fix warnings for gcc 8 and 9.3, compiles windows mex file

src/Makefile

@@ -15,7 +15,7 @@ INCLUDEDIRS=
 
 CUCCOPT:=
 CCOPT=-g -pedantic -Wall -O3 -DMCX_EMBED_CL -DMCX_OPENCL -DUSE_OS_TIMER 
-CPPOPT:=$(CCOPT) -Wno-variadic-macros
+CPPOPT:=$(CCOPT)
 CCOPT+=-std=c99
 
 DLLFLAG=-fPIC
@@ -72,19 +72,21 @@ CLPROGRAM=mcx_core
 ifeq ($(findstring CYGWIN,$(PLATFORM)), CYGWIN)
  CCC=nvcc
  LINKOPT=-L$(LIBOPENCLDIR) -lOpenCL
- INCLUDEDIRS +=-I/c/CUDA/include
+ INCLUDEDIRS +=-I"./mingw64/include"
  CPPOPT =-c -D_CRT_SECURE_NO_DEPRECATE -DWIN32
  OBJSUFFIX=.obj
  EXESUFFIX=.exe
- MEX=cmd /c mex
+ LIBOPENCL ="c:\Windows\System32\OpenCL.dll"
+ MEXCCOPT+=-DMX_COMPAT_32
+ EXTRALIB +=-static
+ MEX :=cmd /c mex.bat -v -f mexopts_msys2_gcc.xml
  DLLFLAG=
 else ifeq ($(findstring MINGW64,$(PLATFORM)), MINGW64)
- MW_MINGW64_LOC=/c/msys64/usr/
- MEX :=cmd //c mex.bat -v
+ MW_MINGW64_LOC=/c/ProgramData/MATLAB/SupportPackages/R2017b/3P.instrset/mingw_w64.instrset/
+ MEX :=cmd //c mex.bat -f mexopts_msys2_gcc.xml
  INCLUDEDIRS+=-I"./mingw64/include"
  LIBOPENCL ="c:\Windows\System32\OpenCL.dll"
- LINKOPT=-g -L$(LIBOPENCLDIR) $(LIBOPENCL) -static
- MKMEXOPT =-f mexopts_msys2_gcc.xml COMPFLAGS='$$COMPFLAGS $(CCFLAGS) $(USERCCFLAGS)' LDFLAGS='$$LDFLAGS -static $(OPENMPLIB) $(LIBOPENCL) $(MEXLINKOPT)' $(FASTMATH) -outdir ../mmclab
+ MEXCCOPT+=-DMX_COMPAT_32
  EXTRALIB +=-static
  DLLFLAG =
 else ifeq ($(findstring Darwin,$(PLATFORM)), Darwin)
@@ -96,10 +98,15 @@ else
  LINKOPT=-g -L$(LIBOPENCLDIR) $(LIBOPENCL)
 endif
 
+ifeq ($(findstring x86_64,$(ARCH)), x86_64)
+ CCOPT +=-m64
+ CPPOPT +=-m64
+endif
+
 all static: CUCCOPT+=
 
 mex: AR=$(MEX)
-mex: LINKOPT+= CXXFLAGS='$$CXXFLAGS -g -DMCX_CONTAINER $(MEXCCOPT) $(USERCCOPT)' LDFLAGS='-L$$TMW_ROOT$$MATLABROOT/sys/os/$$ARCH $$LDFLAGS -g -L$(LIBOPENCLDIR) $(LIBOPENCL) $(USERLINKOPT)'
+mex: LINKOPT+= CXXFLAGS='$$CXXFLAGS -g -DMCX_CONTAINER $(CPPOPT) $(MEXCCOPT) $(USERCCOPT)' LDFLAGS='$$LDFLAGS -g -L$(LIBOPENCLDIR) $(LIBOPENCL) $(USERLINKOPT)' COMPFLAGS='' DEFINES=''
 mex oct: OUTPUT_DIR=../mcxlabcl
 mex: OUTPUTFLAG:=-output
 mex: BINARY=mcxcl

src/buildmcxcl.m

@@ -1,4 +1,4 @@
-function buildmmc(varargin)
+function buildmcxcl(varargin)
 %
 % Format:
 % buildmex or buildmex('option1',value1,'option2',value2,...)
@@ -47,7 +47,7 @@ function buildmmc(varargin)
 opt=struct(varargin{:});
 pname='mcx';
 
