesn’t show up on the boinc list: https://boinc.berkeley.edu/projects.php

Is it not a boinc project?

Boinc-client's built-in project list shows really only a fraction of all public BOINC-based projects. But Orange Kid's sticky thread has most if not all active projects, at least all in which a TeAm AnandTech exists.

TN-Grid is furthermore among those projects in which you can't create an account through boincmgr, but instead need to use a form at their web site instead.

• First, visit the web site: http://gene.disi.unitn.it/test/
• There, follow the link to account creation. In the web form, you need to enter an invitation code along with your user details. That's for spam protection. The code is published right on the main page: science@tn
• After that you can add the project to your client by entering the project URL manually into boincmgr's dialogue: http://gene.disi.unitn.it/test/

 

[Endgame124]

Thanks for the tips and directions! I’ll stick with Rosetta until I start having problems, but then if TN GRID Is the preferred alternative, I’ll probably switch all my hosts

 

[Endgame124]

Can anyone share their average RAC per watt for Rosetta only? Looks like a 4gb raspberry pi 4 running Rosetta w/ 3 processes should run about 800 RAC / 160 RAC per watt. For comparison my old core 2 quad 9650 is pulling 2000 RAC, but only about 16 per watt.

Trying to get a feel for what modern hardware does before I do something silly like buy another 19 pi 4s.

 

[StefanR5R]

I never use RAC myself, because I never run a constant workload for so long that RAC approaches a value which could be used for quantitative comparison. Instead, I usually look at PPD after validation, by copy&pasting a sufficiently large number of results from the results tables at the project web site into a spreadsheet. How many results are needed for meaningful numbers depends on the extent of credit variation at the given project. At Rosetta, variation is very high.

Here are PPD and PPD/W from a narrow set of workunits which I fetched with a small number of requests in short succession on April 6 in the morning, all tasks run with Rosetta v4.12 x86_64-pc-linux-gnu: post #140. Because of the tasks used in this measurement, the numbers are comparable with each other, but not with numbers from other days. Power readings are system power draw at the 230 V wall outlet.

160 RAC/Watt seems high for a computer with 28 nm processor. Are those 5 W a processor spec, or actual system power draw while Rosetta runs? If the latter, was a power meter used which is sufficiently precise for this range of power draw?

 

[Endgame124]

I never use RAC myself, because I never run a constant workload for so long that RAC approaches a value which could be used for quantitative comparison. Instead, I usually look at PPD after validation, by copy&pasting a sufficiently large number of results from the results tables at the project web site into a spreadsheet. How many results are needed for meaningful numbers depends on the extent of credit variation at the given project. At Rosetta, variation is very high.

Here are PPD and PPD/W from a narrow set of workunits which I fetched with a small number of requests in short succession on April 6 in the morning, all tasks run with Rosetta v4.12 x86_64-pc-linux-gnu: post #140. Because of the tasks used in this measurement, the numbers are comparable with each other, but not with numbers from other days. Power readings are system power draw at the 230 V wall outlet.

160 RAC/Watt seems high for a computer with 28 nm processor. Are those 5 W a processor spec, or actual system power draw while Rosetta runs? If the latter, was a power meter used which is sufficiently precise for this range of power draw?

StefanR55, As always you provide excellent information. I didn’t know you could look up individual days worth of points on Rosetta, which will help tremendously in comparisons.

I’m getting the power numbers from a user on her Rosetta forums, who I believe disabled HDMI, usb, Ethernet, and leds to get to that value.

My pi 4 arrives tomorrow, but the best source of power measurement I have is one of my APC UPSes (https://www.apc.com/shop/us/en/products/APC-Power-Saving-Back-UPS-Pro-1500/P-BR1500G). I’ll confirm my power usage after a raspbian lite install with Rosetta running before I get to carried away with other tweaks.

 

[StefanR5R]

You can also look up credits of the last 28 days of a host at stats.free-dc.org, and even better, credits of the last 60 days of a host at boincstats.com.

This can be taken as PPD if the host produces continuously for a few days, reports results without much delay, the project validates the results without much delay, and exports stats properly in 24h periods.

