QuChemPedIA : Quantum Chemistry encycloPed and Intelligence Artificielle.

Invitation code : 3VwMu3-eTCg32

Molecular chemistry is lagging behind in term of open science. Although modelization by quantum mechanics applied to chemistry has become almost mandatory in any major publication, computational raw data is most of the time kept in the labs or destroyed. Furthermore, the software used in this area tend to lack effective quality control and computational details are usually incomplete in the articles and the information may not be reused or reproduced. The first objective of this project is to constitute a large collaborative open platform that will solve and store quantum molecular chemistry results. Original output files will be available to be reused to tackle new chemical studies for different applications. Machine learning and more generally artificial intelligence applied to chemistry data promises to revolutionize this area in the near future, but these methods require a lot of data that this project will be able to provide.

Today, it is impossible for a human to take into account the results, even limited to the most important data, for millions of known molecules. The second objective of this project is to radically change the approach developing artificial intelligence and optimization methods in order to explore efficiently the highly combinatorial molecular space. Generative models aim to provide an artificial assistant, which on the one hand has learned to predict the characteristics of a molecule and estimate its cost of synthesis, and on the other hand is able to browse effectively the molecular space. Generative models would open many perspectives by greatly facilitating the screening of new molecules with many potential applications (energy, medicine, materials, etc.). The bottleneck for our AIs is the computing power needed to verify the properties of the generated molecules.

By supporting this project, you will help chemical researchers around the world by building a unique collection of results. You will also help our AIs to propose much more new targets for the different applications we are addressing than we could do on our own.

Thank you for your help !

Thomas Cauchy (chemist)
Benoit Da Mota (computer scientist)


NWChem long no longer in beta soon
Dear Crunchers.

The latest tests for long units (a few dozen hours) are conclusive with a good success rate. I don't plan to put this application in a VM for Windows and Mac, short units are already enough of a problem. The "NWChem Long" application will therefore come out of its beta phase soon. If you don't want to get these units that can last really long, don't forget to update your preferences.

Thank you for your help and your patience which allowed us to find good parameters.

24 Feb 2020, 17:43:47 UTC · Discuss

NWChem long
Dear crunchers.

Thank you very much ! You are a really great help.

Initially, only two hundred "NWchem long" workunits should have been submitted for testing. Your numerous results and also the numerous failures allow us to better evaluate parameters for this new simulation. I still have to write some scripts for the new inputs, but I should be able to submit jobs soon. Don't hesitate to cancel in progress workunits (NWchem long).

18 Feb 2020, 9:01:04 UTC · Discuss

Molecules are coming!
Dear crunchers.

The new batches of molecules are coming! With them come the new credit system (200 credits per WU) and quorum validation. the expected runtime is 2-3 hours on a recent personal computer.

You can also see a new beta application (NWChem long) that will be used for the bigger calculations we talked about. The inputs are ready since the poll, but I still have to perform some tests. Stay tuned!

3 Feb 2020, 16:10:53 UTC · Discuss

Credits and Gridcoin
Dear Crunchers,

Yesterday, I had to suspend an account for two weeks and remove credits, for obvious credit cheating investigations. I'm quite annoyed that instead of doing science, I have to deal with this kind of behavior. We're small and we're short on time and it doesn't help scientific research...
EDIT : after investigations and fruitful exchanges, the problem has been identified and I'm sorry to have been a bit rough with this user.

The current credit system is too easy to fool, so I'm going to move to something simpler, robust and more generous on average: fixed credits. For short tasks (such as od9), I'm going to award 200 credits. This change requires draining the task queue. At that time, I will submit new tasks. These new tasks will be the opportunity to deploy the new code with checkpoints, system signals and affinity management for large systems (>32 cores). Some errors are to be expected, I can't test everything.

The last point concerns the requests for Gridcoin. I've been asked by the developers and by some of you. I am not against this possibility, but three points do not allow for the moment to be whitelisted. First, I can't guarantee to always have tasks waiting to be calculated. Secondly, the incentive to cheat will increase and I find that increasing the quorum is a waste of resources. Thirdly, I'm struggling with the server to keep it up. The upcoming arrival of larger molecules should settle the first point. For the second point, we are thinking about a validation by analyzing the result. I have already made many optimizations for the third point, at the moment it's much better.

Benoit Da Mota
30 Jan 2020, 9:03:31 UTC · Discuss

New Linux app and new WU
Dear Crunchers,

I have written a new version of the application for Linux (0.12), which is deployed in beta. The checkpoints have been added, but the display of the task progress is not correct. Don't worry, the computation is back to where it was. Moreover, I've added an adhoc management of system signals, to interrupt and resume tasks correctly. WARNING, this code is in beta and has a very high chance to fail. Please only use it if you want to monitor what is going on and help debugging. if the code does not cause a problem, it will quickly become the new reference code (ie. not in beta).

For Mac and Windows users, I am currently looking for workarounds for problems with Virtual Box.

I'll soon be putting short tasks for small molecules in the od9 series. Stay tuned !

28 Jan 2020, 11:08:23 UTC · Discuss

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©2020 Benoit DA MOTA - LERIA, University of Angers, France