Crunching for Covid

[damienh]

Hi Folks,

I thought I would add a new thread for Covid-related crunching, since the WCG challenge thread has turned to this topic.

I still have most CPU on TN-Grid for now. There is a non-FB challenge on there and it is somewhat related to Covid, in that they are now focused on human gene expansion and one of the target genes codes for a protein that is a functional receptor for the coronavirus.

The project that seems to be focused on Covid at the moment, and the one that there has been a lot of press about, is Folding@Home. There is a big groundswell of companies and people getting behind their Covid work as detailed here:

https://foldingathome.org/news/

I know that Richard (Homefarm) and Chris C (ncoded) have moved across to crunch Folding@home. I've enabled 5 GPUs and pointed them at Folding@home, and may yet decide to abandon the TN-Grid sprint and to move CPU over as well, at least through to the next Formula Boinc sprint.

If you do join Folding@home, don't forget to join the UK Boinc Team, which is team ID 45392. Unfortunately it's not a BOINC project and doesn't work quite the same way as our other projects.

The Folding@home software can be found here: https://foldingathome.org/start-folding/. Just don't forget you've installed it, since it will auto-start by default in the future and likely cause issues with your BOINC capability!

Cheers & happy crunching.

[damienh]

As a practical item, I found that I wasn't able to enable GPU folding on Linux. That was despite having both OpenCL and nvidia drivers installed.

Perhaps others will have better luck. I've chosen to run all Windows for now.

You may also find that you don't pick up work units right away, or that they are sparse. There's a huge amount of new resource coming online and the Folding@home folks are working hard to keep up / get ahead.

[UBT - Timbo]

Hi Damien

One thing that should be taken into account about both the Folding@home and TN-Grid efforts on Covid-19 is this:

Whatever may be learned, will not help anyone who has caught the virus now (though it may help to understand the virus and provide a vaccine for the future).

The reason is simple: Any new vaccine or drug must go through lots of testing to be sure that any side-effects are minimal, as well as providing a cure or at least respite from the effects of the virus.

And, one can assume that this will take a while - the fastest drug approval I have heard about is around 15 months after the initial formulation was created until it was approved and available to the general public.

Edit: The BBC website has a news item about a US trial with a newly developed vaccine called "mRNA-1273":

https://www.bbc.co.uk/news/health-51906604

And please note the last paragraph:

But even if these initial safety tests go well, it could still take up to 18 months for any potential vaccine to become available for the public.

So, the challenge (for medical science) is there and is real...but anything that is found from these two projects is not going to benefit anyone quickly...and indeed the virus may well be stopped from spreading and just "die off" within the next few months.

regards
Tim

[UBT - Timbo]

Hi all

I've had a chance to check the Folding @home website and download the Teams and Usernames lists.

So, UBT DOES have a Team on Folding@home - so if you want to get involved, our Team Number is: 45392 - enter this on the Folding@home app "Configure > Identity" tab - and use your BOINC name as your username (if you want)

And currently we are in 6925 position and with a score of: 1,813,773 and having completed 4,727** wus

We do have some current stats as follows:

Code: Select all

username				score	wu	team
Christopher_N._Lewis			1145532	2600	45392
ChrisR					202937	449	45392
UBT_NaRyan				87266	204	45392
Whitecrow				75040	299	45392
melter65				70655	284	45392
Bruto246				46446	227	45392
Deepest-blue				43076	171	45392
DaveIrish				29630	118	45392
sigma-7					25440	53	45392
matthewh4271				21810	77	45392
Koranzite				18730	54	45392
Wompus					15574	62	45392
UBT_Nogbo				11035	25	45392
myddrak					7317	39	45392
UBT-PiezPiedPy				5645	12	45392
garethpl				1325	1	45392
Knightlight				861	3	45392
Cheule					750	6	45392
UBT-Timby				623	2	45392
OwenThomas				562	2	45392
JamesBradbury				506	2	45392
PS3					502	2	45392
59c7a842f5b9640e9d84640e9d6b5b717	500	4	45392
Joc					500	2	45392
stuart264				385	2	45392
Joshrandom				384	1	45392
WTBroughton				307	2	45392
UBT_Cris_keys				234	1	45392
drhen123				220	1	45392
UBT_-_Timbo				201	2	45392
kevan-in-devon				0	21	45392
Total: 31 usernames, 1,813,773 (or 1,813,993 if you add it correctly) score and 4,727 wu

...and YES that DOES appear to be me propping up the bottom of the table. But I don't recognise any of the username as being current forum members on this list so if you already have a Folding@home account, maybe you've not joined the Team? (PS If you joined since Sun Mar 15 18:51:47 GMT 2020, then you won't appear in this listing as that's the time and date of the listing I downloaded).

