sys/objects/init.c

/*

   This file defines part of the initialization of PETSc

  This file uses regular malloc and free because it cannot know
  what malloc is being used until it has already processed the input.
*/

#include <petscsys.h>        /*I  "petscsys.h"   I*/
#include <pthread.h>
#if defined(PETSC_HAVE_STDLIB_H)
#include <stdlib.h>
#endif
#if defined(PETSC_HAVE_MALLOC_H)
#include <malloc.h>
#endif
#if defined(PETSC_HAVE_VALGRIND)
#include <valgrind/valgrind.h>
#endif

/* ------------------------Nasty global variables -------------------------------*/
/*
     Indicates if PETSc started up MPI, or it was
   already started before PETSc was initialized.
*/
PetscBool    PetscBeganMPI         = PETSC_FALSE;
PetscBool    PetscInitializeCalled = PETSC_FALSE;
PetscBool    PetscFinalizeCalled   = PETSC_FALSE;
PetscBool    PetscUseThreadPool    = PETSC_FALSE;
PetscBool    PetscThreadGo         = PETSC_TRUE;
PetscMPIInt  PetscGlobalRank = -1;
PetscMPIInt  PetscGlobalSize = -1;
PetscMPIInt  PetscMaxThreads = 2;
pthread_t*   PetscThreadPoint;
pthread_barrier_t* BarrPoint;
PetscErrorCode ithreaderr;
int*         pVal;

typedef struct {
  pthread_mutex_t mutex;
  pthread_cond_t cond;
  void* (*pfunc)(void*);
  void** pdata;
  pthread_barrier_t* pbarr;
  int iNumJobThreads;
  int iNumReadyThreads;
  PetscBool startJob;
} sjob;
sjob job = {PTHREAD_MUTEX_INITIALIZER,PTHREAD_COND_INITIALIZER,NULL,NULL,NULL,0,0,PETSC_FALSE};

pthread_cond_t  main_cond  = PTHREAD_COND_INITIALIZER;

void*          PetscThreadFunc(void*);
void*          PetscThreadInitialize(PetscInt);
PetscErrorCode PetscThreadFinalize(void);
void           MainWait(void);
PetscErrorCode MainJob(void* (*pFunc)(void*),void**,PetscInt);
void* FuncFinish(void*);
void* PetscThreadRun(MPI_Comm Comm,void* (*pFunc)(void*),int,pthread_t*,void**);
void* PetscThreadStop(MPI_Comm Comm,int,pthread_t*);

#if defined(PETSC_USE_COMPLEX)
#if defined(PETSC_COMPLEX_INSTANTIATE)
template <> class std::complex<double>; /* instantiate complex template class */
#endif
#if !defined(PETSC_HAVE_MPI_C_DOUBLE_COMPLEX)
MPI_Datatype   MPI_C_DOUBLE_COMPLEX;
MPI_Datatype   MPI_C_COMPLEX;
#endif
PetscScalar    PETSC_i;
#else
PetscScalar    PETSC_i = 0.0;
#endif
#if defined(PETSC_USE_REAL___FLOAT128)
MPI_Datatype   MPIU___FLOAT128 = 0;
#endif
MPI_Datatype   MPIU_2SCALAR = 0;
MPI_Datatype   MPIU_2INT = 0;

/*
     These are needed by petscbt.h
*/
#include <petscbt.h>
char      _BT_mask = ' ';
char      _BT_c = ' ';
PetscInt  _BT_idx  = 0;

/*
       Function that is called to display all error messages
*/
PetscErrorCode  (*PetscErrorPrintf)(const char [],...)          = PetscErrorPrintfDefault;
PetscErrorCode  (*PetscHelpPrintf)(MPI_Comm,const char [],...)  = PetscHelpPrintfDefault;
#if defined(PETSC_HAVE_MATLAB_ENGINE)
PetscErrorCode  (*PetscVFPrintf)(FILE*,const char[],va_list)    = PetscVFPrintf_Matlab;
#else
PetscErrorCode  (*PetscVFPrintf)(FILE*,const char[],va_list)    = PetscVFPrintfDefault;
#endif
/*
  This is needed to turn on/off cusp synchronization */
PetscBool   synchronizeCUSP = PETSC_FALSE;