-cflags=' -g -pedantic -Wall -O3 -DMCX_EMBED_CL -DMCX_OPENCL -DUSE_OS_TIMER  -std=c99  -DMCX_CONTAINER -c ';
+cflags=' -g -pedantic -Wall -O3 -DMCX_EMBED_CL -DMCX_OPENCL -DUSE_OS_TIMER -std=c99 -DMCX_CONTAINER -c ';
 
 filelist={'mcx_utils.c','tictoc.c','cjson/cJSON.c','mcx_host.cpp',...
  'mcxcl.c','mcx_shapes.c','mcxlabcl.cpp'};
@@ -71,11 +71,13 @@ function buildmmc(varargin)
 if(~exist('OCTAVE_VERSION','builtin'))
  for i=1:length(filelist)
  flag='CFLAGS';
+ cflag=cflags;
  if(regexp(filelist{i},'\.[Cc][Pp][Pp]$'))
  flag='CXXFLAGS';
+ cflag=regexprep(cflags,'-std=c99','-std=gnu++0x');
  end
- disp(sprintf('mex OBJEXT=.o %s=''%s'' -c ''%s'' ',flag,cflags,filelist{i}));
- eval(sprintf('mex OBJEXT=.o %s=''%s'' -c ''%s'' ',flag,cflags,filelist{i}));
+ disp(sprintf('mex OBJEXT=.o %s=''%s'' -c ''%s'' ',flag,cflag,filelist{i}));
+ eval(sprintf('mex OBJEXT=.o %s=''%s'' -c ''%s'' ',flag,cflag,filelist{i}));
  end
  if(isfield(opt,'lib'))
  linkflags=[linkflags ' ' opt.lib];

src/mcx_utils.c

@@ -308,7 +308,7 @@ void mcx_cleargpuinfo(GPUInfo **gpuinfo){
 
 void mcx_savenii(float *dat, size_t len, char* name, int type32bit, int outputformatid, Config *cfg){
  FILE *fp;
- char fname[MAX_PATH_LENGTH]={'\0'};
+ char fname[MAX_FULL_PATH+100]={'\0'};
  nifti_1_header hdr;
  nifti1_extender pad={{0,0,0,0}};
  float *logval=dat;
@@ -389,7 +389,7 @@ void mcx_savenii(float *dat, size_t len, char* name, int type32bit, int outputfo
 void mcx_savedata(float *dat, int len, Config *cfg){
  FILE *fp;
  char name[MAX_FULL_PATH];
- char fname[MAX_FULL_PATH];
+ char fname[MAX_FULL_PATH+100];
  unsigned int glformat=GL_RGBA32F;
 
  if(cfg->rootpath[0])
@@ -630,7 +630,7 @@ void mcx_readconfig(char *fname, Config *cfg){
  }
  if(fp!=NULL) fclose(fp);
  if(cfg->session[0]=='\0'){
- strncpy(cfg->session,fname,MAX_SESSION_LENGTH);
+ strncpy(cfg->session,fname,MAX_SESSION_LENGTH-1);
  }
  }
  if(cfg->rootpath[0]!='\0'){
@@ -716,7 +716,7 @@ void mcx_loadconfig(FILE *in, Config *cfg){
 #else
  sprintf(comment,"%s/%s",cfg->rootpath,filename);
 #endif
- strncpy(filename,comment,MAX_PATH_LENGTH);
+ memcpy(filename,comment,MAX_PATH_LENGTH);
  }
  comm=fgets(comment,MAX_PATH_LENGTH,in);
 