EDIT: I found out where the extra 21 WU came from - the last name in the table completed 21 tasks, but didn't earn any credits (score) !

regards
Tim

[UBT - Mikee]

Hi

I should be there. Been a member for years but never actually did a WU! Been active since Saturday and done some but not sure why I'm not on the list. Possible GDPR thing?

Mike

[UBT - Timbo]

Hi

I should be there. Been a member for years but never actually did a WU! Been active since Saturday and done some but not sure why I'm not on the list. Possible GDPR thing?

Mike

Hiya Mike

What username did you use and I can check you on the username listing I downloaded

It might also be that if you have ZERO credit score then you are not included (as all the usernames I can see have scores >0 !!)

So, just run the FAH program and make sure you enter the team number as mentioned above.

regards
Tim

[UBT - Mikee]

HI

Couldn't be bothered with the underscores so it's just "UBT-Mikee"

Mike

[UBT - Timbo]

HI

Couldn't be bothered with the underscores so it's just "UBT-Mikee"

Mike

Fair enough

I did a search (of the username listing) and I couldn't find you...

EDIT: BUT I found you here:

https://stats.foldingathome.org/team/45392

regards
Tim

[Woodles]

Never done Folding before but poking around their website I found this - https://foldingathome.org/support/faq/points/passkey/

The interesting part:

Perhaps more interestingly, we have introduced a new Quick Return Bonus (QRB) points program, which is tied to passkeys. To earn this bonus, you must use a passkey.

So sign up for a Passkey and get bonuses

[damienh]

I've submitted the passkey request a couple of times and nothing has shown up in my email.

EDIT: just tried again and it worked, although seems to have re-set my stats ... (?)

[damienh]

I also notice that I'm now crunching a non-covid work unit.

[UBT - Timbo]

Never done Folding before but poking around their website I found this - https://foldingathome.org/support/faq/points/passkey/

The interesting part:

Perhaps more interestingly, we have introduced a new Quick Return Bonus (QRB) points program, which is tied to passkeys. To earn this bonus, you must use a passkey.

So sign up for a Passkey and get bonuses

Hi Mark

Good call - I've set up a passkey - took all of about 20 seconds from visiting the website, entering my info and then getting an email.

Would be nice to get bonuses...but also nice to know one is doing one's "bit" too...though until the end of March, I'll be cracking on with SETI@home and chasing down some "pre-hibernation" credits.

regards
Tim

[UBT - Glenn]

Hi Guys I hope everyone is well. Im back after a little time aways... ill sign up for this now as im one of the "High Risk groups" so finding a cure to me is important.

Best wishes UBT - Glenn

[UBT - Timbo]

Hi Guys I hope everyone is well. Im back after a little time aways... ill sign up for this now as im one of the "High Risk groups" so finding a cure to me is important.

Best wishes UBT - Glenn

Hi Glenn

Long time no see !! Welcome back and good luck crunching.

regards
Tim

[homefarm]

HI

I have a passkey now and registered it, it seems to increase security. However nothing received today, but everything seems in order waiting for units to crunch..... here's hoping.....

[UBT - Timbo]

HI

I have a passkey now and registered it, it seems to increase security. However nothing received today, but everything seems in order waiting for units to crunch..... here's hoping.....

HIya

I've left a vCPU and a GPU "free" for Folding but no tasks have been received

regards
Tim

[homefarm]

Still some outages, see url

https://foldingforum.org/viewtopic.php?p=314382#p314382

[chriscambridge]

The stats on F@H have not been updated in days as they are still showing the folding I did years ago for CureCoin team; since then I have done multiple tasks under UBT.

Personally I have left F@H now for a couple of reasons:

1) They are far more folders than there is F@H work.

2) When 80% of hosts were sitting idle with no work, F@H were sent requests that perhaps they should inform their users that there are other medical projects on BOINC doing similar and/or equally important work.

