Target # 22: corona_RdRp_v2

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hoarfrost
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Message 1813 - Posted: 15 Jan 2023, 17:45:23 UTC

Dear participants,

After doing initial studies on an established SARS-CoV-2 target RNA dependent RNA polymerase (RdRp), we are departing from protease studies and focus on RdRp along with additional NSP targets. Namely, RdRp (NSP12), is responsible for the transcription of viral genes and ultimately replication of the viral genome. The studied active site binds RNA and was previously studied in the context of remdesivir, galidesivir, molnupiravir and several other small molecules. Further reading below:




Figure 1: RdRp in white color along with RNA chain and N4-hydroxycytidine from Molnupiravir in the active site (red stick model).

With best wishes,
Natalia, Marko, Črtomir, hoarfrost.

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hoarfrost
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Message 1815 - Posted: 15 Jan 2023, 18:09:16 UTC

We estimate, that tasks runtime on CPU like Ryzen 3900X (with enabled SMT) will be around 16 hours.
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Crissy

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Message 1849 - Posted: 17 Jan 2023, 15:48:22 UTC

Well it widely varies I guess.
On my "old but still good" XEON2697v2, some tasks cross 40 hrs ....
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Profile Jay Eichelberger
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Message 1850 - Posted: 17 Jan 2023, 17:00:00 UTC - in response to Message 1849.  

@Crissy,
Thanks for posting.
I was about to abort https://www.sidock.si/sidock/result.php?resultid=77569206 - which has been running > 25 hours;
with remaining time = 3days and 10 hours.

does suspend/resume muck up these tasks?

Thanks, Jay
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Profile Jay Eichelberger
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Message 1851 - Posted: 17 Jan 2023, 17:23:51 UTC - in response to Message 1849.  

@Crissy,
Thanks for posting.
I was about to abort https://www.sidock.si/sidock/result.php?resultid=77569206 - which has been running > 25 hours;
with remaining time = 3days and 10 hours.

does suspend/resume muck up these tasks?

Thanks, Jay
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arcturus

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Message 1853 - Posted: 17 Jan 2023, 18:05:40 UTC

I understand the developer is looking into this but these new units are muddying the situation as to whether these are new 'normal' run times or whether they're truly hanging.

Not everyone gets around to checking progress often so I'm guessing we're going to see a stream of 'these units have been hanging for days!' posts soon. Looks like it has begun.
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hoarfrost
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Message 1854 - Posted: 17 Jan 2023, 21:35:05 UTC - in response to Message 1815.  

We estimate, that tasks runtime on CPU like Ryzen 3900X (with enabled SMT) will be around 16 hours.

Now more statistics available. Some workunits shorter, but most of them runs ~ 16 .. 26 hours on Ryzen 3900X with SMT. Powerful machines got a big task. Really big!
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hoarfrost
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Message 1855 - Posted: 17 Jan 2023, 21:36:59 UTC - in response to Message 1851.  
Last modified: 17 Jan 2023, 21:37:44 UTC

...
I was about to abort https://www.sidock.si/sidock/result.php?resultid=77569206 - which has been running > 25 hours;
with remaining time = 3days and 10 hours.
does suspend/resume muck up these tasks?
...

Jay, you can check this tasks.
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[AF>Le_Pommier] Jerome_C2005

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Message 1880 - Posted: 18 Jan 2023, 9:12:36 UTC

I have a small host running this task for more than 3 days and claiming to be at 43% with a 1 day left deadline, in theory more than 4 days of calculation left : is it worth letting it run ? will it get credited (if it ends) ?
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hoarfrost
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Message 1882 - Posted: 18 Jan 2023, 12:30:52 UTC - in response to Message 1880.  
Last modified: 18 Jan 2023, 12:31:11 UTC

I have a small host running this task for more than 3 days and claiming to be at 43% with a 1 day left deadline, in theory more than 4 days of calculation left : is it worth letting it run ? will it get credited (if it ends) ?

This task is hung. It needs restart. *Sprot* tasks is relatively small - for 2 .. 6 hours.
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[AF>Le_Pommier] Jerome_C2005

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Message 1883 - Posted: 18 Jan 2023, 12:46:28 UTC

Mmm I couldn't find how to "restart" a task, I tried to suspend it and let it run again, but it seemed to continue the same way, so I cancelled it :/

Thanks for the answer anyway.
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[AF>Le_Pommier] Jerome_C2005

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Message 1887 - Posted: 19 Jan 2023, 10:52:33 UTC - in response to Message 1883.  
Last modified: 19 Jan 2023, 10:52:51 UTC

+ I confirm the other tasks completed last max 2h30 on that small host.
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Bryn Mawr

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Message 1911 - Posted: 21 Jan 2023, 12:02:10 UTC - in response to Message 1883.  

Mmm I couldn't find how to "restart" a task, I tried to suspend it and let it run again, but it seemed to continue the same way, so I cancelled it :/

Thanks for the answer anyway.


You need to turn “leave non GPU tasks in memory” off before you suspend the task or it won’t force a checkpoint restart.
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[AF>Le_Pommier] Jerome_C2005

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Message 1920 - Posted: 21 Jan 2023, 18:34:00 UTC
Last modified: 21 Jan 2023, 18:34:14 UTC

Thanks for the info.

So far I got another one that ended successfully but it took 1 day 14 hours to complete. And I have another one going the same way.
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Mad_Max

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Message 1948 - Posted: 25 Jan 2023, 18:51:27 UTC - in response to Message 1920.  

For RdRp_v2 target it is a perfectly normal. These are long tasks, even on modern computers the computing time for them can reach up to a day of pure CPU time. On older ones, you can expect 2 days or more.

While WUs for Sprot_delta target are relatively short tasks (like 10-15 times shorter/less computing time compared to RdRp_v2)
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Crissy

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Message 1950 - Posted: 26 Jan 2023, 0:11:41 UTC - in response to Message 1851.  

Hello Jay,

Sometimes "buggy" tasks then drop down to a fraction of time reported but then continue from there.
I had tasks crossing 100 hrs and after suspend/resume they went down to 30 something and completed within normal times.
If I did not stop them, I guess they would have also crossed the deadline without finishing but wasting CPU/energy.

This is why I currently quit this project. Waiting for an improvement to return here :-)

Cheers
Chris
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arcturus

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Message 1951 - Posted: 26 Jan 2023, 15:46:23 UTC - in response to Message 1950.  

This is why I currently quit this project. Waiting for an improvement to return here :-)


The improvement happened days ago with the release of version 2.02 units. I've completed over 150 without one issue.
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Crissy

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Message 1953 - Posted: 26 Jan 2023, 17:44:25 UTC - in response to Message 1951.  

Thanks for the hint, good thing.
I will run dry my Worldcommunitygrid queues and give it another try :-)
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