/*@C PetscStartMatlab - starts up MATLAB with a MATLAB script Logically Collective on MPI_Comm, but only processor zero in the communicator does anything Input Parameters: + comm - MPI communicator . machine - optional machine to run MATLAB on - script - name of script (without the .m) Output Parameter: . fp - a file pointer returned from PetscPOpen() Level: intermediate Notes: This overwrites your matlab/startup.m file The script must be in your MATLAB path or current directory Assumes that all machines share a common file system .seealso: PetscPOpen(), PetscPClose() @*/ PetscErrorCode PetscStartMatlab(MPI_Comm comm,const char machine[],const char script[],FILE **fp) { PetscErrorCode ierr; FILE *fd; char command[512]; #if defined(PETSC_HAVE_UCBPS) && defined(PETSC_HAVE_POPEN) char buf[1024],*found; PetscMPIInt rank; #endif PetscFunctionBegin; #if defined(PETSC_HAVE_UCBPS) && defined(PETSC_HAVE_POPEN) /* check if MATLAB is not already running */ ierr = PetscPOpen(comm,machine,"/usr/ucb/ps -ugxww | grep matlab | grep -v grep","r",&fd);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); if (!rank) found = fgets(buf,1024,fd); ierr = MPI_Bcast(&found,1,MPI_CHAR,0,comm);CHKERRQ(ierr); ierr = PetscPClose(comm,fd,NULL);CHKERRQ(ierr); if (found) PetscFunctionReturn(0); #endif if (script) { /* the remote machine won't know about current directory, so add it to MATLAB path */ /* the extra \" are to protect possible () in the script command from the shell */ sprintf(command,"echo \"delete ${HOMEDIRECTORY}/matlab/startup.m ; path(path,'${WORKINGDIRECTORY}'); %s \" > ${HOMEDIRECTORY}/matlab/startup.m",script); #if defined(PETSC_HAVE_POPEN) ierr = PetscPOpen(comm,machine,command,"r",&fd);CHKERRQ(ierr); ierr = PetscPClose(comm,fd,NULL);CHKERRQ(ierr); #endif } #if defined(PETSC_HAVE_POPEN) ierr = PetscPOpen(comm,machine,"xterm -display ${DISPLAY} -e matlab -nosplash","r",fp);CHKERRQ(ierr); #endif PetscFunctionReturn(0); }
PetscErrorCode PetscLs(MPI_Comm comm,const char libname[],char found[],size_t tlen,PetscBool *flg) { PetscErrorCode ierr; size_t len; char *f,program[PETSC_MAX_PATH_LEN]; FILE *fp; PetscFunctionBegin; ierr = PetscStrcpy(program,"ls ");CHKERRQ(ierr); ierr = PetscStrcat(program,libname);CHKERRQ(ierr); #if defined(PETSC_HAVE_POPEN) ierr = PetscPOpen(comm,PETSC_NULL,program,"r",&fp);CHKERRQ(ierr); #else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP_SYS,"Cannot run external programs on this machine"); #endif f = fgets(found,tlen,fp); if (f) *flg = PETSC_TRUE; else *flg = PETSC_FALSE; while (f) { ierr = PetscStrlen(found,&len);CHKERRQ(ierr); f = fgets(found+len,tlen-len,fp); } if (*flg) {ierr = PetscInfo2(0,"ls on %s gives \n%s\n",libname,found);CHKERRQ(ierr);} #if defined(PETSC_HAVE_POPEN) ierr = PetscPClose(comm,fp);CHKERRQ(ierr); #else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP_SYS,"Cannot run external programs on this machine"); #endif PetscFunctionReturn(0); }
static PetscErrorCode PetscViewerFileClose_ASCII(PetscViewer viewer) { PetscErrorCode ierr; PetscMPIInt rank; PetscViewer_ASCII *vascii = (PetscViewer_ASCII *)viewer->data; int err; PetscFunctionBegin; ierr = MPI_Comm_rank(((PetscObject)viewer)->comm,&rank);CHKERRQ(ierr); if (!rank && vascii->fd != stderr && vascii->fd != PETSC_STDOUT) { if (vascii->fd && vascii->closefile) { err = fclose(vascii->fd); if (err) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SYS,"fclose() failed on file"); } if (vascii->storecompressed) { char par[PETSC_MAX_PATH_LEN],buf[PETSC_MAX_PATH_LEN]; FILE *fp; ierr = PetscStrcpy(par,"gzip ");CHKERRQ(ierr); ierr = PetscStrcat(par,vascii->filename);CHKERRQ(ierr); #if defined(PETSC_HAVE_POPEN) ierr = PetscPOpen(PETSC_COMM_SELF,PETSC_NULL,par,"r",&fp);CHKERRQ(ierr); if (fgets(buf,1024,fp)) { SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error from compression command %s\n%s",par,buf); } ierr = PetscPClose(PETSC_COMM_SELF,fp);CHKERRQ(ierr); #else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP_SYS,"Cannot run external programs on this machine"); #endif } } ierr = PetscFree(vascii->filename);CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode PetscDrawDestroy_X(PetscDraw draw) { PetscDraw_X *win = (PetscDraw_X*)draw->data; PetscErrorCode ierr; #if defined(PETSC_HAVE_POPEN) char command[PETSC_MAX_PATH_LEN]; PetscMPIInt rank; FILE *fd; #endif PetscFunctionBegin; ierr = PetscDrawSynchronizedClear(draw);CHKERRQ(ierr); #if defined(PETSC_HAVE_POPEN) ierr = MPI_Comm_rank(((PetscObject)draw)->comm,&rank);CHKERRQ(ierr); if (draw->savefilename && !rank && draw->savefilemovie) { ierr = PetscSNPrintf(command,PETSC_MAX_PATH_LEN,"ffmpeg -i %s_%%d.Gif %s.m4v",draw->savefilename,draw->savefilename);CHKERRQ(ierr); ierr = PetscPOpen(((PetscObject)draw)->comm,PETSC_NULL,command,"r",&fd);CHKERRQ(ierr); ierr = PetscPClose(((PetscObject)draw)->comm,fd,PETSC_NULL);CHKERRQ(ierr); } #endif XFreeGC(win->disp,win->gc.set); XCloseDisplay(win->disp); ierr = PetscDrawDestroy(&draw->popup);CHKERRQ(ierr); ierr = PetscFree(win->font);CHKERRQ(ierr); ierr = PetscFree(win);CHKERRQ(ierr); PetscFunctionReturn(0); }