F@H response to this was to completely ignore all messages. Both WCG and Rosetta were fully aware of the approach as well as the lack of any response.

2) Rosetta are now publicly promoting via social media the fact that they are actively working on Covid19 related areas

[chriscambridge]

Plenty of Covid19 Rosetta work now...

[homefarm]

Now running Folding GPU tasks, but its only using about 20% or less GPU power.
Not sure why this - but very inefficient??
Using GPUGRID to pick the balance of GPU crunch power.
CPUs given over to Rosetta, postponing all PrimeGrid work for the foreseeable future.

[Woodles]

Looks like Amazon have donated their spare cloud instances to Folding - https://folding.extremeoverclocking.com ... =&t=238068

2.5 BILLION points a day!

[chriscambridge]

It seems to be the "member" EC2Spot

https://folding.extremeoverclocking.com ... =&u=928671

Amazon EC2 Spot instances are spare compute capacity in the AWS cloud available to you at steep discounts compared to On-Demand prices.

[Woodles]

Not bad going for cheap left-overs

[bigsinky]

Folding now running 1.5 Exaflops. That’s a lot of computing power. I couldn’t get folding WUs so have switched all my CPUs to Rosetta. Coming up on my 1st million. Again I’m in a high risk group so a vaccine would be greatly appreciated. Now in 10th day of social distancing. Slowly going stir crazy.

[homefarm]

HI everybody,Hoping you are all well.

I'm 12 week isolated as I'm old and vunerable, except of course I have to feed the cows etc. However so far they are symptom free, as I hope to remain.

I am running Folding in the background on 3 PCs, and on 2 GPUs ( 2080ti and Titan V). F@H shares the GPU, and Afterburner usefully shows the various parameters on the "detach" section at the bottom of the display. Sadly one of my 2080ti has lost it's ability to hold down the temperature. I have set a manual fan profile, which allows it to run short tasks such as GFN-15, taking 25-30 seconds then getting a breather for reload times 2-3 secs. Anything longer and the temp rockets to 84C. (it's normal limit)

In the Boinc arena I have GPUgrid, and Rosetta (mainly Covid) running. Rosetta however throws up loads of error runs, wasting precious CPU time, so I have disabled it for now. The 7890XE runs perfectly on other tasks, so I'm pretty sure it's the Rosetta tasks which are the source of potential errors.

There is a Primegrid 3 day bash, starting tomorrow 12:00 UTC, for Sophie Germain prime hunting. I will move all over to that for the 3 days, then return to Covid.

As a separate task I volunteered to type in 2800 pedigree records for Aberdeen Angus Cattle 1985 herdbook, as the Society is trying to get all records on line. There's about 15 of us slapping on keyboards, and I'm no typist!!

Take care, stay safe.

[damienh]

Glad you're staying safe Richard. I have been helping Tim on his mission to get 10m SETI credits before is all shuts down. Mark has bee in on that too. It's been a good bit of fun.

I have done a fair amount of Folding@home and also a bunch of TN-Grid, which is also somewhat Covid-related.

Other than that, I am slowly going stir crazy at home and have already put on 1kg from comfort eating and ... not going out much ...

Looks like tomorrow will start another Formula Boinc Sprint, so that will be good. Hoping it's Rosetta, so that Chris C will join in.

All the best

[homefarm]

Glad you're ok, Damien, even if you are expanding

Re Seti, I started on it 2 Sep 2004, but later cocked it up and lost a lot of credits.

I also didn't want to wake up the aliens, there's enough nasties already down here. Now we've Covid-19 aliens, but no radio frequency signals from them (yet).

As the Chinese saying goes... May you live in interesting times.

Cheers

[UBT - Timbo]

HI everybody,Hoping you are all well.

I'm 12 week isolated as I'm old and vunerable, except of course I have to feed the cows etc. However so far they are symptom free, as I hope to remain.

Hi Richard

Good to hear from you.