 

[Assimilator1]

Not sure about ppd atm (I'll look into it). But running 12 threads on my Ryzen 3600 restricted to 65w PPT (average clock ~3.75 GHz) it's pulling 135w from the wall atm (also 230v AC).
My rig's done most of the last 37 valid tasks in about 29,000s = about 8hrs (see spoiler). Not time to do the rest of the maths right now, so I'll leave you to do that if you want .

At a very rough & ready look, I'd say the average task credit from those is about 400, so that's 50/hr x12 threads= 600cr/hr x24 = 14,400cr/day.
So on those rough figures, my rig's doing ~107 PPD/w, ......have I done the maths right at least??lol
RAC is a 1 day period right?
Btw, until today, I was only running Rosetta on 10 threads, so the RAC won't be much use.

Spoiler

1156286039	1040084704	1761696	20 Apr 2020, 22:31:41 UTC	22 Apr 2020, 17:26:44 UTC	Completed and validated	29,197.83​	28,497.11​	379.75​	Rosetta Mini v3.78 windows_x86_64
1156246446	1040049859	1761696	20 Apr 2020, 22:27:49 UTC	22 Apr 2020, 17:26:44 UTC	Completed and validated	29,416.81​	28,786.47​	356.10​	Rosetta v4.15 windows_x86_64
1156246450	1040049863	1761696	20 Apr 2020, 22:27:49 UTC	22 Apr 2020, 17:26:44 UTC	Completed and validated	29,210.78​	28,576.56​	403.23​	Rosetta v4.15 windows_x86_64
1156003390	1039842166	1761696	20 Apr 2020, 15:21:24 UTC	22 Apr 2020, 16:07:01 UTC	Completed and validated	29,391.71​	28,480.41​	397.85​	Rosetta Mini v3.78 windows_x86_64
1155941763	1039790257	1761696	20 Apr 2020, 14:48:38 UTC	22 Apr 2020, 15:35:42 UTC	Completed and validated	29,422.43​	28,499.38​	375.31​	Rosetta v4.15 windows_x86_64
1155972128	1037265193	1761696	20 Apr 2020, 14:38:41 UTC	22 Apr 2020, 7:57:09 UTC	Completed and validated	7,940.83​	7,638.52​	100.79​	Rosetta v4.15 windows_x86_64
1155321243	1039260269	1761696	19 Apr 2020, 22:59:01 UTC	22 Apr 2020, 12:19:55 UTC	Completed and validated	29,422.41​	28,372.39​	416.83​	Rosetta v4.15 windows_x86_64
1155284764	1039227980	1761696	19 Apr 2020, 22:05:14 UTC	22 Apr 2020, 11:59:43 UTC	Completed and validated	29,311.41​	28,252.58​	472.25​	Rosetta v4.15 windows_x86_64
1154725297	1038749368	1761696	19 Apr 2020, 9:22:28 UTC	22 Apr 2020, 9:48:19 UTC	Completed and validated	29,960.77​	28,748.13​	381.37​	Rosetta v4.15 windows_x86_64
1154681821	1036087453	1761696	19 Apr 2020, 7:18:48 UTC	22 Apr 2020, 8:19:46 UTC	Completed and validated	25,652.16​	24,450.38​	206.03​	Rosetta v4.15 windows_x86_64
1154618681	1038663694	1761696	19 Apr 2020, 6:42:08 UTC	22 Apr 2020, 7:57:09 UTC	Completed and validated	24,439.55​	23,265.78​	197.65​	Rosetta v4.15 windows_x86_64
1154618740	1038663695	1761696	19 Apr 2020, 6:42:08 UTC	22 Apr 2020, 9:29:25 UTC	Completed and validated	29,913.40​	28,492.19​	381.54​	Rosetta v4.15 windows_x86_64
1154618791	1038663764	1761696	19 Apr 2020, 6:42:08 UTC	22 Apr 2020, 9:27:13 UTC	Completed and validated	29,842.57​	28,434.28​	396.17​	Rosetta v4.15 windows_x86_64
1154618848	1038663767	1761696	19 Apr 2020, 6:42:08 UTC	22 Apr 2020, 9:34:27 UTC	Completed and validated	30,133.09​	28,729.81​	397.26​	Rosetta v4.15 windows_x86_64
1154452322	1038523847	1761696	19 Apr 2020, 2:27:51 UTC	22 Apr 2020, 8:39:03 UTC	Completed and validated	26,953.69​	25,704.09​	222.00​	Rosetta v4.15 windows_x86_64
1154420006	1038496354	1761696	19 Apr 2020, 1:34:04 UTC	22 Apr 2020, 9:16:33 UTC	Completed and validated	29,871.22​	28,658.88​	368.80​	Rosetta v4.15 windows_x86_64
1154420074	1038496355	1761696	19 Apr 2020, 1:34:04 UTC	22 Apr 2020, 5:12:48 UTC	Completed and validated	29,494.37​	28,585.14​	414.48​	Rosetta v4.15 windows_x86_64
1154420108	1038496423	1761696	19 Apr 2020, 1:34:04 UTC	22 Apr 2020, 9:15:07 UTC	Completed and validated	29,112.03​	27,817.45​	374.81​	Rosetta v4.15 windows_x86_64
1154262929	1038365559	1761696	18 Apr 2020, 21:39:07 UTC	22 Apr 2020, 3:51:05 UTC	Completed and validated	29,367.01​	28,589.33​	416.02​	Rosetta v4.15 windows_x86_64
1154262950	1038365608	1761696	18 Apr 2020, 21:39:07 UTC	22 Apr 2020, 4:09:28 UTC	Completed and validated	29,459.16​	28,684.84​	403.90​	Rosetta v4.15 windows_x86_64