static PetscErrorCode PetscViewerFileClose_Binary(PetscViewer v) { PetscViewer_Binary *vbinary = (PetscViewer_Binary*)v->data; PetscErrorCode ierr; PetscMPIInt rank; int err; PetscFunctionBegin; ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)v),&rank);CHKERRQ(ierr); if ((!rank || vbinary->btype == FILE_MODE_READ) && vbinary->fdes) { close(vbinary->fdes); if (!rank && vbinary->storecompressed) { char par[PETSC_MAX_PATH_LEN],buf[PETSC_MAX_PATH_LEN]; FILE *fp; /* compress the file */ ierr = PetscStrcpy(par,"gzip -f ");CHKERRQ(ierr); ierr = PetscStrcat(par,vbinary->filename);CHKERRQ(ierr); #if defined(PETSC_HAVE_POPEN) ierr = PetscPOpen(PETSC_COMM_SELF,NULL,par,"r",&fp);CHKERRQ(ierr); if (fgets(buf,1024,fp)) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error from command %s\n%s",par,buf); ierr = PetscPClose(PETSC_COMM_SELF,fp,NULL);CHKERRQ(ierr); #else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP_SYS,"Cannot run external programs on this machine"); #endif } } if (vbinary->fdes_info) { err = fclose(vbinary->fdes_info); if (err) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SYS,"fclose() failed on file"); } ierr = PetscFree(vbinary->filename);CHKERRQ(ierr); PetscFunctionReturn(0); }
/*@C PetscEmacsClientErrorHandler - Error handler that uses the emacsclient program to load the file where the error occured. Then calls the "previous" error handler. Not Collective Input Parameters: + comm - communicator over which error occured . line - the line number of the error (indicated by __LINE__) . func - the function where error is detected (indicated by __FUNCT__) . file - the file in which the error was detected (indicated by __FILE__) . dir - the directory of the file (indicated by __SDIR__) . mess - an error text string, usually just printed to the screen . n - the generic error number . p - specific error number - ctx - error handler context Options Database Key: . -on_error_emacs <machinename> Level: developer Notes: You must put (server-start) in your .emacs file for the emacsclient software to work Most users need not directly employ this routine and the other error handlers, but can instead use the simplified interface SETERRQ, which has the calling sequence $ SETERRQ(PETSC_COMM_SELF,number,p,mess) Notes for experienced users: Use PetscPushErrorHandler() to set the desired error handler. Developer Note: Since this is an error handler it cannot call CHKERRQ(); thus we just return if an error is detected. Concepts: emacs^going to on error Concepts: error handler^going to line in emacs .seealso: PetscPushErrorHandler(), PetscAttachDebuggerErrorHandler(), PetscAbortErrorHandler() @*/ PetscErrorCode PetscEmacsClientErrorHandler(MPI_Comm comm,int line,const char *fun,const char *file,const char *dir,PetscErrorCode n,PetscErrorType p,const char *mess,void *ctx) { PetscErrorCode ierr; char command[PETSC_MAX_PATH_LEN]; const char *pdir; FILE *fp; PetscInt rval; PetscFunctionBegin; ierr = PetscGetPetscDir(&pdir);if (ierr) PetscFunctionReturn(ierr); sprintf(command,"cd %s; emacsclient --no-wait +%d %s%s\n",pdir,line,dir,file); #if defined(PETSC_HAVE_POPEN) ierr = PetscPOpen(MPI_COMM_WORLD,(char*)ctx,command,"r",&fp);if (ierr) PetscFunctionReturn(ierr); ierr = PetscPClose(MPI_COMM_WORLD,fp,&rval);if (ierr) PetscFunctionReturn(ierr); #else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP_SYS,"Cannot run external programs on this machine"); #endif ierr = PetscPopErrorHandler();if (ierr) PetscFunctionReturn(ierr); /* remove this handler from the stack of handlers */ if (!eh) { ierr = PetscTraceBackErrorHandler(comm,line,fun,file,dir,n,p,mess,0);if (ierr) PetscFunctionReturn(ierr); } else { ierr = (*eh->handler)(comm,line,fun,file,dir,n,p,mess,eh->ctx);if (ierr) PetscFunctionReturn(ierr); } PetscFunctionReturn(ierr); }