I'm not self-isolating as I am a one-man band at work and I have orders to fulfill (mainly to resellers with ecommerce websites) - however, I'm only shipping 2 days a week at present and people are being patient which is nice - as usually they want items shipped "yesterday". The nice thing is that leaving home at around 9am this morning there was virtually no traffic on the roads...and my route takes me over a bridge over the M6 and it too was pretty much empty - so, 9am on a weekday and NO TRAFFIC. It's like a scene from the 50's film version of "Day of the Triffids". It was the same tonight - and driving to and from was so relaxing...as there weren't any twats rushing to overtake you or cut you up... absolute bliss !!

I am running Folding in the background on 3 PCs, and on 2 GPUs ( 2080ti and Titan V). F@H shares the GPU, and Afterburner usefully shows the various parameters on the "detach" section at the bottom of the display. Sadly one of my 2080ti has lost it's ability to hold down the temperature. I have set a manual fan profile, which allows it to run short tasks such as GFN-15, taking 25-30 seconds then getting a breather for reload times 2-3 secs. Anything longer and the temp rockets to 84C. (it's normal limit)

84C on any GPU is far too warm - I found that to my cost when I was running a pair of GTX580's about 5 years ago...but very nice in winter as no central heating was required (in that room)...

I too am running Afterburner and with my specific NVidia GPUs I slide the "Core Voltage" and "Power Limit" DOWN to maybe 60-75% of the "default" settings and this doesn't seem to have any bad effect on crunching times...but it does run the GPU at cooler temps. I've also clicked the "down arrow" to the right of "Power Limit" and this allows you to "Prioritize" the Temp Limit, which you can set manually...so if it gets too hot, it will automatically reduce the Power that the GPU consumes.

You can also adjust the GPU fan speed manually...or leave it on "auto". And if you click on settings, then on the 2nd tab, you can adjust the fan profile such that the fan spins faster at higher temps, which cools it down.

In the Boinc arena I have GPUgrid, and Rosetta (mainly Covid) running. Rosetta however throws up loads of error runs, wasting precious CPU time, so I have disabled it for now. The 7890XE runs perfectly on other tasks, so I'm pretty sure it's the Rosetta tasks which are the source of potential errors.

There is a Primegrid 3 day bash, starting tomorrow 12:00 UTC, for Sophie Germain prime hunting. I will move all over to that for the 3 days, then return to Covid.

As a separate task I volunteered to type in 2800 pedigree records for Aberdeen Angus Cattle 1985 herdbook, as the Society is trying to get all records on line. There's about 15 of us slapping on keyboards, and I'm no typist!!

Take care, stay safe.

I think a lot of people will be tempted to crunch on Rosetta...but as you say there could be issues with tasks that cause them to error out. Hopefully they will resovle that issue once they see lots of "Error" reports.

Good luck with the cattle herdbooks - I s'pose it makes a change from counting sheep !!

regards
Tim

[homefarm]

Thanks Tim, I'll try again with the GPU settings. The only good side is that I'm finding GFN15 primes

[damienh]

Richard, do you know if your GPU fans are actually spinning up? I can only think that one of your fans has failed or your cooler is coming away from the card. I’ve removed a few coolers in my time - it’s worth at least visually checking it and to tighten screws where you see them. You may also spot fan cables underneath the shroud too - they shouldn’t really come loose but worth checking if you do see one. If there’s a lot of dust where you are, you may also need to pull off the outer shroud and clean the heat sink? Just a thought ...

On Tim’s note about power target, although my GPUs are water cooled, I also now tend to run them at 75-80% power target via MSI Afterburner on Windows. I then apply a modest frequency overclock.

Overall I see very little difference vs running them at 100% power.

On Linux I’ve only found ways to reduce GPU frequency rather than the power target. If anyone has seen a tool to adjust power targets on Linux then let me know.

[homefarm]

Thanks Tim, Damien.

Forum benefits, getting valuable tips.

I had been jiggling the parameters, but reducing the power limit to 75, and max temp to 75, has proportionately reduced the Mhz from 1945 to about 1845, allowing it to stabilise. I realised the overclock was high, and previously it had been OK. About 2 weeks ago I used the Afterburner OC button to test and reset the GPU, that must have upset the balances in play.

So, very grateful for the impetus to reset parameters according to your suggestions. It's now running GFN 17 Mega, at 1845, 58C; much better balance.

Thanks guys.

[Woodles]

On Linux I’ve only found ways to reduce GPU frequency rather than the power target. If anyone has seen a tool to adjust power targets on Linux then let me know.

