COVID 19 tasks released on WCG

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Sid Celery

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Message 96508 - Posted: 15 May 2020, 2:35:20 UTC

Not that I'm trying to divert anyone from here as this is my preferred project, but World Community Grid have finally released COVID 19 tasks under OpenPandemics - and I picked up a few today. The expected runtime showed as around 200 minutes, but the way it's running is pointing more toward 250 minutes, so quite manageable

Their announcement is here
Help Stop COVID-19 and Future Pandemics in Their Tracks

And their Forum for OpenPandemics here
Forum: OpenPandemics - COVID-19 Project
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Falconet

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Message 96520 - Posted: 15 May 2020, 11:53:13 UTC

They are working on a GPU version btw.

https://twitter.com/ForliLab/status/1261194223811887109
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Profile yoerik
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Message 96524 - Posted: 15 May 2020, 12:15:44 UTC

looking forward to seeing what results from both projects.
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funkydude

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Message 96537 - Posted: 15 May 2020, 17:39:43 UTC

This is great news. I had originally left Rosetta for WCG because of the file size issues, then came back to Rosetta when they were fixed.
But it seems there is no interest in resolving the latest issues including memory errors and zip failures, so back to WCG I go.

Here are the benefits I personally see: (It's ok if you don't agree)
    Clear and transparent, dedicated section to this specific project with all news posted in one place: https://www.worldcommunitygrid.org/research/opn1/news.do
    Promise of frequent updates
    Longer deadlines (~1 week)
    Lower completion times (~2 hours)
    Lower memory footprint (~200MB)
    All tasks are verified by a wingman for safety
    AVX support
    GPU support nearly done
    The ability to choose to work on only COVID-19
    Badges specifically for COVID-19
    Based on the free and open source AutoDock software instead of the closed source proprietary Rosetta software.
    According to Wikipedia "AutoDock is one of the most cited docking software applications in the research community"



The fact that it's used so much is probably why it's so much more stable.
Although I admit this is from very little testing of the few machines I've swapped over.

I'll give it a week to see how things go, then I'll discuss with my colleagues about moving the work fleet over.

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Falconet

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Message 96544 - Posted: 15 May 2020, 20:55:50 UTC - in response to Message 96537.  
Last modified: 15 May 2020, 20:58:53 UTC

"All tasks are verified by a wingman for safety"

Actually, after a host delivers a certain number of valid results, it becomes quorum 1.
All the AutoDock/AutoDock Vina projects have been that way.
Periodically however, quorum 2 will be re-enabled to make sure the host is doing fine.

The AutoDock software currently in use at OpenPandemics is in a way, a new version, as it includes a new "reactive docking" protocol.
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funkydude

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Message 96560 - Posted: 16 May 2020, 13:34:13 UTC - in response to Message 96544.  

"All tasks are verified by a wingman for safety"

Actually, after a host delivers a certain number of valid results, it becomes quorum 1.
All the AutoDock/AutoDock Vina projects have been that way.
Periodically however, quorum 2 will be re-enabled to make sure the host is doing fine.

The AutoDock software currently in use at OpenPandemics is in a way, a new version, as it includes a new "reactive docking" protocol.


Good to know, thanks.

I've also noticed that after it becomes 1, you will be randomly picked as a wingman for others. So you may still be participating in quorum 2 tasks.

Overall it's good that extra care is taken to have good results. There are multiple people on this forum who like to dismiss Rosetta's bugs as merely a fault in the donators hardware.
This form of verification can help prove otherwise.
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Falconet

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Message 96563 - Posted: 16 May 2020, 14:18:47 UTC - in response to Message 96560.  
Last modified: 16 May 2020, 14:25:19 UTC

"All tasks are verified by a wingman for safety"

Actually, after a host delivers a certain number of valid results, it becomes quorum 1.
All the AutoDock/AutoDock Vina projects have been that way.
Periodically however, quorum 2 will be re-enabled to make sure the host is doing fine.

The AutoDock software currently in use at OpenPandemics is in a way, a new version, as it includes a new "reactive docking" protocol.


Good to know, thanks.

I've also noticed that after it becomes 1, you will be randomly picked as a wingman for others. So you may still be participating in quorum 2 tasks.

Overall it's good that extra care is taken to have good results. There are multiple people on this forum who like to dismiss Rosetta's bugs as merely a fault in the donators hardware.
This form of verification can help prove otherwise.


Exactly, quorum 2 gets re-enabled every now and then to make sure the host is producing valid results.
A quality assurance/extra care measure, like you mentioned.
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Sid Celery

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Message 96565 - Posted: 16 May 2020, 16:05:26 UTC - in response to Message 96537.  

Here are the benefits I personally see: (It's ok if you don't agree)
    Clear and transparent, dedicated section to this specific project with all news posted in one place: https://www.worldcommunitygrid.org/research/opn1/news.do
    Promise of frequent updates
    Longer deadlines (~1 week)
    Lower completion times (~2 hours)
    Lower memory footprint (~200MB)
    All tasks are verified by a wingman for safety
    AVX support
    GPU support nearly done
    The ability to choose to work on only COVID-19
    Badges specifically for COVID-19
    Based on the free and open source AutoDock software instead of the closed source proprietary Rosetta software.
    According to Wikipedia "AutoDock is one of the most cited docking software applications in the research community"



The fact that it's used so much is probably why it's so much more stable.
Although I admit this is from very little testing of the few machines I've swapped over.

I'll give it a week to see how things go, then I'll discuss with my colleagues about moving the work fleet over.


Longer deadlines = lower turnaround time, shorter tasks = less productive output, lower memory footprint = less complex - so many of these things are reasons to prioritise WCG less. Badges... superficiality

But different projects suit different people and it may well be that some users are just too needy for Rosetta. Everyone can make their own decisions.
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Message boards : Cafe Rosetta : COVID 19 tasks released on WCG



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