![(please configure the [header_logo] section in trac.ini)](/trac/issm/chrome/common/trac_banner.png)
Changeset 20840
- Timestamp:
- 07/01/16 13:05:48 (9 years ago)
- Location:
- issm/trunk-jpl/src
- Files:
-
- 5 edited
-
c/classes/IoModel.cpp (modified) (2 diffs)
-
c/classes/IoModel.h (modified) (2 diffs)
-
c/main/kriging.cpp (modified) (2 diffs)
-
m/classes/pairoptions.m (modified) (1 diff)
-
m/contrib/morlighem/gslib/pkriging.m (modified) (1 diff)
Legend:
- Unmodified
- Added
- Removed
-
issm/trunk-jpl/src/c/classes/IoModel.cpp
r20810 r20840 1142 1142 } 1143 1143 /*}}}*/ 1144 void IoModel::FetchData(Option** poption,int index){/*{{{*/ 1145 1146 _error_("not implemented yet"); 1147 1148 /*output: */ 1149 //int code; 1150 //char *name = NULL; 1151 1152 ///*First get option name*/ 1153 //this->FetchData(&name,index); 1154 1155 ///*Get option value*/ 1156 //fid=this->SetFilePointerToData(&code,NULL,index+1); 1157 //switch(code){ 1158 // case 3: {//IssmDouble 1159 // GenericOption<IssmDouble>* option; 1160 // IssmDouble value; 1161 // FetchData(&value,index+1); 1162 // option = new GenericOption<IssmDouble>(); 1163 // option->value = value; 1164 // option->name = name; 1165 // option->numel = 1; 1166 // option->ndims = 1; 1167 // option->size = NULL; 1168 // /*Assign output pointers: */ 1169 // *poption=option; 1170 // break; 1171 // } 1172 // case 4: {//char 1173 // GenericOption<char*>* option; 1174 // char* value = NULL; 1175 // FetchData(&value,index+1); 1176 // option = new GenericOption<char*>(); 1177 // option->value = value; 1178 // option->name = name; 1179 // option->numel = 1; 1180 // option->ndims = 1; 1181 // option->size = NULL; 1182 // *poption=option; 1183 // break; 1184 // } 1185 // default: 1186 // _error_("Option of format " << code << " not supported yet"); 1187 //} 1144 void IoModel::FetchData(Options* options,const char* lastnonoption){/*{{{*/ 1145 1146 /*record descriptions; */ 1147 const char* mddot = "md."; 1148 char* record_name = NULL; 1149 int record_name_size; 1150 int record_length; 1151 int record_code; 1152 1153 /*records: */ 1154 IssmDouble scalar = 0; 1155 char *string = NULL; 1156 int string_size; 1157 1158 /*recover my_rank:*/ 1159 int my_rank=IssmComm::GetRank(); 1160 1161 /*Go find in the binary file, the position of the data we want to fetch: */ 1162 if(my_rank==0){ 1163 fseek(fid,0,SEEK_SET); 1164 for(;;){ 1165 /*Read size of first string name: */ 1166 if(fread(&record_name_size,sizeof(int),1,fid)==0) _error_("could not read record_name"); 1167 if(record_name_size<3 || record_name_size>80) _error_("error while looking in binary file. Found a string of size "<<record_name_size); 1168 1169 /*Allocate string of correct size: */ 1170 record_name=xNew<char>(record_name_size+1); 1171 record_name[record_name_size]='\0'; 1172 1173 /*Read record_name: */ 1174 if(fread(record_name,record_name_size*sizeof(char),1,fid)==0)_error_("Could not find field "<<lastnonoption); 1175 if(strncmp(record_name,mddot,3)!=0) _error_("error while reading binary file: record does not start with \"md.\": "<<record_name); 1176 1177 /*Is this the record sought for? : */ 1178 if(strcmp(record_name,lastnonoption)==0){ 1179 if(fread(&record_length,sizeof(int),1,fid)!=1) _error_("Could not read record_length"); 1180 fseek(fid,record_length,SEEK_CUR); 1181 xDelete<char>(record_name); 1182 break; 1183 } 1184 else{ 1185 if(fread(&record_length,sizeof(int),1,fid)!