remove all warnings raised by gcc 8 and 9.3

commons/Makefile_common.mk

@@ -55,7 +55,7 @@ DLLFLAG=-fPIC
 PLATFORM = $(shell uname -s)
 ifeq ($(findstring MINGW64,$(PLATFORM)), MINGW64)
     MW_MINGW64_LOC=/c/msys64/usr/
-    MKMEX      :=cmd //c mex.bat -v
+    MKMEX      :=cmd //c mex.bat 
     INCLUDEDIRS+=-I"./mingw64/include"
     LIBOPENCL   ="c:\Windows\System32\OpenCL.dll"
     MKMEXOPT    =-f mexopts_msys2_gcc.xml COMPFLAGS='$$COMPFLAGS $(CCFLAGS) $(USERCCFLAGS)' LDFLAGS='$$LDFLAGS -static $(OPENMPLIB) $(LIBOPENCL) $(MEXLINKOPT)' $(FASTMATH) -outdir ../mmclab

src/mcx_utils.c

@@ -7,7 +7,7 @@
 **  \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 Plücker Coordinates,"</a> Biomed. Opt. Express, 1(1) 165-175 (2010).
+**          in Pl¨¹cker 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> 
@@ -438,7 +438,7 @@ void mcx_savenii(OutputType *dat, size_t len, char* name, int type32bit, int out
 void mcx_savedata(OutputType *dat, size_t len, mcconfig *cfg,int isref){
      FILE *fp;
      char name[MAX_FULL_PATH];
-     char fname[MAX_FULL_PATH];
+     char fname[MAX_FULL_PATH+20];
      unsigned int glformat=GL_RGBA32F;
 
      if(cfg->rootpath[0])
@@ -573,7 +573,7 @@ void mcx_readconfig(char *fname, mcconfig *cfg){
         }
         fclose(fp);
         if(cfg->session[0]=='\0'){
-		strncpy(cfg->session,fname,MAX_SESSION_LENGTH);
+		strncpy(cfg->session,fname,MAX_SESSION_LENGTH-1);
 	}
      }
 }
@@ -630,7 +630,7 @@ int mcx_loadjson(cJSON *root, mcconfig *cfg){
      Forward = cJSON_GetObjectItem(root,"Forward");
 
      if(Mesh){
-        strncpy(cfg->meshtag, FIND_JSON_KEY("MeshID","Mesh.MeshID",Mesh,(MMC_ERROR(-1,"You must specify mesh files"),""),valuestring), MAX_PATH_LENGTH);
+        strncpy(cfg->meshtag, FIND_JSON_KEY("MeshID","Mesh.MeshID",Mesh,(MMC_ERROR(-1,"You must specify mesh files"),""),valuestring), MAX_SESSION_LENGTH-1);
         cfg->e0=FIND_JSON_KEY("InitElem","Mesh.InitElem",Mesh,(MMC_ERROR(-1,"InitElem must be given"),0.0),valueint);
         if(!flagset['u'])
 	    cfg->unitinmm=FIND_JSON_KEY("LengthUnit","Mesh.LengthUnit",Mesh,1.0,valuedouble);
@@ -711,7 +711,7 @@ int mcx_loadjson(cJSON *root, mcconfig *cfg){
         }
      }
      if(Session){
-        char val[1];
+        char val[2]={'\0','\0'};
         cJSON *ck;
         if(!flagset['E'])   cfg->seed=FIND_JSON_KEY("RNGSeed","Session.RNGSeed",Session,-1,valueint);
         if(!flagset['n'])   cfg->nphoton=FIND_JSON_KEY("Photons","Session.Photons",Session,0,valueint);
@@ -858,7 +858,7 @@ void mcx_loadconfig(FILE *in, mcconfig *cfg){
 #else
          sprintf(comment,"%s/%s",cfg->rootpath,cfg->meshtag);
 #endif
-         strncpy(cfg->meshtag,comment,MAX_PATH_LENGTH);
+         memcpy(cfg->meshtag,comment,MAX_SESSION_LENGTH);
      }
      comm=fgets(comment,MAX_PATH_LENGTH,in);
 
