mcx.1

.\" Manpage for mcx.
.\" Contact fangqq@gmail.com to correct errors or typos.
.TH man 7 "14 March 2024" "v2024.2" "Monte Carlo eXtreme (MCX) man page"
.SH NAME
mcx \- a GPU-accelerated 3-D photon transport simulator
.SH SYNOPSIS
mcx <-option1 value> <-option2 value> ...
.SH DESCRIPTION
Monte Carlo eXtreme (MCX) is a fast photon transport simulation
software for 3D heterogeneous turbid media. By taking advantage of
the massively parallel threads and extremely low memory latency in a
modern graphics processing unit (GPU), this program is able to perform Monte
Carlo (MC) simulations at a blazing speed, typically hundreds to
a thousand times faster than a fully optimized CPU-based MC
implementation.

The underying algorithm of this software can be found in

Leiming Yu, Fanny Nina-Paravecino, David Kaeli, Qianqian Fang, "Scalableand massively parallel Monte Carlo photon transport simulations forheterogeneous computing platforms," J. Biomed. Opt. 23(1), 010504 (2018).
URL: https://doi.org/10.1117/1.JBO.23.1.010504

Qianqian Fang and David Boas, "Monte Carlo Simulation of Photon Migrationin 3D Turbid Media Accelerated by Graphics Processing Units," Opt. Express,vol. 17, issue 22, pp. 20178-20190 (2009). URL:https://doi.org/10.1364/OE.17.020178

Please see http://mcx.space and http://mcx.space/wiki for detailed
documentation and examples. The MCX project is funded by the USNational Institute of Health (NIH)/National Institute of General MedicalSciences (NIGMS) under grant R01-GM114365 (PI: Qianqian Fang). This software
is written and maintained by Dr. Qianqian Fang (http://fanglab.org).

.SH OPTIONS
Running `mcx` without any parameter prints the help information (same
as -h/--help). One or multiple options can be use in the command line.
If an option appears multiple times, the last apperance overwrites earlier
settings.

The accepted command line options include:
.TP
\fB=========== Required options ===========.TP
\fB-f/--input  <A string>\fR
Use -f to specify an input file.    -f filename.json
or
    -f filename.inp

filename may contain absolute or relative path. If the filename has a '.json'extension, this input file is in the JSON format. If the input file name endswith '.inp', it is in the legacy format. If the file name contains space, onemust use quotation marks to quote the full file name. In Windows, the quotationmust be double quote (""). In Linux or Mac, either single or double quotationmark works.

If this flag is followed by an inline JSON string, such as -f '{...}', theparameter is parsed as an "inline JSON input file".
.TP
\fB--bench  <A string>\fR
.TP
Use --bench to list all built-in benchmarks. As of MCX v2024.2, these benchmarks include
     cube60
     cube60b
     cube60planar
     cubesph60b
     skinvessel
     sphshell
     spherebox
     colin27
One can execute one of the built-in benchmarks by following the benchmark name, such as
    --bench skinvessel

The default settings in each built-in benchmark can be overwritten by the additionalcommand line flags, such as --bench cube60 -n 1e8 runs 1e8 photons instead of thedefault 1e6. Use --bench name --dumpjson to export the benchmark as a standalone JSONinput file.

.TP
\fB=========== MC options ===========
.TP
\fB-n/--photon  <An integer or floating point number>\fR
This flag specifies the total number of photons to be simulated. The format is    -n N
where N can be either an integer, such as 100000 or a floating point number,such as 1e5. If N is a floating point number, it will be rounded to the largestinteger below the current value.

.TP
\fB-r/--repeat  <A positive or negative integer>\fR
Max Value the number can not exceed 2^32-1
Use -r to repeat the simulation so that the total number of photon ismultiplied by the repetition count.
    -r N

where N is a positive integer. When use this option, mcx runs 'nphoton*N'photons with nphoton per batch.
If N is a negative integer, this option splits the total simulation into abs(N)number of smaller batches; in each batch, only nphoton/abs(N) number of photonsare simulated.
This option is useful when one does not have access to a dedicated GPU, i.e.the GPU is used for both display and computation. In such case, the mcxcomputation time is limited to only 5 to 10 seconds due to the graphics driver.One can use the -r option to make the execution time per batch under the timelimit set by the driver.