/* ------------------------------------------------------------------------------*/
/*
   Optional file where all PETSc output from various prints is saved
*/
FILE *petsc_history = PETSC_NULL;

#undef __FUNCT__
#define __FUNCT__ "PetscOpenHistoryFile"
PetscErrorCode  PetscOpenHistoryFile(const char filename[],FILE **fd)
{
  PetscErrorCode ierr;
  PetscMPIInt    rank,size;
  char           pfile[PETSC_MAX_PATH_LEN],pname[PETSC_MAX_PATH_LEN],fname[PETSC_MAX_PATH_LEN],date[64];
  char           version[256];

  PetscFunctionBegin;
  ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
  if (!rank) {
    char        arch[10];
    int         err;
    PetscViewer viewer;

    ierr = PetscGetArchType(arch,10);CHKERRQ(ierr);
    ierr = PetscGetDate(date,64);CHKERRQ(ierr);
    ierr = PetscGetVersion(version,256);CHKERRQ(ierr);
    ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
    if (filename) {
      ierr = PetscFixFilename(filename,fname);CHKERRQ(ierr);
    } else {
      ierr = PetscGetHomeDirectory(pfile,240);CHKERRQ(ierr);
      ierr = PetscStrcat(pfile,"/.petschistory");CHKERRQ(ierr);
      ierr = PetscFixFilename(pfile,fname);CHKERRQ(ierr);
    }

    *fd = fopen(fname,"a"); if (!fd) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Cannot open file: %s",fname);
    ierr = PetscFPrintf(PETSC_COMM_SELF,*fd,"---------------------------------------------------------\n");CHKERRQ(ierr);
    ierr = PetscFPrintf(PETSC_COMM_SELF,*fd,"%s %s\n",version,date);CHKERRQ(ierr);
    ierr = PetscGetProgramName(pname,PETSC_MAX_PATH_LEN);CHKERRQ(ierr);
    ierr = PetscFPrintf(PETSC_COMM_SELF,*fd,"%s on a %s, %d proc. with options:\n",pname,arch,size);CHKERRQ(ierr);
    ierr = PetscViewerASCIIOpenWithFILE(PETSC_COMM_WORLD,*fd,&viewer);CHKERRQ(ierr);
    ierr = PetscOptionsView(viewer);CHKERRQ(ierr);
    ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
    ierr = PetscFPrintf(PETSC_COMM_SELF,*fd,"---------------------------------------------------------\n");CHKERRQ(ierr);
    err = fflush(*fd);
    if (err) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SYS,"fflush() failed on file");
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscCloseHistoryFile"
PetscErrorCode  PetscCloseHistoryFile(FILE **fd)
{
  PetscErrorCode ierr;
  PetscMPIInt    rank;
  char           date[64];
  int            err;

  PetscFunctionBegin;
  ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
  if (!rank) {
    ierr = PetscGetDate(date,64);CHKERRQ(ierr);
    ierr = PetscFPrintf(PETSC_COMM_SELF,*fd,"---------------------------------------------------------\n");CHKERRQ(ierr);
    ierr = PetscFPrintf(PETSC_COMM_SELF,*fd,"Finished at %s\n",date);CHKERRQ(ierr);
    ierr = PetscFPrintf(PETSC_COMM_SELF,*fd,"---------------------------------------------------------\n");CHKERRQ(ierr);
    err = fflush(*fd);
    if (err) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SYS,"fflush() failed on file");
    err = fclose(*fd);
    if (err) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SYS,"fclose() failed on file");
  }
  PetscFunctionReturn(0);
}

/* ------------------------------------------------------------------------------*/

/*
   This is ugly and probably belongs somewhere else, but I want to
  be able to put a true MPI abort error handler with command line args.