=1) _error_("Could not read record_length"); 1186 fseek(fid,record_length,SEEK_CUR); 1187 xDelete<char>(record_name); 1188 } 1189 } 1190 } 1191 1192 /*Go find in the binary file, the position of the data we want to fetch: */ 1193 if(my_rank==0){ //cpu 0{{{ 1194 1195 /*Now march through file looking for the correct data identifiers (bool,int,IssmDouble or string): */ 1196 for(;;){ 1197 1198 /*Read size of first string name: */ 1199 if(fread(&record_name_size,sizeof(int),1,fid)==0){ 1200 /*we have reached the end of the file. break: */ 1201 record_code=0; //0 means bailout 1202 ISSM_MPI_Bcast(&record_code,1,ISSM_MPI_INT,0,IssmComm::GetComm()); /*tell others cpus we are bailing: */ 1203 break; 1204 } 1205 if(record_name_size<3 || record_name_size>80){ 1206 _error_("error while looking in binary file. Found a string of size "<<record_name_size); 1207 } 1208 1209 /*Allocate string of correct size: */ 1210 record_name=xNew<char>(record_name_size+1); 1211 record_name[record_name_size]='\0'; 1212 1213 /*Read record_name: */ 1214 if(fread(record_name,record_name_size*sizeof(char),1,fid)==0){ 1215 _error_("Could not read record name"); 1216 } 1217 if(strncmp(record_name,mddot,3)!=0){ 1218 _error_("error while reading binary file: record does not start with \"md.\": "<<record_name); 1219 } 1220 if(strcmp(record_name,"md.EOF")==0){ 1221 xDelete<char>(record_name); 1222 record_code=0; //0 means bailout 1223 ISSM_MPI_Bcast(&record_code,1,ISSM_MPI_INT,0,IssmComm::GetComm()); /*tell others cpus we are bailing: */ 1224 break; 1225 } 1226 1227 /* Read the record length and the data type code: */ 1228 if(fread(&record_length,sizeof(int),1,this->fid)!=1) _error_("Cound not read record_length"); 1229 if(fread(&record_code ,sizeof(int),1,this->fid)!=1) _error_("Cound not read record_code"); 1230 1231 /*Tell other cpus what we are doing: */ 1232 ISSM_MPI_Bcast(&record_code,1,ISSM_MPI_INT,0,IssmComm::GetComm()); /*tell other cpus what we are going to do: */ 1233 1234 /*Tell other cpus the name of the data, then branch according to the data type: */ 1235 ISSM_MPI_Bcast(&record_name_size,1,ISSM_MPI_INT,0,IssmComm::GetComm()); 1236 ISSM_MPI_Bcast(record_name,record_name_size,ISSM_MPI_CHAR,0,IssmComm::GetComm()); 1237 ISSM_MPI_Bcast(&record_length,1,ISSM_MPI_INT,0,IssmComm::GetComm()); 1238 1239 switch(record_code){ 1240 case 3: 1241 { 1242 if(fread(&scalar,sizeof(IssmPDouble),1,this->fid)!=1) _error_("could not read scalar "); 1243 ISSM_MPI_Bcast(&scalar,1,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); 1244 GenericOption<IssmDouble>* option = new GenericOption<IssmDouble>(); 1245 char* optionname=xNew<char>(strlen(record_name)-3+1); 1246 xMemCpy(optionname,&record_name[3],strlen(record_name)-3+1); 1247 option->value = scalar; 1248 option->name = optionname; 1249 option->numel = 1; 1250 option->ndims = 1; 1251 option->size = NULL; 1252 options->AddOption(option); 1253 } 1254 break; 1255 case 4: 1256 { 1257 /*We have to read a string from disk. First read the dimensions of the string, then the string: */ 1258 if(fread(&string_size,sizeof(int),1,this->fid)!