.TP
\fB-b/--reflect  <0 or 1, if ignored, assumed to be 1>\fR
Use -b to enable or disable reflections at the boundaries.Use '-b' or '-b 1' to enable (default) or '-b 0' to disable

When enabled, mcx will either reflect or transmit the photon at the boundariesbased on the Fresnel's equation.By default, mcx considers refractive index mismatch at the boundaries.

.TP
\fB-B/--bc  <a string up to 12 characters, default '______000000'> \fR

The --bc option describes per-face boundary condition (BC). The first 6 lettersdefines the boundary condition for bounding box faces at -x,-y,-z,+x,+y,+z axes; overwrite -b if given.
The first 6 letters can be one of the following:
    '_': undefined, fallback to -b
    'r': like -b 1, Fresnel reflection BC
    'a': like -b 0, total absorption BC
    'm': mirror or total reflection BC
    'c': cyclic BC, enter from opposite face

if input contains additional 6 letters, the 7th-12th letters can be:
    '0': do not use this face to detect photon, or
    '1': use this face for photon detection (-d 1)
the order of the faces for letters 7-12 is the same as the first 6 letters

For example: --bc ______010 saves photons exiting at plane y=0
.TP
\fB-u/--unitinmm  <a floating point number>\fR
Use -u to set the voxel size in mm.    -u S
where S is a floating point number, denoting the edge length, in mm, of a voxelin the volume. For example, if the volume used in the simulation is 0.1x0.1x0.1mm^3, then, one should use '-u 0.1' in the command line.Only isotrpic voxels are currently supported by mcx.

.TP
\fB-U/--normalize  <0,1,2, if ignored, assumed to be 1>\fR
Use -U to enable or disable solution normalization.    '-U' or '-U 1' toenable (default) or '-U 0' to disable

For fluence, the normalization aims to generate a 'Green's function'. For otherqualities, the normalization produces a stable solution by removing thedependency due to total photon numbers, voxel sizes, and time-gate settings.The detailed equations are explained in the MCX paper.

If one sets -U 2, the normalization is only applied to the fluence in theinterior voxels, and does not apply to the diffuse reflectance (as negativenumbers in the raw output volume) along the air voxels right outside of thenon-zero voxels.

.TP
\fB-E/--seed  <An integer or a string>\fR
Use -E to set the seed of the CPU random number generator (RNG). The CPU RNG inturn initializes the seeds for each GPU thread.    -E -1    // let MCX to automatically seed the CPU-RNG using system clock    -E n     // n is a large positive integer, set the CPU-RNG's seed to n    -E filename.mch // replay detected photons using the seeds saved in the mchfile
Setting a fixed RNG seed is expected to create reproducible results on NVIDIAcards if the thread/block size are kept the same.

.TP
\fB-z/--srcfrom0  <0 or 1, if ignored, assumed to be 1>\fR
Use -z to define the coordinate origin mode of the volume.    -z 0 (default)// assumes the lower-bottom corner of the first voxel as [1 1 1]
    -z or -z 1    // assumes the lower-bottom corner of the first voxel as [0 00]

All source and detector positions are referenced from the origin, determined bythis flag.

.TP
\fB-R/--skipradius  <An integer>\fR
Use -R to specify the scope within which to use atomic operations. The possibleoptions include     -R -2  // this enables full atomic opertions in the entire volume(default)     -R n   // when n is a positive integer, mcx uses atomic operations in the            // shared memory for a n x n x n sub-cubic domain centered at thesource.
     -R 0   // disable all atomic operations, data racing may exist,particularly            // near the source.     -R -1  //use crop0/crop1 to determine atomic zone

Using full atomic operations was very slow in very early CUDA devices, but formost later NVIDIA GPUs, the use of atomic operations is as efficient as thenon-atomic version.

.TP
\fB-k/--voidtime  <0 or 1, if ignored, assumed to be 1>\fR
Use the -k option to tell MCX whether to count the time-of-flight when a photonis launched outside of the volume.    -k 1 (default)  // the time-of-flight of the photon starts at the launch time    -k 0            // the time-of-flight starts when a photon enters the firstnon-zero voxel.


.TP
\fB-V/--specular  <0 or 1, if ignored, assumed to be 1>\fR
Use -V flag to tell MCX whether to consider the specular reflection at theinitial entry of the photon to the domain (entry from a 0-voxel to a non-zerovoxel). By default, the initial specular reflection is considered (thus, photonloses a small fraction of energy, but enters the domain). The reflected energyis no longer modeled. Please be aware that the "absorption fraction" numberprinted at the end of the mcx simulation session should include this energyloss due to specular reflection.
If one sets "-V 0", all launched photon energy preserves after enters thedomain.