    This is so MPI errors in the debugger will leave all the stack
  frames. The default MP_Abort() cleans up and exits thus providing no useful information
  in the debugger hence we call abort() instead of MPI_Abort().
*/

#undef __FUNCT__
#define __FUNCT__ "Petsc_MPI_AbortOnError"
void Petsc_MPI_AbortOnError(MPI_Comm *comm,PetscMPIInt *flag)
{
  PetscFunctionBegin;
  (*PetscErrorPrintf)("MPI error %d\n",*flag);
  abort();
}

#undef __FUNCT__
#define __FUNCT__ "Petsc_MPI_DebuggerOnError"
void Petsc_MPI_DebuggerOnError(MPI_Comm *comm,PetscMPIInt *flag)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  (*PetscErrorPrintf)("MPI error %d\n",*flag);
  ierr = PetscAttachDebugger();
  if (ierr) { /* hopeless so get out */
    MPI_Abort(*comm,*flag);
  }
}

#undef __FUNCT__
#define __FUNCT__ "PetscEnd"
/*@C
   PetscEnd - Calls PetscFinalize() and then ends the program. This is useful if one
     wishes a clean exit somewhere deep in the program.

   Collective on PETSC_COMM_WORLD

   Options Database Keys are the same as for PetscFinalize()

   Level: advanced

   Note:
   See PetscInitialize() for more general runtime options.

.seealso: PetscInitialize(), PetscOptionsView(), PetscMallocDump(), PetscMPIDump(), PetscFinalize()
@*/
PetscErrorCode  PetscEnd(void)
{
  PetscFunctionBegin;
  PetscFinalize();
  exit(0);
  return 0;
}

PetscBool    PetscOptionsPublish = PETSC_FALSE;
extern PetscErrorCode        PetscSetUseTrMalloc_Private(void);
extern PetscBool  petscsetmallocvisited;
static char       emacsmachinename[256];

PetscErrorCode (*PetscExternalVersionFunction)(MPI_Comm) = 0;
PetscErrorCode (*PetscExternalHelpFunction)(MPI_Comm)    = 0;

#undef __FUNCT__
#define __FUNCT__ "PetscSetHelpVersionFunctions"
/*@C
   PetscSetHelpVersionFunctions - Sets functions that print help and version information
   before the PETSc help and version information is printed. Must call BEFORE PetscInitialize().
   This routine enables a "higher-level" package that uses PETSc to print its messages first.

   Input Parameter:
+  help - the help function (may be PETSC_NULL)
-  version - the version function (may be PETSC_NULL)

   Level: developer

   Concepts: package help message

@*/
PetscErrorCode  PetscSetHelpVersionFunctions(PetscErrorCode (*help)(MPI_Comm),PetscErrorCode (*version)(MPI_Comm))
{
  PetscFunctionBegin;
  PetscExternalHelpFunction    = help;
  PetscExternalVersionFunction = version;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsCheckInitial_Private"
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,flgz,flgzout;
  PetscErrorCode ierr;
  PetscReal      si;
  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(PETSC_NULL,"-malloc_log",&flg3);CHKERRQ(ierr);
#if defined(PETSC_USE_DEBUG) && !defined(PETSC_USE_PTHREAD)
  ierr = PetscOptionsGetBool(PETSC_NULL,"-malloc",&flg1,&flg2);CHKERRQ(ierr);
  if ((!flg2 || flg1) && !petscsetmallocvisited) {
#if defined(PETSC_HAVE_VALGRIND)
    if (flg2 || !(RUNNING_ON_VALGRIND)) {
      /* turn off default -malloc if valgrind is being used */
#endif
      ierr = PetscSetUseTrMalloc_Private();CHKERRQ(ierr);
#if defined(PETSC_HAVE_VALGRIND)
    }
#endif
  }
#else
  ierr = PetscOptionsGetBool(PETSC_NULL,"-malloc_dump",&flg1,PETSC_NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetBool(PETSC_NULL,"-malloc",&flg2,PETSC_NULL);CHKERRQ(ierr);
  if (flg1 || flg2 || flg3) {ierr = PetscSetUseTrMalloc_Private();CHKERRQ(ierr);}
#endif
  if (flg3) {
    ierr = PetscMallocSetDumpLog();CHKERRQ(ierr);
  }
  flg1 = PETSC_FALSE;
  ierr = PetscOptionsGetBool(PETSC_NULL,"-malloc_debug",&flg1,PETSC_NULL);CHKERRQ(ierr);
  if (flg1) {
    ierr = PetscSetUseTrMalloc_Private();CHKERRQ(ierr);
    ierr = PetscMallocDebug(PETSC_TRUE);CHKERRQ(ierr);
  }

