Posts by Chilean

1) Message boards : Cafe Rosetta : Record performances with EPYC (Message 95067)
Posted 21 Apr 2020 by Profile Chilean
Post:
The AMD EPYC 7Fx2 series is intended for applications that benefit more from frequency and cache, over raw thread count. However, Rosetta@home is perfectly able to use as many threads as a system has available (provided that the machine has sufficient RAM).

While these frequency-optimized SKUs are impressive for their intended workload, they wouldn't be optimal for Rosetta compared to the existing 2nd generation Epyc lineup.


Isn't Rosetta L3-Cache hungry?

Is it correct that as time goes on, L3 cache will eventually turn into "RAM"? I remember having a computer with 64MB of RAM... and now we have a CPU with 256MB of L3 CACHE.
2) Message boards : News : Rosetta's role in fighting coronavirus (Message 94537)
Posted 15 Apr 2020 by Profile Chilean
Post:
My Android pixel 2xl is an arm64 device but it's not getting any Wu's. Something else I need to do?

The server is currently out of tasks for mobile devices, so you will at least have to wait for more to be created.

I looked at its details. It looks like it should be able to run one task at a time, and possibly two, due to the size or its memory.

You may need to get familiar with the settings that control the limit of how many tasks it will try to run at the same time.


Hmmm, I set my phone to 4 tasks. I don't really check how it's doing in detail, but according to my PC lists, it's doing about 370 RAC, running only at night. My wife's phone is slowly catching up as well.

I'm mostly worried about the writing to storage these WUs might be doing... does anybody know anything about this?

Amazing, these little phones are crunching as fast as my old computer did back when BOINC got first released.
3) Message boards : Cafe Rosetta : DreamLab now available for Android and iOS (Message 94348)
Posted 13 Apr 2020 by Profile Chilean
Post:
I'm not sure I'd use this on my primary phone, just because of heat and battery issues even though it only runs when plugged in... BUT, I did have 2 older phones that I should have recycled long ago in my desk drawer. They are now setup to run this on the corona project 24/7. If those older phones die no big deal.


I set mine to use 3-4 cores, and it barely gets warm. It gets way hotter when I'm bored and play stuff on it. I'm a bit concerned about the disk writing tho. Not sure how much each WU writes to the phone's storage.
4) Message boards : Number crunching : Total R@H Computing Power (Message 94201)
Posted 12 Apr 2020 by Profile Chilean
Post:
Is the "Current GigaFLOPS" stat in the Server Status page accurate?
No.
Such values are usually derived from the RAC/Credit of the attached hosts, or the Tasks themselves. And due to the broken nature of the BOINC Credit mechanism (just look at the huge variability of Credit granted here for different Tasks and different Applications) any such claims of compute performance need to be taken with an ocean of salt. And then you have other BOINC projects that grant Credit in their own way, making their claims of compute performance to be complete and utter fantasy with no basis in reality.
The variability of Rosetta Credit makes me suspect they are using the BOINC Credit New mechanism, which tends to underpay significantly, and as Credit is used to determine FLOPs...


I mean 1 GFLOP reported here = 1 GFLOP reported by Folding@Home.
I've no idea how Folding@home come up with their FLOPs numbers- if they use FLOP counting then they should be pretty close to the true value. If they use some other mechanism then all bets are off.
But the FLOPs between the projects are nowhere near comparable due to the different methods of coming up with the value; you can't even compare FLOPs between BOINC projects, let alone projects outside of the BOINC framework.


I kinda thought this was the case. I just want to know how "far behind" R@H is compared to Folding compute-power wise. I know the difference if probably huge, considering they can use GPUs. But it'd be good to know exactly how much and keep track of it. It'd also be great to see how R@H compares to a TOP500 Supercomputer and stuff like that.
5) Message boards : Number crunching : Total R@H Computing Power (Message 94173)
Posted 11 Apr 2020 by Profile Chilean
Post:
Is the "Current GigaFLOPS" stat in the Server Status page accurate?

