In this episode, we are highlighting the Theory of Nanostructured Materials facility. Our guest, Liang Tan, shares how the facility is finding new ways to collaborate and host fruitful discussions as well as develop coordinated workflows and data management across user groups.
Transcript:
Shannon Ciston
Welcome to this episode of Foundry from Home, a podcast to highlight new developments in remote, virtual, and physically distanced user access to the Molecular Foundry. I’m Shannon Ciston, the User Program Director at the Foundry. Today we’re featuring remote work at the theory of nanostructured materials facility of the Molecular Foundry. The theory facility is focused on expanding understanding of materials and phenomena at the nanoscale, by connecting structural and dynamical properties of materials to their functions, such as information transport, Opto-electronic energy generation, molecular self assembly, and gas separation. They develop and employ a broad range of tools in pursuit of materials and devices that meet global energy and information needs. It’s my pleasure to welcome our guest today, theory facility staff scientist, Dr. Liang Tan. Welcome, Liang.
Let’s get started with talking about ways that user work at the theory facility has and has not changed during the pandemic. So you mentioned that the mechanics of doing the work haven’t changed much but that your interactions to exchange ideas have had to adapt? Can you tell us about that?
Liang Tan
Yes, sure. Well, the the basics of doing the computation or theoretical work hasn’t really changed. At the most basic level, we are still running simulations on computers as before, and we’re still writing papers on that topic as before. But maybe what has changed is the interaction between us and the staff and the users and students and postdocs in the theory facility. It used to be that we can have a conversation with the person next door casually, and walk to the whiteboards outside the offices to write down some equations and have an informal discussion. But nowadays, that’s not possible anymore. Now every interaction has a fixed structure, it has a set time with within 45 minutes or one hour in the zoom meeting. One benefit though, is that we have more unstructured time outside of these zoom meetings. So in a work from home scenario, we’ve had more unstructured, uninterrupted time to think quietly about the deeper problems in our research. But on the whole, it has been a challenge because it’s you can feel like there’s not much exploration of new ideas as before.
Shannon Ciston
Yeah, that I understand. So what’s your facility doing to help foster that intellectual engagement?
Liang Tan
Yes, in the theory facility, we’ve had many zoom seminars over the last few months. Typically, we have at least one every month on the first Friday of the month. This is our regular theory, facility seminar. And the question and answer sessions in those seminars are very useful because they bring people together. And you can have a general discussion over some shared research interests. So these seminars are open to users, and we have got pretty good attendance at many of them, and I encourage anyone who’s interested in the theory, or the goings ons of the theory facility to come join us. The nice thing about using zoom for discussions and collaborative work is that a lot of the work that we do is visual, and this translates very well across video conferencing. For instance, we can, in a zoom session, go directly into a computer terminal and start typing code and the other person can see it immediately. Or maybe we can pull up some visualization software to show, you know, a crystal structure of a material or something and the other person can see it. And having this, is in fact, maybe even better than trying to describe a crystal structure in person using hand gestures and so on. I mean, previously, video conferencing tools were available, but it’s much more common to use it now. And since everyone’s working remotely, using new collaboration tools opens up all these sorts of opportunities.
Shannon Ciston
Yeah, thanks, Liang. That’s great. I agree that the whole remote work environment has really given kind of a push to so many of us to start to communicate in different ways. I’d also like to spend some time for those that might be a little less familiar with the nuts and bolts of the resources available at the theory facility. Can you tell us more about the Foundry compute cluster?
Liang Tan
Yes, the theory facility has a computer cluster. And we can help guide the users to use the code on this compute cluster, or teach them to use some of our codes on that cluster. I’d like to mention though, that user proposals are not for compute time only. The compute element is actually quite important to some users, but there’s always a research component involved in the value that the theory facility adds to many of the user proposals. On one hand, sometimes this in helping the users run some fairly standard calculations, such as density functional theory; Using a publicly available code where we can help provide guidance on the parameters for these calculations, so that you can get the results in a reasonable amount of time. But there are also other projects where there’s a more significant computing element and there’s more code development involved. And in that case, our staff can play a critical role in understanding what needs to be computed, knowing what is the physically interesting quantity, and then helping develop these codes so that they run efficiently on various variety of machines like the Foundry clusters, or maybe the NERSC supercomputers or other supercomputers in different places.
Shannon Ciston
So NERSC, so that’s the National Energy Research Scientific Computing Center is also based out of Berkeley Lab. Does that have any particular benefit for users?
Liang Tan
Yes, definitely. Having access to NERSC is very useful. Many of our users do have accounts and last one advantage is that there is a straight space, where we’re able to run code compiled on the same machine. So we’re not transferring data and code across different machines. And this is saves a lot of time, it makes data sharing much easier. NERSC provides lots of tools for data sharing, when they are definitely worth the effort to get past any additional learning curve. For instance, getting set up with a GLOBUS account, a different endpoint on the user’s machine is pretty easy to do, and makes file sharing and version control much easier.
Shannon Ciston
So besides setting up some of those data sharing tools, is there anything else in particular, you’re finding helps things go smoothly?
Liang Tan
Yes, we are supporting a few different projects that share the same code base on the Foundry site. But each of these different user groups has a different thing that they want to do with the software, or the data that we get from the software. Something that’s become a little bit of a challenge is to have kind of data format that’s consistent across multiple users, to make it efficient for the Foundry staff to work across different projects, since all of these projects come from the same code base. So what we found is that having a common data format is very useful if it is a data format that most people find useful. This includes specifying things in a standard way where the same data is always organized in the same file structure. And surprisingly, this sounds like a very trivial thing, but it’s been a huge time saver for all of us.
Shannon Ciston
Yeah, that’s great. All right. So we’ll wrap it up here. Thanks very much for spending time with us today young. Appreciate it.
Liang Tan
Sure.
Shannon Ciston
It’s interesting to learn more about how the theory facility is supporting user projects and continuing to exchange ideas in this new era of remote work. Thanks for listening everyone. I hope you’ll tune in for more episodes of foundry from home as we highlight developments in virtual remote and distanced user training and access throughout the Molecular Foundry.
This has been a production of the Molecular Foundry’s User Program Office and communications team. The music used in this production was “Still room on the night train” by Ketsa, courtesy of the Free Music Archive. The Molecular Foundry is the US Department of Energy Office of Science user facility at Lawrence Berkeley National Laboratory.
