Contribute your computing resources to fight COVID-19

poissonpoisson OG
edited March 16 in General

https://foldingathome.org/2020/03/15/coronavirus-what-were-doing-and-how-you-can-help-in-simple-terms/

Available for Windows, Mac and Linux. I just set mine up and letting my GTX1070 and Ryzen5-2600X rip.

Only issue was heat lol. I had to remove side cover or else my CPU was cooking due to the extraction fans not keeping up.

EDIT: I created a LES team so if you are keen on having your contribution to science counted as a LES effort, this is LES team code: 240518. You enter it in the identity section in the configuration screen.

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Comments

  • lentrolentro Hosting Provider

    A bit like fluidstack (provider.fluidstack.io) except this one actually helps the world. In guess I’ll run this on my idling servers now ;)

    ISODME: Premium web hosting | Managed VPS services | U.S. based support | 99.99% uptime | isodme.com

  • I think as a community, our guys have plenty of computing power and let's use this to try and strike back at the virus!

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  • poissonpoisson OG
    edited March 16

    In case anyone is wonder, this is legitimate. The lab is based in Stanford, and I got to know of it from a MIT-trained chemistry PhD friend who knows these stuff.

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  • stupid question: is this also hugging network bandwidth? or it's resource intensive but only spent few MBs per hour.
    if you ever run this, share stats please

    3 - 2 - 1 - Backup!

  • @mobile said:
    stupid question: is this also hugging network bandwidth? or it's resource intensive but only spent few MBs per hour.
    if you ever run this, share stats please

    No it doesn't hog bandwidth. It downloads a small amount of data, unpacks, runs the algorithm to do protein folding, and then uploads it back to the server. Here's a sample of the logs of what my CPU slot is currently doing.