  flg1 = PETSC_FALSE;
  ierr = PetscOptionsGetBool(PETSC_NULL,"-malloc_info",&flg1,PETSC_NULL);CHKERRQ(ierr);
  if (!flg1) {
    flg1 = PETSC_FALSE;
    ierr = PetscOptionsGetBool(PETSC_NULL,"-memory_info",&flg1,PETSC_NULL);CHKERRQ(ierr);
  }
  if (flg1) {
    ierr = PetscMemorySetGetMaximumUsage();CHKERRQ(ierr);
  }

  /*
      Set the display variable for graphics
  */
  ierr = PetscSetDisplay();CHKERRQ(ierr);

  /*
      Determine whether user specified maximum number of threads
   */
  ierr = PetscOptionsHasName(PETSC_NULL,"-thread_max",&flg1);CHKERRQ(ierr);
  if(flg1) {
    ierr = PetscOptionsGetInt(PETSC_NULL,"-thread_max",&PetscMaxThreads,PETSC_NULL);CHKERRQ(ierr);
  }

  /*
      Determine whether to use thread pool
   */
  ierr = PetscOptionsHasName(PETSC_NULL,"-use_thread_pool",&flg1);CHKERRQ(ierr);
  if(flg1) {
    PetscUseThreadPool = PETSC_TRUE;
  }
  PetscThreadInitialize(PetscMaxThreads);
  /*
      Print the PETSc version information
  */
  ierr = PetscOptionsHasName(PETSC_NULL,"-v",&flg1);CHKERRQ(ierr);
  ierr = PetscOptionsHasName(PETSC_NULL,"-version",&flg2);CHKERRQ(ierr);
  ierr = PetscOptionsHasName(PETSC_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(PETSC_NULL,"-on_error_abort",&flg1,PETSC_NULL);CHKERRQ(ierr);
  if (flg1) { ierr = PetscPushErrorHandler(PetscAbortErrorHandler,0);CHKERRQ(ierr);}
  flg1 = PETSC_FALSE;
  ierr = PetscOptionsGetBool(PETSC_NULL,"-on_error_mpiabort",&flg1,PETSC_NULL);CHKERRQ(ierr);
  if (flg1) { ierr = PetscPushErrorHandler(PetscMPIAbortErrorHandler,0);CHKERRQ(ierr);}
  flg1 = PETSC_FALSE;
  ierr = PetscOptionsGetBool(PETSC_NULL,"-mpi_return_on_error",&flg1,PETSC_NULL);CHKERRQ(ierr);
  if (flg1) {
    ierr = MPI_Errhandler_set(comm,MPI_ERRORS_RETURN);CHKERRQ(ierr);
  }
  flg1 = PETSC_FALSE;
  ierr = PetscOptionsGetBool(PETSC_NULL,"-no_signal_handler",&flg1,PETSC_NULL);CHKERRQ(ierr);
  if (!flg1) {ierr = PetscPushSignalHandler(PetscDefaultSignalHandler,(void*)0);CHKERRQ(ierr);}
  flg1 = PETSC_FALSE;
  ierr = PetscOptionsGetBool(PETSC_NULL,"-fp_trap",&flg1,PETSC_NULL);CHKERRQ(ierr);
  if (flg1) {ierr = PetscSetFPTrap(PETSC_FP_TRAP_ON);CHKERRQ(ierr);}

