update zmatlib, replace zlib by miniz, update cmake, update version

fangq · Aug 29, 2023 · 11b1c33 · 11b1c33
1 parent 01ed20b
commit 11b1c33
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diff --git a/.github/workflows/build_all.yml b/.github/workflows/build_all.yml
@@ -67,13 +67,13 @@ jobs:
           gcc -v
           mkoctfile --version
           if [[ "$RUNNER_OS" == "Linux" ]]; then
-            make oct LFLAGS='-static-libgcc -static-libstdc++ -Wl,-Bstatic -lz -Wl,-Bdynamic'
+            make oct LFLAGS='-static-libgcc -static-libstdc++'
             ldd ../mmclab/mmc.mex
           elif [[ "$RUNNER_OS" == "macOS" ]]; then
             make oct CC=gcc-11 CXX=g++-11 USEROCTOPT="CXXFLAGS='-pipe -Os -arch x86_64' DL_LD=g++ DL_LDFLAGS='-fopenmp -static-libgcc -static-libstdc++'"
             otool -L ../mmclab/mmc.mex
           else
-            make oct CC=gcc CXX=g++ LIBOPENCL='/c/Windows/System32/OpenCL.dll --verbose' LFLAGS='-static-libgcc -static-libstdc++ -Wl,-Bstatic -lz -Wl,-Bdynamic'
+            make oct CC=gcc CXX=g++ LIBOPENCL='/c/Windows/System32/OpenCL.dll --verbose' LFLAGS='-static-libgcc -static-libstdc++'
             objdump -p ../mmclab/mmc.mex | grep "DLL Name:"
           fi
           octave-cli --eval "fprintf(1,['OCTAVE_ARCH=' regexprep(computer('arch'), 'darwin[0-9.]+-', 'darwin-')])"
@@ -82,7 +82,7 @@ jobs:
         run: |
           cd src
           if [[ "$RUNNER_OS" == "Windows" ]]; then
-            make mex LDFLAGS="-static libzmat.a" EXTRALIB="-Lc:/ProgramData/chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/lib -lz -v"
+            make mex LDFLAGS="-static libzmat.a" EXTRALIB="-Lc:/ProgramData/chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/lib-v"
             objdump -p ../mmclab/mmc.mexw* | grep "DLL Name:"
           elif [[ "$RUNNER_OS" == "macOS" ]]; then
             which mex
@@ -97,13 +97,13 @@ jobs:
           cd src
           make clean
           if [[ "$RUNNER_OS" == "Linux" ]]; then
-            make AR=c++ EXTRALIB="-static-libstdc++ -static-libgcc -Wl,-Bdynamic -lOpenCL -Wl,-Bstatic -lm -lz"
+            make AR=c++ EXTRALIB="-static-libstdc++ -static-libgcc -Wl,-Bdynamic -lOpenCL -Wl,-Bstatic -lm"
             ldd bin/mmc
           elif [[ "$RUNNER_OS" == "macOS" ]]; then
             make CC=gcc-11 CXX=g++-11
             otool -L bin/mmc
           else
-            make CC=gcc CXX=g++ USERARFLAGS="-static-libstdc++ -static-libgcc -Wl,-Bstatic libzmat.a -Lc:/ProgramData/chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/lib -lz"
+            make CC=gcc CXX=g++ USERARFLAGS="-static-libstdc++ -static-libgcc -Wl,-Bstatic libzmat.a -Lc:/ProgramData/chocolatey/lib/mingw/tools/install/mingw64/x86_64-w64-mingw32/lib"
             ldd bin/mmc
           fi
       - name: Create package folder

diff --git a/ChangeLog.txt b/ChangeLog.txt
@@ -1,7 +1,18 @@
 Change Log
 
-== MMC 1.9.6 (v2023.01, Moon Cake), Qianqian Fang <q.fang at neu.edu> ==
+== MMC 2.0.0 (v2023, Moon Cake), Qianqian Fang <q.fang at neu.edu> ==
 
+ 2023-03-04 [465ef20] implement github ci
+ 2023-01-03 [3ddff2b] force flushing in terminal and matlab
+ 2023-01-02 [849d09a] bump up version number
+ 2023-01-02 [423047b] fix travis error after adding cuda related targets
+ 2022-11-02 [9809be0] add cudamex and cudaoct makefile targets
+ 2022-10-25 [f455d1e] reduce photon leakage for edge-immc, still leaks, need more work
+
+
+== MMC 1.9.6 (v2022.10, Moon Cake), Qianqian Fang <q.fang at neu.edu> ==
+
+ 2022-10-08 [4c8bdae] mmc v2022.10
  2022-10-01 [77411c4] using nvidia native atomicadd for float add 40% speedup
  2022-09-21 [e661011] add double-buffer to solve fangq/mcx#41
  2022-05-30 [c3b15b2] print detected photon number in matlab

diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@ Mesh-based Monte Carlo (MMC) - SSE4 and OpenCL
 