.TP
\fB-Y/--replaydet  <A positive integer>\fR
Use the -Y option to specify the ID of the detector for the 'replay'calculations.    -Y n   // n is a positive integer, denoting the index of the detectors to be replayed    -Y 0   // all detected photons will be replayed regardless of detector

If -Y is not specified, MCX replays all detected photons; otherwise, MCX onlyreplays the detected photons from the specified detector. See -E for moredetails.

.TP
\fB-P/--shapes  <A JSON string>\fR
Use the -P option to dynamically define heterogeneities from the command line.The -P flag is followed by a JSON-formatted string. For example
    -P '{"Shapes":[{"ZLayers":[[1,10,1],[11,30,2],[31,60,3]]}]}'
This defines a 3-layer medium: z slices 1-10 is filled with tissue label 1, zslices 11-30 is filled with label 2, and 31-60 is filled with label 3.The shape definition always starts an array object named 'Shapes'. Each elementin the 'Shapes' object defines a primitive object. The supported primitivesincludeName, Origin, Grid, Sphere, Box, Subgrid, {XYZ}Layers, {XYZ}Slabs, Cylinder, UpperSpace.Most objects have a sub-field 'Tag', specifying the tissue label (index to theproperty list). The details of the Shapes objects can be found in this link

.TP
\fB-j / --json  <A JSON string>\fR
Use the -j option to dynamically define simulation parameters to overwrite/modifythe default settings as specified in the .inp/.json file provided after the -fflag. The -j flag is followed by a JSON-formatted string. The format of the JSONconstruct is the same as in an MCX JSON input file. For example

    -j '{"Optode":{"Source":{"Type":"fourier","Param1":[40,0,0,2]}}}'
This changes the source type, whatever it was defined in the input file, to"fourier" source, and sets the source parameter 1 to [40,0,0,2] while keepingeverything else unchanged.

if -f, -j, -P and other parameters (such as -n, -S ...) all present in thecommand line, the priorities are

    all other command line flags > -j > -P > -f

where the settings in -n/-S/-d/... overwrite the settings in -j, which alsooverwrites the input file in -f

.TP
\fB-K / --mediabyte  <A number or a string>\fR
This flag defines the volumetric input data format. Use either a number or a stringfrom below list
     1 or byte: 0-128 tissue labels
     2 or short: 0-65535 (max to 4000) tissue labels
     4 or integer: integer tissue labels
     96 or asgn_float: mua/mus/g/n 4xfloat format
     97 or svmc: split-voxel MC 8-byte format
     98 or mixlabel: label1+label2+label1_percentage
     99 or labelplus: 32bit composite voxel format
     100 or muamus_float: 2x 32bit floats for mua/mus
     101 or mua_float: 1 float per voxel for mua
     102 or muamus_half: 2x 16bit float for mua/mus
     103 or asgn_byte: 4x byte gray-levels for mua/s/g/n
     104 or muamus_short: 2x short gray-levels for mua/s

when formats 99 or 102 is used, the mua/mus values in the input volume
binary data must be pre-scaled by voxel size (unitinmm) if it is not 1.
pre-scaling is not needed when using these 2 formats in mcxlab/pmcx

.TP
\fB-e/--minenergy  <A floating point number>\fR
Use -e to set the min photon packet weight to trigger Russian Roulette.    -e f    // where f is a floating point number between 0 and 1.

.TP
\fB-g/--gategroup  <A positive integer>\fR
Use -g to split a simulation containing many time gates into smaller butmultiple sequential simulations.    -g n    // n is a positive integer
Only use this option when the GPU global memory can not hold the data for allrequired time gates, which only happens when one trys to simulate a very largedomain with very dense time gates (very rare). If one's GPU can only hold thedata for n time gates, while one has to simulate a total of N &gt; n timegates, use -g n to split the total simulations into multiple runs: in the firstrun, MCX will record the results for 1~n time gates, in the second run, MCXwill launch a new kernel to simulate photons for 1~2*n time gates, but onlyrecords the photon fluence for n+1 ~ 2*n time gates and so on. As one can see,this method introduces overhead in the later simulations. Therefore, it isrecommended to avoid.