I mean, it did go up A LOT during the last few weeks, so it does seem to correlate tightly with how much is being proceeded, but is this number comparable to the number given by Folding@Home regarding their total computing power? I mean 1 GFLOP reported here = 1 GFLOP reported by Folding@Home.
6) Message boards : News : Help in the fight against COVID-19! (Message 93983)
Posted 9 Apr 2020 by Profile Chilean
Post:
So, am I supposed to update my client to participate in this new capability? Kind of confused as to whether this is a call to action or just a status update.


You just attach Rosetta to BOINC and that's it. BOINC automatically downloads the executable for you and updates it if necessary,
7) Message boards : Number crunching : Partial use of many CPUs vs. Complete use of one CPU? (Message 93412)
Posted 4 Apr 2020 by Profile Chilean
Post:
Hi all! First time I've used Rosetta@home in a while in light of COVID. I had a technical question. My computer has 4 CPUs and an AMD GPU (which my understanding would suggest that the GPU isn't particularly used by Rosetta@Home).

To optimize Rosetta@Home, would it be better for me to dedicate 1 or 2 of the CPUs at 100% CPU Time or to dedicate all of my CPUs at 50% CPU Time? Is there even a difference?

Thanks!


In my opinion, if your CPU has HT, set it 50% number of threads when working on the PC. If you have a dedicated PC running nothing but Rosetta, then set it to 100% number of threads.

I always leave the CPU time setting at 100%. Much rather have half of my threads running @ 100% than having the whole CPU switching on and off every so many seconds. Kinda makes me think there'd be way more thermal stress that way (heating and cooling so often between 100% usage and 0% usage).
8) Message boards : Number crunching : Munin graphs for Rosetta (Message 93409)
Posted 4 Apr 2020 by Profile Chilean
Post:
Now that they increased the default WU duration, I'd expect to see a decrease in the number of WU being sent back, but an ever increasing RAC as each WU will return more decoys than before,
9) Message boards : Cafe Rosetta : Rosetta volunteers in conversation (Message 92906)
Posted 1 Apr 2020 by Profile Chilean
Post:
Hi from Germany!
Not new to BOINC, but new with R@H since... we all know when.

Stay safe and healthy, everyone!


It's not the virus that concerns me, it's the world falling apart due to virtually nobody working. I already find it hard to buy food, a freezer, a home gym, or brewing sugar. Panic is always worse than the actual thing.


Due to human nature, it kinda IS the virus fault tho, isn't it?. So we should worry about the virus because the virus causes panic (regardless whether its justified or not). Virus, catastrophes, or whatever, they all cause damage by themselves AND by panicking the people. We could make an analogy to our own immune system. The common cold doesn't make you feel like crap because of the virus, it's the immune system itself that makes you feel like crap, usually from overreacting.

This situation also reminds me of to the Chilean 8.8 Earthquake I got to experience back in 2010. The quake itself wasn't the biggest concern. that's what solid building codes are for... it was the PANIC. But can we really expect people to not panic when there's no certainty about anything? That and the aftershocks, those kept you on edge for a few months afterwards too lol

Right now, I truly believe it's better to shutdown EVERYTHING for a few weeks. Otherwise, if we try to contain the economy by sort-of shutting down, then we might not be able to contain it and we'd get the worst of both worlds. Awful economy AND piles of dead bodies. But that's just my guess.
10) Message boards : News : Rosetta's role in fighting coronavirus (Message 92738)
Posted 31 Mar 2020 by Profile Chilean
Post:
Currently, I have 14 machines with 80+ cores and 14+ GPUs. When I switched over to run one of them to Rosetta, from cancer research (WCG), I did NOT receive anything related to covid19. Whenever I would receive ALL WUs for covid19, I will switch over... Till then I will stick with cancer research. Let me know when covid19 is the priority here. I am NOT going to download the fold@home app. If it is not thru BOINC, I do not run it.
James

There has been a discussion that Folding@home is likely to produce a BOINC version soon, Not ready yet, though.