  /*
      Setup debugger information
  */
  ierr = PetscSetDefaultDebugger();CHKERRQ(ierr);
  ierr = PetscOptionsGetString(PETSC_NULL,"-on_error_attach_debugger",string,64,&flg1);CHKERRQ(ierr);
  if (flg1) {
    MPI_Errhandler err_handler;

    ierr = PetscSetDebuggerFromString(string);CHKERRQ(ierr);
    ierr = MPI_Errhandler_create((MPI_Handler_function*)Petsc_MPI_DebuggerOnError,&err_handler);CHKERRQ(ierr);
    ierr = MPI_Errhandler_set(comm,err_handler);CHKERRQ(ierr);
    ierr = PetscPushErrorHandler(PetscAttachDebuggerErrorHandler,0);CHKERRQ(ierr);
  }
  ierr = PetscOptionsGetString(PETSC_NULL,"-debug_terminal",string,64,&flg1);CHKERRQ(ierr);
  if (flg1) { ierr = PetscSetDebugTerminal(string);CHKERRQ(ierr); }
  ierr = PetscOptionsGetString(PETSC_NULL,"-start_in_debugger",string,64,&flg1);CHKERRQ(ierr);
  ierr = PetscOptionsGetString(PETSC_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(PETSC_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_Errhandler_create((MPI_Handler_function*)Petsc_MPI_AbortOnError,&err_handler);CHKERRQ(ierr);
      ierr = MPI_Errhandler_set(comm,err_handler);CHKERRQ(ierr);
    }
    ierr = PetscFree(nodes);CHKERRQ(ierr);
  }

  ierr = PetscOptionsGetString(PETSC_NULL,"-on_error_emacs",emacsmachinename,128,&flg1);CHKERRQ(ierr);
  if (flg1 && !rank) {ierr = PetscPushErrorHandler(PetscEmacsClientErrorHandler,emacsmachinename);CHKERRQ(ierr);}

#if defined(PETSC_USE_SOCKET_VIEWER)
  /*
    Activates new sockets for zope if needed
  */
  ierr = PetscOptionsHasName(PETSC_NULL,"-zope", &flgz);CHKERRQ(ierr);
  ierr = PetscOptionsHasName(PETSC_NULL,"-nostdout", &flgzout);CHKERRQ(ierr);
  if (flgz){
    int  sockfd;
    char hostname[256];
    char username[256];
    int  remoteport = 9999;

    ierr = PetscOptionsGetString(PETSC_NULL, "-zope", hostname, 256, &flgz);CHKERRQ(ierr);
    if (!hostname[0]){
      ierr = PetscGetHostName(hostname,256);CHKERRQ(ierr);
    }
    ierr = PetscOpenSocket(hostname, remoteport, &sockfd);CHKERRQ(ierr);
    ierr = PetscGetUserName(username, 256);CHKERRQ(ierr);
    PETSC_ZOPEFD = fdopen(sockfd, "w");
    if (flgzout){
      PETSC_STDOUT = PETSC_ZOPEFD;
      fprintf(PETSC_STDOUT, "<<<user>>> %s\n",username);
      fprintf(PETSC_STDOUT, "<<<start>>>");
    } else {
      fprintf(PETSC_ZOPEFD, "<<<user>>> %s\n",username);
      fprintf(PETSC_ZOPEFD, "<<<start>>>");
    }
  }
#endif
#if defined(PETSC_USE_SERVER)
  ierr = PetscOptionsHasName(PETSC_NULL,"-server", &flgz);CHKERRQ(ierr);
  if (flgz){
    PetscInt port = PETSC_DECIDE;
    ierr = PetscOptionsGetInt(PETSC_NULL,"-server",&port,PETSC_NULL);CHKERRQ(ierr);
    ierr = PetscWebServe(PETSC_COMM_WORLD,(int)port);CHKERRQ(ierr);
  }
#endif

  /*
        Setup profiling and logging
  */
#if defined (PETSC_USE_INFO)
  {
    char logname[PETSC_MAX_PATH_LEN]; logname[0] = 0;
    ierr = PetscOptionsGetString(PETSC_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,PETSC_NULL);CHKERRQ(ierr);
    }
  }
#endif
#if defined(PETSC_USE_LOG)
  mname[0] = 0;
  ierr = PetscOptionsGetString(PETSC_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(PETSC_NULL,"-log_mpe",&flg1);CHKERRQ(ierr);
  if (flg1) PetscLogMPEBegin();
#endif
  flg1 = PETSC_FALSE;
  flg2 = PETSC_FALSE;
  flg3 = PETSC_FALSE;
  ierr = PetscOptionsGetBool(PETSC_NULL,"-log_all",&flg1,PETSC_NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetBool(PETSC_NULL,"-log",&flg2,PETSC_NULL);CHKERRQ(ierr);
  ierr = PetscOptionsHasName(PETSC_NULL,"-log_summary",&flg3);CHKERRQ(ierr);
  ierr = PetscOptionsHasName(PETSC_NULL,"-log_summary_python",&flg4);CHKERRQ(ierr);
  if (flg1)                      {  ierr = PetscLogAllBegin();CHKERRQ(ierr); }
  else if (flg2 || flg3 || flg4) {  ierr = PetscLogBegin();CHKERRQ(ierr);}

