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MCX-CL v2025 (Harmonic)

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@fangq fangq released this 16 Feb 17:58
v2025
b1da692

Monte Carlo eXtreme (MCX-CL) - OpenCL Edition

v2025

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What's New

MCX-CL v2025 is a maintenance release with multiple bug fixes and minor new features.
It is highly recommended to upgrade for all users.

Notable major bug fixes include

  • a high priority bug fangq/mcx#222, introduced in 198cd34, was fixed. this bug affects all simulations
    since v2023. Particularly, when a photon has a long pathlength, with weight drops to numerical 0,
    its pathlength data is carried in the immediately launched new photon, causing skews in the
    detected photon pathlength distributions

  • multi-GPU simulations was not working (serialized) in v2024.2, this has been fixed

  • further updates to the handling of low absorption medium (fangq/mcx#164), previously affect not-so-low mua values

  • fix incorrect angleinvcdf and invcdf buffer length, ported from fangq/mcx#233

  • fix missing nscat output due to incorrect macro, fix #56

  • add missing --maxjumpdebug flag, accept float, fix #54

  • avoid double-base64-encoding when -Z 2 is used, fangq/mcx#219

  • for all brain related simulations, we have updated the CSF mua value of 0.004/mm that was
    previously used in Custo et al. 2006 paper to 0.0004/mm, matching its upstream reference Strangman et al. 2003.
    However, we want to highlight that both literature may not provide the best mua value for CSF - as such low
    mua/mus CSF properties are mostly for CSF in the inner part of the brain, but not representiative to those in
    the subarachnoid space. A few literature have shown that CSF in the subarachnoid space may have a higher
    mus' value, in the range between 0.16/mm to 0.32/mm, as shown in Okada et al. 2003

  • [Okada_2003] E. Okada and D. T. Delpy, “Near-infrared light propagation in an adult head model. I. Modeling of low-level scattering in the cerebrospinal fluid layer,” Applied Optics 42, 2906–2914 (2003)

  • [Custo_2006] A. Custo, W. M. Wells III., A. H. Barnett, et al., “Effective scattering coefficient of the cerebral spinal fluid in adult head models for diffuse optical imaging,” Applied Optics 45, 4747 (2006)

  • [Strangman_2003] G. Strangman, M. A. Franceschini, and D. A. Boas, “Factors affecting the accuracy of near-infrared spectroscopy concentration calculations for focal changes in oxygenation parameters,” NeuroImage 18, 865–879 (2003)

In addition, in this release, we also added the following key new features

  • optimize thread configurations on Apple processors (M1/M2/M3/M4) and achieve 7x speed acceleration
  • the new -N/--net command line flag allows one to browse and run growing number of community-contributed
    simulations hosted on https://neurojson.io (one can browse the list at https://neurojson.org/db/mcx)
  • mcx can read stdin (standard input) using pipe, allow one to use advanced text processing utilities in the shell,
    such as sed, perl, jq to modify JSON inputs at runtime. For example mcx -N cube60 | jq '.Forward.Dt=1e-10' | mcx -f
  • a new shortcut option -Q for --bench to conveniently browse and run built-in benchmarks
  • mcxlabcl and pmcxcl cam set cfg.flog=1 or 0 to disable printing of mcxcl banner

The detailed updates can be found in the below change log

  • 2025-01-23 [2a9476b] [feat] support reading pipe from command line with -f -
  • 2025-01-22 [febd932] [bug] fix incorrect per-voxel pathlength when mua->0, fangq/mcx#164
  • 2025-01-21 [3640d79] [bug] fix windows -N error
  • 2025-01-21 [44f63c0] [cmake] update cmake to add -N support
  • 2025-01-20 [6de71b0] [neurojson] avoid needing c++11, fix ci
  • 2025-01-20 [3cb78c4] [ci] fix mac warnings and errors
  • 2025-01-20 [29b0f3b] [feat] add -N/--net to download simulations from NeuroJSON.io, add -Q
  • 2024-11-13 [d79f6ed] [ci] remove mac local file
  • 2024-11-13 [96b8dbc] [ci] speedup macos-13 and windows octave download
  • 2024-11-13 [299b920] [ci] add install octave using dmg
  • 2024-11-13 [f8bb370] [ci] add windows octave mex build back
  • 2024-09-30 [0f642c3] [pmcxcl] bump pmcxcl version to 0.2.1 to include fix in fangq/mcx#233
  • 2024-09-29 [42917da] [bug] fix incorrect angleinvcdf and invcdf length, fangq/mcx#233
  • 2024-09-14 [f15814c] [ci] revert pybind11 version further for python3.6
  • 2024-09-14 [d3baf8c] [ci] add ubuntu-24.04 and macos-14
  • 2024-09-14 [e2fa087] [ci] remove DL_LDFLAGS
  • 2024-09-14 [dd99f92] [ci] macos ci fails with -shared
  • 2024-09-14 [7a3e4aa] [ci] test without macos-14
  • 2024-09-13 [4b9e21b] [bug] fix the potential typo in Custo et al for CSF mua, fangq/mcx#232
  • 2024-09-11 [c13dcf2] [ci] remove upx as github disabled upx for macos
  • 2024-09-11 [2191885] [ci] allow make oct to link with OpenCL on macos
  • 2024-09-03 [7c57318] [ci] fix action alert related to download-artifact https://github.com/NeuroJSON/zmat/security/dependabot/1
  • 2024-08-20 [8f84acf] [ci] use gcc-12 on macos runner
  • 2024-08-18 [d7defeb] [bug] fix lzma memory leakage, NeuroJSON/zmat#11, lloyd/easylzma#4
  • 2024-07-19 [9c86f6b] [bug] fix multi-gpu serialization bug on nvidia GPUs the bug was introduced in 9b4d76f
  • 2024-06-12 [953c4e9] [ci] remove compiler warnings
  • 2024-06-12 [57612d0] [test] make mcxcl pass all tests on Alder lake Intel iGPU
  • 2024-06-12 [4609451] [bug] detector radius is not squared, fix #58
  • 2024-06-11 [2b91626] [intel] pass all tests and remove all warnings on old i7-2635QM on mac
  • 2024-06-11 [59d88a0] [test] sync test script between mcx and mcxcl after #57
  • 2024-06-11 [88899f9] [bug] reset replay.tof when tof too big, improve replay test, fix #57
  • 2024-06-09 [6e91fe3] [opencl] optimizing thread number on Apple silicon, gain 7x speedup
  • 2024-06-09 [c2bbf7f] [ci] test on macos-13
  • 2024-06-09 [7b558a4] [bug] fix colin27 failure on Apple silicon, fix #49
  • 2024-06-08 [93c589c] [ci] trying to fix macos-12 build
  • 2024-06-08 [9e84ecc] [bug] apply the same patch to ensure shared mem reset, fangq/mcx#222
  • 2024-06-08 [1154916] [bug] fix missing nscat output due to incorrect macro, fix #56
  • 2024-06-05 [8918150] [bug] add missing --maxjumpdebug flag, accept float, fix #54
  • 2024-06-04 [4b00f6d] [bug] fix double fclose error, close #53
  • 2024-04-25 [027cc55] [bug] avoid double-base64-encoding when -Z 2 is used, fangq/mcx#219
  • 2024-03-29 [cbfa564] [ci] modify DL_LDFLAGS
  • 2024-03-29 [ac879dc] [ci] revert LDFLAGS changes to compare difference on macos-12
  • 2024-03-29 [d175187] [ci] print verbose mkoctfile log to debug macos-12
  • 2024-03-29 [334c882] [package] copy LFLAGS to LDFLAGS, close #50
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