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Large scale experiment: MDAD
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Retvari ZoltanSend message Joined: 20 Jan 09 Posts: 2380 Credit: 16,897,957,044 RAC: 0 Level ![]() Scientific publications ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]()
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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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Send message Joined: 9 Dec 08 Posts: 1006 Credit: 5,068,599 RAC: 0 Level ![]() Scientific publications ![]() ![]() ![]() ![]() |
Good. I've raised the priority for a selection of the WUs because they were coming in too slow. |
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Send message Joined: 28 Sep 17 Posts: 1 Credit: 398,126,739 RAC: 0 Level ![]() Scientific publications ![]() ![]()
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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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Send message Joined: 13 Dec 17 Posts: 1419 Credit: 9,119,446,190 RAC: 891 Level ![]() Scientific publications ![]() ![]() ![]() ![]()
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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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Send message Joined: 13 Mar 20 Posts: 1 Credit: 0 RAC: 0 Level ![]() Scientific publications
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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? |
robertmilesSend message Joined: 16 Apr 09 Posts: 503 Credit: 769,991,668 RAC: 0 Level ![]() Scientific publications ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]()
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[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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Send message Joined: 17 Sep 18 Posts: 11 Credit: 1,857,385,729 RAC: 0 Level ![]() Scientific publications ![]() ![]()
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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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Send message Joined: 1 Jan 15 Posts: 1166 Credit: 12,260,898,501 RAC: 1 Level ![]() Scientific publications ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]()
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Zoltan wrote on March 10th: I expect the number of unsent tasks in the queue will drop significantly during the next days. well, there are still 300.349 left at this point of time (= i.e. 3 days after your posting) :-) |
Retvari ZoltanSend message Joined: 20 Jan 09 Posts: 2380 Credit: 16,897,957,044 RAC: 0 Level ![]() Scientific publications ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]()
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Zoltan wrote on March 10th:The highest number of unsent workunits was over 310.000 so every 5.000 drop is 1.61%.I expect the number of unsent tasks in the queue will drop significantly during the next days. 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. |
robertmilesSend message Joined: 16 Apr 09 Posts: 503 Credit: 769,991,668 RAC: 0 Level ![]() Scientific publications ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]()
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Could you mention whether the MDAD work happens to be related to COVID-19? |
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Send message Joined: 19 Jan 12 Posts: 1 Credit: 20,965,042 RAC: 0 Level ![]() Scientific publications
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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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Send message Joined: 9 Dec 08 Posts: 1006 Credit: 5,068,599 RAC: 0 Level ![]() Scientific publications ![]() ![]() ![]() ![]() |
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. |
robertmilesSend message Joined: 16 Apr 09 Posts: 503 Credit: 769,991,668 RAC: 0 Level ![]() Scientific publications ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]()
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Could you mention whether the MDAD work happens to be related to COVID-19? Thank you. |
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Send message Joined: 2 Jul 07 Posts: 31 Credit: 424,791 RAC: 0 Level ![]() Scientific publications ![]() ![]() ![]() ![]()
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Could you mention whether the MDAD work happens to be related to COVID-19? 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. |
robertmilesSend message Joined: 16 Apr 09 Posts: 503 Credit: 769,991,668 RAC: 0 Level ![]() Scientific publications ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]()
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Rosetta@Home has announced that they are doing some COVID-19 work, CPU only. |
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Send message Joined: 15 Mar 20 Posts: 4 Credit: 752,098 RAC: 0 Level ![]() Scientific publications
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MDAD cosa studia questo progetto? |
BeyondSend message Joined: 23 Nov 08 Posts: 1112 Credit: 6,162,416,256 RAC: 0 Level ![]() Scientific publications ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]()
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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. |
robertmilesSend message Joined: 16 Apr 09 Posts: 503 Credit: 769,991,668 RAC: 0 Level ![]() Scientific publications ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]()
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Rosetta@Home has announced that they are doing some COVID-19 work, CPU only. 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. |
BeyondSend message Joined: 23 Nov 08 Posts: 1112 Credit: 6,162,416,256 RAC: 0 Level ![]() Scientific publications ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]()
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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.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. Exactly. |
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Send message Joined: 12 Jul 17 Posts: 404 Credit: 17,408,899,587 RAC: 0 Level ![]() Scientific publications ![]() ![]()
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Did we do this running ACEMD3??? https://www.youtube.com/watch?v=LlyofuzgsDo |
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