@@ -1440,7 +1440,7 @@ void mcx_parsecmd(int argc, char* argv[], mcconfig *cfg){
 		     	        i=mcx_readarg(argc,argv,i,&(cfg->optlevel),"int");
 		     	        break;
                      case 'D':
-				if(i+1<argc && isalpha(argv[i+1][0]) )
+				if(i+1<argc && isalpha((int)argv[i+1][0]) )
 					cfg->debuglevel=mcx_parsedebugopt(argv[++i]);
 				else
 	                                i=mcx_readarg(argc,argv,i,&(cfg->debuglevel),"int");

src/mcx_utils.h

@@ -43,7 +43,7 @@
 
 #define MAX_FULL_PATH       2048                         /**< max characters in a full file name string */
 #define MAX_PATH_LENGTH     1024                         /**< max characters in a full file name string */
-#define MAX_SESSION_LENGTH  256                          /**< max session name length */
+#define MAX_SESSION_LENGTH  64                           /**< max session name length */
 #define MAX_CHECKPOINT      16                           /**< max number of photon save points */
 #define DET_PHOTON_BUF      100000                       /**< initialize number of detected photons */
 #define SEED_FROM_FILE      -999                         /**< special flag indicating to load seeds from history file */
@@ -206,7 +206,7 @@ typedef struct MMC_config{
 				           0 for wide-field detection pattern*/
 	unsigned char *vol;            /**<pointer to the volume*/
 	char session[MAX_SESSION_LENGTH];/**<session id, a string*/
-        char meshtag[MAX_PATH_LENGTH];   /**<a string to tag all input mesh files*/
+        char meshtag[MAX_SESSION_LENGTH];/**<a string to tag all input mesh files*/
 	char isrowmajor;               /**<1 for C-styled array in vol, 0 for matlab-styled array*/
 	char isreflect;                /**<1 for reflecting photons at boundary,0 for exiting*/
         char isref3;                   /**<1 considering maximum 3 ref. interfaces; 0 max 2 ref*/

src/mmc_host.c

@@ -229,8 +229,6 @@ int mmc_run_mp(mcconfig *cfg, tetmesh *mesh, raytracer *tracer){
 
 		if((cfg->debuglevel & dlProgress) && threadid==0)
 			mcx_progressbar(ncomplete,cfg);
-		if(cfg->issave2pt && cfg->checkpt[0])
-			mesh_saveweightat(mesh,cfg,id+1);
 	}
 
 	for(j=0;j<cfg->srcnum;j++){

src/mmclab.cpp

@@ -7,7 +7,7 @@
 **  \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 Plücker Coordinates,"</a> Biomed. Opt. Express, 1(1) 165-175 (2010).
+**          in Pl¨¹cker 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> 
@@ -447,7 +447,7 @@ void mmc_set_field(const mxArray *root,const mxArray *item,int idx, mcconfig *cf
 	mesh->elemlen=arraydim[1];
 	if(mesh->facenb) free(mesh->facenb);
         mesh->facenb=(int *)malloc(sizeof(int)*arraydim[1]*mesh->ne);
-        for(j=0;j<arraydim[1];j++)
+        for(dimtype j=0;j<arraydim[1];j++)
           for(i=0;i<mesh->ne;i++)
              mesh->facenb[i*arraydim[1]+j]=val[j*mesh->ne+i];
         printf("mmc.facenb=[%d,%d];\n",mesh->ne,mesh->elemlen);
@@ -643,7 +643,7 @@ void mmc_set_field(const mxArray *root,const mxArray *item,int idx, mcconfig *cf
 	arraydim=mxGetDimensions(item);
 	if(arraydim[0]*arraydim[1]>MAX_DEVICE)
 	     mexErrMsgTxt("the workload list can not be longer than 256");
-	for(i=0;i<arraydim[0]*arraydim[1];i++)
+	for(dimtype i=0;i<arraydim[0]*arraydim[1];i++)
 	     cfg->workload[i]=val[i];
         printf("mmc.workload=<<%d>>;\n",arraydim[0]*arraydim[1]);
     }else if(strcmp(name,"isreoriented")==0){

