Large scale experiment: MDAD

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Profile Retvari Zoltan
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Message 53884 - Posted: 10 Mar 2020, 17:39:16 UTC

I'm receiving many tasks which are the last one of their batch:

1nkvA00_450_0-TONI_MDADpr4sn-9-10-RND4090_0

Or near the end of their batch:
1gaxA04_348_0-TONI_MDADpr4sg-8-10-RND1850_0

Total number of tasks in the batch
The sequential number of the given task within the batch (starting number is 0)

I expect the number of unsent tasks in the queue will drop significantly during the next days.
There are 305.826 unsent tasks as I wrote this.
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Toni
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Message 53885 - Posted: 10 Mar 2020, 18:02:11 UTC - in response to Message 53884.  

Good. I've raised the priority for a selection of the WUs because they were coming in too slow.
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Message 53889 - Posted: 12 Mar 2020, 0:21:47 UTC

Why does the ACEMD need so much free disk space?

I cant get work and get an error message:
Message from Server: New version of ACEMD needs 3814.70MB more disk space. You currently have 0.00 MB available and it needs 3814.70 MB.
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Keith Myers
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Message 53890 - Posted: 12 Mar 2020, 1:06:13 UTC - in response to Message 53889.  

You need to increase your disk limits in the Manager or in your Preferences at the website for your host.

That will give enough space to download more work to your host.
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Message 53901 - Posted: 13 Mar 2020, 11:38:02 UTC

So the question on what calculations are actually being executed on the machines is not really answered yet IMO.
"Methods development" sounds rather vague.
Do you plan on open sourcing your code which is being run?
What methods are being developed and evaluated?
Is there any github repo for the MDAD code?
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Message 53904 - Posted: 13 Mar 2020, 13:19:53 UTC - in response to Message 53541.  

[snip]

OAS: Bunkering for serial projects should be banned one way or another. These "races" and "sprints" have some folks requesting as many WUs per host as they can get but they don't get submitted to the work server until after the race start time, i.e. bunkering.

[snip]

A way to stop bunkering: Persuade all projects that have such races or sprints to require that only WUs downloaded during the race count toward the race.
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Message 53906 - Posted: 13 Mar 2020, 13:32:40 UTC - in response to Message 53904.  

Vastly easier to show per-user stats on average turnaround time. Much of the code must already exist as the project already awards bonuses based on turnaround time.

That would quantify the extent of the perceived bunkering 'problem'
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Message 53910 - Posted: 13 Mar 2020, 17:08:09 UTC - in response to Message 53884.  

Zoltan wrote on March 10th:
I expect the number of unsent tasks in the queue will drop significantly during the next days.
There are 305.826 unsent tasks as I wrote this.

well, there are still 300.349 left at this point of time (= i.e. 3 days after your posting)
:-)
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Profile Retvari Zoltan
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Message 53920 - Posted: 14 Mar 2020, 17:59:12 UTC - in response to Message 53910.  

Zoltan wrote on March 10th:
I expect the number of unsent tasks in the queue will drop significantly during the next days.
There are 305.826 unsent tasks as I wrote this.

well, there are still 300.349 left at this point of time (= i.e. 3 days after your posting)
:-)
The highest number of unsent workunits was over 310.000 so every 5.000 drop is 1.61%.
Now there's 297.472 unsent workunits which decreased to this by 5 since I started posting this.
310k to 297k workunits is 4.2% percent decrease in about 13 days.
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Message 53952 - Posted: 20 Mar 2020, 3:41:57 UTC

Could you mention whether the MDAD work happens to be related to COVID-19?
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Message 53953 - Posted: 20 Mar 2020, 4:12:13 UTC - in response to Message 53952.  

Could you mention whether the MDAD work happens to be related to COVID-19?


The last thing that Toni mentioned about the purpose of these workunits was this.

The purpose of the work is (broadly speaking) methods development, i.e. build a dataset to improve the foundation of future MD-based research (not just GPUGRID). More details may come if it works ;)
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Message 53962 - Posted: 21 Mar 2020, 18:21:56 UTC - in response to Message 53952.  

Could you mention whether the MDAD work happens to be related to COVID-19?


MDAD workunits are an ambitious effort to map the protein conformational space. Although the scope of the work is general, we expect that virion proteins will be among the very first test cases.
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Message 53964 - Posted: 21 Mar 2020, 19:31:12 UTC - in response to Message 53962.  

Could you mention whether the MDAD work happens to be related to COVID-19?


MDAD workunits are an ambitious effort to map the protein conformational space. Although the scope of the work is general, we expect that virion proteins will be among the very first test cases.

Thank you.
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Message 54010 - Posted: 24 Mar 2020, 9:28:26 UTC - in response to Message 53962.  

Could you mention whether the MDAD work happens to be related to COVID-19?


MDAD workunits are an ambitious effort to map the protein conformational space. Although the scope of the work is general, we expect that virion proteins will be among the very first test cases.

Do you have also planned any CPU work, or is it GPU only?
Would be happy, if my system can also compute different efforts / methods on COVID.
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Message 54018 - Posted: 24 Mar 2020, 12:48:39 UTC

Rosetta@Home has announced that they are doing some COVID-19 work, CPU only.
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Message 54019 - Posted: 24 Mar 2020, 12:57:51 UTC

MDAD cosa studia questo progetto?
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Message 54075 - Posted: 26 Mar 2020, 0:34:08 UTC - in response to Message 54018.  

Rosetta@Home has announced that they are doing some COVID-19 work, CPU only.

They're being issued, I have 6 machines running the Rosetta Covid-19 WUs.
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Message 54076 - Posted: 26 Mar 2020, 1:42:13 UTC - in response to Message 54075.  

Rosetta@Home has announced that they are doing some COVID-19 work, CPU only.

They're being issued, I have 6 machines running the Rosetta Covid-19 WUs.

They also announced that not all of the workunits related to COVID-19 have COVID-19 in their names. Some of those with foldit in their names are also related.
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Message 54081 - Posted: 26 Mar 2020, 15:03:50 UTC - in response to Message 54076.  
Last modified: 26 Mar 2020, 15:04:42 UTC

Rosetta@Home has announced that they are doing some COVID-19 work, CPU only.
They're being issued, I have 6 machines running the Rosetta Covid-19 WUs.
They also announced that not all of the workunits related to COVID-19 have COVID-19 in their names. Some of those with foldit in their names are also related.

Exactly.
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Message 54112 - Posted: 27 Mar 2020, 14:29:36 UTC

Did we do this running ACEMD3???
https://www.youtube.com/watch?v=LlyofuzgsDo
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