@@ -892,7 +892,11 @@ void mcx_prepdomain(char *filename, Config *cfg){
  if(cfg->shapedata && strstr(cfg->shapedata,":")!=NULL){
  int status;
  Grid3D grid={&(cfg->vol),&(cfg->dim),{1.f,1.f,1.f},cfg->isrowmajor};
- if(cfg->issrcfrom0) memset(&(grid.orig.x),0,sizeof(float3));
+ if(cfg->issrcfrom0){
+ grid.orig.x=0.f;
+ grid.orig.y=0.f;
+ grid.orig.z=0.f;
+ } 
  status=mcx_parse_shapestring(&grid,cfg->shapedata);
  if(status){
  MCX_ERROR(status,mcx_last_shapeerror());
@@ -982,7 +986,7 @@ int mcx_loadjson(cJSON *root, Config *cfg){
  cJSON *meds,*val;
  val=FIND_JSON_OBJ("VolumeFile","Domain.VolumeFile",Domain);
  if(val){
- strncpy(volfile, val->valuestring, MAX_PATH_LENGTH);
+ strncpy(volfile, val->valuestring, MAX_PATH_LENGTH-1);
  if(cfg->rootpath[0]){
 #ifdef WIN32
  sprintf(filename,"%s\\%s",cfg->rootpath,volfile);
@@ -1215,7 +1219,7 @@ int mcx_loadjson(cJSON *root, Config *cfg){
  }
  }
  if(Session){
- char val[1];
+ char val[2]={'\0'};
  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,valuedouble);
  if(cfg->session[0]=='\0') strncpy(cfg->session, FIND_JSON_KEY("ID","Session.ID",Session,"default",valuestring), MAX_SESSION_LENGTH);
@@ -1262,7 +1266,11 @@ int mcx_loadjson(cJSON *root, Config *cfg){
  if(Shapes){
  int status;
  Grid3D grid={&(cfg->vol),&(cfg->dim),{1.f,1.f,1.f},cfg->isrowmajor};
- if(cfg->issrcfrom0) memset(&(grid.orig.x),0,sizeof(float3));
+ if(cfg->issrcfrom0){
+ grid.orig.x=0.f;
+ grid.orig.y=0.f;
+ grid.orig.z=0.f;
+ }
  status=mcx_parse_jsonshapes(root, &grid);
  if(status){
  MCX_ERROR(status,mcx_last_shapeerror());
@@ -1318,7 +1326,11 @@ void mcx_loadvolume(char *filename,Config *cfg){
  if(strstr(filename,".json")!=NULL){
  int status;
  Grid3D grid={&(cfg->vol),&(cfg->dim),{1.f,1.f,1.f},cfg->isrowmajor};
- if(cfg->issrcfrom0) memset(&(grid.orig.x),0,sizeof(float3));
+ if(cfg->issrcfrom0){
+ grid.orig.x=0.f;
+ grid.orig.y=0.f;
+ grid.orig.z=0.f;
+ }
  status=mcx_load_jsonshapes(&grid,filename);
  if(status){
  MCX_ERROR(status,mcx_last_shapeerror());
@@ -1818,7 +1830,7 @@ void mcx_parsecmd(int argc, char* argv[], Config *cfg){
  i=mcx_readarg(argc,argv,i,cfg->compileropt+strlen(cfg->compileropt),"string");
  break;
  case 'D':
- if(i<argc-1 && isalpha(argv[i+1][0]) )
+ if(i<argc-1 && isalpha((int)argv[i+1][0]) )
  cfg->debuglevel=mcx_parsedebugopt(argv[++i],debugflag);
  else
  i=mcx_readarg(argc,argv,i,&(cfg->debuglevel),"int");
@@ -1838,7 +1850,7 @@ void mcx_parsecmd(int argc, char* argv[], Config *cfg){
  if (cfg->issaveref) cfg->issaveref=1;
  break;
  case 'w':
- if(i+1<argc && isalpha(argv[i+1][0]) ){
+ if(i+1<argc && isalpha((int)argv[i+1][0]) ){
  cfg->savedetflag=mcx_parsedebugopt(argv[++i],saveflag);
  }else
  i=mcx_readarg(argc,argv,i,&(cfg->savedetflag),"int");
@@ -1895,7 +1907,7 @@ void mcx_parsecmd(int argc, char* argv[], Config *cfg){
  case 'K':
  i=mcx_readarg(argc,argv,i,&(cfg->maxdetphoton),"int");
  break;
- if(i+1<argc && isalpha(argv[i+1][0]) ){
+ if(i+1<argc && isalpha((int)argv[i+1][0]) ){
  cfg->mediabyte=mcx_keylookup(argv[++i],mediaformat);
  if(cfg->mediabyte==-1)
  MCX_ERROR(-1,"Unsupported media format.");

