Index: /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h =================================================================== --- /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h (revision 5902) +++ /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h (revision 5903) @@ -365,5 +365,5 @@ NodalEnum, ResponseDescriptorsEnum, - SolverStringEnum, + PetscRcEnum, SparsityEnum, TolXEnum, Index: /issm/trunk/src/c/EnumDefinitions/EnumToString.cpp =================================================================== --- /issm/trunk/src/c/EnumDefinitions/EnumToString.cpp (revision 5902) +++ /issm/trunk/src/c/EnumDefinitions/EnumToString.cpp (revision 5903) @@ -327,5 +327,5 @@ case NodalEnum : return "Nodal"; case ResponseDescriptorsEnum : return "ResponseDescriptors"; - case SolverStringEnum : return "SolverString"; + case PetscRcEnum : return "PetscRc"; case SparsityEnum : return "Sparsity"; case TolXEnum : return "TolX"; Index: /issm/trunk/src/c/EnumDefinitions/StringToEnum.cpp =================================================================== --- /issm/trunk/src/c/EnumDefinitions/StringToEnum.cpp (revision 5902) +++ /issm/trunk/src/c/EnumDefinitions/StringToEnum.cpp (revision 5903) @@ -325,5 +325,5 @@ else if (strcmp(name,"Nodal")==0) return NodalEnum; else if (strcmp(name,"ResponseDescriptors")==0) return ResponseDescriptorsEnum; - else if (strcmp(name,"SolverString")==0) return SolverStringEnum; + else if (strcmp(name,"PetscRc")==0) return PetscRcEnum; else if (strcmp(name,"Sparsity")==0) return SparsityEnum; else if (strcmp(name,"TolX")==0) return TolXEnum; Index: /issm/trunk/src/c/modules/ModelProcessorx/CreateParameters.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 5902) +++ /issm/trunk/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 5903) @@ -64,5 +64,5 @@ parameters->AddObject(new DoubleParam(ViscosityOvershootEnum,iomodel->viscosity_overshoot)); parameters->AddObject(new BoolParam(WaitOnLockEnum,iomodel->waitonlock)); - parameters->AddObject(new StringParam(SolverStringEnum,iomodel->solverstring)); + parameters->AddObject(new StringParam(PetscRcEnum,iomodel->petscrc)); parameters->AddObject(new IntParam(NumberOfElementsEnum,iomodel->numberofelements)); parameters->AddObject(new BoolParam(KffEnum,iomodel->kff)); Index: /issm/trunk/src/c/modules/Solverx/Solverx.cpp =================================================================== --- /issm/trunk/src/c/modules/Solverx/Solverx.cpp (revision 5902) +++ /issm/trunk/src/c/modules/Solverx/Solverx.cpp (revision 5903) @@ -27,5 +27,7 @@ PetscTruth flag; int solver_type; - char* solver_string=NULL; + char* petscrc=NULL; + bool fromlocalsize=true; + /*Display message*/ @@ -44,35 +46,41 @@ } else{ - MatGetLocalSize(Kff,&local_m,&local_n);uf=NewVec(local_n,true); + MatGetLocalSize(Kff,&local_m,&local_n);uf=NewVec(local_n,fromlocalsize); } - /*Before preparing the solver, add options to the options database*/ - parameters->FindParam(&solver_string,SolverStringEnum); - PetscOptionsInsertMultipleString(solver_string); - /*Process solver_string to see if we are not using special types of external solvers: */ - PetscOptionsDetermineSolverType(&solver_type,solver_string); + /*Process petscrc to see if we are not using special types of external solvers: */ + parameters->FindParam(&petscrc,PetscRcEnum); + PetscOptionsDetermineSolverType(&solver_type,petscrc); + + /*In serial mode, we don't have a petsc.rc file to boot the Petsc options. Do it now + * using the petscrc string recover in the parameters: */ + #ifdef _SERIAL_ + PetscOptionsInsertMultipleString(petscrc); - #if _PETSC_VERSION_ == 2 - if (solver_type==MUMPSPACKAGE_LU){ - /*Convert Kff to MATTAIJMUMPS: */ - MatConvert(Kff,MATAIJMUMPS,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==MUMPSPACKAGE_CHOL){ - /*Convert Kff to MATTSBAIJMUMPS: */ - MatConvert(Kff,MATSBAIJMUMPS,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==SPOOLESPACKAGE_LU){ - /*Convert Kff to MATTSBAIJMUMPS: */ - MatConvert(Kff,MATAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==SPOOLESPACKAGE_CHOL){ - /*Convert Kff to MATTSBAIJMUMPS: */ - MatConvert(Kff,MATSBAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==SUPERLUDISTPACKAGE){ - /*Convert Kff to MATTSBAIJMUMPS: */ - MatConvert(Kff,MATSUPERLU_DIST,MAT_REUSE_MATRIX,&Kff); - } + /*In serial mode, matrices have been loaded at MPIAIJ or AIJ matrices. + * We need to convert them if we are going to run the solvers successfully: */ + #if _PETSC_VERSION_ == 2 + if (solver_type==MUMPSPACKAGE_LU){ + /*Convert Kff to MATTAIJMUMPS: */ + MatConvert(Kff,MATAIJMUMPS,MAT_REUSE_MATRIX,&Kff); + } + if (solver_type==MUMPSPACKAGE_CHOL){ + /*Convert Kff to MATTSBAIJMUMPS: */ + MatConvert(Kff,MATSBAIJMUMPS,MAT_REUSE_MATRIX,&Kff); + } + if (solver_type==SPOOLESPACKAGE_LU){ + /*Convert Kff to MATTSBAIJMUMPS: */ + MatConvert(Kff,MATAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); + } + if (solver_type==SPOOLESPACKAGE_CHOL){ + /*Convert Kff to MATTSBAIJMUMPS: */ + MatConvert(Kff,MATSBAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); + } + if (solver_type==SUPERLUDISTPACKAGE){ + /*Convert Kff to MATTSBAIJMUMPS: */ + MatConvert(Kff,MATSUPERLU_DIST,MAT_REUSE_MATRIX,&Kff); + } + #endif #endif @@ -82,10 +90,12 @@ KSPSetFromOptions(ksp); - #if _PETSC_VERSION_ == 3 - /*specific solver?: */ - KSPGetPC(ksp,&pc); - if (solver_type==MUMPSPACKAGE_LU){ - PCFactorSetMatSolverPackage(pc,MAT_SOLVER_MUMPS); - } + #ifdef _SERIAL_ + #if _PETSC_VERSION_ == 3 + /*specific solver?: */ + KSPGetPC(ksp,&pc); + if (solver_type==MUMPSPACKAGE_LU){ + PCFactorSetMatSolverPackage(pc,MAT_SOLVER_MUMPS); + } + #endif #endif @@ -98,4 +108,6 @@ } } + + /*Solve: */ KSPSolve(ksp,pf,uf); @@ -106,5 +118,5 @@ /*Free ressources:*/ KSPFree(&ksp); - xfree((void**)&solver_string); + xfree((void**)&petscrc); /*Assign output pointers:*/ Index: /issm/trunk/src/c/modules/SystemMatricesx/SystemMatricesx.cpp =================================================================== --- /issm/trunk/src/c/modules/SystemMatricesx/SystemMatricesx.cpp (revision 5902) +++ /issm/trunk/src/c/modules/SystemMatricesx/SystemMatricesx.cpp (revision 5903) @@ -160,5 +160,5 @@ } } - + /*Assign output pointers: */ if(pKgg) *pKgg=Kgg; Index: /issm/trunk/src/c/objects/IoModel.cpp =================================================================== --- /issm/trunk/src/c/objects/IoModel.cpp (revision 5902) +++ /issm/trunk/src/c/objects/IoModel.cpp (revision 5903) @@ -48,5 +48,5 @@ xfree((void**)&this->gridonpattyn); } - xfree((void**)&this->solverstring); + xfree((void**)&this->petscrc); xfree((void**)&this->elementonbed); xfree((void**)&this->elementonsurface); @@ -182,5 +182,5 @@ IoModelFetchData(&this->connectivity,iomodel_handle,"connectivity"); IoModelFetchData(&this->lowmem,iomodel_handle,"lowmem"); - IoModelFetchData(&this->solverstring,iomodel_handle,"solverstring"); + IoModelFetchData(&this->petscrc,iomodel_handle,"petscrc"); IoModelFetchData(&this->viscosity_overshoot,iomodel_handle,"viscosity_overshoot"); IoModelFetchData(&this->artdiff,iomodel_handle,"artificial_diffusivity"); @@ -227,5 +227,5 @@ this->control_analysis=0; this->control_parameter=NULL; - this->solverstring=NULL; + this->petscrc=NULL; this->numberofvariables=0; this->numvariabledescriptors=0; Index: /issm/trunk/src/c/objects/IoModel.h =================================================================== --- /issm/trunk/src/c/objects/IoModel.h (revision 5902) +++ /issm/trunk/src/c/objects/IoModel.h (revision 5903) @@ -22,5 +22,5 @@ int qmu_analysis; int control_analysis; - char* solverstring; + char* petscrc; /*2d mesh: */ Index: /issm/trunk/src/c/solutions/issm.cpp =================================================================== --- /issm/trunk/src/c/solutions/issm.cpp (revision 5902) +++ /issm/trunk/src/c/solutions/issm.cpp (revision 5903) @@ -42,5 +42,5 @@ /*Initialize Petsc and get start time*/ - PetscInitialize(&argc,&argv,(char *)0,""); + PetscInitialize(&argc,&argv,"petsc.rc",""); MPI_Barrier(MPI_COMM_WORLD); start=MPI_Wtime(); Index: /issm/trunk/src/m/classes/@model/model.m =================================================================== --- /issm/trunk/src/m/classes/@model/model.m (revision 5902) +++ /issm/trunk/src/m/classes/@model/model.m (revision 5903) @@ -270,6 +270,6 @@ %PETSc and MATLAB solver string - md.solverstring=''; - md.solver_type=''; + md.petscoptions=NaN; + md.petscrc=''; %Analysis and sub_analysis Index: /issm/trunk/src/m/classes/@model/setdefaultparameters.m =================================================================== --- /issm/trunk/src/m/classes/@model/setdefaultparameters.m (revision 5902) +++ /issm/trunk/src/m/classes/@model/setdefaultparameters.m (revision 5903) @@ -250,10 +250,6 @@ md.alloc_cleanup=1; -%the string of solverstring is used directly by PETSc to solve finite element -%systems KU=F. By default, we use MUMPS solver +%set petsc options cell array, so that PETSC uses the correct solvers md=solversettomumps(md); - -%Ice solver: 'general' for Matlab's default solver (or 'lu' or 'sholesky') -md.solver_type='general'; %solution speed-up Index: /issm/trunk/src/m/enum/EnumToString.m =================================================================== --- /issm/trunk/src/m/enum/EnumToString.m (revision 5902) +++ /issm/trunk/src/m/enum/EnumToString.m (revision 5903) @@ -322,5 +322,5 @@ case NodalEnum(), string='Nodal'; return case ResponseDescriptorsEnum(), string='ResponseDescriptors'; return -case SolverStringEnum(), string='SolverString'; return +case PetscRcEnum(), string='PetscRc'; return case SparsityEnum(), string='Sparsity'; return case TolXEnum(), string='TolX'; return Index: /issm/trunk/src/m/enum/PetscRcEnum.m =================================================================== --- /issm/trunk/src/m/enum/PetscRcEnum.m (revision 5903) +++ /issm/trunk/src/m/enum/PetscRcEnum.m (revision 5903) @@ -0,0 +1,11 @@ +function macro=PetscRcEnum() +%PETSCRCENUM - Enum of PetscRc +% +% WARNING: DO NOT MODIFY THIS FILE +% this file has been automatically generated by src/c/SynchronizeMatlabEnum +% Please read src/c/README for more information +% +% Usage: +% macro=PetscRcEnum() + +macro=311; Index: sm/trunk/src/m/enum/SolverStringEnum.m =================================================================== --- /issm/trunk/src/m/enum/SolverStringEnum.m (revision 5902) +++ (revision ) @@ -1,11 +1,0 @@ -function macro=SolverStringEnum() -%SOLVERSTRINGENUM - Enum of SolverString -% -% WARNING: DO NOT MODIFY THIS FILE -% this file has been automatically generated by src/c/SynchronizeMatlabEnum -% Please read src/c/README for more information -% -% Usage: -% macro=SolverStringEnum() - -macro=311; Index: /issm/trunk/src/m/enum/StringToEnum.m =================================================================== --- /issm/trunk/src/m/enum/StringToEnum.m (revision 5902) +++ /issm/trunk/src/m/enum/StringToEnum.m (revision 5903) @@ -320,5 +320,5 @@ elseif (strcmpi(name,'Nodal')), enum=NodalEnum(); return elseif (strcmpi(name,'ResponseDescriptors')), enum=ResponseDescriptorsEnum(); return - elseif (strcmpi(name,'SolverString')), enum=SolverStringEnum(); return + elseif (strcmpi(name,'PetscRc')), enum=PetscRcEnum(); return