Is that right? That's a project I've always wanted to run - especially now they're doing COVID work - but I've also been put off by it not being available via Boinc


I agree. If LHC can do a Virtual Machine Wrapper, there's little reason to not have some sort of API/Wrapper/Whatever with Folding (right?). It'd be SO much easier to distribute work between Folding, Rosetta, and GPUGRID. Because right now, it's a manual hassle. It'd be nice to also have some sort of consolidated "credits" thing, to keep track of how much you're contributing.
11) Message boards : News : Rosetta's role in fighting coronavirus (Message 92731)
Posted 31 Mar 2020 by Profile Chilean
Post:
Quick question for anyone, yesterday when it became clear that the server was empty I completed my running units, suspended the rest and did a project reset on my fastest set up. My thinking being that I would send my queue back to the server for redistribution. Is that how it works as although my client is empty, I have a considerable number of tasks in the "in progress" section, although I obviously do not. I had to reset the project a couple of times during the last few days as some work refused to download also but that's understandable given increase in users, and it seems that whatever was in the queue is also listed in that section?

So when you reset does the client not tell the server to redistribute the work you had waiting?


No, I think when you do a reset, it doesn't abandon the WU. In order to correctly do what you were trying to do, you have to ABORT the WUs, and then update the project thru BOINC Manager. Then, on the site, the WU list will show as Abandoned and should get get resent to other people.

By the way, the WUs take the same time regardless of how fast your machine is. If you machine is faster, it'll simply do more models vs a slower machine and get more credit per WU.
12) Message boards : News : Rosetta's role in fighting coronavirus (Message 92700)
Posted 31 Mar 2020 by Profile Chilean
Post:
Not only has the coronavirus spiked volunteer interest with our R@h project, but it is also spiking a lot of interest towards R@h within the lab so the communication should definitely get better. A lot has happened in a short amount of time.

1. As mentioned before we spiked ~4x or more in computing in the last week. So far our infrastructure has been handling this okay but we will definitely look into expansion and optimization as we expect many more volunteers to join in the near future. Also, our bandwidth has maxed out on a few occasions but has been okay since.

2. A number of outside groups have approached us to help.

a. The ARM developer community came together and helped port Rosetta for aarch64. The application is being tested on Ralph@home currently and will be released soon along with an announcement.
b. We are in communication with Microsoft to help us integrate and support Rosetta BOINC builds into the Rosetta Commons build and testing infrastructure and possibly with other developments.
c. We are in communication with Charity Engine to possibly use their infrastructure to run GPU machine learning based jobs and to help integrate such capability to R@h.

3. We have plenty of COVID-19 jobs but there may be a pause from time to time to give us a chance to prepare them based on previous results and new targets/methods etc.
4. We hope to update the Rosetta apps that are currently being tested on Ralph soon and plan to do another update in the near future, so 2 application updates are lined up for the near future.
5. With these updates, we hope to recruit more researchers within the lab to use this resource, but in the immediate future, priority will of course be towards COVID-19, specifically for the design of scaffolds and binders to COVID-19 targets as possible therapeutics.

Thanks Everyone!


Please post this on the homepage! Very informative.

Thanks for the update!
13) Message boards : News : Rosetta's role in fighting coronavirus (Message 92641)
Posted 30 Mar 2020 by Profile Chilean
Post:
My computer does not receive new jobs, maybe they are over. Waiting from China for i5-4690 instead of G1840.


According to the Server Status page, R@H is basically out of WU to send. Over 1.4 MILLION WUs out in the wild being crunched. I don't recall a time when there were so many WUs distributed out in this project.
14) Message boards : News : Rosetta's role in fighting coronavirus (Message 92585)
Posted 30 Mar 2020 by Profile Chilean
Post:
team Challenge
https://www.boincstats.com/stats/challenge/team/chat/1074


Chances are very high that we're gonna finish last lol, but I just signed our tiny, but precious, team up!

If any of y'all are teamless, you're more than welcome to join!
15) Message boards : News : Rosetta's role in fighting coronavirus (Message 92348)
Posted 26 Mar 2020 by Profile Chilean
Post:
To try and maximize my contribution to fighting SARS-CoV-2, I've adopted the approach of running R@h for CPU work, and running Folding@home for my GPUs

Much thanks to the R@h team!