    03:34:31:WU02:FS02:Assigned to work server 128.252.203.9
    03:34:31:WU02:FS02:Requesting new work unit for slot 02: READY cpu:4 from 128.252.203.9
    03:34:31:WU02:FS02:Connecting to 128.252.203.9:8080
    03:34:33:WU02:FS02:Downloading 2.16MiB
    03:34:34:WU02:FS02:Download complete
    03:34:34:WU02:FS02:Received Unit: id:02 state:DOWNLOAD error:NO_ERROR project:13833 run:0 clone:3044 gen:2 core:0xa7 unit:0x0000000380fccb095e6e55e8cbadc0c8
    03:34:34:WU02:FS02:Starting
    03:34:34:WU02:FS02:Running FahCore: /usr/bin/FAHCoreWrapper /var/lib/fahclient/cores/cores.foldingathome.org/v7/lin/64bit/avx/Core_a7.fah/FahCore_a7 -dir 02 -suffix 01 -version 705 -lifeline 2367 -checkpoint 15 -np 4
    03:34:34:WU02:FS02:Started FahCore on PID 11194
    03:34:34:WU02:FS02:Core PID:11198
    03:34:34:WU02:FS02:FahCore 0xa7 started
    03:34:35:WU02:FS02:0xa7:*********************** Log Started 2020-03-16T03:34:34Z ***********************
    03:34:35:WU02:FS02:0xa7:************************** Gromacs [email protected] Core ***************************
    03:34:35:WU02:FS02:0xa7: Type: 0xa7
    03:34:35:WU02:FS02:0xa7: Core: Gromacs
    03:34:35:WU02:FS02:0xa7: Args: -dir 02 -suffix 01 -version 705 -lifeline 11194 -checkpoint 15 -np
    03:34:35:WU02:FS02:0xa7: 4
    03:34:35:WU02:FS02:0xa7:************************************ CBang *************************************
    03:34:35:WU02:FS02:0xa7: Date: Nov 5 2019
    03:34:35:WU02:FS02:0xa7: Time: 06:06:57
    03:34:35:WU02:FS02:0xa7: Revision: 46c96f1aa8419571d83f3e63f9c99a0d602f6da9
    03:34:35:WU02:FS02:0xa7: Branch: master
    03:34:35:WU02:FS02:0xa7: Compiler: GNU 8.3.0
    03:34:35:WU02:FS02:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie -fPIC
    03:34:35:WU02:FS02:0xa7: Platform: linux2 4.19.0-5-amd64
    03:34:35:WU02:FS02:0xa7: Bits: 64
    03:34:35:WU02:FS02:0xa7: Mode: Release
    03:34:35:WU02:FS02:0xa7:************************************ System ************************************
    03:34:35:WU02:FS02:0xa7: CPU: AMD Ryzen 5 2600X Six-Core Processor
    03:34:35:WU02:FS02:0xa7: CPU ID: AuthenticAMD Family 23 Model 8 Stepping 2
    03:34:35:WU02:FS02:0xa7: CPUs: 12
    03:34:35:WU02:FS02:0xa7: Memory: 31.38GiB
    03:34:35:WU02:FS02:0xa7:Free Memory: 24.02GiB
    03:34:35:WU02:FS02:0xa7: Threads: POSIX_THREADS
    03:34:35:WU02:FS02:0xa7: OS Version: 5.3
    03:34:35:WU02:FS02:0xa7:Has Battery: false
    03:34:35:WU02:FS02:0xa7: On Battery: false
    03:34:35:WU02:FS02:0xa7: UTC Offset: 8
    03:34:35:WU02:FS02:0xa7: PID: 11198
    03:34:35:WU02:FS02:0xa7: CWD: /var/lib/fahclient/work
    03:34:35:WU02:FS02:0xa7:******************************** Build - libFAH ********************************
    03:34:35:WU02:FS02:0xa7: Version: 0.0.18
    03:34:35:WU02:FS02:0xa7: Author: Joseph Coffland joseph@cauldrondevelopment.com
    03:34:35:WU02:FS02:0xa7: Copyright: 2019 foldingathome.org
    03:34:35:WU02:FS02:0xa7: Homepage: https://foldingathome.org/
    03:34:35:WU02:FS02:0xa7: Date: Nov 5 2019
    03:34:35:WU02:FS02:0xa7: Time: 06:13:26
    03:34:35:WU02:FS02:0xa7: Revision: 490c9aa2957b725af319379424d5c5cb36efb656
    03:34:35:WU02:FS02:0xa7: Branch: master
    03:34:35:WU02:FS02:0xa7: Compiler: GNU 8.3.0
    03:34:35:WU02:FS02:0xa7: Options: -std=c++11 -O3 -funroll-loops -fno-pie
    03:34:35:WU02:FS02:0xa7: Platform: linux2 4.19.0-5-amd64
    03:34:35:WU02:FS02:0xa7: Bits: 64
    03:34:35:WU02:FS02:0xa7: Mode: Release
    03:34:35:WU02:FS02:0xa7:************************************ Build *************************************
    03:34:35:WU02:FS02:0xa7: SIMD: avx_256
    03:34:35:WU02:FS02:0xa7:********************************************************************************
    03:34:35:WU02:FS02:0xa7:Project: 13833 (Run 0, Clone 3044, Gen 2)
    03:34:35:WU02:FS02:0xa7:Unit: 0x0000000380fccb095e6e55e8cbadc0c8
    03:34:35:WU02:FS02:0xa7:Reading tar file core.xml
    03:34:35:WU02:FS02:0xa7:Reading tar file frame2.tpr
    03:34:35:WU02:FS02:0xa7:Digital signatures verified
    03:34:35:WU02:FS02:0xa7:Calling: mdrun -s frame2.tpr -o frame2.trr -x frame2.xtc -cpt 15 -nt 4
    03:34:35:WU02:FS02:0xa7:Steps: first=500000 total=250000
    03:34:36:WU02:FS02:0xa7:Completed 1 out of 250000 steps (0%)
    03:35:48:WU02:FS02:0xa7:Completed 2500 out of 250000 steps (1%)
    03:37:01:WU02:FS02:0xa7:Completed 5000 out of 250000 steps (2%)
    03:38:11:WU02:FS02:0xa7:Completed 7500 out of 250000 steps (3%)
    03:39:21:WU02:FS02:0xa7:Completed 10000 out of 250000 steps (4%)
    03:40:31:WU02:FS02:0xa7:Completed 12500 out of 250000 steps (5%)

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  • poissonpoisson OG
    edited March 16

    By the way, if you decide to contribute and there is constantly an error using your CPU, it is very likely because the library that is needed doesn't support too many cores. I tried with a ten core and it failed. So far I have been able to get it working setting number of cores at 4.

