Posts by Jim1348

61) Message boards : Number crunching : Validate error- Work Unit (Message 1358)
Posted 16 Feb 2021 by Jim1348
Post:
As I can understand, this project requires virtualization to send work units, does it?

You only need virtualization on a Windows machine. You don't need it on Linux (at least Ubuntu 18.04/20.04 work OK).
62) Questions and Answers : Web site : Please make it clearer on the webpage that you require Virtualbox (Message 1353)
Posted 13 Feb 2021 by Jim1348
Post:
Good idea, except that it isn't if you run Linux, as I do.
https://quchempedia.univ-angers.fr/athome/results.php?hostid=5947

But the Windows users could use the instruction to avoid a lot of confusion.
63) Questions and Answers : Unix/Linux : Not respecting BOINC compute limits (Message 1315)
Posted 17 Jan 2021 by Jim1348
Post:
Set Max # CPUs 1
Also, unhide your computer if you want more help.
64) Message boards : Number crunching : Ubuntu 20.04.1 does not validate (Message 1285)
Posted 23 Dec 2020 by Jim1348
Post:
They are now running fine and completing OK.
Just don't use BOINC 7.16.4.
https://quchempedia.univ-angers.fr/athome/results.php?hostid=5132
65) Message boards : Number crunching : Ubuntu 20.04.1 does not validate (Message 1281)
Posted 22 Dec 2020 by Jim1348
Post:
I can whitelist your host if you want to test ? Just give me the host id.

I would like to try it on ID: 5132
That is a Ryzen 3600 that I had upgraded to Ubuntu 20.04.1 and was causing problems with BOINC 7.16.14.
It is now working on VirtualBox projects, and even though I am not using VB for QuChemPedIA, I think the problems are related.
66) Message boards : Number crunching : Ubuntu 20.04.1 does not validate (Message 1279)
Posted 22 Dec 2020 by Jim1348
Post:
I think the problem is solved, but I can't check it since my machine is not allowed now.
It was not the Linux kernel version, but BOINC 7.16.14, which I obtained from PPA costamagnagianfranco.

I fixed it with the expert advice from Gunde on the LHC forum, where I could not run CMS (a VirtualBox project).
https://lhcathome.cern.ch/lhcathome/forum_thread.php?id=5560
Basically, if you have that PPA version, you go to "software and update" and uncheck line for that PPA then:
sudo apt remove boinc-client boinc-manager
sudo apt install boinc-client boinc-manager

That will install BOINC from the apt repository.
In the case of Ubuntu 20.04.1, it will be BOINC 7.16.6.
In the case of Ubuntu 18.04.5, it will be BOINC 7.9.3.
Either should work with QuChemPedIA, I expect.
67) Message boards : Number crunching : Ubuntu 20.04.1 does not validate (Message 1264)
Posted 18 Dec 2020 by Jim1348
Post:
I am going to update the linux kernel on this machine and see what happens.

Not surprisingly, after updating to the 5.4.0-58 Linux kernel, all the remaining twelve work units ended in "Validate error" after running only a few seconds.
https://quchempedia.univ-angers.fr/athome/results.php?hostid=3052&offset=0&show_names=0&state=5&appid=

So there is the smoking gun. It is something that changed between 5.4.0-52 and 5.4.0.-58.
(Or else between BOINC 7.16.11 and 7.16.14).
Maybe that will help.
68) Message boards : Number crunching : Ubuntu 20.04.1 does not validate (Message 1263)
Posted 18 Dec 2020 by Jim1348
Post:
install extension pack for your virtual box

I don't use VirtualBox. I run it in Ubuntu.
69) Message boards : Number crunching : Ubuntu 20.04.1 does not validate (Message 1254)
Posted 18 Dec 2020 by Jim1348
Post:
I ran these seven on an i7-9700 with the 5.4.0-52 linux kernel. They ran the full length, and did not crash early.

The first three have a validation problem on all machines:
https://quchempedia.univ-angers.fr/athome/workunit.php?wuid=1957005
https://quchempedia.univ-angers.fr/athome/workunit.php?wuid=1957007
https://quchempedia.univ-angers.fr/athome/workunit.php?wuid=1956677

The last four are awaiting validation, and may be OK:
https://quchempedia.univ-angers.fr/athome/workunit.php?wuid=1996081
https://quchempedia.univ-angers.fr/athome/workunit.php?wuid=1996118
https://quchempedia.univ-angers.fr/athome/workunit.php?wuid=1996349
https://quchempedia.univ-angers.fr/athome/workunit.php?wuid=1995982

I am going to update the linux kernel on this machine and see what happens.
70) Message boards : Number crunching : Ubuntu 20.04.1 does not validate (Message 1250)
Posted 18 Dec 2020 by Jim1348
Post:
put first line (number of processor) at 50% and computing time(second line) at 100%

That does not fix it for my Ryzen 3900X (kernel 5.4.0-58)
https://quchempedia.univ-angers.fr/athome/results.php?hostid=5331&offset=0&show_names=0&state=5&appid=
71) Message boards : Number crunching : Ubuntu 20.04.1 does not validate (Message 1248)
Posted 18 Dec 2020 by Jim1348
Post:
As the troubles began apparently since kernel 4.15]

I was on a fairly recent version, probably 5.4.0-45 or close to it, before the trouble began with 5.4.0.-58.
72) Message boards : Number crunching : Ubuntu 20.04.1 does not validate (Message 1237)
Posted 16 Dec 2020 by Jim1348
Post:
And now I just updated my Ryzen 3900X (Ubuntu 18.04.5).
It updated to the latest Linux kernel (5.4.0.-58), and it also updated BOINC to 7.16.14.

