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MCX-CL v2023 (Fractal)
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@fangq fangq released this 07 Oct 20:09
· 77 commits to master since this release
v2023
04a7155

Monte Carlo eXtreme (MCX-CL) - OpenCL Edition

v2023

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What's New

The last official MCX-CL release was v2020 nearly 3 years ago. Many new
features have been implemented in MCX/MCX-CL since then. Some of the key
updates made to the v2023 version of MCX-CL are listed below

MCX-CL v2023 is significantly faster than the previous releases due to
two major updates. First, on NVIDIA GPUs, an native PTX-based atomic function
is used to gain 40% acceleration on NVIDIA hardware. Secondly, a highly
efficient DDA (Digital Differential Analyzer) ray-marching algorithm was
implemented to MCX and ported to MCX-CL. This also brings up to 40% speedup
in certain benchmarks such as cube60. Moreover, MCX-CL v2023 provides an
official Python mcx module (pmcxcl) to run stream-lined MCX simulations
in Python, offering intuitive mcxlab-like interface. During the past year,
a large effort was committed to build automated continuous integration (CI)
pipelines using Github Action, allowing us to automatically create, test,
and distribute portable packages across Linux, Windows, MacOS OSes, and
MATLAB, GNU Octave and Python environments.

Starting in MCX-CL v2023, we have completed the migration from MCX-specific binary output
formats (.mc2/.mch) to human-readable, extensible and future-proof JSON-based portable
data formats defined by the NeuroJSON project. The NeuroJSON
project aims at simplify scientific data exchange using portable data formats that are
readable, searchable, shareable, can be readily validated and served in the web and cloud.
The NeuroJSON project is also led by MCX's author, Dr. Qianqian Fang, funded by the
US NIH U24-NS124027 grant.

As a result of this migration, the MCX-CL executable's default output formats are now
.jnii for volumetric output data, and .jdat for detected photon/trajectory data.
Both data formats are JSON compatible. Details on how to read/write these data files
can be found below.

In summary, v2023 is packed with exciting updates, including

  • pmcxcl (https://pypi.org/project/pmcxcl/) - a Python interface to mcxcl
  • New continuous integration (CI) and testing system based on Github Action
  • CMake based building environment
  • Use NVIDIA PTX-based float atomicadd to gain >30% speedup
  • Efficient DDA (Digital Differential Analyzer) ray-marching algorithm, gain 40% speedup
  • Fixed loss of accuracy near the source (fangq/mcx#41)
  • Trajectory-only output with debuglevel=T
  • Adopted standardized NeuroJSON JNIfTI and JData formats to ease data exchange