=1) _error_("could not read length of string "); 1259 ISSM_MPI_Bcast(&string_size,1,ISSM_MPI_INT,0,IssmComm::GetComm()); 1260 1261 if(string_size){ 1262 string=xNew<char>(string_size+1); 1263 string[string_size]='\0'; 1264 1265 /*Read string, then broadcast: */ 1266 if(fread(string,string_size*sizeof(char),1,this->fid)!=1)_error_(" could not read string "); 1267 ISSM_MPI_Bcast(string,string_size,ISSM_MPI_CHAR,0,IssmComm::GetComm()); 1268 } 1269 else{ 1270 string=xNew<char>(1); 1271 string[0]='\0'; 1272 } 1273 1274 /*Add string to parameters: */ 1275 GenericOption<char*>* option = new GenericOption<char*>(); 1276 char* optionname=xNew<char>(strlen(record_name)-3+1); 1277 xMemCpy(optionname,&record_name[3],strlen(record_name)-3+1); 1278 option->value = string; 1279 option->name = optionname; 1280 option->numel = 1; 1281 option->ndims = 1; 1282 option->size = NULL; 1283 options->AddOption(option); 1284 1285 } 1286 break; 1287 default: 1288 _error_("record type not supported:" << record_code); 1289 break; 1290 } 1291 xDelete<char>(record_name); 1292 } 1293 } //}}} 1294 else{ //cpu ~0 {{{ 1295 for(;;){ //wait on cpu 0 1296 ISSM_MPI_Bcast(&record_code,1,ISSM_MPI_INT,0,IssmComm::GetComm()); /*get from cpu 0 what we are going to do: */ 1297 if(record_code==0){ 1298 break; //we are done, break from the loop 1299 } 1300 else{ 1301 ISSM_MPI_Bcast(&record_name_size,1,ISSM_MPI_INT,0,IssmComm::GetComm()); 1302 _assert_(record_name_size); 1303 record_name=xNew<char>((record_name_size+1)); record_name[record_name_size]='\0'; 1304 ISSM_MPI_Bcast(record_name,record_name_size,ISSM_MPI_CHAR,0,IssmComm::GetComm()); 1305 ISSM_MPI_Bcast(&record_length,1,ISSM_MPI_INT,0,IssmComm::GetComm()); 1306 switch(record_code){ 1307 case 3: 1308 { 1309 if(fread(&scalar,sizeof(IssmPDouble),1,this->fid)!=1) _error_("could not read scalar "); 1310 ISSM_MPI_Bcast(&scalar,1,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); 1311 char* optionname=xNew<char>(strlen(record_name)-3+1); 1312 xMemCpy(optionname,&record_name[3],strlen(record_name)-3+1); 1313 GenericOption<IssmDouble>* option = new GenericOption<IssmDouble>(); 1314 option->value = scalar; 1315 option->name = optionname; 1316 option->numel = 1; 1317 option->ndims = 1; 1318 option->size = NULL; 1319 options->AddOption(option); 1320 } 1321 break; 1322 case 4: 1323 { 1324 /*We have to read a string from disk. First read the dimensions of the string, then the string: */ 1325 if(fread(&string_size,sizeof(int),1,this->fid)!=1) _error_("could not read length of string "); 1326 ISSM_MPI_Bcast(&string_size,1,ISSM_MPI_INT,0,IssmComm::GetComm()); 1327 1328 if(string_size){ 1329 string=xNew<char>(string_size+1); 1330 string[string_size]='\0'; 1331 1332 /*Read string, then broadcast: */ 1333 if(fread(string,string_size*sizeof(char),1,this->fid)!=1)_error_(" could not read string "); 1334 ISSM_MPI_Bcast(string,string_size,ISSM_MPI_CHAR,0,IssmComm::GetComm()); 1335 } 1336 else{ 1337 string=xNew<char>(1); 1338 string[0]='\0'; 1339 } 1340 1341 /*Add string to parameters: */ 1342 char* optionname=xNew<char>(strlen(record_name)-3+1); 1343 xMemCpy(optionname,&record_name[3],strlen(record_name)-3+1); 1344 GenericOption<char*>* option = new GenericOption<char*>(); 1345 option->value = string; 1346 option->name = optionname; 1347 option->numel = 1; 1348 option->ndims = 1; 1349 option->size = NULL; 1350 options->AddOption(option); 1351 } 1352 break; 1353 default: 1354 _error_("record type not