/* PetscInitializeNoPointers - Calls PetscInitialize() from C/C++ without the pointers to argc and args Collective Level: advanced Notes: this is called only by the PETSc MATLAB and Julia interface. Even though it might start MPI it sets the flag to indicate that it did NOT start MPI so that the PetscFinalize() does not end MPI, thus allowing PetscInitialize() to be called multiple times from MATLAB and Julia without the problem of trying to initialize MPI more than once. Turns off PETSc signal handling because that can interact with MATLAB's signal handling causing random crashes. .seealso: PetscInitialize(), PetscInitializeFortran(), PetscInitializeNoArguments() */ PetscErrorCode PetscInitializeNoPointers(int argc,char **args,const char *filename,const char *help) { PetscErrorCode ierr; int myargc = argc; char **myargs = args; PetscFunctionBegin; ierr = PetscInitialize(&myargc,&myargs,filename,help);CHKERRQ(ierr); ierr = PetscPopSignalHandler();CHKERRQ(ierr); PetscBeganMPI = PETSC_FALSE; PetscFunctionReturn(ierr); }
void Msg::Init(int argc, char **argv) { #if defined(HAVE_MPI) int flag; MPI_Initialized(&flag); if(!flag) MPI_Init(&argc, &argv); MPI_Comm_rank(MPI_COMM_WORLD, &_commRank); MPI_Comm_size(MPI_COMM_WORLD, &_commSize); MPI_Errhandler_set(MPI_COMM_WORLD, MPI_ERRORS_RETURN); #endif #if defined(HAVE_PETSC) int sargc = 0; char **sargv = new char*[argc + 1]; // prune argv from gmsh-specific options that make PETSc verbose for(int i = 0; i < argc; i++){ std::string val(argv[i]); if(val != "-info" && val != "-help" && val != "-v") sargv[sargc++] = argv[i]; } PetscInitialize(&sargc, &sargv, PETSC_NULL, PETSC_NULL); PetscPopSignalHandler(); #if defined(HAVE_SLEPC) SlepcInitialize(&sargc, &sargv, PETSC_NULL, PETSC_NULL); #endif delete [] sargv; #endif time_t now; time(&now); _launchDate = ctime(&now); _launchDate.resize(_launchDate.size() - 1); _commandLine.clear(); for(int i = 0; i < argc; i++){ if(i) _commandLine += " "; _commandLine += argv[i]; } if(argc && argv){ CTX::instance()->argv0 = std::string(argv[0]); // add the directory where the binary is installed to the path where Python // looks for modules, and to the path for executables (this allows us to // find the onelab.py module or subclients automatically) addGmshPathToEnvironmentVar("PYTHONPATH"); addGmshPathToEnvironmentVar("PATH"); } InitializeOnelab("Gmsh"); }
MooseInit::MooseInit(int argc, char *argv[], MPI_Comm COMM_WORLD_IN) : LibMeshInit(argc, argv, COMM_WORLD_IN) { #ifdef LIBMESH_HAVE_PETSC PetscPopSignalHandler(); // get rid of Petsc error handler #endif // Set the number of OpenMP threads to the same as the number of threads libMesh is going to use #ifdef LIBMESH_HAVE_OPENMP omp_set_num_threads(libMesh::n_threads()); #endif ParallelUniqueId::initialize(); // Make sure that any calls to the global random number generator are consistent among processes MooseRandom::seed(0); }