src/mcx_utils.h

@@ -13,7 +13,7 @@
 
 #define MAX_FULL_PATH 2048
 #define MAX_PATH_LENGTH 1024
-#define MAX_SESSION_LENGTH 256
+#define MAX_SESSION_LENGTH 64
 #define MAX_DEVICE 256
 
 #define MCX_ASSERT(x) mcx_assess((x),"assert error",__FILE__,__LINE__)

src/mcxlabcl.cpp

@@ -78,7 +78,7 @@ void mcx_validate_config(Config *cfg);
 void mcxlab_usage();
 
 float *detps=NULL; //! buffer to receive data from cfg.detphotons field
-int  dimdetps[2]={0,0}; //! dimensions of the cfg.detphotons array
+uint dimdetps[2]={0,0}; //! dimensions of the cfg.detphotons array
 int seedbyte=0;
 
 /** @brief Mex function for the MCX host function for MATLAB/Octave
@@ -96,7 +96,7 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]){
  dimtype fielddim[5];
  int errorflag=0;
  int threadid=0;
- cl_uint detected=0,workdev;
+ cl_uint  workdev;
  cl_device_id devices[MAX_DEVICE];
 
  const char *outputtag[]={"data"};
@@ -120,7 +120,6 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]){
  */
  if(nrhs==1 && mxIsChar(prhs[0])){
  char shortcmd[MAX_SESSION_LENGTH];
- int totaldev=0;
  mxGetString(prhs[0], shortcmd, MAX_SESSION_LENGTH);
  shortcmd[MAX_SESSION_LENGTH-1]='\0';
  if(strcmp(shortcmd,"gpuinfo")==0){
@@ -138,7 +137,7 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]){
  workdev=MAX_DEVICE;
 
  plhs[0] = mxCreateStructMatrix(gpuinfo[0].devcount,1,15,gpuinfotag);
- for(int i=0;i<workdev;i++){
+ for(uint i=0;i<workdev;i++){
  mxSetField(plhs[0],i,"name",mxCreateString(gpuinfo[i].name));
  SET_GPU_INFO(plhs[0],i,id);
  SET_GPU_INFO(plhs[0],i,devcount);
@@ -193,7 +192,7 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]){
  */
  for (jstruct = 0; jstruct < ncfg; jstruct++) { /* how many configs */
  try{
- unsigned int partialdata,hostdetreclen;
+ unsigned int partialdata,hostdetreclen=0;
  printf("Running simulations for configuration #%d ...\n", jstruct+1);
 
  /** Initialize cfg with default values first */
@@ -381,7 +380,7 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]){
 
  /** return the relative workload between multiple GPUs */
  val = mxCreateDoubleMatrix(1,workdev,mxREAL);
- for(int i=0;i<workdev;i++)
+ for(uint i=0;i<workdev;i++)
  *(mxGetPr(val)+i) = cfg.workload[i];
  mxSetFieldByNumber(stat,0,5, val);
 
@@ -420,7 +419,7 @@ void mcx_set_field(const mxArray *root,const mxArray *item,int idx, Config *cfg)
  const char *name=mxGetFieldNameByNumber(root,idx);
  const dimtype *arraydim;
  char *jsonshapes=NULL;
- int i,j;
+ int j;
 
  if(strcmp(name,"nphoton")==0 && cfg->replay.seed!=NULL)
  return;
@@ -470,6 +469,7 @@ void mcx_set_field(const mxArray *root,const mxArray *item,int idx, Config *cfg)
  GET_VEC4_FIELD(cfg,srcparam2)
  else if(strcmp(name,"vol")==0){
  dimtype dimxyz;
+ int i;
  cfg->mediabyte=0;
  arraydim=mxGetDimensions(item);
 