supported:" << record_code); 1355 break; 1356 } 1357 1358 } 1359 } 1360 } //}}} 1188 1361 1189 1362 } … … 1956 2129 1957 2130 _error_("Could not find constant \""<<constant_name <<"\""); 1958 }1959 /*}}}*/1960 void IoModel::LastIndex(int *pindex){/*{{{*/1961 1962 int my_rank;1963 int lastindex,index;1964 int record_length;1965 1966 /*recover my_rank:*/1967 my_rank=IssmComm::GetRank();1968 1969 /*Go find in the binary file, the position of the data we want to fetch: */1970 if(my_rank==0){1971 1972 /*First set FILE* position to the beginning of the file: */1973 fseek(fid,0,SEEK_SET);1974 1975 /*Now march through file looking for the correct data identifier: */1976 for(;;){1977 /*Read name for this size of first string name: */1978 if(fread(&index,sizeof(int),1,fid)==0){1979 /*Ok, we have reached the end of the file. break: */1980 break;1981 }1982 1983 /*read the record length, and use it to skip this record: */1984 if(fread(&record_length,sizeof(int),1,fid)!=1) _error_("Could not read record_length");1985 fseek(fid,record_length,SEEK_CUR);1986 lastindex=index;1987 }1988 }1989 /*Broadcast code and vector type: */1990 ISSM_MPI_Bcast(&lastindex,1,ISSM_MPI_INT,0,IssmComm::GetComm());1991 1992 /*Assign output pointers:*/1993 *pindex=lastindex;1994 2131 } 1995 2132 /*}}}*/ -
issm/trunk-jpl/src/c/classes/IoModel.h
r20810 r20840 124 124 void FetchData(IssmDouble** pscalarmatrix,int* pM,int* pN,const char* data_name); 125 125 void FetchData(IssmDouble*** pmatrixarray,int** pmdims,int** pndims, int* pnumrecords,const char* data_name); 126 void FetchData(Option **poption,int index);126 void FetchData(Options *options,const char* data_name); 127 127 void FetchData(int num,...); 128 128 void FetchDataToInput(Elements* elements,const char* vector_name,int input_enum); … … 134 134 void FetchMultipleData(int** pvector, int* pnum_instances,const char* data_name); 135 135 void FetchMultipleData(IssmDouble** pvector, int* pnum_instances,const char* data_name); 136 void LastIndex(int *pindex);137 136 fpos_t* SetFilePointersToData(int** pcodes,int** pvector_types, int* pnum_instances, const char* data_name); 138 137 FILE* SetFilePointerToData(int* pcode,int* pvector_type, const char* data_name); -
issm/trunk-jpl/src/c/main/kriging.cpp
r20690 r20840 132 132 void ProcessInputfile(IssmDouble **px,IssmDouble **py,IssmDouble **pdata,int *pnobs,IssmDouble **px_interp,IssmDouble **py_interp,int *pninterp,Options **poptions,FILE* fid){ 133 133 134 int ninterp,nobs,numoptions; 135 IssmDouble *x = NULL; 136 IssmDouble *y = NULL; 137 IssmDouble *data = NULL; 138 IssmDouble *x_interp = NULL; 139 IssmDouble *y_interp = NULL; 140 Options *options = NULL; 141 Option *option = NULL; 134 int ninterp ,nobs; 135 IssmDouble *x = NULL; 136 IssmDouble *y = NULL; 137 IssmDouble *data = NULL; 138 IssmDouble *x_interp = NULL; 139 IssmDouble *y_interp = NULL; 140 Options *options = NULL; 142 141 143 142 int M,N; … … 145 144 iomodel->fid=fid; 146 145 iomodel->CheckFile(); 147 iomodel->FetchData(&x,&M,&N,"md. 0"); nobs=M*N;148 iomodel->FetchData(&y,&M,&N,"md. 1"); _assert_(M*N==nobs);149 iomodel->FetchData(&data,&M,&N,"md. 2"); _assert_(M*N==nobs);150 iomodel->FetchData(&x_interp,&M,&N,"md. 3"); ninterp=M*N;151 iomodel->FetchData(&y_interp,&M,&N,"md. 4"); _assert_(M*N==ninterp);146 iomodel->FetchData(&x,&M,&N,"md.x"); nobs=M*N; 