[feat] test zipped mesh in json, migrate from float3 to FLOAT3, add b…

…enchmark
fangq · Mar 9, 2024 · efc4101 · efc4101
1 parent cc3f362
commit efc4101
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Showing 15 changed files with 498 additions and 342 deletions.
diff --git a/commons/Makefile_common.mk b/commons/Makefile_common.mk
@@ -306,7 +306,7 @@ pretty:
 	    --suffix=none \
 	    --formatted \
 	    --break-blocks \
-	    --exclude=mmc_bench.h \
+	    --exclude=mmc_bench.c \
 	   "*.c" "*.h" "*.cpp" "*.cu" "*.cl"
 
 .PHONY: regression clean arch makedirs dep $(SUBDIRS)

diff --git a/examples/validation/cube2.json b/examples/validation/cube2.json
@@ -1,5 +1,16 @@
 {
-    "Domain": {
+    "Session": {
+	"Photons":  30000000,
+	"RNGSeed":  27182818,
+	"ID":       "cube2"
+    },
+    "Domain" : {
+         "Media": [
+             {"mua": 0.00, "mus": 0.0, "g": 1.00, "n": 1.0},
+             {"mua": 0.005,"mus": 1.0, "g": 0.01, "n": 1.37}
+         ]
+    },
+    "Mesh": {
         "MeshNode": [
             [ 0, 0, 0],
             [60, 0, 0],
@@ -9,25 +20,16 @@
             [60, 0,60],
             [ 0,60,60],
             [60,60,60]
-         ],
+        ],
         "MeshElem": [
 	    [1, 2, 8, 4, 1],
 	    [1, 3, 4, 8, 1],
 	    [1, 2, 6, 8, 1],
 	    [1, 5, 8, 6, 1],
 	    [1, 3, 8, 7, 1],
 	    [1, 5, 7, 8, 1]
-         ],
-	 "InitElem": 2,
-         "Media": [
-             {"mua": 0.00, "mus": 0.0, "g": 1.00, "n": 1.0},
-             {"mua": 0.005,"mus": 1.0, "g": 0.01, "n": 1.37}
-         ]
-    },
-    "Session": {
-	"Photons":  30000000,
-	"RNGSeed":  27182818,
-	"ID":       "cube"
+        ],
+	"InitElem": 2
     },
     "Forward": {
 	"T0": 0.0e+00,

diff --git a/src/Makefile b/src/Makefile
@@ -1,7 +1,7 @@
 ROOTDIR = ..
 BINARY=mmc
 
-FILES=mmc_rand_xorshift128p mmc_mesh mmc_raytrace mmc_utils mmc_tictoc mmc_host mmc_highorder mmc_cl_utils mmc_cl_host
+FILES=mmc_rand_xorshift128p mmc_mesh mmc_raytrace mmc_utils mmc_tictoc mmc_host mmc_highorder mmc_bench mmc_cl_utils mmc_cl_host
 CLPROGRAM=mmc_core
 
 ifeq ($(findstring Darwin,$(PLATFORM)), Darwin)

