Release MMC v2020 (Moon Cake beta) · fangq/mmc

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Full ChangeLog: http://mcx.space/wiki/index.cgi?MMC/ChangeLog
Release note: http://mcx.space/wiki/index.cgi?MMC/Doc/ReleaseNotes/v2020

What's New

MMC v2020 (1.9) is a major update to MMC. For the first time, MMC adds GPU
support via the newly implemented OpenCL version. The released package
simultaneously supports CPU-only multi-threading with SSE4 (standard MMC) and
OpenCL-based MMC on a wide variety of CPU/GPU devices across vendors. Using
up-to-date GPU hardware, the MMC simulation speed was increased by 100x to 400x
compared to single-threaded SSE4-based MMC simulation. The detailed description
of the GPU accelerated MMC can be found in the below paper [Fang2019].

One can choose between the SSE4 and OpenCL based simulation modes using the -G
or cfg.gpuid input options. A device ID of -1 enables SSE4 CPU based MMC, and a
number 1 or above chooses the supported OpenCL device (using mmc -L or
mmclab('gpuinfo') to list).

A detailed (long) list of updates can be found in the ChangeLog.txt or the
Github commit history: https://github.com/fangq/mmc/commits/master

To highlight a few most important updates:

Supported GPU using OpenCL in both binary and mmclab
Supported using multiple NVIDIA GPUs
GPU MMC (or MMCL) had been rigirously validated across a range of benchmarks
Supported photon sharing for multiple patterns
Charactrized the speed improvement of MMCL simulations over standard MMC
Created mmc and octave-mmclab official Fedora packages and disseminate via Fedora repositories
Implemented xorshift128+ RNG unit and used as default for both CPU/GPU MMC
Fixed a list of bugs in both SSE4/OpenCL MMC
Created 6 standard benchmarks (B1:cube60, B1D:d-cube60, B2:sphshells,
B2D:d-sphshells, B3:colin27, B4:skin-vessel) for comparisons

Please file bug reports to https://github.com/fangq/mmc/issues

Moreover, over the past year, we have also published a high-quality brain
3D mesh generation pipeline and rigirously compared mmc with voxel based
MCX, and showed improvement in modeling accuracy. The detail of the mesh
generation software (Brain2mesh: http://mcx.space/brian2mesh) and the
benchmarks can be found in the below [Brain2Mesh2020] paper.

Lastly, we also implemented the photon sharing algorithm to simultaneously
simulate multiple pattern sources. This paper is detailed in the recently
published OL paper, see [Yan2020].

Reference:

[Fang2019] Qianqian Fang and Shijie Yan, “GPU-accelerated mesh-based
Monte Carlo photon transport simulations,” J. of Biomedical Optics, 24(11),
115002 (2019) URL: http://dx.doi.org/10.1117/1.JBO.24.11.115002

[Brain2Mesh2020] Anh Phong Tran† , Shijie Yan† , Qianqian Fang*, (2020) "Improving
model-based fNIRS analysis using mesh-based anatomical and light-transport models,"
Neurophotonics, 7(1), 015008, URL: https://doi.org/10.1117/1.NPh.7.1.015008

[Yan2020] Yan S, Yao R, Intes X, and Fang Q*, "Accelerating Monte Carlo modeling
of structured-light-based diffuse optical imaging via 'photon sharing'," Opt. Lett. 45, 2842-2845 (2020)
URL: https://www.biorxiv.org/content/10.1101/2020.02.16.951590v2