I've seen a couple of people recommending nvidia-smi for controlling Nvidia cards (TSBT )

Not tried this myself.

[Edit] '-pl' (power limit) seems to be the parameter that you want - "nvidia-smi -pl 85" sets the power limit to 85%

[damienh]

I've seen a couple of people recommending nvidia-smi for controlling Nvidia cards (TSBT )

Not tried this myself.

[Edit] '-pl' (power limit) seems to be the parameter that you want - "nvidia-smi -pl 85" sets the power limit to 85%

That's great - thank you. I will see if I can make that work.

[UBT - Timbo]

Richard, do you know if your GPU fans are actually spinning up? I can only think that one of your fans has failed or your cooler is coming away from the card. I’ve removed a few coolers in my time - it’s worth at least visually checking it and to tighten screws where you see them. You may also spot fan cables underneath the shroud too - they shouldn’t really come loose but worth checking if you do see one. If there’s a lot of dust where you are, you may also need to pull off the outer shroud and clean the heat sink? Just a thought ...

Good call Damien.

I had assumed that maybe Richards fans would have been working OK...but obviously if the PC case is all sealed up and the PSU and CPU fans are making a noise then any GPU fan noise could easily be "obscured"...so a rise in temps could easily be due to fan failure.

Maybe Richard needs to carefully remove the side of the case cover - the left hand one is usually best, if it's a normal desktop tower type case - and take a peek inside and see - of course, the PC needs to be "on" and running - so don't physically move the PC itself while it's "powered up" as you could damage the hard drive.

So might be best to quit any applications and then check - all you need to see is that the GPU fan is actually running. A small torch and maybe a mirror might help too?

regards
Tim

[damienh]

Sounds like he's figured it out - he had a nasty overclock on the card! That would explain it ...

He's now under-clocked it a bit.

[damienh]

I've seen a couple of people recommending nvidia-smi for controlling Nvidia cards (TSBT )

Not tried this myself.

[Edit] '-pl' (power limit) seems to be the parameter that you want - "nvidia-smi -pl 85" sets the power limit to 85%

So I've tried this and it works, with a couple of small ammendments.

1. It requires to be run as root, so 'sudo nvidia-smi -pl' followed by the power limit target
2. The power limit target is not in % like MSI afterburner and is instead in watts

Note that it is a function of the nvidia proprietary driver, so that needs to be already installed.

I looked up the TDP of my card and did the calculation myself. My 2080ti was runing at about 1890MHz @260w. I applied a 200w limit (~78%) then applied a 100MHz overclock. The card is now running at around 1790Mhz, so I'm getting close to 95% of the compute for 78% of the power (and heat). That's a win

I might adjust it even lower though. I'm generally finding that clocks don't drop rapidly with power reductions.

[homefarm]

Richard, do you know if your GPU fans are actually spinning up? I can only think that one of your fans has failed or your cooler is coming away from the card. I’ve removed a few coolers in my time - it’s worth at least visually checking it and to tighten screws where you see them. You may also spot fan cables underneath the shroud too - they shouldn’t really come loose but worth checking if you do see one. If there’s a lot of dust where you are, you may also need to pull off the outer shroud and clean the heat sink? Just a thought ...

Good call Damien.

I had assumed that maybe Richards fans would have been working OK...but obviously if the PC case is all sealed up and the PSU and CPU fans are making a noise then any GPU fan noise could easily be "obscured"...so a rise in temps could easily be due to fan failure.

Maybe Richard needs to carefully remove the side of the case cover - the left hand one is usually best, if it's a normal desktop tower type case - and take a peek inside and see - of course, the PC needs to be "on" and running - so don't physically move the PC itself while it's "powered up" as you could damage the hard drive.

So might be best to quit any applications and then check - all you need to see is that the GPU fan is actually running. A small torch and maybe a mirror might help too?

regards
Tim

Hi Guys

Don't worry as I built the PCs, and have checked them for hardware failure etc. Cheers

[UBT - Mikee]

Hi

LinusTechTips have donated server hardware and bandwidth to Covid19 folding@home research.
2 videos showing a basic 'how to' guide, 2nd showing building and commissioning of the server.

https://www.youtube.com/watch?v=HaMjPs66cTs

https://www.youtube.com/watch?v=KU4qOebhkfs

Mike