diff --git a/src/mmc_bench.c b/src/mmc_bench.c
@@ -0,0 +1,177 @@
+/***************************************************************************//**
+**  \mainpage Mesh-based Monte Carlo (MMC) - a 3D photon simulator
+**
+**  \author Qianqian Fang <q.fang at neu.edu>
+**  \copyright Qianqian Fang, 2010-2024
+**
+**  \section sref Reference:
+**  \li \c (\b Fang2010) Qianqian Fang, <a href="http://www.opticsinfobase.org/abstract.cfm?uri=boe-1-1-165">
+**          "Mesh-based Monte Carlo Method Using Fast Ray-Tracing
+**          in Plucker Coordinates,"</a> Biomed. Opt. Express, 1(1) 165-175 (2010).
+**  \li \c (\b Fang2012) Qianqian Fang and David R. Kaeli,
+**           <a href="https://www.osapublishing.org/boe/abstract.cfm?uri=boe-3-12-3223">
+**          "Accelerating mesh-based Monte Carlo method on modern CPU architectures,"</a>
+**          Biomed. Opt. Express 3(12), 3223-3230 (2012)
+**  \li \c (\b Yao2016) Ruoyang Yao, Xavier Intes, and Qianqian Fang,
+**          <a href="https://www.osapublishing.org/boe/abstract.cfm?uri=boe-7-1-171">
+**          "Generalized mesh-based Monte Carlo for wide-field illumination and detection
+**           via mesh retessellation,"</a> Biomed. Optics Express, 7(1), 171-184 (2016)
+**  \li \c (\b Fang2019) Qianqian Fang and Shijie Yan,
+**          <a href="http://dx.doi.org/10.1117/1.JBO.24.11.115002">
+**          "Graphics processing unit-accelerated mesh-based Monte Carlo photon transport
+**           simulations,"</a> J. of Biomedical Optics, 24(11), 115002 (2019)
+**  \li \c (\b Yuan2021) Yaoshen Yuan, Shijie Yan, and Qianqian Fang,
+**          <a href="https://www.osapublishing.org/boe/fulltext.cfm?uri=boe-12-1-147">
+**          "Light transport modeling in highly complex tissues using the implicit
+**           mesh-based Monte Carlo algorithm,"</a> Biomed. Optics Express, 12(1) 147-161 (2021)
+**
+**  \section slicense License
+**          GPL v3, see LICENSE.txt for details
+*******************************************************************************/
+
+/***************************************************************************//**
+\file    mmc_bench.c
+
+@brief   MMC builtin benchmarks
+*******************************************************************************/
+
+#include "mmc_bench.h"
+
+#define MSTR(...) #__VA_ARGS__
+
+const char* benchname[MAX_MCX_BENCH] = {"dmmc-cube60", "dmmc-cube60b", ""};
+
+const char* benchjson[MAX_MCX_BENCH] = {
+MSTR(
+{
+    "Session": {
+        "ID": "dmmc-cube60",
+        "Photons": 1e6,
+        "RNGSeed": 1648335518,
+        "DoMismatch": 0
+    },
+    "Domain" : {
+         "Media": [
+             {"mua": 0.00, "mus": 0.0, "g": 1.00, "n": 1.0},
+             {"mua": 0.005,"mus": 1.0, "g": 0.01, "n": 1.37}
+         ]
+    },
+    "Mesh": {
+        "MeshNode": [
+            [ 0, 0, 0],
+            [60, 0, 0],
+            [ 0,60, 0],
+            [60,60, 0],
+            [ 0, 0,60],
+            [60, 0,60],
+            [ 0,60,60],
+            [60,60,60]
+        ],
+        "MeshElem": [
+            [1, 2, 8, 4, 1],
+            [1, 3, 4, 8, 1],
+            [1, 2, 6, 8, 1],
+            [1, 5, 8, 6, 1],
+            [1, 3, 8, 7, 1],
+            [1, 5, 7, 8, 1]
+        ],
+        "InitElem": 2
+    },
+    "Forward": {
+        "T0": 0.0e+00,
+        "T1": 5.0e-09,
+        "Dt": 5.0e-09
+    },
+    "Optode": {
+        "Source": {
+            "Pos": [30.1, 30.2, 0.0],
+            "Dir": [0.0, 0.0, 1.0]
+        },
+        "Detector": [
+            {
+                "Pos": [30.0, 20.0, 0.0],
+                "R": 1.0
+            },
+            {
+                "Pos": [30.0, 40.0, 0.0],
+                "R": 1.0
+            },
+            {
+                "Pos": [20.0, 30.0, 0.0],
+                "R": 1.0
+            },
+            {
+                "Pos": [40.0, 30.0, 0.0],
+                "R": 1.0
+            }
+        ]
+    }
+}),
+
+MSTR(
+{
+    "Session": {
+        "ID": "dmmc-cube60b",
+        "Photons": 1e6,
+        "RNGSeed": 1648335518,
+        "DoMismatch": 1
+    },
+    "Domain" : {
+         "Media": [
+             {"mua": 0.00, "mus": 0.0, "g": 1.00, "n": 1.0},
+             {"mua": 0.005,"mus": 1.0, "g": 0.01, "n": 1.37}
+         ]
+    },
+    "Mesh": {
+        "MeshNode": [
+            [ 0, 0, 0],
+            [60, 0, 0],
+            [ 0,60, 0],
+            [60,60, 0],
+            [ 0, 0,60],
+            [60, 0,60],
+            [ 0,60,60],
+            [60,60,60]
+        ],
+        "MeshElem": [
+            [1, 2, 8, 4, 1],
+            [1, 3, 4, 8, 1],
+            [1, 2, 6, 8, 1],
+            [1, 5, 8, 6, 1],
+            [1, 3, 8, 7, 1],
+            [1, 5, 7, 8, 1]
+        ],
+        "InitElem": 2
+    },
+    "Forward": {
+        "T0": 0.0e+00,
+        "T1": 5.0e-09,
+        "Dt": 5.0e-09
+    },
+    "Optode": {
+        "Source": {
+            "Pos": [30.1, 30.2, 0.0],
+            "Dir": [0.0, 0.0, 1.0]
+        },
+        "Detector": [
+            {
+                "Pos": [30.0, 20.0, 0.0],
+                "R": 1.0
+            },
+            {
+                "Pos": [30.0, 40.0, 0.0],
+                "R": 1.0
+            },
+            {
+                "Pos": [20.0, 30.0, 0.0],
+                "R": 1.0
+            },
+            {
+                "Pos": [40.0, 30.0, 0.0],
+                "R": 1.0
+            }
+        ]
+    }
+})
+
+};
diff --git a/src/mmc_bench.h b/src/mmc_bench.h
@@ -30,127 +30,16 @@
 *******************************************************************************/
 