 -   Author: Qianqian Fang (q.fang at neu.edu)
 -   License: GNU General Public License version 3 (GPL v3), see License.txt
--   Version: 1.9.6 (v2023.01, Moon Cake)
+-   Version: 2.0.0 (v2023, Moon Cake)
 -   URL: <http://mcx.space/mmc>
 
 [![Build Status](https://travis-ci.com/fangq/mmc.svg?branch=master)](https://travis-ci.com/fangq/mmc)
@@ -35,7 +35,7 @@ Table of Content:
 What's New
 -------------
 
-MMC v2023.01 (1.9.6) includes a major feature upgrade - implicit MMC (iMMC) - to
+MMC v2023 (2.0.0) includes a major feature upgrade - implicit MMC (iMMC) - to
 enable simulations of highly complex anatomical structures. The details of the
 iMMC algorithm, developed by Yaoshen Yuan, are described in his recent paper 
 [Yuan2021]. Briefly, iMMC permits one to associate cylindrical inclusions, 

diff --git a/README.txt b/README.txt
@@ -6,7 +6,7 @@
 
 *Author:  Qianqian Fang <q.fang at neu.edu>
 *License: GNU General Public License version 3 (GPL v3), see License.txt
-*Version: 1.9.6 (v2023.01, Moon Cake)
+*Version: 2.0.0 (v2023, Moon Cake)
 *URL:     http://mcx.space/mmc
 
 ---------------------------------------------------------------------
@@ -19,7 +19,7 @@ Table of Content:
 
 == # What's New ==
 
-MMC v2023.01 (1.9.6) includes a major feature upgrade - implicit MMC (iMMC) - to
+MMC v2023 (2.0.0) includes a major feature upgrade - implicit MMC (iMMC) - to
 enable simulations of highly complex anatomical structures. The details of the
 iMMC algorithm, developed by Yaoshen Yuan, are described in his recent paper 
 [Yuan2021]. Briefly, iMMC permits one to associate cylindrical inclusions, 

diff --git a/commons/Makefile_common.mk b/commons/Makefile_common.mk
@@ -13,15 +13,15 @@
 # and linking
 ########################################################
 
-ROOTDIR ?= .
+ROOTDIR ?= ..
 MMCDIR  ?= $(ROOTDIR)
 
 MMCSRC :=$(MMCDIR)/src
 
 CXX        := g++
 AR         := $(CC)
 CUDACC     :=nvcc
-BIN        := bin
+BIN        := $(MMCDIR)/bin
 BUILT      := built
 BINDIR     := $(BIN)
 OBJDIR 	   := $(BUILT)
@@ -30,8 +30,8 @@ INCLUDEDIR := $(MMCDIR)/src -I$(MMCDIR)/src/zmat/easylzma -I$(MMCDIR)/src/ubj
 AROUTPUT   += -o
 MAKE       ?= make
 
-ZMATLIB    :=libzmat.a
-USERARFLAGS?=$(ZMATLIB) -lz
+ZMATLIB    :=lib/libzmat.a
+USERARFLAGS?=$(ZMATLIB)
 
 LIBOPENCLDIR ?= /usr/local/cuda/lib64
 LIBOPENCL  ?=-lOpenCL

diff --git a/examples/colin27/run_test.sh b/examples/colin27/run_test.sh
@@ -1,3 +1,3 @@
 #!/bin/sh
 
-time ../../src/bin/mmc -f brain.inp -s brain -n 1e6 -b 1 -D TP -F nii $@
+time ../../bin/mmc -f brain.inp -s brain -n 1e6 -b 1 -D TP -F nii $@
diff --git a/examples/dcs/run_test.sh b/examples/dcs/run_test.sh
@@ -1,3 +1,3 @@
 #!/bin/sh
 
