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damotbe
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Message 428 - Posted: 14 Jan 2020, 14:24:40 UTC

Dear Quchempedia crunchers!

First generation of our newly generated small molecules is almost finished. Thanks again.

We have two propositions for the new phase of calculations :

1. Make a pause (maybe a month or so), in order to parse and treat the recent calculations, learn from the success and failures of the calculations and then generate new small molecules. Probably with a little bit more than 9 atoms.

2. Take some of the newly generated compounds, add them to a core (BTX) used in the chemistry lab here in Angers (see the abstract of this article https://pubs.rsc.org/en/content/articlelanding/2019/nj/c9nj05804d/unauth#!divAbstract) to demonstrate how we can use our newly generated molecules inside a real system, to show how a fragment can modify the core properties and to serve as a screening example. These calculations are very interesting and can lead to very nice applications (drugs and materials).

Beware that the second choice, means that the molecules will have more than 9 heavy atoms, probably more than 30 and so calculations could take days. The good news is that the next workunits will implement checkpointing. Boinc will not be able to display the real level of progress and will think that the calculation starts again from the beginning. But we've run some tests and the calculations restart from the very last step. The expected calculation times will always be very approximate and unreliable, we will voluntarily choose a slightly high value.

If you choose the first option, we will calculate the BTX ones with our private ressources and we will post a news when we will have treated and generated new small molecules.

Thank you for giving your choices and opinions under this post.

Kindly,
Thomas and Benoit
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rbpeake

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Message 429 - Posted: 14 Jan 2020, 14:47:16 UTC

I am willing to try the second option. Sounds like BOINC could be a big help.

Thanks.
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[VENETO] boboviz

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Message 430 - Posted: 14 Jan 2020, 14:48:21 UTC - in response to Message 428.  

Thank you for giving your choices and opinions under this post.

For me, the second one. New science.
No problems if wus are long if there are checkpoints
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Aurum
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Message 431 - Posted: 14 Jan 2020, 16:07:12 UTC

I'm fine with either option and you can count on me either way to continue to support this project.
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swiftmallard
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Message 432 - Posted: 14 Jan 2020, 16:09:41 UTC

Option #2 sounds good!
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Sibe Bleuzé

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Message 433 - Posted: 14 Jan 2020, 16:16:48 UTC

I prefer the second option, keep us calculating yeah.
Just a question: if you are going to make checkpoints that BOINC doesn't understand,
wouldn't it be better for you to make each of these checkpoints a separate WU?
So that the expected time matches and BOINC doesn't think you're starting over?
I don't know if this is something you can actually do, it's just an idea.
Anyway I'll keep crunching them, other projects have days long tasks too.
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Zalster

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Message 436 - Posted: 14 Jan 2020, 18:37:44 UTC

I prefer the second one as well. My computer is solely devoted to this project and I don't check on it for several days to weeks other than the error rates here on the website.
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marsinph

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Message 438 - Posted: 14 Jan 2020, 18:54:31 UTC - in response to Message 428.  

Dear Quchempedia crunchers!

First generation of our newly generated small molecules is almost finished. Thanks again.

We have two propositions for the new phase of calculations :

1. Make a pause (maybe a month or so), in order to parse and treat the recent calculations, learn from the success and failures of the calculations and then generate new small molecules. Probably with a little bit more than 9 atoms.

2. Take some of the newly generated compounds, add them to a core (BTX) used in the chemistry lab here in Angers (see the abstract of this article https://pubs.rsc.org/en/content/articlelanding/2019/nj/c9nj05804d/unauth#!divAbstract) to demonstrate how we can use our newly generated molecules inside a real system, to show how a fragment can modify the core properties and to serve as a screening example. These calculations are very interesting and can lead to very nice applications (drugs and materials).

Beware that the second choice, means that the molecules will have more than 9 heavy atoms, probably more than 30 and so calculations could take days. The good news is that the next workunits will implement checkpointing. Boinc will not be able to display the real level of progress and will think that the calculation starts again from the beginning. But we've run some tests and the calculations restart from the very last step. The expected calculation times will always be very approximate and unreliable, we will voluntarily choose a slightly high value.

If you choose the first option, we will calculate the BTX ones with our private ressources and we will post a news when we will have treated and generated new small molecules.

Thank you for giving your choices and opinions under this post.

Kindly,
Thomas and Benoit


Taka a pause !? OK but you forget yopur project is now in world competition between teams !
So remove it .