The detailed updates can be found in the below change log

  • 2023-09-13 [0722c09] support ASCII escape code in Windows terminals
  • 2023-08-27 [080855a] fix pmcxcl gpu hanging bug, import utils from pmcx, v0.0.12
  • 2023-08-27 [e342756] port negative pattern support from mcx
  • 2023-08-27 [7a7b456] update debuglevel=R for RNG testing
  • 2023-08-25 [b8095a8] add mcxlab('version'), use MCX_VERSION macro, update msg, port many bug fixes from mcx
  • 2023-08-04 [9b4d76f] fix boundary condition handling, port from mcx
  • 2023-07-30 [50940de] update zmatlib to 0.9.9, use miniz, drop zlib
  • 2023-07-30 [370128a] support compileropt and kernelfile in mcxlab/pmcxcl, fix omp
  • 2023-07-30 [1b28a6d] fix windows gomp multiple linking bug
  • 2023-07-29 [4916939] automatically build and upload Python module via github action
  • 2023-07-28 [09c61b7] bump pmcxcl version, fix windows pypi version check
  • 2023-07-25 [4b5606e] port python module action scripts from mcx
  • 2023-07-25 [f92425e] add initial draft of pmcxcl for Python, add cmake
  • 2023-07-25 [3c2c735] update missing output structs
  • 2023-07-23 [87f3c0e] allow early termination if -d 3 or cfg.issavedet=3 is set
  • 2023-07-23 [c8ccc04] support outputtype=length/l for saving total path lengths per voxel
  • 2023-07-23 [57c3b9b] fix incorrect comment regarding gaussian src, fangq/mcx#165
  • 2023-07-23 [7d5bd16] update mcxplotphoton to mcx
  • 2023-07-23 [1cafd3e] allow to get fluence in non-absorbing medium, fangq/mcx#174
  • 2023-07-23 [8dbc397] update neurojson repo paths
  • 2023-07-23 [0d780bd] support trajectory only output with debuglevel=T
  • 2023-07-23 [e4ade36] fix replay test result matching
  • 2023-07-03 [b57b157] fix macos error
  • 2023-07-02 [99a4486] port zmat ci changes to mcxcl
  • 2023-06-03 [980cc9f] enable doxygen documentation via make doc
  • 2023-05-17 [a25f302] allow device query to handle open-source AMD ocl runtime, fix #44
  • 2023-03-12 [c9697a9] update action from mmc to mcxcl
  • 2023-03-12 [11938a3] copy mmc's merged action script
  • 2023-03-07 [ee7e940] add github action
  • 2022-10-08 [ae7f6e3] update version to 1.0
  • 2022-10-03 [695d2f3] run test on all platforms
  • 2022-10-03 [85beae7] revert debugging information, fix cyclic bc for mac
  • 2022-10-02 [53ec9e7] attempt to fix cyclic bc
  • 2022-10-02 [263abb2] test cyclic bc
  • 2022-10-02 [6c588fa] debug cyclic bc
  • 2022-10-02 [fc481ba] debug cyclic test on the mac
  • 2022-10-02 [8bdc33e] disable zmat and file IO functions in mex/oct targets
  • 2022-10-02 [c6e280a] fix CI error after using voxel index dda
  • 2022-10-01 [24bf948] allow disabling PTX based f32 atomicadd
  • 2022-10-01 [2277f7f] using nvidia native atomicadd for float add 30% speedup
  • 2022-09-29 [f0d0bad] update skipvoid
  • 2022-09-29 [b3d94d2] update to match mcx flipdir use
  • 2022-09-23 [1931489] adopt voxel-index based dda, like fangq/mcx b873f90c6
  • 2022-09-21 [d9e5eaa] add jammy to ci
  • 2022-09-21 [3e71eac] making double-buffer finally work to solve fangq/mcx#41, thanks to @ShijieYan
  • 2022-09-21 [2216686] sync mcxcl's json2mcx with the latest version from mcx
  • 2022-05-21 [39913fc] complete reformat of source code using astyle with 'make pretty'
  • 2022-05-21 [f7d69d5] sync mcx2json from mcx repo
  • 2022-01-27 [2559135] sync mcxdetphoton.m with mcx, move location
  • 2021-10-29 [867314a] Update README.md
  • 2021-06-23 [818f3a1] set maximum characters to read for fscanf, fix #41
  • 2021-06-23 [38d56a6] handle empty detector array in json2mcx
  • 2021-05-26 [4c18305] fix a few minor memory leaks based on valgrind output, still leaks on nvidia GPUs
  • 2021-05-15 [bbee39e] save volume in jdata format by default
  • 2021-02-26 [8eba2cd] add MATLAB_MEX_FILE in the makefile
  • 2021-02-24 [8f793a0] use memcpy to avoid strncpy warning from gcc 10
  • 2021-02-24 [89b46a9] update windows compilation commands
  • 2021-02-24 [49c6217] allow compiling GNU Octave mex on windows
  • 2021-02-07 [e9d2ce7] following Debian script suffix rule
  • 2020-09-06 [a39f271] update numeral version number
  • 2020-09-06 [6ea10b2] add back wiki versions of the README file for easy website update
  • 2020-09-04 [de59205] patch mcxcl for fangq/mcx#103 and fangq/mcx#104
  • 2020-09-01 [9b5431e] sync with mcx, add cubesph60b to match example/benchmark2
  • 2020-08-31 [7e7eb06] flush output for mcxlabcl
  • 2020-08-31 [6079b17] fix pattern3d demo script bug
  • 2020-08-31 [7b36ee8] fix photon sharing mcxlab crash
  • 2020-08-30 [f498e29] fix typo
  • 2020-08-29 [b001786] update mcxlabcl, update ChangeLog

Contributors

ShijieYan
Assets 2
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