/* PFStringCreateFunction - Creates a function from a string Collective over PF Input Parameters: + pf - the function object - string - the string that defines the function Output Parameter: . f - the function pointer. .seealso: PFSetFromOptions() */ PetscErrorCode PETSCVEC_DLLEXPORT PFStringCreateFunction(PF pf,char *string,void **f) { #if defined(PETSC_USE_DYNAMIC_LIBRARIES) PetscErrorCode ierr; char task[1024],tmp[256],lib[PETSC_MAX_PATH_LEN],username[64]; FILE *fd; PetscTruth tmpshared,wdshared,keeptmpfiles = PETSC_FALSE; MPI_Comm comm; #endif PetscFunctionBegin; #if defined(PETSC_USE_DYNAMIC_LIBRARIES) ierr = PetscStrfree(pf->data);CHKERRQ(ierr); ierr = PetscStrallocpy(string,(char**)&pf->data);CHKERRQ(ierr); /* create the new C function and compile it */ ierr = PetscSharedTmp(((PetscObject)pf)->comm,&tmpshared);CHKERRQ(ierr); ierr = PetscSharedWorkingDirectory(((PetscObject)pf)->comm,&wdshared);CHKERRQ(ierr); if (tmpshared) { /* do it in /tmp since everyone has one */ ierr = PetscGetTmp(((PetscObject)pf)->comm,tmp,PETSC_MAX_PATH_LEN);CHKERRQ(ierr); comm = ((PetscObject)pf)->comm; } else if (!wdshared) { /* each one does in private /tmp */ ierr = PetscGetTmp(((PetscObject)pf)->comm,tmp,PETSC_MAX_PATH_LEN);CHKERRQ(ierr); comm = PETSC_COMM_SELF; } else { /* do it in current directory */ ierr = PetscStrcpy(tmp,".");CHKERRQ(ierr); comm = ((PetscObject)pf)->comm; } ierr = PetscOptionsGetTruth(((PetscObject)pf)->prefix,"-pf_string_keep_files",&keeptmpfiles,PETSC_NULL);CHKERRQ(ierr); if (keeptmpfiles) { sprintf(task,"cd %s ; mkdir ${USERNAME} ; cd ${USERNAME} ; \\cp -f ${PETSC_DIR}/src/pf/impls/string/makefile ./makefile ; ke MIN=%d NOUT=%d petscdlib STRINGFUNCTION=\"%s\" ; sync\n",tmp,(int)pf->dimin,(int)pf->dimout,string); } else { sprintf(task,"cd %s ; mkdir ${USERNAME} ;cd ${USERNAME} ; \\cp -f ${PETSC_DIR}/src/pf/impls/string/makefile ./makefile ; make MIN=%d NOUT=%d -f makefile petscdlib STRINGFUNCTION=\"%s\" ; \\rm -f makefile petscdlib.c libpetscdlib.a ; sync\n",tmp,(int)pf->dimin,(int)pf->dimout,string); } #if defined(PETSC_HAVE_POPEN) ierr = PetscPOpen(comm,PETSC_NULL,task,"r",&fd);CHKERRQ(ierr); ierr = PetscPClose(comm,fd);CHKERRQ(ierr); #else SETERRQ(PETSC_ERR_SUP_SYS,"Cannot run external programs on this machine"); #endif ierr = MPI_Barrier(comm);CHKERRQ(ierr); /* load the apply function from the dynamic library */ ierr = PetscGetUserName(username,64);CHKERRQ(ierr); sprintf(lib,"%s/%s/libpetscdlib",tmp,username); ierr = PetscDLLibrarySym(comm,PETSC_NULL,lib,"PFApply_String",f);CHKERRQ(ierr); #endif PetscFunctionReturn(0); }
static PetscErrorCode PetscPythonFindLibrary(char pythonexe[PETSC_MAX_PATH_LEN],char pythonlib[PETSC_MAX_PATH_LEN]) { const char cmdline[] = "-c 'import sys; print(sys.exec_prefix); print(sys.version[:3])'"; char command[PETSC_MAX_PATH_LEN+1+sizeof(cmdline)+1]; char prefix[PETSC_MAX_PATH_LEN],version[8],sep[2]={PETSC_DIR_SEPARATOR, 0},*eol; FILE *fp = NULL; char path[PETSC_MAX_PATH_LEN+1]; PetscBool found = PETSC_FALSE; PetscErrorCode ierr; PetscFunctionBegin; #if defined(PETSC_PYTHON_LIB) ierr = PetscStrcpy(pythonlib,PETSC_PYTHON_LIB);CHKERRQ(ierr); PetscFunctionReturn(0); #endif /* call Python to find out the name of the Python dynamic library */ ierr = PetscStrncpy(command,pythonexe,PETSC_MAX_PATH_LEN);CHKERRQ(ierr); ierr = PetscStrcat(command," ");CHKERRQ(ierr); ierr = PetscStrcat(command,cmdline);CHKERRQ(ierr); #if defined(PETSC_HAVE_POPEN) ierr = PetscPOpen(PETSC_COMM_SELF,NULL,command,"r",&fp);CHKERRQ(ierr); if (!fgets(prefix,sizeof(prefix),fp)) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Python: bad output from executable: %s",pythonexe); if (!fgets(version,sizeof(version),fp)) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Python: bad output from executable: %s",pythonexe); ierr = PetscPClose(PETSC_COMM_SELF,fp,NULL);CHKERRQ(ierr); #else SETERRQ(PETSC_COMM_SELF,1,"Python: Aborted due to missing popen()"); #endif /* remove newlines */ ierr = PetscStrchr(prefix,'\n',&eol);CHKERRQ(ierr); if (eol) eol[0] = 0; ierr = PetscStrchr(version,'\n',&eol);CHKERRQ(ierr); if (eol) eol[0] = 0; /* test for $prefix/lib64/libpythonX.X[.so]*/ ierr = PetscStrcpy(pythonlib,prefix);CHKERRQ(ierr); ierr = PetscStrcat(pythonlib,sep);CHKERRQ(ierr); ierr = PetscStrcat(pythonlib,"lib64");CHKERRQ(ierr); ierr = PetscTestDirectory(pythonlib,'r',&found);CHKERRQ(ierr); if (found) { ierr = PetscStrcat(pythonlib,sep);CHKERRQ(ierr); ierr = PetscStrcat(pythonlib,"libpython");CHKERRQ(ierr); ierr = PetscStrcat(pythonlib,version);CHKERRQ(ierr); ierr = PetscDLLibraryRetrieve(PETSC_COMM_SELF,pythonlib,path,PETSC_MAX_PATH_LEN,&found);CHKERRQ(ierr); if (found) PetscFunctionReturn(0); } /* test for $prefix/lib/libpythonX.X[.so]*/ ierr = PetscStrcpy(pythonlib,prefix);CHKERRQ(ierr); ierr = PetscStrcat(pythonlib,sep);CHKERRQ(ierr); ierr = PetscStrcat(pythonlib,"lib");CHKERRQ(ierr); ierr = PetscTestDirectory(pythonlib,'r',&found);CHKERRQ(ierr); if (found) { ierr = PetscStrcat(pythonlib,sep);CHKERRQ(ierr); ierr = PetscStrcat(pythonlib,"libpython");CHKERRQ(ierr); ierr = PetscStrcat(pythonlib,version);CHKERRQ(ierr); ierr = PetscDLLibraryRetrieve(PETSC_COMM_SELF,pythonlib,path,PETSC_MAX_PATH_LEN,&found);CHKERRQ(ierr); if (found) PetscFunctionReturn(0); } /* nothing good found */ ierr = PetscMemzero(pythonlib,PETSC_MAX_PATH_LEN);CHKERRQ(ierr); ierr = PetscInfo(0,"Python dynamic library not found\n");CHKERRQ(ierr); PetscFunctionReturn(0); }