1154244105	1038349816	1761696	18 Apr 2020, 21:13:47 UTC	22 Apr 2020, 0:51:45 UTC	Completed and validated	28,207.63​	27,616.83​	615.08​	Rosetta v4.15 windows_x86_64
1154244147	1038349813	1761696	18 Apr 2020, 21:13:47 UTC	22 Apr 2020, 1:28:58 UTC	Completed and validated	29,501.92​	28,827.70​	444.72​	Rosetta v4.15 windows_x86_64
1154145594	1038267933	1761696	18 Apr 2020, 18:50:45 UTC	22 Apr 2020, 1:10:49 UTC	Completed and validated	29,388.77​	28,739.95​	438.20​	Rosetta v4.15 windows_x86_64
1154031385	1038172190	1761696	18 Apr 2020, 16:15:13 UTC	21 Apr 2020, 23:54:57 UTC	Completed and validated	28,905.15​	28,463.53​	408.13​	Rosetta v4.15 windows_x86_64
1154031324	1038172189	1761696	18 Apr 2020, 16:15:13 UTC	21 Apr 2020, 23:44:03 UTC	Completed and validated	28,137.56​	27,731.63​	231.85​	Rosetta v4.15 windows_x86_64
1154004310	1038149439	1761696	18 Apr 2020, 15:35:48 UTC	21 Apr 2020, 19:43:57 UTC	Completed and validated	28,460.40​	28,266.89​	394.13​	Rosetta v4.15 windows_x86_64
1154004323	1038149184	1761696	18 Apr 2020, 15:35:48 UTC	21 Apr 2020, 19:43:57 UTC	Completed and validated	28,665.70​	28,476.73​	430.58​	Rosetta v4.15 windows_x86_64
1154004188	1038149197	1761696	18 Apr 2020, 15:35:48 UTC	21 Apr 2020, 19:43:57 UTC	Completed and validated	28,736.66​	28,539.69​	438.77​	Rosetta v4.15 windows_x86_64
1154004451	1038149438	1761696	18 Apr 2020, 15:35:48 UTC	21 Apr 2020, 22:45:54 UTC	Completed and validated	27,388.24​	27,103.23​	220.11​	Rosetta v4.15 windows_x86_64
1153802810	1037987789	1761696	18 Apr 2020, 11:05:18 UTC	21 Apr 2020, 17:01:32 UTC	Completed and validated	28,766.89​	28,548.22​	476.42​	Rosetta v4.15 windows_x86_64
1153802885	1037987878	1761696	18 Apr 2020, 11:05:18 UTC	21 Apr 2020, 17:00:14 UTC	Completed and validated	28,739.17​	28,537.06​	408.84​	Rosetta v4.15 windows_x86_64
1153802685	1037987776	1761696	18 Apr 2020, 11:05:18 UTC	21 Apr 2020, 17:16:40 UTC	Completed and validated	28,787.48​	28,603.45​	435.21​	Rosetta v4.15 windows_x86_64
1153691526	1037899929	1761696	18 Apr 2020, 8:27:05 UTC	21 Apr 2020, 15:54:51 UTC	Completed and validated	28,723.94​	28,500.47​	425.79​	Rosetta v4.15 windows_x86_64
1153688032	1037897125	1761696	18 Apr 2020, 8:21:53 UTC	21 Apr 2020, 15:52:59 UTC	Completed and validated	28,622.57​	28,397.58​	418.92​	Rosetta v4.15 windows_x86_64
1153666719	1037879856	1761696	18 Apr 2020, 7:51:35 UTC	21 Apr 2020, 10:45:56 UTC	Completed and validated	28,458.59​	28,335.47​	416.25​	Rosetta v4.15 windows_x86_64
1153666550	1037879803	1761696	18 Apr 2020, 7:51:35 UTC	21 Apr 2020, 9:01:54 UTC	Completed and validated	28,558.00​	28,396.69​	428.51​	Rosetta v4.15 windows_x86_64
1152653061	1037020023	1761696	17 Apr 2020, 8:14:41 UTC	20 Apr 2020, 8:34:24 UTC	Completed and validated	26,211.09​	26,029.69​	238.99​	Rosetta v4.15 windows_x86_64