Full Change Log

MMC 1.9 (v2020, Moon Cake - beta), Qianqian Fang <q.fang at neu.edu>

2020-08-09*[874c5bf] support multiple NVIDIA GPUs, patch from fangq/mcxcl@c1e3ebb
2020-07-25 [41d4aef] Update README.md
2020-07-24 [f9dd4dd] add markdown version of README, add travis badge
2020-07-24 [3cbccd1] fix oct for travis linux
2020-07-24 [b532d76] use MSYS for travis windows
2020-07-22*[214fc47] add travis ci script
2020-06-28 [a3c98c5] use the new gitfilter format
2020-04-18 [867b2b9] test gpu pointer to avoid error
2020-04-11 [46e1fbe] wrapping opencl api with return value tests, fix a few small memory leaks
2020-04-08 [cb30b31] fix beam focusing issue reported by Luka Rogelj
2020-04-06 [123dc0d] remove mingw64 compilation warnings
2020-04-06 [e65c3a3] define function pointer to update progressbar
2020-04-06 [f3c3b56] fix error when cfg.gpuid is a string
2020-04-05 [e9e04a7] update function name in help info
2020-04-05 [1abe23d] make creating octave mex file work again
2020-04-04 [c6c5d55] prevent ioctl linking with mingw64 gcc compiler
2020-04-03 [c986ab7] use more portable output handle
2020-04-03 [66b8f4f] flush octave compilation command
2020-04-03 [5d3df36] replace %I64u by %zu
2020-04-03 [c20ed88] compile on windows
2020-04-03 [50fbcc7] remove all matlab mex compilation warnings on windows, add installation instruction
2020-04-02 [c8884a4] remove all warnings raised by gcc 8 and 9.3
2020-04-02 [d7becea] add mingw64 mexopts xml file for matlab r2014 or newer
2020-04-02 [085420c] need to select both c and c++ compiler
2020-04-02 [9e8918d] add CL header for better portability
2020-04-02 [8f90d58] add missing header files from mingw64 compiler on windows
2020-04-02 [72f6ded] test buildmmc script on linux
2020-04-02*[387e3ba] add matlab script to build mmclab mex file
2020-03-31 [c01b6ae] test on msys2 gcc compiler
2020-03-30 [92b19e3] switch windows building environment to msys2
2020-03-29 [48e397f] make byte alignment compatible with MS VS
2020-03-25 [a2948be] force updating elemprop if elem contains more than 4 columns
2020-03-25 [18fb6fc] prevent mmclab from crashing if the source is not enclosed
2020-03-25 [d6de33e] use cfg.steps to specify voxel size in DMMC mode, instead of unitinmm
2020-03-25 [7e04588] allow users to set cfg.maxdetphoton in mmclab
2020-03-03*[99312c3] fix wrong ray-tracer problem when compile with omp, finish fedora packaging
2020-02-26 [d4608f4] fix gpuid=-1 does not work bug in mmclab
2020-02-25 [acef8db] update onecube filtering command, fix #51
2020-02-20 [36c4f5f] remove mexsse and octsse, add mexomp and octomp targets
2020-02-20 [8527d82] allow make omp to work again, but currently results are not correct, do not use
2020-02-05 [dbea367] fix all warnings for gcc 7
2020-02-05 [a5ac4a9] update cjson to the latest git version
2019-11-19 [75a4844] use detp.prop and detp.unitinmm if present, similar to mcx #83
2019-11-19 [a89457a] fix time/weight scaling, see mcx bug #83
2019-11-05 [a10b743] revert the previous change, use a more robust condition to find ppath
2019-11-05 [3c3ab43] remove the unneeded condition when converting ppath in loadmch.m, fix mcx bug #82
2019-10-29 [4d7d94f] partially update documentation
2019-10-29 [a9c4732] rename mmcl executable to mmc
2019-10-29*[0c3f19f] Merge branch 'mmcl' to 'master', now mmcl is official!
2019-10-27 [206bedf] fix skinvessel example
2019-10-18 [a3823b8] add the missing -d 1 flag
2019-10-14 [4940761] fix end-of-line markers
2019-10-14 [2139721] fix example file permissions and end-of-line markers
2019-10-12 [373459a] remove commented lines
2019-10-12 [e321340] add initial element search for wide-field sources; update mmcl examples
2019-10-11 [8e6f561] bug fixing; update mmclab examples
2019-10-11*[1a8e81f] bug fixing; add support of surface diffuse reflectance for mmcl
2019-10-07 [3262326] resolve some compiling issues,e.g. missing argument in functions; missing fields in data struct