/*@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; }
PetscErrorCode PetscOptionsCheckInitial_Private(void) { char string[64],mname[PETSC_MAX_PATH_LEN],*f; MPI_Comm comm = PETSC_COMM_WORLD; PetscBool flg1 = PETSC_FALSE,flg2 = PETSC_FALSE,flg3 = PETSC_FALSE,flg4 = PETSC_FALSE,flag; PetscErrorCode ierr; PetscReal si,logthreshold; int i; PetscMPIInt rank; char version[256]; PetscFunctionBegin; ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); /* Setup the memory management; support for tracing malloc() usage */ ierr = PetscOptionsHasName(NULL,"-malloc_log",&flg3);CHKERRQ(ierr); logthreshold = 0.0; ierr = PetscOptionsGetReal(NULL,"-malloc_log_threshold",&logthreshold,&flg1);CHKERRQ(ierr); if (flg1) flg3 = PETSC_TRUE; #if defined(PETSC_USE_DEBUG) ierr = PetscOptionsGetBool(NULL,"-malloc",&flg1,&flg2);CHKERRQ(ierr); if ((!flg2 || flg1) && !petscsetmallocvisited) { if (flg2 || !(PETSC_RUNNING_ON_VALGRIND)) { /* turn off default -malloc if valgrind is being used */ ierr = PetscSetUseTrMalloc_Private();CHKERRQ(ierr); } } #else ierr = PetscOptionsGetBool(NULL,"-malloc_dump",&flg1,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,"-malloc",&flg2,NULL);CHKERRQ(ierr); if (flg1 || flg2 || flg3) {ierr = PetscSetUseTrMalloc_Private();CHKERRQ(ierr);} #endif if (flg3) { ierr = PetscMallocSetDumpLogThreshold((PetscLogDouble)logthreshold);CHKERRQ(ierr); } flg1 = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-malloc_debug",&flg1,NULL);CHKERRQ(ierr); if (flg1) { ierr = PetscSetUseTrMalloc_Private();CHKERRQ(ierr); ierr = PetscMallocDebug(PETSC_TRUE);CHKERRQ(ierr); } flg1 = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-malloc_test",&flg1,NULL);CHKERRQ(ierr); #if defined(PETSC_USE_DEBUG) if (flg1 && !PETSC_RUNNING_ON_VALGRIND) { ierr = PetscSetUseTrMalloc_Private();CHKERRQ(ierr); ierr = PetscMallocSetDumpLog();CHKERRQ(ierr); ierr = PetscMallocDebug(PETSC_TRUE);CHKERRQ(ierr); } #endif flg1 = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-malloc_info",&flg1,NULL);CHKERRQ(ierr); if (!flg1) { flg1 = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-memory_info",&flg1,NULL);CHKERRQ(ierr); } if (flg1) { ierr = PetscMemorySetGetMaximumUsage();CHKERRQ(ierr); } /* Set the display variable for graphics */ ierr = PetscSetDisplay();CHKERRQ(ierr); /* Print the PETSc version information */ ierr = PetscOptionsHasName(NULL,"-v",&flg1);CHKERRQ(ierr); ierr = PetscOptionsHasName(NULL,"-version",&flg2);CHKERRQ(ierr); ierr = PetscOptionsHasName(NULL,"-help",&flg3);CHKERRQ(ierr); if (flg1 || flg2 || flg3) { /* Print "higher-level" package version message */ if (PetscExternalVersionFunction) { ierr = (*PetscExternalVersionFunction)(comm);CHKERRQ(ierr); } ierr = PetscGetVersion(version,256);CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm,"--------------------------------------------\ ------------------------------\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm,"%s\n",version);CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm,"%s",PETSC_AUTHOR_INFO);CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm,"See docs/changes/index.html for recent updates.\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm,"See docs/faq.html for problems.\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm,"See docs/manualpages/index.html for help. \n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm,"Libraries linked from %s\n",PETSC_LIB_DIR);CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm,"--------------------------------------------\ ------------------------------\n");CHKERRQ(ierr); } /* Print "higher-level" package help message */ if (flg3) { if (PetscExternalHelpFunction) { ierr = (*PetscExternalHelpFunction)(comm);CHKERRQ(ierr); } } /* Setup the error handling */ flg1 = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-on_error_abort",&flg1,NULL);CHKERRQ(ierr); if (flg1) { ierr = MPI_Comm_set_errhandler(PETSC_COMM_WORLD,MPI_ERRORS_ARE_FATAL);CHKERRQ(ierr); ierr = PetscPushErrorHandler(PetscAbortErrorHandler,0);CHKERRQ(ierr); } flg1 = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-on_error_mpiabort",&flg1,NULL);CHKERRQ(ierr); if (flg1) { ierr = PetscPushErrorHandler(PetscMPIAbortErrorHandler,0);CHKERRQ(ierr);} flg1 = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-mpi_return_on_error",&flg1,NULL);CHKERRQ(ierr); if (flg1) { ierr = MPI_Comm_set_errhandler(comm,MPI_ERRORS_RETURN);CHKERRQ(ierr); } flg1 = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-no_signal_handler",&flg1,NULL);CHKERRQ(ierr); if (!flg1) {ierr = PetscPushSignalHandler(PetscSignalHandlerDefault,(void*)0);CHKERRQ(ierr);} flg1 = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-fp_trap",&flg1,NULL);CHKERRQ(ierr); if (flg1) {ierr = PetscSetFPTrap(PETSC_FP_TRAP_ON);CHKERRQ(ierr);} /* Setup debugger information */ ierr = PetscSetDefaultDebugger();CHKERRQ(ierr); ierr = PetscOptionsGetString(NULL,"-on_error_attach_debugger",string,64,&flg1);CHKERRQ(ierr); if (flg1) { MPI_Errhandler err_handler; ierr = PetscSetDebuggerFromString(string);CHKERRQ(ierr); ierr = MPI_Comm_create_errhandler((MPI_Handler_function*)Petsc_MPI_DebuggerOnError,&err_handler);CHKERRQ(ierr); ierr = MPI_Comm_set_errhandler(comm,err_handler);CHKERRQ(ierr); ierr = PetscPushErrorHandler(PetscAttachDebuggerErrorHandler,0);CHKERRQ(ierr); } ierr = PetscOptionsGetString(NULL,"-debug_terminal",string,64,&flg1);CHKERRQ(ierr); if (flg1) { ierr = PetscSetDebugTerminal(string);CHKERRQ(ierr); } ierr = PetscOptionsGetString(NULL,"-start_in_debugger",string,64,&flg1);CHKERRQ(ierr); ierr = PetscOptionsGetString(NULL,"-stop_for_debugger",string,64,&flg2);CHKERRQ(ierr); if (flg1 || flg2) { PetscMPIInt size; PetscInt lsize,*nodes; MPI_Errhandler err_handler; /* we have to make sure that all processors have opened connections to all other processors, otherwise once the debugger has stated it is likely to receive a SIGUSR1 and kill the program. */ ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); if (size > 2) { PetscMPIInt dummy = 0; MPI_Status status; for (i=0; i<size; i++) { if (rank != i) { ierr = MPI_Send(&dummy,1,MPI_INT,i,109,PETSC_COMM_WORLD);CHKERRQ(ierr); } } for (i=0; i<size; i++) { if (rank != i) { ierr = MPI_Recv(&dummy,1,MPI_INT,i,109,PETSC_COMM_WORLD,&status);CHKERRQ(ierr); } } } /* check if this processor node should be in debugger */ ierr = PetscMalloc(size*sizeof(PetscInt),&nodes);CHKERRQ(ierr); lsize = size; ierr = PetscOptionsGetIntArray(NULL,"-debugger_nodes",nodes,&lsize,&flag);CHKERRQ(ierr); if (flag) { for (i=0; i<lsize; i++) { if (nodes[i] == rank) { flag = PETSC_FALSE; break; } } } if (!flag) { ierr = PetscSetDebuggerFromString(string);CHKERRQ(ierr); ierr = PetscPushErrorHandler(PetscAbortErrorHandler,0);CHKERRQ(ierr); if (flg1) { ierr = PetscAttachDebugger();CHKERRQ(ierr); } else { ierr = PetscStopForDebugger();CHKERRQ(ierr); } ierr = MPI_Comm_create_errhandler((MPI_Handler_function*)Petsc_MPI_AbortOnError,&err_handler);CHKERRQ(ierr); ierr = MPI_Comm_set_errhandler(comm,err_handler);CHKERRQ(ierr); } ierr = PetscFree(nodes);CHKERRQ(ierr); } ierr = PetscOptionsGetString(NULL,"-on_error_emacs",emacsmachinename,128,&flg1);CHKERRQ(ierr); if (flg1 && !rank) {ierr = PetscPushErrorHandler(PetscEmacsClientErrorHandler,emacsmachinename);CHKERRQ(ierr);} /* Setup profiling and logging */ #if defined(PETSC_USE_INFO) { char logname[PETSC_MAX_PATH_LEN]; logname[0] = 0; ierr = PetscOptionsGetString(NULL,"-info",logname,250,&flg1);CHKERRQ(ierr); if (flg1 && logname[0]) { ierr = PetscInfoAllow(PETSC_TRUE,logname);CHKERRQ(ierr); } else if (flg1) { ierr = PetscInfoAllow(PETSC_TRUE,NULL);CHKERRQ(ierr); } } #endif #if defined(PETSC_USE_LOG) mname[0] = 0; ierr = PetscOptionsGetString(NULL,"-history",mname,PETSC_MAX_PATH_LEN,&flg1);CHKERRQ(ierr); if (flg1) { if (mname[0]) { ierr = PetscOpenHistoryFile(mname,&petsc_history);CHKERRQ(ierr); } else { ierr = PetscOpenHistoryFile(0,&petsc_history);CHKERRQ(ierr); } } #if defined(PETSC_HAVE_MPE) flg1 = PETSC_FALSE; ierr = PetscOptionsHasName(NULL,"-log_mpe",&flg1);CHKERRQ(ierr); if (flg1) {ierr = PetscLogMPEBegin();CHKERRQ(ierr);} #endif flg1 = PETSC_FALSE; flg2 = PETSC_FALSE; flg3 = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-log_all",&flg1,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,"-log",&flg2,NULL);CHKERRQ(ierr); ierr = PetscOptionsHasName(NULL,"-log_summary",&flg3);CHKERRQ(ierr); ierr = PetscOptionsHasName(NULL,"-log_summary_python",&flg4);CHKERRQ(ierr); if (flg1) { ierr = PetscLogAllBegin();CHKERRQ(ierr); } else if (flg2 || flg3 || flg4) { ierr = PetscLogBegin();CHKERRQ(ierr);} ierr = PetscOptionsGetString(NULL,"-log_trace",mname,250,&flg1);CHKERRQ(ierr); if (flg1) { char name[PETSC_MAX_PATH_LEN],fname[PETSC_MAX_PATH_LEN]; FILE *file; if (mname[0]) { sprintf(name,"%s.