src/simpmesh.c

@@ -154,8 +154,8 @@ void mesh_error(const char *msg,const char *file,const int linenum){
  * @param[in] cfg: the simulation configuration structure
  */
 
-void mesh_filenames(const char *format,char *foutput,mcconfig *cfg){
-	char filename[MAX_FULL_PATH];
+void mesh_filenames(const char format[64],char *foutput,mcconfig *cfg){
+	char filename[MAX_PATH_LENGTH];
 	sprintf(filename,format,cfg->meshtag);
 
 	if(cfg->rootpath[0]) 
@@ -871,36 +871,6 @@ float mc_next_scatter(float g, float3 *dir,RandType *ran, RandType *ran0, mcconf
     return nextslen;
 }
 
-/**
- * @brief Save a snapshot of the simulation output
- *
- * save snapshot of the simulation output during a lengthy simulation
- * the snapshots are specified by a set of "check-points", i.e. the index 
- * of the photons that being completed.
- *
- * @param[in] mesh: the mesh object
- * @param[in] cfg: the simulation configuration
- * @param[in] id: the index of the current photon
- */
-
-void mesh_saveweightat(tetmesh *mesh,mcconfig *cfg,int id){
-	char sess[MAX_SESSION_LENGTH];
-	int i,found=0;
-	for(i=0;i<MAX_CHECKPOINT;i++){
-           if(cfg->checkpt[i]==0)  return;
-	   if(id==cfg->checkpt[i]) {
-		found=1;
-		break;
-	   }
-	}
-        if(!found) return;
-	memcpy(sess,cfg->session,MAX_SESSION_LENGTH);
-	sprintf(cfg->session,"%s_%d",sess,id);
-	mesh_saveweight(mesh,cfg,0);
-	memcpy(cfg->session,sess,MAX_SESSION_LENGTH);
-}
-
-
 /**
  * @brief Save the fluence output to a file
  *

src/simpmesh.h

@@ -7,7 +7,7 @@
 **  \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 Plücker Coordinates,"</a> Biomed. Opt. Express, 1(1) 165-175 (2010).
+**          in Pl¨¹cker 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> 
@@ -140,7 +140,6 @@ float mesh_normalize(tetmesh *mesh, mcconfig *cfg, float Eabsorb, float Etotal,
 void mesh_build(tetmesh *mesh);
 void mesh_error(const char *msg, const char *file,const int linenum);
 void mesh_filenames(const char *format,char *foutput,mcconfig *cfg);
-void mesh_saveweightat(tetmesh *mesh,mcconfig *cfg,int id);
 void mesh_saveweight(tetmesh *mesh,mcconfig *cfg,int isref);
 void mesh_savedetphoton(float *ppath, void *seeds, int count, int seedbyte, mcconfig *cfg);
 void mesh_getdetimage(float *detmap, float *ppath, int count, mcconfig *cfg, tetmesh *mesh);

src/sse_math/sse_math.h

@@ -72,7 +72,7 @@ _PS_CONST_TYPE(min_norm_pos, int, 0x00800000);
 _PS_CONST_TYPE(mant_mask, int, 0x7f800000);
 _PS_CONST_TYPE(inv_mant_mask, int, ~0x7f800000);
 
-_PS_CONST_TYPE(sign_mask, int, 0x80000000);
+_PS_CONST_TYPE(sign_mask, unsigned int, 0x80000000);
 _PS_CONST_TYPE(inv_sign_mask, int, ~0x80000000);
 
 _PI32_CONST(1, 1);