Meep

Description

From the Meep Homepage: Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems, along with our MPB eigenmode package. Its features include:

• Free software under the GNU GPL.
• Simulation in 1d, 2d, 3d, and cylindrical coordinates.
• Distributed memory parallelism on any system supporting the MPI standard. Portable to any Unix-like system (GNU/Linux is fine).
• Arbitrary anisotropic electric permittivity ε and magnetic permeability μ, along with dispersive ε(ω) and μ(ω) (including loss/gain) and nonlinear (Kerr & Pockels) dielectric and magnetic materials, and electric/magnetic conductivities σ.
• PML absorbing boundaries and/or perfect conductor and/or Bloch-periodic boundary conditions.
• Exploitation of symmetries to reduce the computation size — even/odd mirror symmetries and 90°/180° rotations.
• Complete scriptability — either via a Scheme scripting front-end (as in libctl and MPB), or callable as a C++ library.
• Field output in the HDF5 standard scientific data format, supported by many visualization tools.
• Arbitrary material and source distributions.
• Field analyses including flux spectra, frequency extraction, and energy integrals; completely programmable.
• Multi-parameter optimization, root-finding, integration, etcetera (via libctl).
  Meep officially stands for MIT Electromagnetic Equation Propagation, but we also have several unofficial meanings of the acronym.

• Meep Home Page

Version

• 1.2.1

Authorized Users

• CIRCE account holders

Platform

• CIRCE cluster

Running Meep on CIRCE

It is highly recommended that you read the tutorials on using Meep from the Meep webpage. Please refer to the Additional Documentation section for a link to the tutorial.

Meep Utilities

Ensure that you’ve loaded the module apps/meep/1.2.1 into your environment to access the various HDF5 utilities for converting and working with output data. Load it persistently so that we can avoid having to deal with it again later:

[user@login0 ~]$ module add apps/meep/1.2.1
[user@login0 ~]$ module initadd apps/meep/1.2.1

Loading the Meep module will automatically provide the following dependencies:

• compilers/intel/2013sp1_cluster_xe

Running a Parallel Job

To run Meep, we will use the run command which creates our job script and submits our job to the cluster for us. We will also use the /work filesystem since Meep relies on HDF5’s parallel I/O facilities:

#!/bin/bash
#
#SBATCH --ntasks=8
#SBATCH --job-name=meep-test
#SBATCH --output=%j.out
#SBATCH --time=01:00:00

#### Slurm 8 processor MEEP test to run for 1 hour.

module load apps/meep/1.2.1
time mpirun meep-mpi input.ctl

#### cleanup output
mkdir -p $SLURM_JOB_ID
mv $SLURM_JOB_ID.out $SLURM_JOB_ID
mv *.h5 $SLURM_JOB_ID

 
Here, we run Meep on 8 processors for a maximum of one hour, specifying the input ctl file `input.ctl`. See the tutorials linked in Additional Documentation for information on creating the ctl (Scheme-based) input file.

Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./meep-test.sh

• You can view the status of your job with the “squeue -u <username>” command

Additional Documentation

• Meep Tutorial
  • http://ab-initio.mit.edu/wiki/index.php/Meep_Tutorial

More Job Information

See the following for more detailed job submission information:

• SLURM User’s Guide
• Scheduling and Dispatch Policies
• Advanced Submit Techniques

Reporting Bugs

Report bugs with Meep to the IT Help Desk: rc-help@usf.edu