Lattice Microbes

Lattice Microbes is a software package for efficiently sampling trajectories from the chemical and reaction-diffusion master equations (CME/RDME) on high performance computing (HPC) infrastructure using both exact and approximate methods.

pyLM is a problem solving environment written in Python that leverages the high-performance nature of the Lattice Microbes package while providing ease of use for common stochastic simulations and high customizability for complex biological applications.

Lattice Microbes is licensed under the University of Illinois Open Source License. More info on Lattice Microbes can be found at http://www.scs.illinois.edu/schulten/lm/.

See here for a document describing prerequisites and setup steps for all HPC containers.

See here for a document describing the steps to pull NGC containers.

Running Lattice Microbes

There are 3 options to run the Lattice Microbes container.

1. Running lm interactively within the container with pre-existing models
2. Running pyLM scripts interactively in the container
3. Running lm models from the nvidia-docker run command.

Running Lattice Microbes interactively

To run the Lattice Microbes container interactively, use the following command:

nvidia-docker run -ti --rm -v $(pwd):/workspace nvcr.io/hpc/lattice-microbes:2018.03 bash

This will start a shell the container, and map the current working directory to /workspace.

To start an RDME simulation model saved in “system.lm”, run the following command:

/opt/lm/bin/lm -r 1 -sp -f /workspace/system.lm

Running pyLM

First, start an interactive container as described in Section 1.1. Next, set up the environment for pyLM:

export PYTHONPATH=/opt/lm/lib:/opt/lm/lib/python

You can then run python3 and import pyLM:

# python3
Python 3.5.2 (default, Nov 23 2017, 16:37:01) 
[GCC 5.4.0 20160609] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyLM

You may now run any pyLM scripts that are in the /workspace directory.

Running Lattice Microbes via docker run

To run the Lattice Microbes on a model “system.lm” in the current working directory, use the following command:

nvidia-docker run -it --rm -v $(pwd):/workspace nvcr.io/hpc/lattice-microbes:2018.03 /opt/lm/bin/lm -r 1 -f /workspace/system.lm

This will map the current working directory to /workspace in the container, and run an RDME simulation.

Suggested Reading

• Lattice Microbes Website
• Lattice Microbes User Guide
• Lattice Microbes Tutorial
• pyLM Reference