@@ -562,7 +562,7 @@ void mcx_set_field(const mxArray *root,const mxArray *item,int idx, Config *cfg)
  if(cfg->detpos) free(cfg->detpos);
  cfg->detpos=(float4 *)malloc(cfg->detnum*sizeof(float4));
  for(j=0;j<4;j++)
- for(i=0;i<cfg->detnum;i++)
+ for(uint i=0;i<cfg->detnum;i++)
  ((float *)(&cfg->detpos[i]))[j]=val[j*cfg->detnum+i];
  printf("mcx.detnum=%d;\n",cfg->detnum);
  }else if(strcmp(name,"prop")==0){
@@ -574,7 +574,7 @@ void mcx_set_field(const mxArray *root,const mxArray *item,int idx, Config *cfg)
  if(cfg->prop) free(cfg->prop);
  cfg->prop=(Medium *)malloc(cfg->medianum*sizeof(Medium));
  for(j=0;j<4;j++)
- for(i=0;i<cfg->medianum;i++)
+ for(uint i=0;i<cfg->medianum;i++)
  ((float *)(&cfg->prop[i]))[j]=val[j*cfg->medianum+i];
  printf("mcx.medianum=%d;\n",cfg->medianum);
  }else if(strcmp(name,"session")==0){
@@ -662,7 +662,7 @@ void mcx_set_field(const mxArray *root,const mxArray *item,int idx, Config *cfg)
  double *val=mxGetPr(item);
  if(cfg->srcpattern) free(cfg->srcpattern);
  cfg->srcpattern=(float*)malloc(arraydim[0]*arraydim[1]*dimz*sizeof(float));
- for(i=0;i<arraydim[0]*arraydim[1]*dimz;i++)
+ for(int i=0;i<arraydim[0]*arraydim[1]*dimz;i++)
  cfg->srcpattern[i]=val[i];
  printf("mcx.srcpattern=[%d %d %d];\n",arraydim[0],arraydim[1],dimz);
  }else if(strcmp(name,"shapes")==0){
@@ -738,7 +738,7 @@ void mcx_set_field(const mxArray *root,const mxArray *item,int idx, Config *cfg)
  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(int i=0;i<arraydim[0]*arraydim[1];i++)
  cfg->workload[i]=val[i];
  printf("mcx.workload=<<%d>>;\n",arraydim[0]*arraydim[1]);
  }else{
@@ -766,7 +766,7 @@ void mcx_set_field(const mxArray *root,const mxArray *item,int idx, Config *cfg)
 
 
 void mcx_replay_prep(Config *cfg){
- int i,j, hasdetid=0, offset;
+ int hasdetid=0, offset;
  float plen;
 
  if(cfg->seed==SEED_FROM_FILE && detps==NULL)
@@ -789,14 +789,14 @@ void mcx_replay_prep(Config *cfg){
  cfg->replay.detid=(int*)calloc(cfg->nphoton,sizeof(int));
 
  cfg->nphoton=0;
- for(i=0;i<dimdetps[1];i++){
+ for(uint i=0;i<dimdetps[1];i++){
  if(cfg->replaydet<=0 || cfg->replaydet==(int)(detps[i*dimdetps[0]])){
  if(i!=cfg->nphoton)
  memcpy((char *)(cfg->replay.seed)+cfg->nphoton*seedbyte, (char *)(cfg->replay.seed)+i*seedbyte, seedbyte);
  cfg->replay.weight[cfg->nphoton]=1.f;
  cfg->replay.tof[cfg->nphoton]=0.f;
  cfg->replay.detid[cfg->nphoton]=(hasdetid) ? (int)(detps[i*dimdetps[0]]) : 1;
- for(j=hasdetid;j<cfg->medianum-1+hasdetid;j++){
+ for(uint j=hasdetid;j<cfg->medianum-1+hasdetid;j++){
  plen=detps[i*dimdetps[0]+offset+j]*cfg->unitinmm;
  cfg->replay.weight[cfg->nphoton]*=expf(-cfg->prop[j-hasdetid+1].mua*plen);
  cfg->replay.tof[cfg->nphoton]+=plen*R_C0*cfg->prop[j-hasdetid+1].n;
@@ -821,7 +821,8 @@ void mcx_replay_prep(Config *cfg){
  */
 