.TP
\fB-a/--array  <0 or 1, if ignored, assumed to be 1>\fR
Use -a to tell mcx if the input volume data is a MATLAB-like data(column-major) or a C-like data (row-major).Format    -a 0 (default) // the input volume is a MATLAB-array    -a 1           // the input volume is a C-array
If an MATLAB array is used, the fastest loop index is the left-most index of anarray; while for a C array, it is the right-most index.

.TP
\fB=========== MC options ===========
.TP
\fB-L/--listgpu  <0 or 1, if ignored, assumed to be 1>\fR
Use the -L flag to list all available GPUs on your system without running thesimulation. For example
$mcx -L
    =========================   GPU Information  ============================
    Device 1 of 2:		GeForce GTX 980 Ti
    Compute Capability:	5.2
    Global Memory:		2147287040 B
    Constant Memory:	65536 B
    Shared Memory:		49152 B
    Registers:		65536
    Clock Speed:		1.19 GHz
    Number of MPs:		22
    Number of Cores:	2816
    SMX count:		22
    =========================   GPU Information  ============================
    Device 2 of 2:		GeForce GT 730
    Compute Capability:	3.5
    Global Memory:		1073545216 B
    Constant Memory:	65536 B
    Shared Memory:		49152 B
    Registers:		65536
    Clock Speed:		0.90 GHz
    Number of MPs:		2
    Number of Cores:	384
    SMX count:		2


.TP
\fB-t/--thread  <An integer>\fR
Use -t to specify the number of threads.    -t N
where N is a positive integer. The thread number N must be a multiple of 32 -the size of a warp - on all CUDA devices. If N is not a multiple of 32, mcxwill round it to the nearest multiple less than N. To achieve the best efficiency, it is recommended to launch a large number ofthreads to mazimize the utility of the GPU resources; a thread number largerthan 10000 is generally sufficient.
You should not manually specify the thread number using this option when youuse the autopilot mode (-A).

.TP
\fB-T/--blocksize  <An integer>\fR
Use -T to specify the size of a block.    -T N
where N is a positive integer. The block size N must be a multiple of 32 - thesize of a warp - on all CUDA devices. If N is not a multiple of 32, mcx willround it to the nearest multiple less than N. Because mcx does not need inter-thread communication, a small block size, suchas 32 or 64, is generally recommended.
You should not manually specify the block size using this option when you usethe autopilot mode (-A).

.TP
\fB-A/--autopilot  <0 or 1, if ignored, assumed to be 1>\fR
Use -A to enable automatic thread/block configuration (i.e. autopilot).    -A 1

When the autopilot mode is enabled, mcx will compute the 'optimal' threadnumber and block size using a heuristic algorithm.

.TP
\fB-G/--gpu  <An integer or a string made of '0's and '1's>\fR
Use -G to specify one or multiple GPUs to run the simulation. Format    -G 1    // use only the first GPU device (device orders based on 'mcx -L'output)    -G n    // n is a positive integer, use only the n-th GPU device    -G 1110 // when -G is followed by a string made of only 0s and 1s, itspecifies            // a mask for active GPUs, for example, 1110 means to use GPU 1-3            // together while the 4th GPU is not used.
When multiple GPU devices are specified, one need to use the -W/--workload flagto optimally partition the total photons to be simulated. By default, photonswill be evenly distributed among multiple GPU devices.

.TP
\fB-W/--workload  <A list of floating point/integer values, separated bycommas>\fR
Use -W to partition the total simulated photon numbers between multipledevices. Format    -W w1,w2,w3,...  // w_i is a numerical value, corresponding to the relativeportions                     // of the workload of the i-th GPU device. The total load                     // is proportional to the sum of w_i.

For example, -W 10,20,20 indicates a 1:2:2 workload split between 3 activeGPUs.If one needs to simulate 1e6 photons, the 1st GPU will run 2e5 photons,while the 2nd and the 3rd GPUs will run 4e5 photons each.

.TP
\fB-I/--printgpu  <0 or 1, if ignored, assumed to be 1>\fR
The -I option lists all available GPU, same as -L, but it also run the actualsimulation.

.TP
\fB=========== Output options ===========
.TP
\fB-s/--session  <A string>\fR
Use -s to specify a session ID for the simulation.    -s session_name // session_name is a string, it can not contain &lt;&gt;:"/|?*
If -s is set, the output fluence file (.mc2), detected photon file (.mch) andthe log file (.log) will be named as session_name.{mc2,mch,log}. Otherwise, theinput file name following the -f option will be used in the place ofsession_name.