int main(int argc, char *args[]) { HandlerCtx user; PetscErrorCode ierr; user.exitHandler = 0; ierr = PetscInitialize(&argc, &args, (char*) 0, help);CHKERRQ(ierr); ierr = PetscPushSignalHandler(handleSignal, &user);CHKERRQ(ierr); while (!user.exitHandler) { if (user.signum > 0) { ierr = PetscPrintf(PETSC_COMM_SELF, "Caught signal %d\n", user.signum);CHKERRQ(ierr); user.signum = -1; } } ierr = PetscPopSignalHandler();CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
/*@C PetscFinalize - Checks for options to be called at the conclusion of the program. MPI_Finalize() is called only if the user had not called MPI_Init() before calling PetscInitialize(). Collective on PETSC_COMM_WORLD Options Database Keys: + -options_table - Calls PetscOptionsView() . -options_left - Prints unused options that remain in the database . -objects_dump [all] - Prints list of objects allocated by the user that have not been freed, the option all cause all outstanding objects to be listed . -mpidump - Calls PetscMPIDump() . -malloc_dump - Calls PetscMallocDump() . -malloc_info - Prints total memory usage - -malloc_log - Prints summary of memory usage Level: beginner Note: See PetscInitialize() for more general runtime options. .seealso: PetscInitialize(), PetscOptionsView(), PetscMallocDump(), PetscMPIDump(), PetscEnd() @*/ PetscErrorCode PetscFinalize(void) { PetscErrorCode ierr; PetscMPIInt rank; PetscInt nopt; PetscBool flg1 = PETSC_FALSE,flg2 = PETSC_FALSE,flg3 = PETSC_FALSE; #if defined(PETSC_HAVE_AMS) PetscBool flg = PETSC_FALSE; #endif #if defined(PETSC_USE_LOG) char mname[PETSC_MAX_PATH_LEN]; #endif PetscFunctionBegin; if (!PetscInitializeCalled) { printf("PetscInitialize() must be called before PetscFinalize()\n"); PetscFunctionReturn(PETSC_ERR_ARG_WRONGSTATE); } ierr = PetscInfo(NULL,"PetscFinalize() called\n");CHKERRQ(ierr); #if defined(PETSC_SERIALIZE_FUNCTIONS) ierr = PetscFPTDestroy();CHKERRQ(ierr); #endif #if defined(PETSC_HAVE_AMS) ierr = PetscOptionsGetBool(NULL,"-options_gui",&flg,NULL);CHKERRQ(ierr); if (flg) { ierr = PetscOptionsAMSDestroy();CHKERRQ(ierr); } #endif #if defined(PETSC_HAVE_SERVER) flg1 = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-server",&flg1,NULL);CHKERRQ(ierr); if (flg1) { /* this is a crude hack, but better than nothing */ ierr = PetscPOpen(PETSC_COMM_WORLD,NULL,"pkill -9 petscwebserver","r",NULL);CHKERRQ(ierr); } #endif ierr = PetscHMPIFinalize();CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,"-malloc_info",&flg2,NULL);CHKERRQ(ierr); if (!flg2) { flg2 = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-memory_info",&flg2,NULL);CHKERRQ(ierr); } if (flg2) { ierr = PetscMemoryShowUsage(PETSC_VIEWER_STDOUT_WORLD,"Summary of Memory Usage in PETSc\n");CHKERRQ(ierr); } #if defined(PETSC_USE_LOG) flg1 = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-get_total_flops",&flg1,NULL);CHKERRQ(ierr); if (flg1) { PetscLogDouble flops = 0; ierr = MPI_Reduce(&petsc_TotalFlops,&flops,1,MPI_DOUBLE,MPI_SUM,0,PETSC_COMM_WORLD);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Total