 /***************************************************************************//**
-\file    mcx_bench.h
+\file    mmc_bench.h
 
-@brief   MCX builtin benchmarks
+@brief   MMC builtin benchmarks
 *******************************************************************************/
 
 #ifndef _MCEXTREME_BENCHMARK_H
 #define _MCEXTREME_BENCHMARK_H
 
-#define MSTR(...) #__VA_ARGS__
-
-const char *benchname[]={"d-cube60","d-cube60b",""};
-const char *benchjson[]={
-MSTR(
-{
-    "Session": {
-	"ID":       "d-cube60",
-	"Photons":  1e6,
-	"RNGSeed":  1648335518,
-	"DoMismatch": 0
-    },
-    "Domain": {
-        "Dim":    [60,60,60],
-        "OriginType": 1,
-        "Media": [
-             {"mua": 0, "mus": 0, "g": 1, "n": 1},
-             {"mua": 0.005,"mus": 1.0, "g": 0.01, "n": 1.37},
-             {"mua": 0.002,"mus": 5, "g": 0.90, "n": 1}
-        ]
-    },
-    "Shapes": [
-        {"Name":     "cubic60"},
-        {"Origin":   [0,0,0]},
-        {"Grid":     {"Tag":1, "Size":[60,60,60]}}
-    ],
-    "Forward": {
-	"T0": 0.0e+00,
-	"T1": 5.0e-09,
-	"Dt": 5.0e-09
-    },
-    "Optode": {
-	"Source": {
-	    "Type":"pencil",
-	    "Pos": [29.0, 29.0, 0.0],
-	    "Dir": [0.0, 0.0, 1.0]
-	},
-	"Detector": [
-	    {
-		"Pos": [29.0,  19.0,  0.0],
-		"R": 1.0
-	    },
-            {
-                "Pos": [29.0,  39.0,  0.0],
-                "R": 1.0
-            },
-            {
-                "Pos": [19.0,  29.0,  0.0],
-                "R": 1.0
-            },
-            {
-                "Pos": [39.0,  29.0,  0.0],
-                "R": 1.0
-            }
-	]
-    }
-}),
-
-
-MSTR(
-{
-    "Session": {
-	"ID":       "d-cube60b",
-	"Photons":  1e6,
-	"RNGSeed":  1648335518,
-	"DoMismatch": true
-    },
-    "Domain": {
-        "Dim":    [60,60,60],
-        "OriginType": 1,
-        "Media": [
-             {"mua": 0.00, "mus": 0.0, "g": 1.00, "n": 1.0},
-             {"mua": 0.005,"mus": 1.0, "g": 0.01, "n": 1.37},
-             {"mua": 0.002,"mus": 5.0, "g": 0.90, "n": 1.0}
-        ]
-    },
-    "Shapes": [
-        {"Name":     "cube60b"},
-        {"Origin":   [0,0,0]},
-        {"Grid":     {"Tag":1, "Size":[60,60,60]}}
-    ],
-    "Forward": {
-	"T0": 0.0e+00,
-	"T1": 5.0e-09,
-	"Dt": 5.0e-09
-    },
-    "Optode": {
-	"Source": {
-	    "Type":"pencil",
-	    "Pos": [29.0, 29.0, 0.0],
-	    "Dir": [0.0, 0.0, 1.0]
-	},
-	"Detector": [
-	    {
-		"Pos": [29.0,  19.0,  0.0],
-		"R": 1.0
-	    },
-            {
-                "Pos": [29.0,  39.0,  0.0],
-                "R": 1.0
-            },
-            {
-                "Pos": [19.0,  29.0,  0.0],
-                "R": 1.0
-            },
-            {
-                "Pos": [39.0,  29.0,  0.0],
-                "R": 1.0
-            }
-	]
-    }
-})
-
-};
+#define MAX_MCX_BENCH  3                           /**< Total number of built-in benchmarks */
+extern const char* benchname[MAX_MCX_BENCH];       /**< String list defining the names of each built-in benchmark */
+extern const char* benchjson[MAX_MCX_BENCH];       /**< JSON-formatted input configuration for each built-in benchmark */
 