    For my GPU, it works with no problems, but you need an Nvidia GPU with CUDA installed.

    EDIT: you can set up multiple slots each with the number of cores you are comfortable with contributing so that you can contribute all your idle CPU power.

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  • edited March 16

    @poisson said:
    By the way, if you decide to contribute and there is constantly an error using your CPU, it is very likely because the library that is needed doesn't support too many cores. I tried with a ten core and it failed. So far I have been able to get it working setting number of cores at 4.

    For my GPU, it works with no problems, but you need an Nvidia GPU with CUDA installed.

    EDIT: you can set up multiple slots each with the number of cores you are comfortable with contributing so that you can contribute all your idle CPU power.

    that's interesting, probably need to put it on container like podman or openshift to makes it run efficiently in lots of cores workstation.

    source code is more interesting for me so i hopped to this page
    https://foldingathome.org/support/faq/opensource/
    https://github.com/FoldingAtHome


    03:34:35:WU02:FS02:0xa7: SIMD: avx_256
    i wonder if they just listed this AVX, if there's a NEON port i'd imagine it's also viable to run in arm devices.
    like x264 for example (this isn't that scientific though lol)

    it's just sad to see people buying or gifted with raspberry pi (and it's siblings) without knowing what to do with it
    i think people will be happy seeing their paperweight Pi contribute something in science with low power cost
    that tiny spark of dopamine probably worth it for average joe. man im so sleepy

    3 - 2 - 1 - Backup!

  • @mobile said:

    it's just sad to see people buying or gifted with raspberry pi (and it's siblings) without knowing what to do with it
    i think people will be happy seeing their paperweight Pi contribute something in science with low power cost
    that tiny spark of dopamine probably worth it for average joe. man im so sleepy

    My BeagleBone Black has been running [email protected] for two years.
    I have Raspberry Pi 3B and 4B. It overheats if I run [email protected]

    [email protected] download page doesn't seem to have ARMv7 or ARMv8 clients.
    People needs to start writing everything in Go so it's portable to every platform.

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  • havochavoc OG
    edited March 16

    Looks like [email protected] is swamped by the interest...no more project available temporarily.

    Alternatively check out BOINC / world computing grid - same concept

    13:05:52:WU00:FS00:Connecting to 65.254.110.245:8080
    13:05:52:WARNING:WU00:FS00:Failed to get assignment from '65.254.110.245:8080': No WUs available for this configuration
    13:05:52:WU00:FS00:Connecting to 18.218.241.186:80
    13:05:53:WARNING:WU00:FS00:Failed to get assignment from '18.218.241.186:80': No WUs available for this configuration
    13:05:53:ERROR:WU00:FS00:Exception: Could not get an assignment

  • It requires python-gnome2 to be installed. Will that pull any X related packages?

    I don't want any X related stuff installed on my cli only small vps...

    Plus, my Debian 10 installation complains about not finding this package...

    The all seeing eye sees everything...

  • AndreiAndrei Services Provider

    Putting 4 GPUs towards this:

    Uptime report + real time cpu/ram/network/disk usage:
    http://hetrixtools.com/report/uptime/6dacf09a7cbcba0b12c28e23ba129e2a/

    Go team LowEndSpirit!
    Cheers.

    Thanked by (4)ehab saibal Mason poisson
  • How often is the team stats updated? Can't see my username there yet lol.