2019-10-07 [261fe69] manually resolve merge conflicts
2019-09-09 [9a2ad2a] download colin27 mesh from github instead
2019-08-31 [7e8ad7a] fix .mch file header due to wrong history data structure
2019-08-24 [4dc1228] fix memory crash due to wrong output data length for plucker, havel & badouel ray-tracer when basisorder is 0
2019-08-20 [ca4d675] allow photons that exit into 0-label elements to be detected
2019-08-20 [26477c7] add gpu parameter specifier to make RGA happy
2019-07-26*[9e800e0] fix output detected photon information for SSE-MMCL and GPU-MMCL
2019-07-25 [a3b7714] fix maximum time gate rounding bug
2019-07-24 [eb109e0] return detected photon info in mmclabcl,print progress bar
2019-07-18 [7995941] compile on new mac
2019-07-18 [9f50a7f] hacky workaround to avoid convert_float error for -1 returned by vectorized isgreater on Intel GPU
2019-07-16 [ef0ef3f] use mmclab('gpuinfo') to query gpu devices
2019-07-16 [a45f5a1] undo the revert
2019-07-16 [cfe52b4] fix rng bug on mac
2019-07-16 [72ce3a2] fix RNG error for SSE MMC on windows - long is 32bit on windows
2019-07-16 [c242112] long is only 32bit on windows, fix incorrect mmc results
2019-07-15 [c8c1cb9] Merge branch 'master' into mmcx
2019-07-12 [04565c2] compile for mac with static gcc and gomp
2019-07-12 [afcfda1] mac opencl does not accept more than 8 constant inputs
2019-07-12 [57880f1] allow to compile on windows
2019-07-12 [1e5455d] changes to compile on mac
2019-07-12 [3621fc9] make mmcl compile on mac
2019-07-12 [167ec74] output oct file with correct name
2019-07-12 [95f65bf] disable dref demo as mmcl has not fully merged with master
2019-07-08 [9e622d5] fix index issue for branchless ray-tracer 0-basisorder
2019-07-05 [23f1159] merge with master
2019-07-04 [a78760b] fix normalization indexing bug
2019-07-03 [522e21b] add matlab scripts to create plots for the paper, paper ready to submit
2019-07-02 [7779235] change line color
2019-07-02 [9fc9d0a] revert the mua change made yesterday for dmmc, thanks to Shijie
2019-07-01 [5f58a5f] update benchmark 4, correct alignment in benchmark 1
2019-07-01 [d3ebb41] change prefix in mmclab printing
2019-07-01 [a36c408] update run benchmark script
2019-07-01 [e1e567f] update mmcl bench mmclab script
2019-07-01 [f5aeac9] add benchmark scripts for mmcl
2019-07-01 [c1ec5f1] group 1/mua to normalization
2019-06-30 [5a29aa0] fix double summation and oldidx bug in method=elem
2019-06-30*[4d9013f] mmclabcl is working
2019-06-29 [acba8db] save nii for non-grid ray-tracers
2019-06-29 [fe9c83d] add b2 run_mmc script
2019-06-29 [727e89d] change b2 mesh
2019-06-28 [e537021] further update benchmark script
2019-06-28*[5b7e840] benchmark script to run on different host
2019-06-28 [3fb9a9c] fix param priority from command line
2019-06-28 [5325e53] fix cl build error
2019-06-28 [4fd89e3] make dual-mode mmc again, remove unneeded registers
2019-06-28 [ad13d2a] revert code back to 03/28 version
2019-06-28 [fba4b95] update benchmark script
2019-06-27 [420c0d4] b3 test script
2019-06-27 [d2f193f] update script
2019-06-27 [8b7e3ff] save output to bin
2019-06-27 [827b30d] add mmcl benchmark master script
2019-06-27 [d87e999] reduce colin27 photon
2019-06-27 [7f1e3ee] add spherical_shell demo
2019-06-27 [b971de3] add DMMC paper figure 1 mmclab demo script
2019-06-27 [f1876ba] add dmmc example mesh file
2019-06-27 [422a9da] add skinvessel mmc and dmmc example
2019-06-27 [02f208a] add mmc2json script to convert mmclab cfg to json
2019-06-27 [f0ff69b] fix the ray-tracer after dref related changes in the master branch
2019-06-26 [454de4f] update code variant name
2019-06-26*[d81fd9a] dualmode mmc - support both SSE4+cpu (-G -1) and CPU, rename to mmcl
2019-06-26 [4c65a21] merge with the latest master branch
2019-06-26 [90d0d20] fix outputtype=fluence and wp output, fix #36
2019-06-26 [45d3711] make mmc functions compatible with mcx output
2019-05-24 [0494f23] 2nd attempt to fix the reflection when mirror bc is used