This is the best approach in my opinion. GPU for Folding, CPU for Rosetta.

For me it makes little sense to do CPU for Folding since they can already do the same work with GPU which are way faster for that kind of work.
16) Message boards : Number crunching : Good bye Rosetta !!! (Message 91023)
Posted 13 Aug 2019 by Profile Chilean
Post:
Sorry, I leave this projet.
Admin publish information as links. Nice to be informed about . The latest is three years old !!!
The only recent (16july19 by admin) is about "audacious projects". Nice, but is not a part of Boinc.
And this link send us to donation requests !

And about projects who has nothing to do with sciencetific research, as educating people, sexual abuse,...
Of course there are also very important subjects, but
Does we think they not need the computing power of Boinc ?

But what they do to solve the problems of a lot of users ? Abnormal running, app crash,......
Nothing ! Or even good as nothing.Never answer about technical problems. The admin fully ignare the Boinc cruncher.
They just ignore us !


Bye bye.
17) Message boards : Number crunching : Rosetta v4.08 x86_64-pc-linux-gnu or Rosetta v4.07 i686-pc-linux-gnu (Message 90396)
Posted 19 Feb 2019 by Profile Chilean
Post:
Well, you can't execute the benchmark since that are all your completed WUs. Whatever you did, will sort itself out with time.
You can force 64-bit only with <no_alt_platform> in cc_config.xml, but I would wait with that and see if the 64-bit application is really faster than the 32-bit, that's not always the case. Just watch the GFLOPS values. If it really is faster, the server will send most WUs to that application anyway, so no really need to do anything.


I was surprised to see that Rosetta 4.08 is the only 64-bit binary for Linux. Both copies of Minirosetta are 32-bit.
The 32-bit binaries end up with a smaller code footprint and pass parameters on the stack. The parameter list quickly spills to the stack, but they will be in the L1 cache which has a 1-cycle access time.

A 64-bt version will always be faster if compiled properly, unless you aggressively inline functions. The larger code footprint is causing front-end icache miss stalls.
I want to see how hard it is to modify the source to redefine their 3-dimensional "vector" object into a 4-dimensional vector so they can use packed SSE or AVX. Right now all Rosetta computation uses scalar operations.

thanks again.


I have nothing to add, but I started reading your post and when it started going over my head I went "yo this dude knows his stuff...", then I saw the username and said "of course, it's rjs5" lol
18) Message boards : Number crunching : GPU calculation (Message 90270)
Posted 29 Jan 2019 by Profile Chilean
Post:
Rosetta "could" run on GPU if each GPU thread could handle a single model trajectory. But apparently each trajectory uses a lot of memory.
19) Message boards : Number crunching : AMD 1950x Threadripper performance (Message 90250)
Posted 23 Jan 2019 by Profile Chilean
Post:
I might throttle back to maybe 75% or 24 hyper-threads. See what happens. I went out and bought 2x16 GBs of DDR4 memory. So the system seems to recognize all 48 GBs of memory. I do not see much of a change in BIONC usage of memory. With 32 Active simulations, my memory foot print is around 13 GBs.


You only had 1 stick before?

You now have Dual Channel at least.
20) Message boards : Number crunching : AMD 1950x Threadripper performance (Message 90239)
Posted 21 Jan 2019 by Profile Chilean
Post:
I fiddled with that setting. It seems to really cut my real cpu utilization. I set in the manager under options, computing preference, use at most 50% of the CPUs. I thought that would have run close to 100% of the 16 cores, but it seems to cut the real cpu utilization in half. Makes my brain hurt. I maybe making a run to MIcrocenter soon. Will ponder more memory, but it seems to do reasonably well with 16 GBs of RAM.


This is expected. If I half the CPU core usage % in BOINC Manager, I'll see 50% total CPU usage and the workload is distributed evenly in the threads available. To Windows, you "do" have 32 cores... but in real life you don't really. You simply have 32 threads, but 16 cores. So 50% on thread 0 and thread 1 should mean 100% of core 0. Less heat, more cache hits, less RAM usage.

You can maybe run it at 75%. That's what I do. Makes running BOINC completely unnoticeable.


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