  • Def legit, was part of a folding team for OCN years ago, can get very competitive and lots of fun. Better in the winter to save on heating your office

  • Just grabbed the LES team stats! The term "wu" stands for work units or basically number of jobs done.


    Tue Mar 17 01:52:15 GMT 2020
    team teamname score wu
    240518 LowEndSpirit 153869 30

    I contributed 73443 points and 8 work units in 24 hours (mostly GPU).

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  • poissonpoisson OG
    edited March 17

    @Andrei said:
    Putting 4 GPUs towards this:

    Uptime report + real time cpu/ram/network/disk usage:
    http://hetrixtools.com/report/uptime/6dacf09a7cbcba0b12c28e23ba129e2a/

    Go team LowEndSpirit!
    Cheers.

    Four Tesla T4s! My little GTX1070 is blown away :)

    And you contributed almost as much as me in what, four hours? :)

    Tue Mar 17 00:51:57 GMT 2020
    name score wu team
    HetrixTools 66501 13 240518

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  • In case anyone is wondering whether donating your computing resources really work, here's a link to previous work by the same team on the Ebola virus which they used distributed computing to find a pocket in Ebola viral protein that is is a potential site for drugs and confirmed the findings using actual experiments: https://www.biorxiv.org/content/10.1101/2020.02.09.940510v1.abstract

    Here's the abstract:

    Many proteins are classified as ‘undruggable,’ especially those that engage in protein-protein and protein-nucleic acid interactions. Discovering ‘cryptic’ pockets that are absent in available structures but open due to protein dynamics could provide new druggable sites. Here, we integrate atomically-detailed simulations and biophysical experiments to search for cryptic pockets in viral protein 35 (VP35) from the highly lethal Ebola virus. VP35 plays multiple essential roles in Ebola’s replication cycle, including binding the viral RNA genome to block a host’s innate immunity. However, VP35 has so far proved undruggable. Using adaptive sampling simulations and allosteric network detection algorithms, we uncover a cryptic pocket that is allosterically coupled to VP35’s key RNA-binding interface. Experimental tests corroborate the predicted pocket and confirm that stabilizing the open form allosterically disrupts RNA binding. These results demonstrate simulations’ power to characterize hidden conformations and dynamics, uncovering cryptic pockets and allostery that present new therapeutic opportunities.

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  • Update on LES contributions to fight Covid-19 with computational resources:

    Team Statistics

    Thu Mar 19 01:50:51 GMT 2020
    team teamname score wu
    240518 LowEndSpirit 3771115 123

    Individual Statistics

    Thu Mar 19 01:50:51 GMT 2020
    name score wu team
    HetrixTools 3329922 72 240518
    json 268505 20 240518
    aaronng82 137837 14 240518
    darB 26101 4 240518
    Mr_Tom 6860 9 240518
    Laton 900 1 240518
    NekkiBasara 590 2 240518
    Xenos 400 1 240518

    Thanks everyone for the effort! If you would like to join, go to the link in the original post!

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  • Quick update on LES contributions to fight Covid-19 with computational resources again. Going strong!

    Team Statistics

    Thu Mar 19 01:50:51 GMT 2020
    team teamname score wu
    240518 LowEndSpirit 4445640 196

    Individual Statistics

    Thu Mar 19 01:50:51 GMT 2020
    name score wu team
    HetrixTools 3329922 72 240518
    json 697060 38 240518
    aaronng82 317973 29 240518
    darB 58296 9 240518
    Mr_Tom 30468 34 240518
    NekkiBasara 7001 10 240518
    Xenos 4020 3 240518
    Laton 900 1 240518

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  • Intensive CPU usage on VPS may break the rules of provider. Is this CPU intensive?

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  • Very. The assumption is that you'd run this on dedis, VDS with unlimited CPU usage per ToS, or owned hardware (e.g., homelab).

    Don't run [email protected] on a LES NAT VPS, just ... don't

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  • mikhomikho Hosting ProviderOG

    Leaving this here

    Get 4 or more NAT servers (mix/match between packages) and get a 20 % recurring discount. https://clients.mrvm.net

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