New WU will implemente check point !?!? It is aready under Windows in VirtualBox !!!
But WU take some days without error and doing nothing (exept the cjeck point)

Sometimes, you suggest to abort. Nice unusefull advise.
I have one WU running 4 days, two WU running 3 days, one running 2 days.
No any in error.
https://quchempedia.univ-angers.fr/athome/result.php?resultid=854441
https://quchempedia.univ-angers.fr/athome/result.php?resultid=853808
and so on.....
Here the four days WU : https://quchempedia.univ-angers.fr/athome/result.php?resultid=813148

I delete this project. There are much more stable as this one.

A lot of complaints and no change, except to say the new WU will take some days.

To Admin : do you really think we will wait, days and days before to be obliged to cancel ???

Best regards
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Aurum
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Message 439 - Posted: 14 Jan 2020, 19:02:12 UTC - in response to Message 438.  
Last modified: 14 Jan 2020, 19:06:14 UTC

marsinph is nothing if not consistent. He seems obsessed with the Formula-BOINC.org contest. I believe he's on the BOINC.BE Team.
There are two dozen projects and QCP is in the Top Five of most scientifically significant. In alphabetical order:
GPUGrid
QuChem
Rosetta@home
TN-Grid
World Community Grid

Pay him no mind, just adieu or saluu.
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Woodles

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Message 441 - Posted: 14 Jan 2020, 20:09:53 UTC

I'm fine with either option.

My only thought it that if the second option is chosen with longer tasks (with checkpoints) wouldn't it be harder to tell if the task has crashed but not marked as finished as is happening at the moment? Do we then have to wait even longer before aborting stuck workunits?

Do the checkpoints still occur with stuck workunits so the user can tell that work is still ongoing?
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Jim1348

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Message 442 - Posted: 14 Jan 2020, 22:31:30 UTC - in response to Message 428.  

#2 Yes!
I leave my machine running 24/7 anyway.

Please try to use more memory also. I have 16 GB in my Ryzen 2600 (11 cores in use), and can easily double that to 32 GB if you need it.
64 GB may be possible.
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RFGuy_KCCO

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Message 443 - Posted: 14 Jan 2020, 23:14:40 UTC

Choice #2 is fine with me.

However, if the WU's do end up taking days to complete, perhaps consider paying bonus credit for completing them, as some other projects - PrimeGrid, for example - do for long WU's.
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[VENETO] boboviz

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Message 445 - Posted: 15 Jan 2020, 8:11:14 UTC
Last modified: 15 Jan 2020, 8:12:30 UTC

Up to now.

Choice 1: 0
Choice 2: 7
It's the same: 2
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STE\/E

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Message 446 - Posted: 15 Jan 2020, 8:55:54 UTC - in response to Message 428.  

Option 2
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Henk Haneveld

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Message 447 - Posted: 15 Jan 2020, 9:08:50 UTC

Do both and run them as seperate applications.

Create in the users preference setttings the option for the users to choose wich of these they want to run or even if they want to run them both.
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Tom_unoduetre

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Message 448 - Posted: 15 Jan 2020, 10:31:44 UTC - in response to Message 447.  

Do both and run them as seperate applications.

Create in the users preference setttings the option for the users to choose wich of these they want to run or even if they want to run them both.

I second this. Like QuChem short and QuChem long.

In any case a deadline increase for option two would be nice, something like 2-3 weeks.
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sjmielh

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Message 449 - Posted: 15 Jan 2020, 12:58:45 UTC - in response to Message 447.  

Do both and run them as seperate applications.

Create in the users preference setttings the option for the users to choose wich of these they want to run or even if they want to run them both.


I vote for this option as well. Then you not only have the speedy crunchers, but also the modest ones. On forums you see more of the speedy crunchers.

Sjmielh
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[VENETO] boboviz

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Message 450 - Posted: 15 Jan 2020, 12:59:35 UTC - in response to Message 445.  

Up to now.


Updated:
Choice 1: 0
Choice 2: 8
It's the same: 2
Both (with two apps): 2
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Bill Michael

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Message 452 - Posted: 15 Jan 2020, 17:43:13 UTC

I would also vote for both with two apps, BUT... you really DO need to get your act together on how BOINC works. There is no reason for the "will think it restarts" thing, any more than there is any excuse for the current WUs 'hanging' and having to be aborted. Both are bugs in your code. I realize that the bugs only exist because of VirtualBox, but you chose to use it. Sorry if that sounds harsh, but MANY other projects have dealt with these VB issues, they are well known, they are hard to solve, and even once solved may reoccur with a new version. My normal stance is to refuse to run any VB-based project - but your goals seemed to be worth the "pain" so I joined.
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Senilix

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Message 453 - Posted: 15 Jan 2020, 18:43:10 UTC

I second the 2-apps approach.
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Message boards : News : Updates and poll

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