  ierr = PetscOptionsGetString(PETSC_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

  /*
      Setup building of stack frames for all function calls
  */
#if defined(PETSC_USE_DEBUG) && !defined(PETSC_USE_PTHREAD)
  ierr = PetscStackCreate();CHKERRQ(ierr);
#endif

  ierr = PetscOptionsGetBool(PETSC_NULL,"-options_gui",&PetscOptionsPublish,PETSC_NULL);CHKERRQ(ierr);

  /*
       Print basic help message
  */
  ierr = PetscOptionsHasName(PETSC_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);
#if defined(PETSC_USE_LOG)
    ierr = (*PetscHelpPrintf)(comm," -get_total_flops: total flops over all processors\n");CHKERRQ(ierr);
    ierr = (*PetscHelpPrintf)(comm," -log[_all _summary]: 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 upshot\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);
  }

  ierr = PetscOptionsGetReal(PETSC_NULL,"-petsc_sleep",&si,&flg1);CHKERRQ(ierr);
  if (flg1) {
    ierr = PetscSleep(si);CHKERRQ(ierr);
  }

  ierr = PetscOptionsGetString(PETSC_NULL,"-info_exclude",mname,PETSC_MAX_PATH_LEN,&flg1);CHKERRQ(ierr);
  ierr = PetscStrstr(mname,"null",&f);CHKERRQ(ierr);
  if (f) {
    ierr = PetscInfoDeactivateClass(PETSC_NULL);CHKERRQ(ierr);
  }

#if defined(PETSC_HAVE_CUSP)
  ierr = PetscOptionsHasName(PETSC_NULL,"-log_summary",&flg3);CHKERRQ(ierr);
  if (flg3) flg1 = PETSC_TRUE;
  else flg1 = PETSC_FALSE;
  ierr = PetscOptionsGetBool(PETSC_NULL,"-cusp_synchronize",&flg1,PETSC_NULL);CHKERRQ(ierr);
  if (flg1) synchronizeCUSP = PETSC_TRUE;
#endif

  PetscFunctionReturn(0);
}

void* PetscThreadFunc(void* arg) {
  int ierr,iVal;
  int* pId = (int*)arg;
  int ThreadId = *pId;
  PetscErrorCode iterr;

  ierr = pthread_mutex_lock(&job.mutex);
  job.iNumReadyThreads++;
  if(job.iNumReadyThreads==PetscMaxThreads) {
    ierr = pthread_cond_signal(&main_cond);
  }
  //the while loop needs to have an exit
  //the 'main' thread can terminate all the threads by performing a broacast
  //and calling FuncFinish
  while(PetscThreadGo) {
    //need to check the condition to ensure we don't have to wait
    //waiting when you don't have to causes problems
    //also need to wait if another thread sneaks in and messes with the predicate
    while(job.startJob==PETSC_FALSE&&job.iNumJobThreads==0) {
      //upon entry, automically releases the lock and blocks
      //upon return, has the lock
      ierr = pthread_cond_wait(&job.cond,&job.mutex);
    }
    job.startJob = PETSC_FALSE;
    job.iNumJobThreads--;
    job.iNumReadyThreads--;
    iVal = PetscMaxThreads-job.iNumReadyThreads-1;
    pthread_mutex_unlock(&job.mutex);
    if(job.pdata==NULL) {
      iterr = (PetscErrorCode)(long int)job.pfunc(job.pdata);
    }
    else {
      iterr = (PetscErrorCode)(long int)job.pfunc(job.pdata[iVal]);
    }
    if(iterr!=0) {
      ithreaderr = 1;
    }
    //the barrier is necessary BECAUSE: look at job.iNumReadyThreads
    //what happens if a thread finishes before they all start? BAD!
    //what happens if a thread finishes before any else start? BAD!
    pthread_barrier_wait(job.pbarr); //ensures all threads are finished
    //reset job
    if(PetscThreadGo) {
      pthread_mutex_lock(&job.mutex);
      job.iNumReadyThreads++;
      if(job.iNumReadyThreads==PetscMaxThreads) {
	//signal the 'main' thread that the job is done! (only done once)
	ierr = pthread_cond_signal(&main_cond);
      }
    }
  }
  return NULL;
}