.TP
\fB-d/--savedet  <0 or 1, if ignored, assumed to be 1>\fR
Use -d to enable or disable saving the detailed path data for all detectedphotons.    '-d' or '-d 1' to enable (default) or    '-d 0' to disable
    '-d 3' to terminate simulation when detected photon buffer is filled

When this option is enabled, a binary file, with a suffix of .mch, will beproduced in additional to the '.mc2' output. The .mch file contains the partialpath data for all photons enters the aperatures of the detectors.


.TP
\fB-w/--savedetflag <a string or number, if ignored, assumed to be 'dp'>\fR
A case-insensitive string controlling the presence of each detected photondata fields. The presence of a letter denotes that the corresponding detectedphoton data is saved, otherwise, it is not saved. The below list shows allsupported data fields (the data columns of each field is shown in the parentheses)

     1 D output detector ID (1)
     2 S output partial scat. even counts (#media)
     4 P output partial path-lengths (#media)
     8 M output momentum transfer (#media)
     16 X output exit position (3)
     32 V output exit direction (3)
     64 W output initial weight (1)

For example, -w dspmxvw asks mcx to save all supported field. If a domaincontains 2 tissue types (#media=2), this results in a 2D floating point arraymade of 14 columns and #detected photon rows.

.TP
\fB-x/--saveexit  <0 or 1, if ignored, assumed to be 1>\fR
1 to save photon exit positions and directions
setting -x to 1 also implies setting '-d' to 1

.TP
\fB-X/--saveref  <0 or 1, if ignored, assumed to be 1>\fR
1 to save diffuse reflectance at the air-voxels
right outside of the domain; if non-zero voxels
appear at the boundary, pad 0s before using -X

.TP
\fB-q/--saveseed  <0 or 1, if ignored, assumed to be 1>\fR
1 to save photon RNG seed for replay; 0 not save

.TP
\fB-M/--dumpmask  <0 or 1, if ignored, assumed to be 1>\fR
Use -M to dump the modified volume data for debugging purposes. The dumpedvolume is saved in a binary file with Nx x Ny x Nz bytes, each byte containsthe tissue label as the input volume, and the highest bit of each byte denoteswhether the voxel is next to a detector.

.TP
\fB-m/--momentum  <0 or 1, if ignored, assumed to be 1>\fR
Use -m to save the momentum transfer for all detected photons. One can use thisoutput for diffuse correlation spectroscopy (DCS) simulations. This informationis stored in the .mch file. One can load the data using loadmch.m and processthe saved data using the mcxdcsg1.m script, both matlab scripts can be foundunder mcx/utils.

.TP
\fB-H/--maxdetphoton  <An integer>\fR
Use -H to specify the maximum number of detected photons.    -H n    // nis a positive integer, signifying mcx to allocate a buffer to hold n detectedphotons
By default, mcx can save up to 1e6 detected photons. If the detected photonsexceed this limit, mcx will show a warning. Users may use the -H option torerun the simulation and use the number in the warning to reallocate the buffer.

.TP
\fB-S/--save2pt  <0 or 1, if ignored, assumed to be 1>\fR
Use -S to enable or disable saving volumetric fluence distributions (or therequested output specified by the -X flag).
.TP
\fB-O/--outputtype  <A single character (case insensitive)>\fR
Use -O to specify the type of data to be saved in the volumetric output. Thesupported formats include
 'X' - output time-resolved fluence rate (1/mm^2), i.e. TPSF
 'F' - output time-resolved fluence rate integrated in each time-gate, 'E' - energy deposit at each voxel (normalized or unnormalized, depends on -n)
 'J' - Jacobian (replay mode), 'P' - scattering event counts at each voxel (replay mode only)


.TP
\fB-F/--outputformat  <A string, if ignored, set 'mc2'>\fR
Use -F to specify the volumetric data output format:
    mc2 - MCX mc2 format (binary 32bit float) (default)
    nii - Nifti format (fluence after taking log10())
    jnii - JNIfTI format (https://neurojson.org)
    bnii - Binary JNIfTI (https://neurojson.org)
    hdr - Analyze 7.5 hdr/img format
    tx3 - GL texture data for rendering (GL_RGBA32F)

the bnii/jnii formats support compression (-Z) and generate small files
load jnii (JSON) and bnii (UBJSON) files using below lightweight libs:
    MATLAB/Octave: JNIfTI toolbox https://github.com/NeuroJSON/jnifti,
    MATLAB/Octave: JSONLab toolbox https://github.com/fangq/jsonlab,
    Python: PyJData: https://pypi.org/project/jdata
    JavaScript: JSData: https://github.com/NeuroJSON/jsdata

