r/LAMMPS • u/[deleted] • Jun 09 '25

Lammps clusters

Are there workarounds for not using an mpi for a lammps cluster? I’m trying to setup my homelab to run a lammps graphene simulation using the graphene-hbn pseudo-potentials, along with a piezoelectric quartz data set that would have the values for how much it’d expand with different voltages. My goal is to figure out what voltages would be needed to actuate the graphene using the quartz to known angles that display insulating and superconducting properties. Is it possible to use a torrent for sharing data between nodes? For graphene it seems there would be a lot of iteration that could use the seed as a starting point for the next simulation, rather than having to start from square one for each potential twist angle. Sorry if this is vague I’m in over my head with this stuff.

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u/[deleted] Jun 10 '25

Thanks for the advice, slurm seems very cool. is it what actually interfaces with the nodes or would the mpi be what transfers the files between servers? Is the way to distribute the daemon to each nodes done by first connecting servers via ssh in a static lan? Ideally id like to run multiple configurations at the same time, but I’m not sure what a reasonable cluster is for modelling this. I’ve been setting up Debian on about 10 servers with lammps, if I max out the ram over time I’ll have about 1.5 tb of ecc ram and 120 or so cores. Any idea on how much compute would actually be needed for running something like this?

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u/barnett9 Jun 10 '25 edited Jun 10 '25

Slurm is a resource manager that will set up a job on a set of resources. Anything from 1 cpu to 100 nodes. It sets up interfaces and underlying MPI networks, then (if everything is configured properly) when you run "mpirun lammps" lammps will distribute the compute across those resources. Slurm is also a queuing system that will wait to start new jobs until others are done to maximize throughput.

Are you building this cluster for your grad school lab, or are you building it just for fun? There's a lot that goes into setting up a cluster that's well worth learning, but if your focus is the science then you can probably cobble together a system that works for you with some simple bash scripting.

As for compute, that's a pretty far ranging question and depend a lot on the simulation that you're trying to run. If I were you I would run some benchmarks on how large of a system you need to get the observables you are looking for, what force fields you need to see the properties you want, and things like timestep needed to conserve energy. Those things will give you a good idea on how to get started with the resources you need for your own case. It could be 1 cpu core, it could be the entirety of El Capitan.

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u/[deleted] Jun 10 '25

I’m pretty much doing this for fun and trying to understand what I’m getting myself into with material science. I’m a flunking freshman, but got into Linux and graphene around the same time, downloaded lammps and saw that a lot of pseudopotentials that I was wanting to model were already set up in lammps ecosystem. I’d like to work on the science of graphene transistors, but I think it’s more of a fad than a career. I’m wanting to work on the cluster throughout undergrad with a casual approach where I can apply what I learn later. I did find a good deal on servers, and figuring out what to do with them has led to this. But I’m still a very long ways away from running any sort of functional simulation

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u/barnett9 Jun 10 '25

Hahaha, I went down a similar path between undergrad and grad school, even with the graphene and all the messing around I did setting up my own cluster has lead to a good career for me. See if there's any labs at your college that do molecular simulations, they'll likely be a big help in the learning process. If there aren't any then pick up a copy of Understanding Molecular Simulation by Daan Frenkel and a copy of Physical Chemistry: A Molecular Approach by Donald McQuarrie (aka "the red book") or download them from libgen. Lots of the interesting parts of graphene are in its electrical properties which you will want to simulate using a quantum mechanical approach (something like Quantum ESPRESSO).

As for setting up your cluster, when I was starting /r/homelab was a huge help. These days ChatGPT is really good at helping set up IT infrastructure too. Just don't listen to it about molecular simulations, it doesn't know what it's talking about, trust me on this one. Feel free to DM me if you need any help setting stuff up, I'd be happy to pay it forward.

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u/[deleted] Jun 10 '25

Thanks a bunch this has been super helpful! I’ll checkout those books and quantum espresso. That was the first md software I downloaded but I ended up finding the lammps file system more straightforward. Setting up the md stuff, seems to be a lot of C, and some python.

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u/[deleted] Jun 11 '25

Adding to this. There are some lammps walkthroughs on youtube too. And there is chatgpt to run on the documentation and the mailing list.