-../../src/bin/mmc -s dcs -f dcs.inp -b 1 -m 1 -D P -d 1
+../../bin/mmc -s dcs -f dcs.inp -b 1 -m 1 -D P -d 1
diff --git a/examples/meshtest/run_test.sh b/examples/meshtest/run_test.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 
-time ../../src/bin/mmc -f mesh0.inp -s mesh0 -n 30000000 -b 0 -l -D TP
-time ../../src/bin/mmc -f mesh1.inp -s mesh1 -n 30000000 -b 0 -l -D TP
-time ../../src/bin/mmc -f mesh2.inp -s mesh2 -n 30000000 -b 0 -l -D TP
+time ../../bin/mmc -f mesh0.inp -s mesh0 -n 30000000 -b 0 -l -D TP
+time ../../bin/mmc -f mesh1.inp -s mesh1 -n 30000000 -b 0 -l -D TP
+time ../../bin/mmc -f mesh2.inp -s mesh2 -n 30000000 -b 0 -l -D TP
 
diff --git a/examples/onecube/run_test.sh b/examples/onecube/run_test.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-../../src/bin/mmc -n 20 -f onecube.inp -s onecube -G -1 -D M  | grep '^M' | sed -e 's/^M/1/g' -e 's/^B/0/g' -e 's/P/2/g'| sed '$d' > mov.txt
-../../src/bin/mmc -n 20 -f onecube.inp -s onecube -G -1 -D MA | grep '^[A-Z]' | sed -e 's/^[A-Z] //g' | sed '$d' > ad.txt
+../../bin/mmc -n 20 -f onecube.inp -s onecube -G -1 -D M  | grep '^M' | sed -e 's/^M/1/g' -e 's/^B/0/g' -e 's/P/2/g'| sed '$d' > mov.txt
+../../bin/mmc -n 20 -f onecube.inp -s onecube -G -1 -D MA | grep '^[A-Z]' | sed -e 's/^[A-Z] //g' | sed '$d' > ad.txt
diff --git a/examples/planar/run_test.sh b/examples/planar/run_test.sh
@@ -1,10 +1,10 @@
 #!/bin/sh
 
-../../src/bin/mmc -n 100000 -f planar.inp -s planar -b 1 -x 1 -D E > debug.txt
+../../bin/mmc -n 100000 -f planar.inp -s planar -b 1 -x 1 -D E > debug.txt
 grep '^x ' debug.txt | sed -e 's/^x //g'> exitpos.txt
 grep '^e ' debug.txt | sed -e 's/^e //g'> enterpos.txt
 
-#../../src/bin/mmc -n 1 -f planar.inp -s planar -b 1 -x 1 -D M  | sed -e 's/^M/1/g' -e 's/^B/0/g' -e 's/P/2/g'| sed '$d' > mov.txt
-#../../src/bin/mmc -n 1 -f planar.inp -s planar -b 1 -x 1 -D MA | sed -e 's/^[A-Z] //g' | sed '$d' > ad.txt
+#../../bin/mmc -n 1 -f planar.inp -s planar -b 1 -x 1 -D M  | sed -e 's/^M/1/g' -e 's/^B/0/g' -e 's/P/2/g'| sed '$d' > mov.txt
+#../../bin/mmc -n 1 -f planar.inp -s planar -b 1 -x 1 -D MA | sed -e 's/^[A-Z] //g' | sed '$d' > ad.txt
 
-#../../src/bin/mmc -n 1000000 -f planar.inp -s planar -b 1 -x 1 -D TP
+#../../bin/mmc -n 1000000 -f planar.inp -s planar -b 1 -x 1 -D TP
diff --git a/examples/reftest/run_test.sh b/examples/reftest/run_test.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-../../src/bin/mmc -n 20 -f onecube.inp -s onecube -b 1 -D M  | sed -e 's/^M/1/g' -e 's/^B/0/g' -e 's/P/2/g' -e 's/T/3/g'| sed '$d' > mov.txt
-../../src/bin/mmc -n 20 -f onecube.inp -s onecube -b 1 -D MA | sed -e 's/^[A-Z] //g' | sed '$d' > ad.txt
+../../bin/mmc -n 20 -f onecube.inp -s onecube -b 1 -D M  | sed -e 's/^M/1/g' -e 's/^B/0/g' -e 's/P/2/g' -e 's/T/3/g'| sed '$d' > mov.txt
+../../bin/mmc -n 20 -f onecube.inp -s onecube -b 1 -D MA | sed -e 's/^[A-Z] //g' | sed '$d' > ad.txt
diff --git a/examples/regression/exitangle/run_test_planar.sh b/examples/regression/exitangle/run_test_planar.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 date 
 