%d",mname,rank); ierr = PetscFixFilename(name,fname);CHKERRQ(ierr); file = fopen(fname,"w"); if (!file) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Unable to open trace file: %s",fname); } else file = PETSC_STDOUT; ierr = PetscLogTraceBegin(file);CHKERRQ(ierr); } #endif ierr = PetscOptionsGetBool(NULL,"-options_gui",&PetscOptionsPublish,NULL);CHKERRQ(ierr); #if defined(PETSC_HAVE_CUDA) ierr = PetscOptionsHasName(NULL,"-cuda_show_devices",&flg1);CHKERRQ(ierr); if (flg1) { struct cudaDeviceProp prop; int devCount; int device; ierr = cudaGetDeviceCount(&devCount);CHKERRQ(ierr); for (device = 0; device < devCount; ++device) { ierr = cudaGetDeviceProperties(&prop, device);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "CUDA device %d: %s\n", device, prop.name);CHKERRQ(ierr); } } { int size; ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); if (size>1) { int devCount, device, rank; ierr = cudaGetDeviceCount(&devCount);CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); device = rank % devCount; ierr = cudaSetDevice(device);CHKERRQ(ierr); } else { int device; /* the code below works for serial GPU simulations */ ierr = PetscOptionsGetInt(NULL,"-cuda_set_device", &device, &flg1);CHKERRQ(ierr); if (flg1) { ierr = cudaSetDevice(device);CHKERRQ(ierr); } } } #endif /* Print basic help message */ ierr = PetscOptionsHasName(NULL,"-help",&flg1);CHKERRQ(ierr); if (flg1) { ierr = (*PetscHelpPrintf)(comm,"Options for all PETSc programs:\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -help: prints help method for each option\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -on_error_abort: cause an abort when an error is detected. Useful \n ");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," only when run in the debugger\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -on_error_attach_debugger [gdb,dbx,xxgdb,ups,noxterm]\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," start the debugger in new xterm\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," unless noxterm is given\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -start_in_debugger [gdb,dbx,xxgdb,ups,noxterm]\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," start all processes in the debugger\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -on_error_emacs <machinename>\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," emacs jumps to error file\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -debugger_nodes [n1,n2,..] Nodes to start in debugger\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -debugger_pause [m] : delay (in seconds) to attach debugger\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -stop_for_debugger : prints message on how to attach debugger manually\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," waits the delay for you to attach\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -display display: Location where graphics and debuggers are displayed\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -no_signal_handler: do not trap error signals\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -mpi_return_on_error: MPI returns error code, rather than abort on internal error\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -fp_trap: stop on floating point exceptions\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," note on IBM RS6000 this slows run greatly\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -malloc_dump <optional filename>: dump list of unfreed memory at conclusion\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -malloc: use our error checking malloc\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -malloc no: don't use error checking malloc\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -malloc_info: prints total memory usage\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -malloc_log: keeps log of all memory allocations\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -malloc_debug: enables extended checking for memory corruption\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -options_table: dump list of options inputted\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -options_left: dump list of unused options\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -options_left no: don't dump list of unused options\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -tmp tmpdir: alternative /tmp directory\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -shared_tmp: tmp directory is shared by all processors\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -not_shared_tmp: each processor has separate tmp directory\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -memory_info: print memory usage at end of run\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -server <port>: Run PETSc webserver (default