 void mcx_validate_config(Config *cfg){
- int i,gates,idx1d;
+ int i;
+ uint gates;
  const char boundarycond[]={'_','r','a','m','c','\0'};
  unsigned int partialdata=(cfg->medianum-1)*(SAVE_NSCAT(cfg->savedetflag)+SAVE_PPATH(cfg->savedetflag)+SAVE_MOM(cfg->savedetflag));
  unsigned int hostdetreclen=partialdata+SAVE_DETID(cfg->savedetflag)+3*(SAVE_PEXIT(cfg->savedetflag)+SAVE_VEXIT(cfg->savedetflag))+SAVE_W0(cfg->savedetflag);
@@ -845,9 +846,9 @@ void mcx_validate_config(Config *cfg){
  cfg->crop0.x=MAX((int)(cfg->srcpos.x-cfg->sradius),0);
  cfg->crop0.y=MAX((int)(cfg->srcpos.y-cfg->sradius),0);
  cfg->crop0.z=MAX((int)(cfg->srcpos.z-cfg->sradius),0);
- cfg->crop1.x=MIN((int)(cfg->srcpos.x+cfg->sradius),cfg->dim.x-1);
- cfg->crop1.y=MIN((int)(cfg->srcpos.y+cfg->sradius),cfg->dim.y-1);
- cfg->crop1.z=MIN((int)(cfg->srcpos.z+cfg->sradius),cfg->dim.z-1);
+ cfg->crop1.x=MIN((int)(cfg->srcpos.x+cfg->sradius),(int)cfg->dim.x-1);
+ cfg->crop1.y=MIN((int)(cfg->srcpos.y+cfg->sradius),(int)cfg->dim.y-1);
+ cfg->crop1.z=MIN((int)(cfg->srcpos.z+cfg->sradius),(int)cfg->dim.z-1);
  }else if(cfg->sradius==0.f){
  memset(&(cfg->crop0),0,sizeof(uint3));
  memset(&(cfg->crop1),0,sizeof(uint3));
@@ -879,15 +880,15 @@ void mcx_validate_config(Config *cfg){
  mexErrMsgTxt("unknown boundary condition specifier");
 
  if(cfg->medianum){
- for(int i=0;i<cfg->medianum;i++)
+ for(uint i=0;i<cfg->medianum;i++)
  if(cfg->prop[i].mus==0.f){
  cfg->prop[i].mus=EPS;
  cfg->prop[i].g=1.f;
  }
  }
  if(cfg->unitinmm!=1.f){
  cfg->steps.x=cfg->unitinmm; cfg->steps.y=cfg->unitinmm; cfg->steps.z=cfg->unitinmm;
- for(i=1;i<cfg->medianum;i++){
+ for(uint i=1;i<cfg->medianum;i++){
  cfg->prop[i].mus*=cfg->unitinmm;
  cfg->prop[i].mua*=cfg->unitinmm;
  }
@@ -905,7 +906,7 @@ void mcx_validate_config(Config *cfg){
  if(cfg->seed<0 && cfg->seed!=SEED_FROM_FILE) cfg->seed=time(NULL);
  if((cfg->outputtype==otJacobian || cfg->outputtype==otWP) && cfg->seed!=SEED_FROM_FILE)
  mexErrMsgTxt("Jacobian output is only valid in the reply mode. Please define cfg.seed"); 
- for(i=0;i<cfg->detnum;i++){
+ for(uint i=0;i<cfg->detnum;i++){
  if(!cfg->issrcfrom0){
  cfg->detpos[i].x--;cfg->detpos[i].y--;cfg->detpos[i].z--; /*convert to C index*/
  }