Posts by damotbe

1) Message boards : News : Project update (Message 1783)
Posted 29 Aug 2022 by damotbe
Dear crunchers.

The project was developed a few years ago with an intern and a very limited budget. Despite many project submissions, we did not get any funding. Sometimes we are told that our project is too ambitious, sometimes not enough... It is discouraging! The truth is that the public funding of research in France is extremely low.

Our prototype programs are outdated. At the beginning, I struggled with VMs, then security changes in the Linux kernel started to prevent the application from running properly.

Despite everything and thanks to you (thank you!), we are coming to the end of a computing campaign and the integration of the data will take me a lot of time. The project is obviously not finished and we could still submit many calculations. But today the priority is to analyze and valorize what we already have. I'll go through the last calculations that had problems and see if I can resubmit some tasks, but very soon there will be no more WU.

We have made a lot of progress with little funding, we will continue to share our scientific publications with you. Moreover, we are currently finishing writing an article and I can already tell you that we have developed a way to greatly reduce the calculations of unstable molecules.

See you soon
Kind regards,
2) Message boards : News : Presensation of our work (Message 1717)
Posted 31 Mar 2022 by damotbe
Hello everybody.

In the context of the Molecular Modeling and Drug Discovery (M2D2) talks, organized by the Valence Discovery lab, Thomas Cauchy made a presentation of our work. This video is intended for researchers but Thomas makes, as always, an important effort to popularize the subject. I hope you will enjoy it !

3) Message boards : Number crunching : Virtualbox and memory error (Message 1693)
Posted 5 Mar 2022 by damotbe
it's strange... Did you try to reset the project ?
4) Message boards : Science : What are we working on? (Message 1692)
Posted 5 Mar 2022 by damotbe
We work on methods able to find new materials but photoreactive drugs are also of interest.
Your calculations allow us to explore the chemical space to find new chemical environments to train our AI models
5) Message boards : Science : NWChemEx (Message 1691)
Posted 5 Mar 2022 by damotbe
Thomas Cauchy could explain this better than I could. NWChemEX is not suitable for our uses (small molecules) and brings nothing in terms of performance
6) Message boards : Science : GPU Client ? (Message 1690)
Posted 5 Mar 2022 by damotbe
No, we are not allowed to use Gaussian, we use NWChem which is open source. There is no GPU code that suits our needs
7) Questions and Answers : Unix/Linux : Any alternative to the current taskset clobbering? (Message 1630)
Posted 13 Jan 2022 by damotbe
When we had a developer, it was the only solution that works in conjunction with mpirun and boinc wrapper. That is not perfect, of course
8) Message boards : Number crunching : Inconclusive validation (Message 1629)
Posted 13 Jan 2022 by damotbe
curious issue...
9) Message boards : Number crunching : What happens with certificates ? (Message 1513)
Posted 13 Oct 2021 by damotbe
Wrong. The only conclusion is 50% of the project are down or use Let's encrypt certificates.

The role of the certificate is that the Boinc client can verify that the server is the real one and not an impostor or a hacker. So a third actor is needed: a certification authority (CA). The Let's encrypt CA certificate has been revoked. So only projects that depend on Let's encrypt are impacted. This is the case of the QuChemPedia server. At the time the certificate was revoked, my server renewed the certificate with the new Let's encrypt certificate. Except that for the Boinc client to be aware of this, the new CA certificate must be added in the BOINC client's list of trusted CAs.

Technically advanced problem... 3 different actors are involved in HTTPS
10) Message boards : Number crunching : What happens with certificates ? (Message 1511)
Posted 13 Oct 2021 by damotbe

Same issue from my side, 72 tasks are waiting to be uploaded for several days now, and it seems that anybody really cares about that.
Even if the issue is coming from the boinc client on windows only; it impacts directly some projects (including QuChemPedIA@home), and I don't really see any of these project admins taking this problem seriously.

It's frustrating for me too. The certificate problem is a problem that I understand very well but I can't do anything directly!

The solution is always the same: install a Linux VM with Virtualbox for example, then install Boinc in it and join the project from the VM.
11) Message boards : Number crunching : What happens with certificates ? (Message 1508)
Posted 12 Oct 2021 by damotbe
I have no problem with my Linux machines. The problem is with the BOINC clients on Windows. The project receives about 8000 valid tasks per 24 hours according to my dashboard and no problems are reported.
12) Message boards : Number crunching : What happens with certificates ? (Message 1495)
Posted 6 Oct 2021 by damotbe
So, it comes from the let's encrypt certificate, i.e. your OS or your boinc client certificate. Old system are not maintained (Windows 8 and before) and let's encrypt change the certificate.
First solution : use a recent and up-to-date OS or fixed boinc client
second solution : install new certificate by hand / by-pass the certificate check

EDIT: the link to boinc forum explain that the windows boinc client have its own certificates file.
13) Message boards : News : New scientific publication (Message 1484)
Posted 5 Oct 2021 by damotbe
Dear crunchers,

We are very pleased to announce the release of our latest publication associated with the quchempedia project.

Link :
The article is freely available. Feel free to have a look at it even if some parts of the article are quite technical and intended for specialists.

The most important is that the results of this article are based on the calculations of this BOINC project!
With the molecules we generated and you calculated, it was possible to probe the vast space of chemistry.
You are mentioned in the acknowledgements but we would like to renew our gratitude to you here.

We have many more projects.

Benoit and Thomas
14) Message boards : Number crunching : What happens with certificates ? (Message 1483)
Posted 5 Oct 2021 by damotbe
Is the problem solved or not ?
15) Message boards : Number crunching : Fast wu,s invalid (Message 1478)
Posted 17 Sep 2021 by damotbe
The error messages for affinity are normal since the execution is finished
For the short jobs, it is a know issue. Many users experiment this error with recent Linux distribution (ubuntu >=20.04 and Debian 11)
I suspect changes in the kernel or library but at the moment, we have no engineer and no time...
16) Questions and Answers : Unix/Linux : Workunits failure after upgrading Debian to 11 (bullseye) (Message 1474)
Posted 8 Sep 2021 by damotbe
you can know the Linux version with the command
uname -a

and the OS with
cat /etc/os-release 
17) Questions and Answers : Unix/Linux : Workunits failure after upgrading Debian to 11 (bullseye) (Message 1471)
Posted 7 Sep 2021 by damotbe
I'm totally busy and I don't have intern or engineer to work on this. The guy who compile nwchem for the project has gone and I'm not able to update the executable. The straightforward workaround is to run an old linux (in a VM) to compute for the project or it works if you have chance....

:( :( :(
18) Message boards : News : Server shutdown for maintenance (Message 1457)
Posted 23 Aug 2021 by damotbe
Server up and running !
19) Message boards : News : Server shutdown for maintenance (Message 1456)
Posted 15 Aug 2021 by damotbe
Dear members.

For electrical checking reasons (in the whole university), the server must be shut down from tomorrow August 16th for about a week. I hope to be able to restart everything on August 23rd.

20) Message boards : Cafe : 2021 BOINC Workshop ✨ (Message 1446)
Posted 21 Jul 2021 by damotbe
Sorry, I didn't see that thread... we were totally overhelmed.

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