Index: /issm/trunk/src/c/Container/Results.cpp =================================================================== --- /issm/trunk/src/c/Container/Results.cpp (revision 6388) +++ /issm/trunk/src/c/Container/Results.cpp (revision 6389) @@ -158,7 +158,9 @@ int i; FILE *fid = NULL; + bool io_gather=true; /*Recover file descriptor: */ parameters->FindParam(&fid,OutputFilePointerEnum); + parameters->FindParam(&io_gather,IoGatherEnum); for(i=0;iSize();i++){ @@ -167,5 +169,5 @@ /*write result to disk: */ - result->WriteData(fid); + result->WriteData(fid,io_gather); } Index: /issm/trunk/src/c/io/pfclose.cpp =================================================================== --- /issm/trunk/src/c/io/pfclose.cpp (revision 6388) +++ /issm/trunk/src/c/io/pfclose.cpp (revision 6389) @@ -17,6 +17,4 @@ /*Close file handle: */ extern int my_rank; - if(my_rank==0){ - if(fclose(fid)!=0)ISSMERROR("%s%s","could not close file ",filename); - } + if(fclose(fid)!=0)ISSMERROR("%s%s","could not close file ",filename); } Index: /issm/trunk/src/c/io/pfopen.cpp =================================================================== --- /issm/trunk/src/c/io/pfopen.cpp (revision 6388) +++ /issm/trunk/src/c/io/pfopen.cpp (revision 6389) @@ -19,8 +19,6 @@ /*Open handle to data on disk: */ - if(my_rank==0){ - fid=fopen(filename,format); - if(fid==NULL) ISSMERROR("%s%s%s","could not open file ",filename," for binary reading or writing"); - } + fid=fopen(filename,format); + if(fid==NULL) ISSMERROR("%s%s%s","could not open file ",filename," for binary reading or writing"); return fid; Index: /issm/trunk/src/c/modules/OutputResultsx/OutputResultsx.cpp =================================================================== --- /issm/trunk/src/c/modules/OutputResultsx/OutputResultsx.cpp (revision 6388) +++ /issm/trunk/src/c/modules/OutputResultsx/OutputResultsx.cpp (revision 6389) @@ -58,5 +58,4 @@ /*What strategy? : */ parameters->FindParam(&io_gather,IoGatherEnum); - if(io_gather){ @@ -76,4 +75,5 @@ #endif + /*Write results to disk (in parallel), or to memory (in serial mode): */ #ifdef _SERIAL_ @@ -83,5 +83,4 @@ #endif - /*Delete and reinitialize results, in parallel: */ #ifdef _PARALLEL_ @@ -89,4 +88,12 @@ #endif + /*Close output file? :*/ + if((step==1) && (time==0)){ + if(io_gather){ + if(my_rank==0) pfclose(fid,outputfilename); + } + else pfclose(fid,cpu_outputfilename); + } + /*Assign output pointers:*/ *presults=results; Index: /issm/trunk/src/c/objects/ExternalResults/BoolExternalResult.cpp =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/BoolExternalResult.cpp (revision 6388) +++ /issm/trunk/src/c/objects/ExternalResults/BoolExternalResult.cpp (revision 6389) @@ -143,5 +143,5 @@ /*BoolExternalResult management: */ /*FUNCTION BoolExternalResult::WriteData{{{1*/ -void BoolExternalResult::WriteData(FILE* fid){ +void BoolExternalResult::WriteData(FILE* fid,bool io_gather){ int length; Index: /issm/trunk/src/c/objects/ExternalResults/BoolExternalResult.h =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/BoolExternalResult.h (revision 6388) +++ /issm/trunk/src/c/objects/ExternalResults/BoolExternalResult.h (revision 6389) @@ -55,5 +55,5 @@ /*ExternalResult management: {{{1*/ int EnumType(){return enum_type;} - void WriteData(FILE* fid); + void WriteData(FILE* fid,bool io_gather); char* GetResultName(void); #ifdef _SERIAL_ Index: /issm/trunk/src/c/objects/ExternalResults/DoubleExternalResult.cpp =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/DoubleExternalResult.cpp (revision 6388) +++ /issm/trunk/src/c/objects/ExternalResults/DoubleExternalResult.cpp (revision 6389) @@ -143,5 +143,5 @@ /*DoubleExternalResult management: */ /*FUNCTION DoubleExternalResult::WriteData{{{1*/ -void DoubleExternalResult::WriteData(FILE* fid){ +void DoubleExternalResult::WriteData(FILE* fid,bool io_gather){ int length; Index: /issm/trunk/src/c/objects/ExternalResults/DoubleExternalResult.h =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/DoubleExternalResult.h (revision 6388) +++ /issm/trunk/src/c/objects/ExternalResults/DoubleExternalResult.h (revision 6389) @@ -56,5 +56,5 @@ /*ExternalResult management: {{{1*/ int EnumType(){return enum_type;} - void