 #endif
diff --git a/src/mmc_cl_host.c b/src/mmc_cl_host.c
@@ -281,7 +281,7 @@ void mmc_run_cl(mcconfig* cfg, tetmesh* mesh, raytracer* tracer) {
     memcpy(propdet + param.maxpropdet, tracer->n, (param.normbuf << 2)*sizeof(float4));
 
     for (i = 0; i < workdev; i++) {
-        OCL_ASSERT(((gnode[i] = clCreateBuffer(mcxcontext, RO_MEM, sizeof(float3) * (mesh->nn), mesh->node, &status), status)));
+        OCL_ASSERT(((gnode[i] = clCreateBuffer(mcxcontext, RO_MEM, sizeof(FLOAT3) * (mesh->nn), mesh->node, &status), status)));
         OCL_ASSERT(((gelem[i] = clCreateBuffer(mcxcontext, RO_MEM, sizeof(int4) * (mesh->ne), mesh->elem, &status), status)));
         OCL_ASSERT(((gtype[i] = clCreateBuffer(mcxcontext, RO_MEM, sizeof(int) * (mesh->ne), mesh->type, &status), status)));
         OCL_ASSERT(((gfacenb[i] = clCreateBuffer(mcxcontext, RO_MEM, sizeof(int4) * (mesh->ne), mesh->facenb, &status), status)));

diff --git a/src/mmc_highorder.cpp b/src/mmc_highorder.cpp
@@ -92,7 +92,7 @@ void mesh_10nodetet(tetmesh* mesh, mcconfig* cfg) {
     pos = 0;
 
     mesh->nn += edgelist.size();
-    mesh->node = (float3*)realloc((void*)mesh->node, sizeof(float3) * (mesh->nn));
+    mesh->node = (FLOAT3*)realloc((void*)mesh->node, sizeof(FLOAT3) * (mesh->nn));
     mesh->weight = (double*)realloc((void*)mesh->weight, sizeof(double) * mesh->nn * cfg->maxgate);
     memset(mesh->weight, 0, sizeof(double)*mesh->nn * cfg->maxgate); // if mesh->weight is filled, need to allocate a new buffer, and copy the old buffer gate by gate