elseif (strcmpi(name,'Sparsity')), enum=SparsityEnum(); return elseif (strcmpi(name,'TolX')), enum=TolXEnum(); return Index: /issm/trunk/src/m/model/PetscOptions2PetscRc.m =================================================================== --- /issm/trunk/src/m/model/PetscOptions2PetscRc.m (revision 5903) +++ /issm/trunk/src/m/model/PetscOptions2PetscRc.m (revision 5903) @@ -0,0 +1,47 @@ +function petscstring=PetscOptions2PetscRc(petscoptions,filename) +%PETSCOPTIONS2PETSCRC: build a Petsc compatible options file, from the petscoptions model field + return options string +% +% Usage: petscstring=PetscOptions2PetscRc(petscoptions,filename); +% +% Example: md.petscsrc=PetscOptions2PetscRc(md.petscoptions,'petsc.rc'); +% +% See also: solversettomumps, solversettoasm, etc ... + + +%open file for writing +fid=fopen(filename,'w'); +if fid==-1, + error(['PetscOptions2PetscRc error: could not open ' filename ' for writing']); +end + +%write header +fprintf(fid,'%s%s%s\n\n','%Petsc options file: ',filename,' written from Matlab petscoptions array'); + +%initialize petscstring: +petscstring=''; + +%start writing options +for i=1:length(petscoptions), + option=petscoptions{i}; + if isempty(option), + %do nothing + elseif length(option)==1, + %this option has only one argument + fprintf(fid,'-%s\n',option{1}); + petscstring=[petscstring ' -' option{1}]; + elseif length(option)==2, + %option with value. value can be string or scalar + if isscalar(option{2}), + fprintf(fid,'-%s %g\n',option{1},option{2}); + petscstring=[petscstring ' -' option{1} ' ' num2str(option{2})]; + elseif ischar(option{2}), + fprintf(fid,'-%s %s\n',option{1},option{2}); + petscstring=[petscstring ' -' option{1} ' ' option{2}]; + else + error(['PetscOptions2PetscRc error: option #' num2str(i) ' is not well formatted']); + end + else + error(['PetscOptions2PetscRc error: option #' num2str(i) ' is not well formatted']); + end + +end Index: /issm/trunk/src/m/model/marshall.m =================================================================== --- /issm/trunk/src/m/model/marshall.m (revision 5902) +++ /issm/trunk/src/m/model/marshall.m (revision 5903) @@ -134,5 +134,5 @@ WriteData(fid,md.lowmem,'Integer','lowmem'); WriteData(fid,md.optscal,'Mat','optscal'); -WriteData(fid,md.solverstring,'String','solverstring'); +WriteData(fid,md.petscrc,'String','petscrc'); WriteData(fid,md.viscosity_overshoot,'Scalar','viscosity_overshoot'); WriteData(fid,md.stokesreconditioning,'Scalar','stokesreconditioning'); Index: /issm/trunk/src/m/model/presolve.m =================================================================== --- /issm/trunk/src/m/model/presolve.m (revision 5902) +++ /issm/trunk/src/m/model/presolve.m (revision 5903) @@ -33,2 +33,5 @@ count=count+numpairsforthisrift; end + +%deal with petsc options +md.petscrc=PetscOptions2PetscRc(md.petscoptions,'petsc.rc'); Index: /issm/trunk/src/m/model/queue/LaunchQueueJob.m =================================================================== --- /issm/trunk/src/m/model/queue/LaunchQueueJob.m (revision 5902) +++ /issm/trunk/src/m/model/queue/LaunchQueueJob.m (revision 5903) @@ -22,5 +22,5 @@ %compress the files into one zip. - compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue ']; + compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue petsc.rc']; if md.qmu_analysis, compressstring=[compressstring md.name '.qmu.in']; Index: /issm/trunk/src/m/model/solvers/solversettoasm.m =================================================================== --- /issm/trunk/src/m/model/solvers/solversettoasm.m (revision 5902) +++ /issm/trunk/src/m/model/solvers/solversettoasm.m (revision 5903) @@ -5,5 +5,5 @@ % md=solversettoasm(md) -%md.solverstring=' -mat_type aij -ksp_type cgs -pc_type asm -sub_mat_type mumps -sub_pc_type lu -pc_asm_overlap 4 -pc_factor_shift_positive_definite true'; -%md.solverstring=' -mat_type aij -ksp_type cgs -pc_type asm -sub_pc_type lu -pc_asm_overlap 4 '; -md.solverstring=' -mat_type aij -ksp_type gmres -pc_type asm -sub_pc_type lu -pc_asm_overlap 4 '; +%md.petscoptions={{'mat_type','aij'},{'ksp_type','cgs'},{'pc_type','asm'},{sub_mat_type','mumps'},{'sub_pc_type','lu'},{'pc_asm_overlap',4},{'pc_factor_shift_positive_definite','true'}}; +%md.petscoptions={{'mat_type','aij'},{'ksp_type','cgs'},{'pc_type','asm'},{'sub_pc_type','lu'},{'pc_asm_overlap',4}}; +md.petscoptions={{'mat_type','aij'},{'ksp_type','gmres'},{'pc_type','asm'},{'sub_pc_type','lu'},{'pc_asm_overlap',4}}; Index: /issm/trunk/src/m/model/solvers/solversettomatlab.m =================================================================== --- /issm/trunk/src/m/model/solvers/solversettomatlab.m (revision 5902) +++ /issm/trunk/src/m/model/solvers/solversettomatlab.m (revision 5903) @@ -5,3 +5,3 @@ % md=solversettomatlab(md) -md.solverstring='-ksp_type matlab'; +md.petscoptions={{'ksp_type','matlab'}}; Index: /issm/trunk/src/m/model/solvers/solversettomumps.m =================================================================== --- /issm/trunk/src/m/model/solvers/solversettomumps.m (revision 5902) +++ /issm/trunk/src/m/model/solvers/solversettomumps.m (revision 5903) @@ -5,6 +5,3 @@ % md=solversettomumps(md) -md.solverstring='-mat_type aijmumps -ksp_type preonly -pc_type lu -mat_mumps_icntl_14 120 -pc_factor_shift_positive_definite true'; - -%optional -%md.solverstring=[md.solverstring ' -mat_mumps_icntl_14 40 -mat_mumps_icntl_4 0 -mat_mumps_sym 1 -mat_ignore_lower_triangular']; +md.petscoptions={{'mat_type','aijmumps'},{'ksp_type','preonly'},{'pc_type','lu'},{'mat_mumps_icntl_14',120},{'pc_factor_shift_positive_definite','true'}}; Index: /issm/trunk/src/m/model/solvers/solversettosor.m =================================================================== --- /issm/trunk/src/m/model/solvers/solversettosor.m (revision 5902) +++ /issm/trunk/src/m/model/solvers/solversettosor.m (revision 5903) @@ -5,6 +5,3 @@ % md=solversettosor(md) -md.mat_type='aij'; -md.ksp_type='cg'; -md.pc_type='sor'; -md.solver_extra_option=' -pc_sor_omega 1.1 -pc_sor_its 2 '; +md.petscoptions={{'mat_type','aij'},{'ksp_type','cg'},{'pc_type','sor'},{'pc_sor_omega',1.1},{pc_sor_its',2}}; Index: /issm/trunk/src/mex/Solver/Solver.cpp =================================================================== --- /issm/trunk/src/mex/Solver/Solver.cpp (revision 5902) +++ /issm/trunk/src/mex/Solver/Solver.cpp (revision 5903) @@ -12,5 +12,5 @@ Vec uf0 = NULL; Vec uf = NULL; - char *solver_string = NULL; + char *petscrc = NULL; Parameters *parameters = NULL; int verbose; @@ -27,9 +27,9 @@ /*First, check solver string: */ FetchParams(¶meters,PARAMETERS); - parameters->FindParam(&solver_string,SolverStringEnum); + parameters->FindParam(&petscrc,PetscRcEnum); int verbose; parameters->FindParam(&verbose,VerboseEnum); /*Fetch rest of data only if not running the matlab solver: */ - if (strcmp(solver_string,matlabstring)!=0){ + if (strcmp(petscrc,matlabstring)!=0){ /*Input datasets: */ FetchData(&Kff,KFF); @@ -55,5 +55,5 @@ VecFree(&uf); delete parameters; - xfree((void**)&solver_string); + xfree((void**)&petscrc); MODULEEND(); Index: /issm/trunk/test/NightlyRun/test104.m =================================================================== --- /issm/trunk/test/NightlyRun/test104.m (revision 5902) +++ /issm/trunk/test/NightlyRun/test104.m (revision 5903) @@ -5,4 +5,5 @@ md=setelementstype(md,'macayeal','all'); md.cluster=oshostname; +md.verbose=1; md=solve(md,'analysis_type',DiagnosticSolutionEnum);