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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 of Lattice Microbes while providing ease of use for common stochastic simulations and high customizability for complex biological applications.
Visit the Lattice Microbes website for more information.
You have the option to download and install Lattice Microbes on bare-metal or pull and run the container from NVIDIA GPU Cloud.
Installing applications in an HPC environment can be challenging. and containers let you run the application without installing it on the system, making it easy to deploy the most recent version of the application while optimizing performance.
Running Lattice Microbes through containers is very straightforward and can be set up in minutes.
Once you pull the Lattice Microbes container from NGC, there are three options to run it.
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 of 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
First, start an interactive container as described in option 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.
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.
The Lattice Microbes container is optimized and tested for reliability to run on NVIDIA® Pascal™- and NVIDIA Volta-powered systems with NVIDIA CUDA® 9 or newer. All the HPC application containers available on NVIDIA GPU Cloud can run on the following systems: