Release Notes for Mesh-based Monte Carlo 1.4.8-2 (v2019.4)

code name: Pork Rinds, released on April 29, 2019

Click this link to download MMC/MMCLAB v2019.4

Acknowledgement: This software release is made possible with the funding support from the NIH/NIGMS under grant R01-GM114365.

1. Introduction
2. About this release
3. What's new compared to previous release
3.1. new features
4. System requirements
5. Known issues
6. Reference

1. Introduction

Mesh-based Monte Carlo, or MMC, is a Monte Carlo light transport simulator designed for high accuracy for modeling tissues or domains with complex and smooth boundaries. Unlikely other existing MC software designed for layered (such as MCML) or voxel-based media (tMCimg, mcxyz and MCX), MMC can use a tetrahedral mesh to represent a complex domain, making it computationally and memory efficient.

MMC supports multi-threading based parallel computing. You can obtain a nearly linear speed-up when using more CPU cores in your simulation. Starting from version 0.8, MMC also supports the Single-Instruction Multiple-Data (SIMD) parallelism on modern CPUs, allowing MMC to take further advantage in parallel computing.

MMCLAB is the MATLAB mex version of the MMC software. It can be directly called inside MATLAB. This makes it easy to use with streamlined pre-processing (mesh generation using the Iso2Mesh toolbox) and post processing (visualization and data analysis).

2. About this release

MMC/MMCLAB v2019.4 is a maintenance release, containing several critical bug fixes compared to v2019.3, released just a month days ago.

One of the critical bug-fixes concerns all simulations using the -M S (branchless Badouel method) and -M G (dual-grid MMC). With this fix, the handling to edge-crossing photons is more robust and yields more accurate solutions, especially when the mesh density is high.

Another bug fixed was the incorrect headers of the .mch files created from v2019.3 and v2019.3-1 binaries (mmclab is not affected). The mch files produced by the recent releases becomes garbled when loaded with loadmch.m. This is now fixed in v2019.4.

In addition to these bug fixes, MMC v2019.4 gains a new feature to output diffuse reflectance on the surface mesh (similar to mcx).

3. What's new compared to previous release

The v2019.4 release was improved upon the previous version, v2019.3 by fixing a list of high priority bugs. They are:

3.1. new features

  1. !!key!! mmc can now https://github.com/fangq/mmc/issues/4 save diffuse reluctance on the surface], use --saveref or cfg.saveref
  2. !!key!! fix a ray-tracing bug related to the Branchless Badouel and DMMC ray-tracing modes
  3. !!key!! fix a bug that caused incorrect .mch file output format and garbled data
  4. !!key!! removed the libgomp-1.dll that failed on some windows 10 systems, and used a newer version
  5. optimizing DMMC memory utility and further accelerate
  6. adding mesh file for dmmc validation example

Pre-compiled MMC binaries are provided for Windows, Linux and Mac OS. In all cases, a binary compiled with SSE4-accelerated ray-tracing algorithms is provided for each platform.

The best simulation speed can be typically achieved by using 

  mmc -M S -C 0 ....

One can recompile all binaries using an Intel C++ Compiler. It can generate binaries up to 25% faster than the equivalent binaries compiled with GCC.

The detailed change logs can be found in the ChangeLog and Git commit history pages.

4. System requirements

Although MMC/MMCLAB can be executed independently once all input data (including mesh data) are provided, most pre- and post-processing scripts in both packages require the installation of Iso2Mesh Toolbox - a MATLAB based 3D mesh generator. Please browse http://iso2mesh.sf.net for download and installation information.

The default ray-tracer in the released binaries require your computer to support SSE4 instructions. This can be determined by using the following command on Linux/MacOS 

  grep 'sse4' /proc/cpuinfo

or using a freeware "CPU-Z" on windows. If you attempt to run the SSE4 on an unsupported computer, you will get an error when executing the binary. In that case, you should recompile MMC using "make omp" command.

5. Known issues

  • One must use savemmcmesh.m to generate all mesh input files for MMC; otherwise, the element orientation is not guaranteed.
  • Currently, this code only supports element-based optical properties; nodal-based optical properties (for continuously varying media) will be added in a future release
  • The maximum photon number per MMC session is 2^32-1=4,294,967,295, if you need to run a large number of photons, we suggest you splitting the job into smaller jobs with each one running a smaller chunk of photons (for example 1E8). Each job should initialized with a different seed (-E).

6. Reference

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