-../../../src/bin/mmc -n 1000000 -f tank_planar.inp -s tank_planar -b 1 -x 1 -U 0 -D TP
+../../../bin/mmc -n 1000000 -f tank_planar.inp -s tank_planar -b 1 -x 1 -U 0 -D TP
 
 date
diff --git a/examples/replay/run_test.sh b/examples/replay/run_test.sh
@@ -1,11 +1,11 @@
 #!/bin/sh
 
 # first run to get the seeds for each detected photon (-q 1)
-../../src/bin/mmc -f replaytest.inp -s step1 -n 3e6 -b 0 -q 1 -x 1 -d 1 -D TP
+../../bin/mmc -f replaytest.inp -s step1 -n 3e6 -b 0 -q 1 -x 1 -d 1 -D TP
 
 # replay the detected photons (-E *.mch) detected by detector#1 (-P 1) without normalization (-U 0)
-../../src/bin/mmc -f replaytest.inp -E step1.mch -s step2 -P 1 -b 0 -q 1 -x 1 -d 1 -O L -D TP
+../../bin/mmc -f replaytest.inp -E step1.mch -s step2 -P 1 -b 0 -q 1 -x 1 -d 1 -O L -D TP
 
 # replay the detected photons (-E *.mch) detected by detector#1 (-P 1) without normalization (-U 0)
-../../src/bin/mmc -f replaytest.inp -E step1.mch -s step3 -P 1 -b 0 -q 1 -x 1 -d 1 -O P -D TP
+../../bin/mmc -f replaytest.inp -E step1.mch -s step3 -P 1 -b 0 -q 1 -x 1 -d 1 -O P -D TP
 
diff --git a/examples/replaywide/run_test.sh b/examples/replaywide/run_test.sh
@@ -1,13 +1,13 @@
 #!/bin/sh
 
 # first run to get the seeds for each detected photon (-q 1)
-../../src/bin/mmc -f init_MC.inp -s init -n 3e7 -b 1 -q 1 -x 1 -D TP
+../../bin/mmc -f init_MC.inp -s init -n 3e7 -b 1 -q 1 -x 1 -D TP
 
 # replay the detected photons (-E *.mch) for full illumination & half detection (-P 0) under wl mode
-../../src/bin/mmc -f replay1.inp -E init.mch -s replay1 -P 0 -b 1 -O L -D TP
+../../bin/mmc -f replay1.inp -E init.mch -s replay1 -P 0 -b 1 -O L -D TP
 
 # replay the detected photons (-E *.mch) for half illumination & full detection (-P 0) under wp mode
-../../src/bin/mmc -f replay2.inp -E init.mch -s replay2 -P 0 -b 1 -O L -D TP
+../../bin/mmc -f replay2.inp -E init.mch -s replay2 -P 0 -b 1 -O L -D TP
 
 # replay the detected photons (-E *.mch) for half illumination & half detection (-P 0) under wl mode
-../../src/bin/mmc -f replay3.inp -E init.mch -s replay3 -P 0 -b 1 -O L -D TP
+../../bin/mmc -f replay3.inp -E init.mch -s replay3 -P 0 -b 1 -O L -D TP
diff --git a/examples/sfdi2layer/run_test.sh b/examples/sfdi2layer/run_test.sh
@@ -1,3 +1,3 @@
 #!/bin/sh
 
-../../src/bin/mmc -n 3000000 -f sfdi.inp -s sfdi -b 0 -k 0 -D TP -M S $@
+../../bin/mmc -n 3000000 -f sfdi.inp -s sfdi -b 0 -k 0 -D TP -M S $@
diff --git a/examples/sharing/run_test.sh b/examples/sharing/run_test.sh
@@ -1,3 +1,3 @@
 #!/bin/sh
 
-../../src/bin/mmc -n 1000000 -f sharing.inp -s sharing -b 1 -k 0 -D TP
+../../bin/mmc -n 1000000 -f sharing.inp -s sharing -b 1 -k 0 -D TP
diff --git a/examples/skinvessel/run_dmmc.sh b/examples/skinvessel/run_dmmc.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-../../src/bin/mmc -f dmmc_skinvessel.json -n 1e8 -F bin $@
+../../bin/mmc -f dmmc_skinvessel.json -n 1e8 -F bin $@
 
diff --git a/examples/skinvessel/run_mmc.sh b/examples/skinvessel/run_mmc.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-../../src/bin/mmc -f skinvessel.json -n 1e8 -F bin $@
+../../bin/mmc -f skinvessel.json -n 1e8 -F bin $@
 
diff --git a/examples/sphere/run_test.sh b/examples/sphere/run_test.sh
@@ -1,10 +1,10 @@
 #!/bin/sh
 