2019-05-24 [a7ac195] allow internal reflections when mirror bc is set
2019-05-16*[24e2bb0] use isreflect=2 for total absorption on outer surf, 3 for perfect mirror
2019-04-30 [a2dda44] allow point sources to use initial elements
2019-04-30 [cbdcb1e] avoid initial elem search in cone/arcsine source launch
2019-04-24 [caa0a65] fix output format in both dmmc and mmc mode
2019-04-24 [cb93d6c] remove mac compilation error
2019-04-22 [565ad68] fix bugs and finally get diffuse reflectance output to work
2019-04-21 [5b79f08] save diffuse reflectance on surface
2019-04-21 [44d1865] copy initial test from plucker to other 3 ray tracers
2019-04-21 [ed8dbdd] saving dref on surface, support saveref option, feature incomplete
2019-04-17 [f3623ff] minor update to function parameter type
2019-04-16 [492aa3e] restore the capability to save mch files
2019-04-02 [6407e74] update loadmch to support user defined output
2019-03-28 [5312319] use DO_NOT_SAVE flag to remove memory operations
2019-03-26 [22fe07f] remove unused variables
2019-03-26 [eeccd6d] fix a bug found by Shijie
2019-03-25 [fb51a41] fix the missing energy loss for the first step in new voxel
2019-03-24 [78622ef] merge with master from github
2019-03-24 [2508642] first step to make mmc cl kernel cuda compatible
2019-03-23 [0e0f96f] fix bug in writing compression
2019-03-23 [752753d] use atomic call to return raytet counts
2019-03-23 [3676918] disable buffer fanning in the kernel
2019-03-23 [3f52cb2] only write to memory when moving out of a voxel
2019-03-23 [370e91d] use macro to dynamically select dmmc vs elem-mmc
2019-03-21 [0b647e7] fix export data length
2019-03-21 [109910e] use a better random number to distribute the writing location
2019-03-21 [1b9d645] use --buffer to set copy of memory to reduce racing
2019-03-21 [2f2aec3] matching the branchless badouel algorithm in mmc, thanks to Shijie
2019-03-21 [0477ade] avoid mac compiler error
2019-03-21 [9f5eaf9] fix a critical bug for dmmc ray-tracer
2019-03-21 [c6c0721] disable volume saving if --save2pt is set to 0
2019-03-21 [bc67cc8] fix incorrect results on AMD devices
2019-03-21 [4ec96ed] update printed program name
2019-03-20 [5dd80a1] no need to convert char lookup in string
2019-03-20 [cfaf43b] merge with mmc v2019.3 master branch
2019-03-20 [4efb7b7] fix OpenCL-precision-induced ray-tracing accuracy issue in Branchless-badouel ray-tracer
2019-03-05 [ae6de41] update change log and README for v2019.3 release
2019-03-05 [10f72ea] support mc2 and nii output for DMMC
2019-03-04 [f403303] disable linking with iomp5 to avoid crash in older matlab
2019-03-01 [996f765] add USC 19.5 atlas example, Fig9a in TranYan2019(submitted)
2019-02-11 [8acc8d7] really reduce register count, fix DMMC output crash
2019-02-10*[61ef773] fix dmmc, 5x speed increase from normal mmc
2019-02-10 [2417416] fix infinite loop, thanks Shijie!
2019-02-10 [5ef4499] return total ray-tet intersection counts
2019-02-09 [7fab7dd] moving node,elem,type,facenb,normal,srcelem to constant mem
2019-02-09 [ec0e183] optimized based on vtune profiling on intel cpu
2019-02-09 [84e87e4] add xorshift128+ RNG, seed each thread by host RNG
2019-02-06 [fe76503] convert output weight to double
2019-01-31*[5c571cf] now can run on cuda and cpu
2019-01-30 [29ae3e1] need debugging, but very close to bug free for the ray-tracing
2019-01-27 [75fbcde] mmcx now can compile, no error
2019-01-18 [53fda23] fix mmclab crash due to racing in multi-thread, similar to mcx issue #60
2019-01-17 [2f61bfe] a very rough draft of the cl kernel, converted ray-tracer from SIMD to float3
2019-01-14*[43aae8f] sync internal mmcx branch with master, mmcx branch was started in 2018

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MMC v2020 (Moon Cake beta)

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What's New

Full Change Log

MMC 1.9 (v2020, Moon Cake - beta), Qianqian Fang <q.fang at neu.edu>