147 iomodel->FetchData(&y,&M,&N,"md.y"); _assert_(M*N==nobs); 148 iomodel->FetchData(&data,&M,&N,"md.data"); _assert_(M*N==nobs); 149 iomodel->FetchData(&x_interp,&M,&N,"md.x_interp"); ninterp=M*N; 150 iomodel->FetchData(&y_interp,&M,&N,"md.y_interp"); _assert_(M*N==ninterp); 152 151 153 152 /*Read options*/ 154 153 options = new Options(); 155 iomodel->LastIndex(&N); 156 numoptions=(int)((N-4)/2); 157 for(int i=0;i<numoptions;i++){ 158 iomodel->FetchData(&option,5+2*i); 159 options->AddOption(option); 160 option=NULL; 161 } 154 iomodel->FetchData(options,"md.y_interp"); 162 155 163 156 /*Assign output pointer*/ -
issm/trunk-jpl/src/m/classes/pairoptions.m
r20690 r20840 284 284 end 285 285 end % }}} 286 function marshall(self,fid,firstindex)% {{{ 287 288 error('needs to be revised with new marhsall format...'); 286 function marshall(self,fid)% {{{ 287 289 288 for i=1:size(self.list,1), 290 289 name = self.list{i,1}; 291 290 value = self.list{i,2}; 292 291 293 %Write option name294 WriteData(fid,prefix,'enum',(firstindex-1)+2*i-1,'data',name,'format','String');295 296 292 %Write option value 297 293 if (isnumeric(value) & numel(value)==1), 298 WriteData(fid, prefix,'enum',(firstindex-1)+2*i,'data',value,'format','Double');294 WriteData(fid,'','name',['md.' name],'data',value,'format','Double'); 299 295 elseif ischar(value), 300 WriteData(fid, prefix,'enum',(firstindex-1)+2*i,'data',value,'format','String');296 WriteData(fid,'','name',['md.' name],'data',value,'format','String'); 301 297 else 302 298 error(['Cannot marshall option ' name ': format not supported yet']); -
issm/trunk-jpl/src/m/contrib/morlighem/gslib/pkriging.m
r20446 r20840 18 18 end 19 19 20 %First, write MaximumNumberOfDefinitionsEnum to make sure that the Enums are synchronized21 WriteData(fid,'enum',MaximumNumberOfDefinitionsEnum(),'data',true,'format','Boolean');22 23 20 %Write all data 24 WriteData(fid,'enum',0,'data',x,'format','DoubleMat'); 25 WriteData(fid,'enum',1,'data',y,'format','DoubleMat'); 26 WriteData(fid,'enum',2,'data',observations,'format','DoubleMat'); 27 WriteData(fid,'enum',3,'data',x_interp,'format','DoubleMat'); 28 WriteData(fid,'enum',4,'data',y_interp,'format','DoubleMat'); 29 30 %Last, write MaximumNumberOfEnum+1 to make sure that the binary file is not corrupt 31 WriteData(fid,'enum',MaximumNumberOfDefinitionsEnum()+1,'data',true,'format','Boolean'); 21 WriteData(fid,'','name','md.x','data',x,'format','DoubleMat'); 22 WriteData(fid,'','name','md.y','data',y,'format','DoubleMat'); 23 WriteData(fid,'','name','md.data','data',observations,'format','DoubleMat'); 24 WriteData(fid,'','name','md.x_interp','data',x_interp,'format','DoubleMat'); 25 WriteData(fid,'','name','md.y_interp','data',y_interp,'format','DoubleMat'); 32 26 33 27 %Now, write number of options 34 options.marshall(fid,5); 35 st=fclose(fid); 36 if st==-1, 37 error(['marshall error message: could not close file ' name '.bin']); 38 end 39 % ========================================= MARSHALL.m ================================================= 28 options.marshall(fid); 29 30 %Last, write "md.EOF" to make sure that the binary file is not corrupt 31 WriteData(fid,'','name','md.EOF','data',true,'format','Boolean'); 40 32 41 33 %Launch job on remote cluster
Note:
See TracChangeset
for help on using the changeset viewer.