-#../../src/bin/mmc -n 100000 -f planar.inp -s planar -b 1 -x 1 -D E > debug.txt
+#../../bin/mmc -n 100000 -f planar.inp -s planar -b 1 -x 1 -D E > debug.txt
 #grep '^x ' debug.txt | sed -e 's/^x //g'> exitpos.txt
 #grep '^e ' debug.txt | sed -e 's/^e //g'> enterpos.txt
 
-#../../src/bin/mmc -n 1 -f planar.inp -s planar -b 1 -x 1 -D M  | sed -e 's/^M/1/g' -e 's/^B/0/g' -e 's/P/2/g'| sed '$d' > mov.txt
-#../../src/bin/mmc -n 1 -f planar.inp -s planar -b 1 -x 1 -D MA | sed -e 's/^[A-Z] //g' | sed '$d' > ad.txt
+#../../bin/mmc -n 1 -f planar.inp -s planar -b 1 -x 1 -D M  | sed -e 's/^M/1/g' -e 's/^B/0/g' -e 's/P/2/g'| sed '$d' > mov.txt
+#../../bin/mmc -n 1 -f planar.inp -s planar -b 1 -x 1 -D MA | sed -e 's/^[A-Z] //g' | sed '$d' > ad.txt
 
-../../src/bin/mmc -n 10000000 -f planar.inp -s planar -b 1 -x 1 -D TP
+../../bin/mmc -n 10000000 -f planar.inp -s planar -b 1 -x 1 -D TP
diff --git a/examples/sphshells/run_dmmc.sh b/examples/sphshells/run_dmmc.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-../../src/bin/mmc -f dmmc_sphshells.json -n 1e8 -F bin $@
+../../bin/mmc -f dmmc_sphshells.json -n 1e8 -F bin $@
 
diff --git a/examples/sphshells/run_mmc.sh b/examples/sphshells/run_mmc.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-../../src/bin/mmc -f sphshells.json -n 1e8 -F bin $@
+../../bin/mmc -f sphshells.json -n 1e8 -F bin $@
 
diff --git a/examples/statnoise/run_test.sh b/examples/statnoise/run_test.sh
@@ -3,5 +3,5 @@
 for i in {1..10}
 do
     echo "run #$i"
-    ../../src/bin/mmc -f vartest.json -s v_$i -n 10000000 -b 0 -l -D TP -E 9876543$i
+    ../../bin/mmc -f vartest.json -s v_$i -n 10000000 -b 0 -l -D TP -E 9876543$i
 done
diff --git a/examples/validation/benchspeed.sh b/examples/validation/benchspeed.sh
@@ -1,3 +1,3 @@
 #!/bin/sh
 
-time ../../src/bin/mmc -f cube.inp -s cube -n 100000 -b 0 -D PT
+time ../../bin/mmc -f cube.inp -s cube -n 100000 -b 0 -D PT
diff --git a/examples/validation/run_tess.sh b/examples/validation/run_tess.sh
@@ -1,3 +1,3 @@
 #!/bin/sh
 
-time ../../src/bin/mmc -f cube2.inp -s cube2 -n 1e8 -b 0 -D TP -M G -F bin $@
+time ../../bin/mmc -f cube2.inp -s cube2 -n 1e8 -b 0 -D TP -M G -F bin $@
diff --git a/examples/validation/run_test.sh b/examples/validation/run_test.sh
@@ -1,3 +1,3 @@
 #!/bin/sh
 
-time ../../src/bin/mmc -f cube.inp -s cube -n 1e8 -b 0 -F bin -D TP $@
+time ../../bin/mmc -f cube.inp -s cube -n 1e8 -b 0 -F bin -D TP $@
diff --git a/examples/widedet/run_test.sh b/examples/widedet/run_test.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
 # run with -x 2 to record detected photons in the form of time-resolved images
-../../src/bin/mmc -f widedet.inp -s widedet -n 1000000 -x 2 -b 1 -D TP
+../../bin/mmc -f widedet.inp -s widedet -n 1000000 -x 2 -b 1 -D TP
diff --git a/src/buildmmc.m b/src/buildmmc.m
@@ -62,6 +62,15 @@ function buildmmc(varargin)
 opt=struct(varargin{:});
 pname='mmc';
 