port is 8080) see PetscWebServe()\n");CHKERRQ(ierr); #if defined(PETSC_USE_LOG) ierr = (*PetscHelpPrintf)(comm," -get_total_flops: total flops over all processors\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -log[_summary _summary_python]: logging objects and events\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -log_trace [filename]: prints trace of all PETSc calls\n");CHKERRQ(ierr); #if defined(PETSC_HAVE_MPE) ierr = (*PetscHelpPrintf)(comm," -log_mpe: Also create logfile viewable through Jumpshot\n");CHKERRQ(ierr); #endif ierr = (*PetscHelpPrintf)(comm," -info <optional filename>: print informative messages about the calculations\n");CHKERRQ(ierr); #endif ierr = (*PetscHelpPrintf)(comm," -v: prints PETSc version number and release date\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -options_file <file>: reads options from file\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -petsc_sleep n: sleeps n seconds before running program\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm,"-----------------------------------------------\n");CHKERRQ(ierr); } #if defined(PETSC_HAVE_SERVER) flg1 = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-server",&flg1,NULL);CHKERRQ(ierr); if (flg1) { ierr = PetscPOpen(PETSC_COMM_WORLD,NULL,"${PETSC_DIR}/${PETSC_ARCH}/bin/petscwebserver","r",NULL);CHKERRQ(ierr); } #endif ierr = PetscOptionsGetReal(NULL,"-petsc_sleep",&si,&flg1);CHKERRQ(ierr); if (flg1) { ierr = PetscSleep(si);CHKERRQ(ierr); } ierr = PetscOptionsGetString(NULL,"-info_exclude",mname,PETSC_MAX_PATH_LEN,&flg1);CHKERRQ(ierr); ierr = PetscStrstr(mname,"null",&f);CHKERRQ(ierr); if (f) { ierr = PetscInfoDeactivateClass(0);CHKERRQ(ierr); } #if defined(PETSC_HAVE_CUSP) ierr = PetscOptionsHasName(NULL,"-log_summary",&flg3);CHKERRQ(ierr); if (flg3) flg1 = PETSC_TRUE; else flg1 = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-cusp_synchronize",&flg1,NULL);CHKERRQ(ierr); if (flg1) PetscCUSPSynchronize = PETSC_TRUE; #endif PetscFunctionReturn(0); }
/*@C PetscFileRetrieve - Obtains a library from a URL or compressed and copies into local disk space as uncompressed. Collective on MPI_Comm Input Parameter: + comm - processors accessing the library . libname - name of library, including entire URL (with or without .gz) - llen - length of llibname Output Parameter: + llibname - name of local copy of library - found - if found and retrieved the file Level: developer @*/ PetscErrorCode PetscFileRetrieve(MPI_Comm comm,const char libname[],char llibname[],size_t llen,PetscBool *found) { char buf[1024],tmpdir[PETSC_MAX_PATH_LEN],urlget[PETSC_MAX_PATH_LEN],*par; const char *pdir; FILE *fp; PetscErrorCode ierr; int i; PetscMPIInt rank; size_t len = 0; PetscBool flg1,flg2,flg3,sharedtmp,exists; #if defined(PETSC_HAVE_POPEN) int rval; #endif PetscFunctionBegin; *found = PETSC_FALSE; /* if file does not have an ftp:// or http:// or .gz then need not process file */ ierr = PetscStrstr(libname,".gz",&par);CHKERRQ(ierr); if (par) {ierr = PetscStrlen(par,&len);CHKERRQ(ierr);} ierr = PetscStrncmp(libname,"ftp://",6,&flg1);CHKERRQ(ierr); ierr = PetscStrncmp(libname,"http://",7,&flg2);CHKERRQ(ierr); ierr = PetscStrncmp(libname,"file://",7,&flg3);CHKERRQ(ierr); if (!flg1 && !flg2 && !flg3 && (!par || len != 3)) { ierr = PetscStrncpy(llibname,libname,llen);CHKERRQ(ierr); ierr = PetscTestFile(libname,'r',found);CHKERRQ(ierr); if (*found) { ierr = PetscInfo1(NULL,"Found file %s\n",libname);CHKERRQ(ierr); } else { ierr = PetscInfo1(NULL,"Did not find file %s\n",libname);CHKERRQ(ierr); } PetscFunctionReturn(0); } if (par && len == 3){ size_t llen; ierr = PetscStrlen(libname,&llen);CHKERRQ(ierr); ierr = PetscStrncpy(llibname,libname,llen);CHKERRQ(ierr); llibname[llen-len] = 0; ierr = PetscTestFile(llibname,'r',found);CHKERRQ(ierr); if (*found) { ierr = PetscInfo1(NULL,"Found uncompressed version of file %s\n",llibname);CHKERRQ(ierr); PetscFunctionReturn(0); } else { ierr = PetscInfo1(NULL,"Did not find uncompressed version of file %s\n",libname);CHKERRQ(ierr); } } /* Determine if all processors share a common /tmp */ ierr = PetscSharedTmp(comm,&sharedtmp);CHKERRQ(ierr); ierr = PetscOptionsGetenv(comm,"PETSC_TMP",tmpdir,PETSC_MAX_PATH_LEN,&flg1);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); if (!rank || !sharedtmp) { /* Construct the script to get URL file */ ierr = PetscGetPetscDir(&pdir);CHKERRQ(ierr); ierr = PetscStrcpy(urlget,pdir);CHKERRQ(ierr); ierr = PetscStrcat(urlget,"/bin/urlget");CHKERRQ(ierr); ierr = PetscTestFile(urlget,'r',&exists);CHKERRQ(ierr); if (!exists) { ierr = PetscTestFile("urlget",'r',&exists);CHKERRQ(ierr); if (!exists) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Cannot locate PETSc script urlget in %s or current directory",urlget); ierr = PetscStrcpy(urlget,"urlget");CHKERRQ(ierr); } ierr = PetscStrcat(urlget," ");CHKERRQ(ierr); /* are we using an alternative /tmp? */ if (flg1) { ierr = PetscStrcat(urlget,"-tmp ");CHKERRQ(ierr); ierr = PetscStrcat(urlget,tmpdir);CHKERRQ(ierr); ierr = PetscStrcat(urlget," ");CHKERRQ(ierr); } ierr = PetscStrcat(urlget,libname);CHKERRQ(ierr); ierr = PetscStrcat(urlget," 2>&1 ");CHKERRQ(ierr); #if defined(PETSC_HAVE_POPEN) ierr = PetscPOpen(PETSC_COMM_SELF,NULL,urlget,"r",&fp);CHKERRQ(ierr); #else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP_SYS,"Cannot run external programs on this machine"); #endif if (!fgets(buf,1024,fp)) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"No output from ${PETSC_DIR}/bin/urlget in getting file %s",libname); ierr = PetscInfo1(0,"Message back from urlget: %s\n",buf);CHKERRQ(ierr); ierr = PetscStrncmp(buf,"Error",5,&flg1);CHKERRQ(ierr); ierr = PetscStrncmp(buf,"Traceback",9,&flg2);CHKERRQ(ierr); #if defined(PETSC_HAVE_POPEN) ierr = PetscPClose(PETSC_COMM_SELF,fp,&rval);CHKERRQ(ierr); #endif if (flg1 || flg2) *found = PETSC_FALSE; else { *found = PETSC_TRUE; /* Check for \n and make it 0 */ for (i=0; i<1024; i++) { if (buf[i] == '\n') { buf[i] = 0; break; } } ierr = PetscStrncpy(llibname,buf,llen);CHKERRQ(ierr); } } if (sharedtmp) { /* send library name to all processors */ ierr = MPI_Bcast(found,1,MPIU_BOOL,0,comm);CHKERRQ(ierr); if (*found) { ierr = MPI_Bcast(llibname,llen,MPI_CHAR,0,comm);CHKERRQ(ierr); ierr = MPI_Bcast(found,1,MPIU_BOOL,0,comm);CHKERRQ(ierr); } } PetscFunctionReturn(0); }
PetscErrorCode waitForSignal(PetscInt waitTime) { PetscErrorCode ierr; FILE *fd1; PetscViewer fd; PetscInt iDone=0; PetscInt zero=0; PetscInt one=1; PetscInt fp; PetscInt numsignalfiles = 2; PetscTruth flg; if (firstTime) { ierr = PetscPrintf(PETSC_COMM_WORLD,"Initializing signaling module ...\n");CHKERRQ(ierr); ierr = PetscOptionsGetString(PETSC_NULL,"-signalscript",externalSignalScriptName,PETSC_MAX_PATH_LEN-1,&useExternalSignalScript);CHKERRQ(ierr); ierr = PetscOptionsHasName(PETSC_NULL,"-signalfiles",&useSignalFiles);CHKERRQ(ierr); if ((useExternalSignalScript) && (useSignalFiles)) { SETERRQ(1,"Cannot specify both an external signal script and signal files!"); } if ((!useExternalSignalScript) && (!useSignalFiles)) { SETERRQ(1,"Must specify an external signal script OR signal files!"); } if (useExternalSignalScript) { ierr = PetscPrintf(PETSC_COMM_WORLD,"External signaling script has been specified: %s\n",externalSignalScriptName);CHKERRQ(ierr); } if (useSignalFiles) { ierr = PetscOptionsGetStringArray(PETSC_NULL,"-signalfiles",signalfiles,&numsignalfiles,&flg);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Signal files have been specified: %s, %s\n",signalfiles[0],signalfiles[1]);CHKERRQ(ierr); ierr = PetscOptionsGetInt(PETSC_NULL,"-signalwaittime",&signalWaitTime,&flg);CHKERRQ(ierr); if (flg) { ierr = PetscPrintf(PETSC_COMM_WORLD,"Signal wait time of %d seconds has been specified\n",signalWaitTime);CHKERRQ(ierr); } else { signalWaitTime = -1; } } firstTime = PETSC_FALSE; } else { if (useExternalSignalScript) { ierr = PetscPOpen(PETSC_COMM_WORLD,PETSC_NULL,externalSignalScriptName,"r",&fd1);CHKERRQ(ierr); ierr = PetscPClose(PETSC_COMM_WORLD,fd1);CHKERRQ(ierr); } else { if (signalWaitTime>0) waitTime = signalWaitTime; /* overwrite with runtime option */ /* overwrite external signal file */ ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,signalfiles[1],FILE_MODE_WRITE,&fd);CHKERRQ(ierr); ierr = PetscViewerBinaryGetDescriptor(fd,&fp);CHKERRQ(ierr); ierr = PetscBinarySynchronizedWrite(PETSC_COMM_WORLD,fp,&zero,1,PETSC_INT,PETSC_FALSE);CHKERRQ(ierr); ierr = PetscViewerDestroy(fd);CHKERRQ(ierr); /* send "ready" signal */ ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD,signalfiles[0],&fd);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(fd,"%d\n",one);CHKERRQ(ierr); ierr = PetscViewerDestroy(fd);CHKERRQ(ierr); /* wait for external signal */ while (iDone==0) { ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,signalfiles[1],FILE_MODE_READ,&fd);CHKERRQ(ierr); ierr = PetscViewerBinaryGetDescriptor(fd,&fp);CHKERRQ(ierr); ierr = PetscBinarySynchronizedRead(PETSC_COMM_WORLD,fp,&iDone,1,PETSC_INT);CHKERRQ(ierr); ierr = PetscViewerDestroy(fd);CHKERRQ(ierr); PetscSleep(waitTime); } /* send "busy" signal */ ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD,signalfiles[0],&fd);CHKERRQ(ierr); ierr = PetscViewerASCIIPrintf(fd,"%d\n",zero);CHKERRQ(ierr); ierr = PetscViewerDestroy(fd);CHKERRQ(ierr); } } return 0; }