.TP
\fB-Z/--zip  <A string, if ignored, assume to be 'zlib'>\fR
Set compression method if -F jnii or --dumpjson is used (when saving data to JSON/JNIfTI format)
must be 0-6 or one of 'zlib', 'gzip','base64','lzip','lzma','lz4' or 'lz4hc', case insensitive
    0 zlib: zip format (moderate compression,fast)
    1 gzip: gzip format (compatible with *.gz)
    2 base64: base64 encoding with no compression
    3 lzip: lzip format (high compression,very slow)
    4 lzma: lzma format (high compression,very slow)
    5 lz4: LZ4 format (low compression,extrem. fast)
    6 lz4hc: LZ4HC format (moderate compression,fast)

.TP
\fB--dumpjson  <A file name or number, if ignored, assume to be '-'>\fR
Must be a number (1-3), empty, '-' or a file name
Export all settings,including volume data using JSON/JData (https://neurojson.org)format for easy sharing; can be reused using -f

if followed by nothing or '-', mcx will print the JSON to the console;write to a file if file name is specified;by default, prints settings after pre-processing;--dumpjson 2 prints raw inputs before pre-processing
--dumpjson 3 prints raw inputs after pre-processing

.TP
\fB=========== User IO options ===========
.TP
\fB-h/--help\fR
se the -h flag to print the built-in help of all supported command line flags

.TP
\fB-v/--version\fR

Use the -v flag to print the version of MCX

.TP
\fB-l/--log  <0 or 1, if ignored, assumed to be 1>\fR
Use the -l flag to save the MCX's command line output into a log file. Format    '-l' or '-l 1' to enable (default) or    '-l 0' to disable

The output file name is 'session_name.log' where 'session_name' is the stringspecified by the -s flag. If -l is used, no message will be printed in thecommand line.

.TP
\fB-i/--interactive  <0 or 1, if ignored, assumed to be 1>\fR
Use -i when one wants to type in the domain settings in an item-by-item promptmode. The -i option can not be used together with -f. When -i is used, one canuse the redirect operator to include an input file, i.e.    mcx -i &lt; input.inp    mcx -f input.inp
can produce the same answer.

.TP
\fB=========== Debug options ===========
.TP
\fB-D/--debug  <An integer or a string>\fR
Use -D to print debug information (you can use an integer or a string bycombining the following flags)
  1 R  debug RNG
  2 M  store photon trajectory info (saved in a .mct file, can be loaded withloadmch.m)
  4 P  print progress bar
  8 T  save trajectory data only, disable flux/detp

combine multiple items by using a string, or add selected numbers together

.TP
\fB=========== Additional options ===========
.TP
\fB--gscatter  <An integer>\fR
after a photon completes the specified number of
scattering events, mcx then ignores anisotropy g
and only performs isotropic scattering for speed

.TP
\fB--maxvoidstep  <An integer>\fR
maximum distance (in voxel unit) of a photon that
can travel before entering the domain, iflaunched outside (i.e. a widefield source)

.TP
\fB--maxjumpdebug  <An integer>\fR
when trajectory is requested (i.e. -D M),
use this parameter to set the maximum positions
stored (default: 1e7)

.SH EXAMPLES
\fBListing supported GPUs\fR
    mcx -L

\fBListing built-in benchmarks\fR
    mcx --bench

\fBRunning built-in benchmarks\fR
    mcx --bench cube60

\fBDump JSON configuration file for the built-in benchmark\fR
    mcx --bench cube60 --dumpjson

\fBRunning mcx using autopilot mode\fR
    mcx -A 1 -n 1e7 --bench cube60b -G 1 -D P

\fBUsing multiple devices (1st,2nd and 4th GPUs) with equal load\fR
    mcx -A -n 1e7 --bench cube60 -G 1101 -W 10,10,10

\fBUsing JSON-based inline domain definition\fR
    mcx -f input.json -P '{"Shapes":[{"ZLayers":[[1,10,1],[11,30,2],[31,60,3]]}]}'

\fBUsing inline JSON setting modifier\fR
    mcx -f input.json -j '{"Optode":{"Source":{"Type":"isotropic"}}}'

.SH SEE ALSO
mmc(7), mcxcl(7)
.SH AUTHOR
Qianqian Fang (q.fang@neu.edu)