WriteData(FILE* fid); + void WriteData(FILE* fid,bool io_gather); char* GetResultName(void); #ifdef _SERIAL_ Index: /issm/trunk/src/c/objects/ExternalResults/DoubleMatExternalResult.cpp =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/DoubleMatExternalResult.cpp (revision 6388) +++ /issm/trunk/src/c/objects/ExternalResults/DoubleMatExternalResult.cpp (revision 6389) @@ -180,5 +180,5 @@ /*DoubleMatExternalResult management: */ /*FUNCTION DoubleMatExternalResult::WriteData{{{1*/ -void DoubleMatExternalResult::WriteData(FILE* fid){ +void DoubleMatExternalResult::WriteData(FILE* fid,bool io_gather){ int length; @@ -188,6 +188,8 @@ extern int my_rank; - /*return if now on cpu 0: */ - if(my_rank) return; + if(io_gather){ + /*we are gathering the data on cpu 0, don't write on other cpus: */ + if(my_rank) return; + } /*First write enum: */ Index: /issm/trunk/src/c/objects/ExternalResults/DoubleMatExternalResult.h =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/DoubleMatExternalResult.h (revision 6388) +++ /issm/trunk/src/c/objects/ExternalResults/DoubleMatExternalResult.h (revision 6389) @@ -57,5 +57,5 @@ /*ExternalResult managemnet: {{{1*/ int EnumType(){return enum_type;} - void WriteData(FILE* fid); + void WriteData(FILE* fid,bool io_gather); char* GetResultName(void); #ifdef _SERIAL_ Index: /issm/trunk/src/c/objects/ExternalResults/DoubleVecExternalResult.cpp =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/DoubleVecExternalResult.cpp (revision 6388) +++ /issm/trunk/src/c/objects/ExternalResults/DoubleVecExternalResult.cpp (revision 6389) @@ -168,5 +168,5 @@ /*DoubleVecExternalResult management: */ /*FUNCTION DoubleVecExternalResult::WriteData{{{1*/ -void DoubleVecExternalResult::WriteData(FILE* fid){ +void DoubleVecExternalResult::WriteData(FILE* fid,bool io_gather){ int length; Index: /issm/trunk/src/c/objects/ExternalResults/DoubleVecExternalResult.h =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/DoubleVecExternalResult.h (revision 6388) +++ /issm/trunk/src/c/objects/ExternalResults/DoubleVecExternalResult.h (revision 6389) @@ -56,5 +56,5 @@ /*ExternalResult management: {{{1*/ int EnumType(){return enum_type;} - void WriteData(FILE* fid); + void WriteData(FILE* fid,bool io_gather); char* GetResultName(void); #ifdef _SERIAL_ Index: /issm/trunk/src/c/objects/ExternalResults/ExternalResult.h =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/ExternalResult.h (revision 6388) +++ /issm/trunk/src/c/objects/ExternalResults/ExternalResult.h (revision 6389) @@ -31,5 +31,5 @@ /*Virtual functions:{{{1*/ virtual int EnumType()=0; - virtual void WriteData(FILE* fid)=0; + virtual void WriteData(FILE* fid,bool io_gather)=0; virtual char* GetResultName(void)=0; #ifdef _SERIAL_ Index: /issm/trunk/src/c/objects/ExternalResults/IntExternalResult.cpp =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/IntExternalResult.cpp (revision 6388) +++ /issm/trunk/src/c/objects/ExternalResults/IntExternalResult.cpp (revision 6389) @@ -143,5 +143,5 @@ /*IntExternalResult management: */ /*FUNCTION IntExternalResult::WriteData{{{1*/ -void IntExternalResult::WriteData(FILE* fid){ +void IntExternalResult::WriteData(FILE* fid,bool io_gather){ int length; Index: /issm/trunk/src/c/objects/ExternalResults/IntExternalResult.h =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/IntExternalResult.h (revision 6388) +++ /issm/trunk/src/c/objects/ExternalResults/IntExternalResult.h (revision 6389) @@ -54,5 +54,5 @@ /*ExternalResult managemnet: {{{1*/ int EnumType(){return enum_type;} - void WriteData(FILE* fid); + void WriteData(FILE* fid,bool io_gather); char* GetResultName(void); #ifdef _SERIAL_ Index: /issm/trunk/src/c/objects/ExternalResults/PetscVecExternalResult.cpp =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/PetscVecExternalResult.cpp (revision 6388) +++ /issm/trunk/src/c/objects/ExternalResults/PetscVecExternalResult.cpp (revision 6389) @@ -199,5 +199,5 @@ /*PetscVecExternalResult management: */ /*FUNCTION PetscVecExternalResult::WriteData{{{1*/ -void PetscVecExternalResult::WriteData(FILE* fid){ +void PetscVecExternalResult::WriteData(FILE* fid,bool io_gather){ int length; Index: /issm/trunk/src/c/objects/ExternalResults/PetscVecExternalResult.h =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/PetscVecExternalResult.h (revision 6388) +++ /issm/trunk/src/c/objects/ExternalResults/PetscVecExternalResult.h (revision 6389) @@ -56,5 +56,5 @@ /*ExternalResult management: {{{1*/ int EnumType(){return enum_type;} - void WriteData(FILE* fid); + void WriteData(FILE* fid,bool io_gather); char* GetResultName(void); #ifdef _SERIAL_ Index: /issm/trunk/src/c/objects/ExternalResults/StringExternalResult.cpp =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/StringExternalResult.cpp (revision 6388) +++ /issm/trunk/src/c/objects/ExternalResults/StringExternalResult.cpp (revision 6389) @@ -158,5 +158,5 @@ /*StringExternalResult management: */ /*FUNCTION StringExternalResult::WriteData{{{1*/ -void StringExternalResult::WriteData(FILE* fid){ +void StringExternalResult::WriteData(FILE* fid,bool io_gather){ int length; Index: /issm/trunk/src/c/objects/ExternalResults/StringExternalResult.h =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/StringExternalResult.h (revision 6388) +++ /issm/trunk/src/c/objects/ExternalResults/StringExternalResult.h (revision 6389) @@ -56,5 +56,5 @@ /*ExternalResult management: {{{1*/ int EnumType(){return enum_type;} - void WriteData(FILE* fid); + void WriteData(FILE* fid,bool io_gather); char* GetResultName(void); #ifdef _SERIAL_ Index: /issm/trunk/src/c/solutions/issm.cpp =================================================================== --- /issm/trunk/src/c/solutions/issm.cpp (revision 6388) +++ /issm/trunk/src/c/solutions/issm.cpp (revision 6389) @@ -100,5 +100,4 @@ /*Close output file and write lock file if requested*/ - femmodel->parameters->FindParam(&output_fid,OutputFilePointerEnum); pfclose(output_fid,argv[5]); if (waitonlock>0){ _printf_("write lock file:\n"); Index: /issm/trunk/src/m/classes/clusters/astrid.m =================================================================== --- /issm/trunk/src/m/classes/clusters/astrid.m (revision 6388) +++ /issm/trunk/src/m/classes/clusters/astrid.m (revision 6389) @@ -71,12 +71,17 @@ fprintf(fid,'#!/bin/sh\n'); if mem_debug==0, - fprintf(fid,'mpirun -np %i %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',cluster.np,cluster.codepath,EnumToString(analysis_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); + fprintf(fid,'mpirun -np %i %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog ',cluster.np,cluster.codepath,EnumToString(analysis_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); else - %fprintf(fid,'LD_PRELOAD=%s mpirun -np %i %s --leak-check=full --gen-suppressions=all --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(analysis_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); - fprintf(fid,'LD_PRELOAD=%s mpirun -np %i %s --leak-check=full --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup, cluster.codepath,EnumToString(analysis_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); + %fprintf(fid,'LD_PRELOAD=%s mpirun -np %i %s --leak-check=full --gen-suppressions=all --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(analysis_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); + fprintf(fid,'LD_PRELOAD=%s mpirun -np %i %s --leak-check=full --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup, cluster.codepath,EnumToString(analysis_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname); end if md.gprof, fprintf(fid,'\n gprof %s/issm.exe gmon.out > %s.performance',cluster.codepath,modelname); + end + + if ~md.io_gather, + %concatenate the output files: + fprintf(fid,'\ncat %s.outbin.* > %s.outbin',modelname,modelname); end Index: /issm/trunk/src/m/model/parseresultsfromdisk.m =================================================================== --- /issm/trunk/src/m/model/parseresultsfromdisk.m (revision 6388) +++ /issm/trunk/src/m/model/parseresultsfromdisk.m (revision 6389) @@ -21,5 +21,9 @@ %Add result - results(result.step).(result.fieldname)=result.field; + if (length(results)>=result.step & isfield(results,result.fieldname)), + results(result.step).(result.fieldname)=[ results(result.step).(result.fieldname); result.field]; + else + results(result.step).(result.fieldname)=result.field; + end %read next result