flops over all processors %g\n",flops);CHKERRQ(ierr); } #endif #if defined(PETSC_USE_LOG) #if defined(PETSC_HAVE_MPE) mname[0] = 0; ierr = PetscOptionsGetString(NULL,"-log_mpe",mname,PETSC_MAX_PATH_LEN,&flg1);CHKERRQ(ierr); if (flg1) { if (mname[0]) {ierr = PetscLogMPEDump(mname);CHKERRQ(ierr);} else {ierr = PetscLogMPEDump(0);CHKERRQ(ierr);} } #endif mname[0] = 0; ierr = PetscOptionsGetString(NULL,"-log_summary",mname,PETSC_MAX_PATH_LEN,&flg1);CHKERRQ(ierr); if (flg1) { PetscViewer viewer; if (mname[0]) { ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD,mname,&viewer);CHKERRQ(ierr); ierr = PetscLogView(viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); } else { viewer = PETSC_VIEWER_STDOUT_WORLD; ierr = PetscLogView(viewer);CHKERRQ(ierr); } } mname[0] = 0; ierr = PetscOptionsGetString(NULL,"-log_summary_python",mname,PETSC_MAX_PATH_LEN,&flg1);CHKERRQ(ierr); if (flg1) { PetscViewer viewer; if (mname[0]) { ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD,mname,&viewer);CHKERRQ(ierr); ierr = PetscLogViewPython(viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); } else { viewer = PETSC_VIEWER_STDOUT_WORLD; ierr = PetscLogViewPython(viewer);CHKERRQ(ierr); } } ierr = PetscOptionsGetString(NULL,"-log_detailed",mname,PETSC_MAX_PATH_LEN,&flg1);CHKERRQ(ierr); if (flg1) { if (mname[0]) {ierr = PetscLogPrintDetailed(PETSC_COMM_WORLD,mname);CHKERRQ(ierr);} else {ierr = PetscLogPrintDetailed(PETSC_COMM_WORLD,0);CHKERRQ(ierr);} } mname[0] = 0; ierr = PetscOptionsGetString(NULL,"-log_all",mname,PETSC_MAX_PATH_LEN,&flg1);CHKERRQ(ierr); ierr = PetscOptionsGetString(NULL,"-log",mname,PETSC_MAX_PATH_LEN,&flg2);CHKERRQ(ierr); if (flg1 || flg2) { if (mname[0]) PetscLogDump(mname); else PetscLogDump(0); } #endif /* Free all objects registered with PetscObjectRegisterDestroy() such as PETSC_VIEWER_XXX_(). */ ierr = PetscObjectRegisterDestroyAll();CHKERRQ(ierr); ierr = PetscStackDestroy();CHKERRQ(ierr); flg1 = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-no_signal_handler",&flg1,NULL);CHKERRQ(ierr); if (!flg1) { ierr = PetscPopSignalHandler();CHKERRQ(ierr);} flg1 = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-mpidump",&flg1,NULL);CHKERRQ(ierr); if (flg1) { ierr = PetscMPIDump(stdout);CHKERRQ(ierr); } flg1 = PETSC_FALSE; flg2 = PETSC_FALSE; /* preemptive call to avoid listing this option in options table as unused */ ierr = PetscOptionsHasName(NULL,"-malloc_dump",&flg1);CHKERRQ(ierr); ierr = PetscOptionsHasName(NULL,"-objects_dump",&flg1);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,"-options_table",&flg2,NULL);CHKERRQ(ierr); if (flg2) { PetscViewer viewer; ierr = PetscViewerASCIIGetStdout(PETSC_COMM_WORLD,&viewer);CHKERRQ(ierr); ierr = PetscOptionsView(viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); } /* to prevent PETSc -options_left from warning */ ierr = PetscOptionsHasName(NULL,"-nox",&flg1);CHKERRQ(ierr); ierr = PetscOptionsHasName(NULL,"-nox_warning",&flg1);CHKERRQ(ierr); if (!PetscHMPIWorker) { /* worker processes skip this because they do not usually process options */ flg3 = PETSC_FALSE; /* default value is required */ ierr = PetscOptionsGetBool(NULL,"-options_left",&flg3,&flg1);CHKERRQ(ierr); ierr = PetscOptionsAllUsed(&nopt);CHKERRQ(ierr); if (flg3) { if (!flg2) { /* have not yet printed the options */ PetscViewer viewer; ierr = PetscViewerASCIIGetStdout(PETSC_COMM_WORLD,&viewer);CHKERRQ(ierr); ierr = PetscOptionsView(viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); } if (!nopt) { ierr = PetscPrintf(PETSC_COMM_WORLD,"There are no unused options.\n");CHKERRQ(ierr); } else if (nopt == 1) { ierr = PetscPrintf(PETSC_COMM_WORLD,"There is one unused database option. It is:\n");CHKERRQ(ierr); } else { ierr = PetscPrintf(PETSC_COMM_WORLD,"There are %D unused database options. They are:\n",nopt);CHKERRQ(ierr); } } #if defined(PETSC_USE_DEBUG) if (nopt && !flg3 && !flg1) { ierr = PetscPrintf(PETSC_COMM_WORLD,"WARNING! There are options you set that were not used!\n");CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"WARNING! could be spelling mistake, etc!\n");CHKERRQ(ierr); ierr = PetscOptionsLeft();CHKERRQ(ierr); } else if (nopt && flg3) { #else if (nopt && flg3) { #endif ierr = PetscOptionsLeft();CHKERRQ(ierr); } } { PetscThreadComm tcomm_world; ierr = PetscGetThreadCommWorld(&tcomm_world);CHKERRQ(ierr); /* Free global thread communicator */ ierr = PetscThreadCommDestroy(&tcomm_world);CHKERRQ(ierr); } /* List all objects the user may have forgot to free */ ierr = PetscOptionsHasName(NULL,"-objects_dump",&flg1);CHKERRQ(ierr); if (flg1) { MPI_Comm local_comm; char string[64]; ierr = PetscOptionsGetString(NULL,"-objects_dump",string,64,NULL);CHKERRQ(ierr); ierr = MPI_Comm_dup(MPI_COMM_WORLD,&local_comm);CHKERRQ(ierr); ierr = PetscSequentialPhaseBegin_Private(local_comm,1);CHKERRQ(ierr); ierr = PetscObjectsDump(stdout,(string[0] == 'a') ? PETSC_TRUE : PETSC_FALSE);CHKERRQ(ierr); ierr = PetscSequentialPhaseEnd_Private(local_comm,1);CHKERRQ(ierr); ierr = MPI_Comm_free(&local_comm);CHKERRQ(ierr); } PetscObjectsCounts = 0; PetscObjectsMaxCounts = 0; ierr = PetscFree(PetscObjects);CHKERRQ(ierr); #if defined(PETSC_USE_LOG) ierr = PetscLogDestroy();CHKERRQ(ierr); #endif /* Destroy any packages that registered a finalize */ ierr = PetscRegisterFinalizeAll();CHKERRQ(ierr); /* Destroy all the function registration lists created */ ierr = PetscFinalize_DynamicLibraries();CHKERRQ(ierr); /* Print PetscFunctionLists that have not been properly freed ierr = PetscFunctionListPrintAll();CHKERRQ(ierr); */ if (petsc_history) { ierr = PetscCloseHistoryFile(&petsc_history);CHKERRQ(ierr); petsc_history = 0; } ierr = PetscInfoAllow(PETSC_FALSE,NULL);CHKERRQ(ierr); { char fname[PETSC_MAX_PATH_LEN]; FILE *fd; int err; fname[0] = 0; ierr = PetscOptionsGetString(NULL,"-malloc_dump",fname,250,&flg1);CHKERRQ(ierr); flg2 = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-malloc_test",&flg2,NULL);CHKERRQ(ierr); #if