#undef __FUNCT__
#define __FUNCT__ "PetscThreadInitialize"
void* PetscThreadInitialize(PetscInt N) {
  PetscInt i;
  int status;

  if(PetscUseThreadPool) {
    pVal = (int*)malloc(N*sizeof(int));
    //allocate memory in the heap for the thread structure
    PetscThreadPoint = (pthread_t*)malloc(N*sizeof(pthread_t));
    BarrPoint = (pthread_barrier_t*)malloc((N+1)*sizeof(pthread_barrier_t)); //BarrPoint[0] makes no sense, don't use it!
    job.pdata = (void**)malloc(N*sizeof(void*));
    for(i=0; i<N; i++) {
      pVal[i] = i;
      status = pthread_create(&PetscThreadPoint[i],NULL,PetscThreadFunc,&pVal[i]);
      //error check to ensure proper thread creation
      status = pthread_barrier_init(&BarrPoint[i+1],NULL,i+1);
      //error check
    }
  }
  else {
  }
  return NULL;
}


#undef __FUNCT__
#define __FUNCT__ "PetscThreadFinalize"
PetscErrorCode PetscThreadFinalize() {
  int i,ierr;
  void* jstatus;

  PetscFunctionBegin;

  if(PetscUseThreadPool) {
    MainJob(FuncFinish,NULL,PetscMaxThreads);  //set up job and broadcast work
    //join the threads
    for(i=0; i<PetscMaxThreads; i++) {
      ierr = pthread_join(PetscThreadPoint[i],&jstatus);
      //do error checking
    }
    free(BarrPoint);
    free(PetscThreadPoint);
  }
  else {
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MainWait"
void MainWait() {
  int ierr;
  ierr = pthread_mutex_lock(&job.mutex);
  while(job.iNumReadyThreads<PetscMaxThreads||job.startJob==PETSC_TRUE) {
    ierr = pthread_cond_wait(&main_cond,&job.mutex);
  }
  ierr = pthread_mutex_unlock(&job.mutex);
}

#undef __FUNCT__
#define __FUNCT__ "MainJob"
PetscErrorCode MainJob(void* (*pFunc)(void*),void** data,PetscInt n) {
  int ierr;
  PetscErrorCode ijoberr = 0;
  if(PetscUseThreadPool) {
    MainWait();
    ierr = pthread_mutex_lock(&job.mutex);
    job.pfunc = pFunc;
    job.pdata = data;
    job.pbarr = &BarrPoint[n];
    job.iNumJobThreads = n;
    job.startJob = PETSC_TRUE;
    ierr = pthread_cond_broadcast(&job.cond);
    ierr = pthread_mutex_unlock(&job.mutex);
    if(pFunc!=FuncFinish) {
      MainWait(); //why wait after? guarantees that job gets done
    }
  }
  else {
    pthread_t* apThread = (pthread_t*)malloc(n*sizeof(pthread_t));
    PetscThreadRun(MPI_COMM_WORLD,pFunc,n,apThread,data);
    PetscThreadStop(MPI_COMM_WORLD,n,apThread); //ensures that all threads are finished with the job
    free(apThread);
  }
  if(ithreaderr) {
    ijoberr = ithreaderr;
  }
  return ijoberr;
}

void* FuncFinish(void* arg) {
  PetscThreadGo = PETSC_FALSE;
  return(0);
}