GPU-Accelerated Lattice Microbes

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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 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.

Installation

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.

Running Jobs

Once you pull the Lattice Microbes container from NGC, there are three options to run it.

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

1. 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 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

2. Running pyLM Scripts Interactively

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.

3. 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.

Recommended System Configurations

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:

  • Workstation: Powered by NVIDIA Titan V and x86 CPU
  • NVIDIA® DGX™ Systems
  • HPC cluster with Pascal/Volta GPUs, CUDA 9, x86 CPU
  • Cloud (AWS, Google Cloud Platform and more)

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