 

[Endgame124]

Well, I have my pi4, installed raspbian (seriously, ssh is disabled by default on the image?), configured it to use zram to stretch the host ram to appx 7GB, did some power tweaking, setup boinctui and attached to rosetta.... and? Rosetta is down for maintenance.

Guess I need to hold my horses a little longer

 

[Endgame124]

I have 4 work units processing on my pi4. Its using between 3 and 5 watts per my UPS (generally 4) and it has already completed 4 work units. Currently I only have the hdmi turned off.

Pi 4 Temperatures with Flirc aluminum case with 4 WUs processing:
Plastic cap on: 58c
Plastic cap off: 55c
Plastic cap off + large heatsink (old thermaltake volcano cu) placed where cap normally is: 45c.

I want to pickup at least 2 more Pi 4s, as I want to test a bunch of different conditions and configurations including:
Does Ubuntu w/ linux kernel 5 improve performance?
Does wifi use less power than ethernet + usb?
What if I only turn on wifi when I need to send / receive data?
Can I setup a pico net using bluetooth to connect to a wired pi so I can disable wifi and ethernet?
How does overclocking change the power usage and ppd with a good case?
Can I PXE boot the pi, store everything on my freenas, and save power and cost not using a sd card?

 

[TennesseeTony]

Turing Pi Cluster Board Lets You Make a Raspberry Pi Server Rack

Support up to seven Raspberry Pi Compute Modules at once.

www.tomshardware.com

 

[Endgame124]

Very interesting on that pi cluster board. It doesn't use conventional pis though, and is limited to at best Pi 3B+, so it may not be an ideal platform for rosetta.

Speaking of which, a little more detail on the thermals of my Pi 4:

Ambient temp 68 degrees (my basement is pretty steady temp wise, but I didn't check between tests if the pi had increased the basement temp)
Each configuration was run for 2 hours, and temps were recorded at 10 second intervals. Max temp recorded (unfortunately I discarded the dataset between runs, so I can't give average temp)
HDMI is disabled for the testing.

w/ top on 58c
w/ top off 55c
w/ top off + heatsink 51c
w/ top off + heatsink + 60mm fan (side) 38c
w/ top off + heatsink + 60mm fan (front) 35c

I'm leaving this one as my reference pi, but will be ordering another one later this week, and I'll probably try some overclocking at 2Ghz.

 

[Endgame124]

I setup a pi3 b+ (1gb ram) to run Rosetta, which, uh, kind of works when you configure zram to compress data in memory.

I want to set it to run 2 (maybe even just 1) rosetta process, and then, say, 2 of some other project that is light weight on ram. I created this app_config.xml, but it doesn't seem to work - I'm still getting 4 rosetta processes and thrashing data in and out of swap. Any suggestions?

/var/lib/boinc-client/projects/boinc.bakerlab.org_rosetta/app_config.xml

<app_config>
<project_max_concurrent>2</project_max_concurrent>
</app_config>

 

[biodoc]

@Endgame124 , that app_config.xml looks good. I'm assuming you chose 'options' then 'read config files' in boinc manager. If the computer is using the swap file heavily it may take some time to respond?

 

[Endgame124]

@Endgame124 , that app_config.xml looks good. I'm assuming you chose 'options' then 'read config files' in boinc manager. If the computer is using the swap file heavily it may take some time to respond?

I actually ran "sudo systemctl stop boinc-client; sudo systemctl start boinc-client".

Is restarting the service insufficient?

 

[biodoc]

Is restarting the service insufficient?

No, that should work. Is there a line in the boinc log that confirms reading the rosetta app_config upon restarting the client?

Sun 26 Apr 2020 07:51:00 AM EDT | Rosetta@home | Found app_config.xml

 

[Endgame124]

No, that should work. Is there a line in the boinc log that confirms reading the rosetta app_config upon restarting the client?

Sun 26 Apr 2020 07:51:00 AM EDT | Rosetta@home | Found app_config.xml

I think It May have been the copy paste from browser to vim. I dos2unix’d the file, restarted the service, and it seems to be happy so far. I’ll check in on it again in an hour. Thanks for the assist so far - I’ll check that log when I check on it again.

 

[StefanR5R]

CERN's data center is donating computer time to Folding@home and Rosetta@home. In addition, CERN has initiatives to develop and produce medical supplies, protective gear, and equipment for hospitals such as ventilators, and are supporting local ambulances and isolated people with CERN personnel and vehicles.

Like many organisations, CERN is also affected by the COVID-19 pandemic. Researchers in the CERN community are trying to help out in different ways, as explained on this web page.

As part of this effort to fight COVID-19, we also contribute computing power to Folding@home and Rosetta@home from temporarily available servers that were about to be decommissioned.

During periods like this with little work from LHC@home, we also encourage you to participate in other BOINC projects such as Rosetta@home and contribute to the global fight of the pandemic.

Many thanks for your contributions to LHC@home and continued happy crunching!

With the best of wishes of good health for your and your families from the LHC@home team.

 

[StefanR5R]

(Dug up an old thread.)

In case some Rosetta@home connoisseurs among us haven't seen it:
We have a quick Rosetta race going on: 2020 Formula Boinc Sprints

The race lasts until Sunday, 22:00 UTC (18:00 EDT, 15:00 PDT).
--> stats, updated at each full hour <--

 

[Endgame124]

Rosetta@Home also announced a breakthrough for Covid on their Twitter feed - a lab successful anti viral:

https://twitter.com/x/status/1276324129390555136

 

[ZipSpeed]

Rosetta@Home also announced a breakthrough for Covid on their Twitter feed - a lab successful anti viral:

https://twitter.com/x/status/1276324129390555136

I'll admit, sometimes I'll wonder if I'm wasting thousands of dollars on hardware and electricity for no reason. Reading about these successes makes me happy and it's not all for naught.

 

[Assimilator1]

Rosetta@Home also announced a breakthrough for Covid on their Twitter feed - a lab successful anti viral:

https://twitter.com/x/status/1276324129390555136

Great to hear!

 

[Markfw]

I'll admit, sometimes I'll wonder if I'm wasting thousands of dollars on hardware and electricity for no reason. Reading about these successes makes me happy and it's not all for naught.

Take your WCG CPUs off-line for 24 hours and put them on Rosetta. We might have a chance for 1st place.

 

[ZipSpeed]

Take your WCG CPUs off-line for 24 hours and put them on Rosetta. We might have a chance for 1st place.

Done. I moved what I can, but I won't have access to some of my other rigs until Monday. Looks like the Rosetta portion is done tomorrow.

 

[StefanR5R]

Uh oh... some Rosetta tasks are occupying >3 GB RAM now.

In other news...

A group called Science To Save the World has created a great video that explains how Rosetta is used to investigate COVID-19, and to model the spike protein before laboratory techniques of structure discovery could be completed.
https://www.youtube.com/watch?v=HBq3izp5X-I

It's a ~6 minutes long introductory video. Some basic bits about viruses and their role in this biosphere are in it too.

 

[Endgame124]

3GB Rosetta processes? Even an 8GB pi won’t be enough for that! I’ll have to get, like, serious x86 hardware or something.