Now all the tasks invalidate immediately. I am having to pull if off of QuChemPedIA.
https://quchempedia.univ-angers.fr/athome/results.php?hostid=5331&offset=0&show_names=0&state=5&appid=
73) Message boards : Number crunching : Ubuntu 20.04.1 does not validate (Message 1236)
Posted 15 Dec 2020 by Jim1348
Post:
this problem is discouraging... no idea of what occured...

On Universe, it has been found that Ubuntu 20.04 is about twice as fast as Ubuntu 18.04
I did not find it first, but see the linked messages 4446 and 4460:
https://universeathome.pl/universe/forum_thread.php?id=551

That is the only project I have found where it makes a difference, but it shows there have been changes to the libraries (or something; I am not a Linux expert).

Good luck.
74) Message boards : Number crunching : Ubuntu 20.04.1 does not validate (Message 1230)
Posted 11 Dec 2020 by Jim1348
Post:
My computer, running Ubuntu 18.04.5 LTS, is also having a problem with work units only running for 4 seconds then finishing.

Well I see the same thing on my i7-8700 running Ubuntu 18.04.5
https://quchempedia.univ-angers.fr/athome/results.php?hostid=5332&offset=0&show_names=0&state=5&appid=

On the other hand, my Ryzen 3900X that is also running Ubuntu 18.04.5 is doing OK, or at least not badly.
https://quchempedia.univ-angers.fr/athome/results.php?hostid=5331&offset=0&show_names=0&state=4&appid=

So it seems to be a combination of the hardware and the OS. That is a bit limiting.
75) Message boards : Number crunching : Ubuntu 20.04.1 does not validate (Message 1220)
Posted 27 Nov 2020 by Jim1348
Post:
Did you use the same way as described in your previous post to configure your installation ?
Yes, it is my standard technique. And I always do a clean install by first wiping out the SSD by doing a Secure Erase with PartedMagic.
I don't want any leftovers from previous installations hanging around.

So everything should be the standard libraries, fully updated. Maybe Damotbe can find it.
I will be happy to try again.
76) Message boards : Number crunching : Ubuntu 20.04.1 does not validate (Message 1213)
Posted 26 Nov 2020 by Jim1348
Post:
After running QuChemPedIA for a long time on an i7-9700 under Ubuntu 18.04.5, I set up a Ryzen 3600 on Ubuntu 20.04.1.
Now not just most of the tasks fail to validate, but they all do. There seems to be some basic problem with this OS.
https://quchempedia.univ-angers.fr/athome/results.php?hostid=5132
77) Message boards : Number crunching : Validate error. (Message 1178)
Posted 11 Nov 2020 by Jim1348
Post:
I thought a Ryzen 3900X might be better than the Intel i7-9700 I was using, in order to reduce the invalids and validation inconclusives, but it did not make much difference.
I will wait until they figure out what the problem is before jumping in again. Good luck.
78) Message boards : Science : Scientists make digital breakthrough in chemistry that could revolutionize the drug industry (Message 1159)
Posted 27 Oct 2020 by Jim1348
Post:
One force driving that explosion has been the Defense Advanced Research Projects Agency (DARPA). It’s wrapping up a four-year program called Make-It, of which both the Chemputer and AutoSyn are alumni. The long-term goal of the program’s manager, Anne Fischer, is to speed up the discovery of useful molecules, which has historically involved a lot of waiting around while chemists laboriously smithed atoms into novel configurations. “The slow step is always making and testing the molecules,” she says.

 But now that Make-It has helped produce robotic tools to build molecules like the Chemputer, AutoSyn, and others, she’s directing a new DARPA program, Accelerated Molecular Discovery, that looks to the next stage: developing smarter software to tell the robots what molecules to make, and how to make them.  
This is still a very new science. It’s started to explode really in the last 18 months.

 ″We’re now trying now to harness what we’ve done in Make-It and expand it out so we can teach computers how to discover new molecules,” she says.

 The secret to doing so, many believe, is machine learning. And some machines capable of rudimentary chemical learning are well underway. Connor Coley, a chemist at MIT, is a member of a team that last year paired an automated flow chemistry system with an algorithm to direct it. The algorithm trained on databases of hundreds of thousands of reactions and was able to predict recipes for new products. “It tries to understand, based on those patterns, what kind of transformations should work for new molecules it’s never seen before,” Coley said.

https://www.cnbc.com/2020/10/24/how-a-digital-breakthrough-could-revolutionize-drug-industry.html

I suppose that is what we are doing here in effect.
79) Message boards : Number crunching : The aborted and resend WU (Message 1112)
Posted 29 Sep 2020 by Jim1348
Post:
When I tried to verify that on my Win7 64-bit machine, I had so many errors that I could not get very far. My conclusion was that so many cores were left idle that the remaining work units of course ran faster on the other cores.

That is always the case with virtual cores. They run faster when lightly loaded.
But there may be other reasons as well, and your experience may be different.
80) Questions and Answers : Unix/Linux : Linux vs Windows (Message 1051)
Posted 8 Sep 2020 by Jim1348
Post:
I normally crunch on Ubuntu 18.04 (now 20.04), but was going to try it out on Win7 64-bit. However, I got too many "VBox unmanageable" errors to give it a good test. I had to about about half of them. It was an i7-4771 with 32 GB memory, so it was not a memory problem. And I tried both VirtualBox 6.1.14 and 5.2.42; same results. Maybe someone else can give it a try.


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