+clsource = fileread('mmc_core.cl');
+clsrc = sprintf('0x%02x, ', char(clsource));
+clhex = ['unsigned char mmc_core_cl[] = {' sprintf('\n') clsrc(1:end-2) sprintf('\n')  ...
+    sprintf('};\nunsigned int mmc_core_cl_len = %d;\n', length(clsource))];
+
+fp=fopen('mmc_core.clh','wb');
+fwrite(fp, clhex, 'char');
+fclose(fp);
+
 cflags='-c -Wall -g -DMCX_EMBED_CL -fno-strict-aliasing -m64 -DMMC_USE_SSE -DHAVE_SSE2 -msse -msse2 -msse3 -mssse3 -msse4.1 -O3 -fopenmp  -DUSE_OS_TIMER -DUSE_OPENCL';
 
 filelist={'mmc_rand_xorshift128p.c','mmc_mesh.c','mmc_raytrace.c',...

diff --git a/src/mmc_const.h b/src/mmc_const.h
@@ -32,6 +32,11 @@
 #ifndef _MCEXTREME_CONSTANT_H
 #define _MCEXTREME_CONSTANT_H
 
+#define MMC_VERSION        "v2023"
+#define MMC_VERSION_MAJOR  2
+#define MMC_VERSION_MINOR  0
+#define MMC_VERSION_PATCH  0
+
 #define DET_MASK           0xFFFF0000
 #define MED_MASK           0x0000FFFF
 

diff --git a/src/mmc_utils.c b/src/mmc_utils.c
@@ -2921,7 +2921,7 @@ void mcx_savedetphoton(float* ppath, void* seeds, int count, int doappend, mccon
  */
 
 void mcx_version(mcconfig* cfg) {
-    MMC_ERROR(MMC_INFO, "MMC $Rev::      $v2023.01");
+    MMC_ERROR(MMC_INFO, "MMC $Rev::      $" MMC_VERSION);
 }
 
 /**
@@ -2931,18 +2931,22 @@ void mcx_version(mcconfig* cfg) {
  */
 
 void mcx_printheader(mcconfig* cfg) {
-    MMC_FPRINTF(cfg->flog, S_YELLOW"\
+    MMC_FPRINTF(cfg->flog, S_YELLOW "\
 ###############################################################################\n\
 #                     Mesh-based Monte Carlo (MMC) - OpenCL                   #\n\
-#          Copyright (c) 2010-2022 Qianqian Fang <q.fang at neu.edu>          #\n\
-#                            http://mcx.space/#mmc                            #\n\
+#          Copyright (c) 2010-2023 Qianqian Fang <q.fang at neu.edu>          #\n\
+#" S_BLUE "              https://mcx.space/#mmc  &  https://neurojson.org/              " S_YELLOW "#\n\
 #                                                                             #\n\
 #Computational Optics & Translational Imaging (COTI) Lab  [http://fanglab.org]#\n\
 #   Department of Bioengineering, Northeastern University, Boston, MA, USA    #\n\
-#                                                                             #\n\
-#                Research funded by NIH/NIGMS grant R01-GM114365              #\n\
 ###############################################################################\n\
-$Rev::      $v2023.01$Date::                       $ by $Author::             $\n\
+#    The MCX Project is funded by the NIH/NIGMS under grant R01-GM114365      #\n\
+###############################################################################\n\
+#  Open-source codes and reusable scientific data are essential for research, #\n\
+# MCX proudly developed human-readable JSON-based data formats for easy reuse,#\n\
+#  Please consider using JSON (" S_BLUE "https://neurojson.org/" S_YELLOW ") for your research data #\n\
+###############################################################################\n\
+$Rev::      $ " S_GREEN MMC_VERSION S_YELLOW "  $Date::                       $ by $Author::             $\n\
 ###############################################################################\n"S_RESET);
 }
 

diff --git a/src/mmclab.cpp b/src/mmclab.cpp
@@ -45,6 +45,7 @@
 #endif
 
 #include "mex.h"
+#include "mmc_const.h"
 #include "mmc_mesh.h"
 #include "mmc_host.h"
 #ifdef USE_OPENCL
@@ -1162,7 +1163,7 @@ extern "C" int mmc_throw_exception(const int id, const char* msg, const char* fi
  */
 
 void mmclab_usage() {
-    printf("MMCLAB v2023.01\nUsage:\n    [flux,detphoton]=mmclab(cfg);\n\nPlease run 'help mmclab' for more details.\n");
+    printf("MMCLAB " MMC_VERSION "\nUsage:\n    [flux,detphoton]=mmclab(cfg);\n\nPlease run 'help mmclab' for more details.\n");
 }
 
 /**