defined(PETSC_USE_DEBUG) if (PETSC_RUNNING_ON_VALGRIND) flg2 = PETSC_FALSE; #else flg2 = PETSC_FALSE; /* Skip reporting for optimized builds regardless of -malloc_test */ #endif if (flg1 && fname[0]) { char sname[PETSC_MAX_PATH_LEN]; sprintf(sname,"%s_%d",fname,rank); fd = fopen(sname,"w"); if (!fd) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Cannot open log file: %s",sname); ierr = PetscMallocDump(fd);CHKERRQ(ierr); err = fclose(fd); if (err) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SYS,"fclose() failed on file"); } else if (flg1 || flg2) { MPI_Comm local_comm; ierr = MPI_Comm_dup(MPI_COMM_WORLD,&local_comm);CHKERRQ(ierr); ierr = PetscSequentialPhaseBegin_Private(local_comm,1);CHKERRQ(ierr); ierr = PetscMallocDump(stdout);CHKERRQ(ierr); ierr = PetscSequentialPhaseEnd_Private(local_comm,1);CHKERRQ(ierr); ierr = MPI_Comm_free(&local_comm);CHKERRQ(ierr); } } { char fname[PETSC_MAX_PATH_LEN]; FILE *fd = NULL; fname[0] = 0; ierr = PetscOptionsGetString(NULL,"-malloc_log",fname,250,&flg1);CHKERRQ(ierr); ierr = PetscOptionsHasName(NULL,"-malloc_log_threshold",&flg2);CHKERRQ(ierr); if (flg1 && fname[0]) { int err; if (!rank) { fd = fopen(fname,"w"); if (!fd) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Cannot open log file: %s",fname); } ierr = PetscMallocDumpLog(fd);CHKERRQ(ierr); if (fd) { err = fclose(fd); if (err) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SYS,"fclose() failed on file"); } } else if (flg1 || flg2) { ierr = PetscMallocDumpLog(stdout);CHKERRQ(ierr); } } /* Can be destroyed only after all the options are used */ ierr = PetscOptionsDestroy();CHKERRQ(ierr); PetscGlobalArgc = 0; PetscGlobalArgs = 0; #if defined(PETSC_USE_REAL___FLOAT128) ierr = MPI_Type_free(&MPIU___FLOAT128);CHKERRQ(ierr); #if defined(PETSC_HAVE_COMPLEX) ierr = MPI_Type_free(&MPIU___COMPLEX128);CHKERRQ(ierr); #endif ierr = MPI_Op_free(&MPIU_MAX);CHKERRQ(ierr); ierr = MPI_Op_free(&MPIU_MIN);CHKERRQ(ierr); #endif #if defined(PETSC_HAVE_COMPLEX) #if !defined(PETSC_HAVE_MPI_C_DOUBLE_COMPLEX) ierr = MPI_Type_free(&MPIU_C_DOUBLE_COMPLEX);CHKERRQ(ierr); ierr = MPI_Type_free(&MPIU_C_COMPLEX);CHKERRQ(ierr); #endif #endif #if (defined(PETSC_HAVE_COMPLEX) && !defined(PETSC_HAVE_MPI_C_DOUBLE_COMPLEX)) || defined(PETSC_USE_REAL___FLOAT128) ierr = MPI_Op_free(&MPIU_SUM);CHKERRQ(ierr); #endif ierr = MPI_Type_free(&MPIU_2SCALAR);CHKERRQ(ierr); #if defined(PETSC_USE_64BIT_INDICES) || !defined(MPI_2INT) ierr = MPI_Type_free(&MPIU_2INT);CHKERRQ(ierr); #endif ierr = MPI_Op_free(&PetscMaxSum_Op);CHKERRQ(ierr); ierr = MPI_Op_free(&PetscADMax_Op);CHKERRQ(ierr); ierr = MPI_Op_free(&PetscADMin_Op);CHKERRQ(ierr); /* Destroy any known inner MPI_Comm's and attributes pointing to them Note this will not destroy any new communicators the user has created. If all PETSc objects were not destroyed those left over objects will have hanging references to the MPI_Comms that were freed; but that is ok because those PETSc objects will never be used again */ { PetscCommCounter *counter; PetscMPIInt flg; MPI_Comm icomm; union {MPI_Comm comm; void *ptr;} ucomm; ierr = MPI_Attr_get(PETSC_COMM_SELF,Petsc_InnerComm_keyval,&ucomm,&flg);CHKERRQ(ierr); if (flg) { icomm = ucomm.comm; ierr = MPI_Attr_get(icomm,Petsc_Counter_keyval,&counter,&flg);CHKERRQ(ierr); if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_CORRUPT,"Inner MPI_Comm does not have expected tag/name counter, problem with corrupted memory"); ierr = MPI_Attr_delete(PETSC_COMM_SELF,Petsc_InnerComm_keyval);CHKERRQ(ierr); ierr = MPI_Attr_delete(icomm,Petsc_Counter_keyval);CHKERRQ(ierr); ierr = MPI_Comm_free(&icomm);CHKERRQ(ierr); } ierr = MPI_Attr_get(PETSC_COMM_WORLD,Petsc_InnerComm_keyval,&ucomm,&flg);CHKERRQ(ierr); if (flg) { icomm = ucomm.comm; ierr = MPI_Attr_get(icomm,Petsc_Counter_keyval,&counter,&flg);CHKERRQ(ierr); if (!flg) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_CORRUPT,"Inner MPI_Comm does not have expected tag/name counter, problem with corrupted memory"); ierr = MPI_Attr_delete(PETSC_COMM_WORLD,Petsc_InnerComm_keyval);CHKERRQ(ierr); ierr = MPI_Attr_delete(icomm,Petsc_Counter_keyval);CHKERRQ(ierr); ierr = MPI_Comm_free(&icomm);CHKERRQ(ierr); } } ierr = MPI_Keyval_free(&Petsc_Counter_keyval);CHKERRQ(ierr); ierr = MPI_Keyval_free(&Petsc_InnerComm_keyval);CHKERRQ(ierr); ierr = MPI_Keyval_free(&Petsc_OuterComm_keyval);CHKERRQ(ierr); #if defined(PETSC_HAVE_CUDA) { PetscInt p; for (p = 0; p < PetscGlobalSize; ++p) { if (p == PetscGlobalRank) cublasShutdown(); ierr = MPI_Barrier(PETSC_COMM_WORLD);CHKERRQ(ierr); } } #endif if (PetscBeganMPI) { #if defined(PETSC_HAVE_MPI_FINALIZED) PetscMPIInt flag; ierr = MPI_Finalized(&flag);CHKERRQ(ierr); if (flag) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"MPI_Finalize() has already been called, even though MPI_Init() was called by PetscInitialize()"); #endif ierr = MPI_Finalize();CHKERRQ(ierr); } /* Note: In certain cases PETSC_COMM_WORLD is never MPI_Comm_free()ed because the communicator has some outstanding requests on it. Specifically if the flag PETSC_HAVE_BROKEN_REQUEST_FREE is set (for IBM MPI implementation). See src/vec/utils/vpscat.c. Due to this the memory allocated in PetscCommDuplicate() is never freed as it should be. Thus one may obtain messages of the form [ 1] 8 bytes PetscCommDuplicate() line 645 in src/sys/mpiu.c indicating the memory was not freed. */ ierr = PetscMallocClear();CHKERRQ(ierr); PetscInitializeCalled = PETSC_FALSE; PetscFinalizeCalled = PETSC_TRUE; PetscFunctionReturn(ierr); } #if defined(PETSC_MISSING_LAPACK_lsame_) PETSC_EXTERN int lsame_(char *a,char *b) { if (*a == *b) return 1; if (*a + 32 == *b) return 1; if (*a - 32 == *b) return 1; return 0; } #endif #if defined(PETSC_MISSING_LAPACK_lsame) PETSC_EXTERN int lsame(char *a,char *b) { if (*a == *b) return 1; if (*a + 32 == *b) return 1; if (*a - 32 == *b) return 1; return 0; }
PETSC_EXTERN void PETSC_STDCALL petscpopsignalhandler_(int *__ierr ){ *__ierr = PetscPopSignalHandler(); }