xref: /petsc/src/sys/objects/pinit.c (revision 192daf7cd86056b082984d0d4358c7fe5ba67f57)

#define PETSC_DLL
/*
   This file defines the initialization of PETSc, including PetscInitialize()
*/

#include "petsc.h"        /*I  "petsc.h"   I*/
#include "petscsys.h"

#if defined(PETSC_USE_LOG)
EXTERN PetscErrorCode PetscLogBegin_Private(void);
#endif
extern PetscTruth PetscOpenMPWorker;

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

extern FILE *petsc_history;

EXTERN PetscErrorCode PetscInitialize_DynamicLibraries(void);
EXTERN PetscErrorCode PetscFinalize_DynamicLibraries(void);
EXTERN PetscErrorCode PetscFListDestroyAll(void);
EXTERN PetscErrorCode PetscSequentialPhaseBegin_Private(MPI_Comm,int);
EXTERN PetscErrorCode PetscSequentialPhaseEnd_Private(MPI_Comm,int);
EXTERN PetscErrorCode PetscLogCloseHistoryFile(FILE **);
EXTERN PetscErrorCode PetscOptionsHelpDestroyList(void);

/* this is used by the _, __, and ___ macros (see include/petscerror.h) */
PetscErrorCode __gierr = 0;

/* user may set this BEFORE calling PetscInitialize() */
MPI_Comm PETSC_COMM_WORLD = 0;

/*
     Declare and set all the string names of the PETSc enums
*/
const char *PetscTruths[]    = {"FALSE","TRUE","PetscTruth","PETSC_",0};
const char *PetscDataTypes[] = {"INT", "DOUBLE", "COMPLEX",
                                "LONG","SHORT",  "FLOAT",
                                "CHAR","LOGICAL","ENUM","TRUTH","LONGDOUBLE","PetscDataType","PETSC_",0};

PetscTruth PetscPreLoadingUsed = PETSC_FALSE;
PetscTruth PetscPreLoadingOn   = PETSC_FALSE;

/*
       Checks the options database for initializations related to the
    PETSc components
*/
#undef __FUNCT__
#define __FUNCT__ "PetscOptionsCheckInitial_Components"
PetscErrorCode PETSC_DLLEXPORT PetscOptionsCheckInitial_Components(void)
{
  PetscTruth flg1;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscOptionsHasName(PETSC_NULL,"-help",&flg1);CHKERRQ(ierr);
  if (flg1) {
#if defined (PETSC_USE_LOG)
    MPI_Comm   comm = PETSC_COMM_WORLD;
    ierr = (*PetscHelpPrintf)(comm,"------Additional PETSc component options--------\n");CHKERRQ(ierr);
    ierr = (*PetscHelpPrintf)(comm," -log_summary_exclude: <vec,mat,pc.ksp,snes>\n");CHKERRQ(ierr);
    ierr = (*PetscHelpPrintf)(comm," -info_exclude: <null,vec,mat,pc,ksp,snes,ts>\n");CHKERRQ(ierr);
    ierr = (*PetscHelpPrintf)(comm,"-----------------------------------------------\n");CHKERRQ(ierr);
#endif
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscInitializeNoArguments"
/*@C
      PetscInitializeNoArguments - Calls PetscInitialize() from C/C++ without
        the command line arguments.

   Collective

   Level: advanced

.seealso: PetscInitialize(), PetscInitializeFortran()
@*/
PetscErrorCode PETSC_DLLEXPORT PetscInitializeNoArguments(void)
{
  PetscErrorCode ierr;
  int            argc = 0;
  char           **args = 0;

  PetscFunctionBegin;
  ierr = PetscInitialize(&argc,&args,PETSC_NULL,PETSC_NULL);
  PetscFunctionReturn(ierr);
}

#undef __FUNCT__
#define __FUNCT__ "PetscInitialized"
/*@
      PetscInitialized - Determine whether PETSc is initialized.

7   Level: beginner

.seealso: PetscInitialize(), PetscInitializeNoArguments(), PetscInitializeFortran()
@*/
PetscErrorCode PETSC_DLLEXPORT PetscInitialized(PetscTruth *isInitialized)
{
  PetscFunctionBegin;
  PetscValidPointer(isInitialized, 1);
  *isInitialized = PetscInitializeCalled;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscFinalized"
/*@
      PetscFinalized - Determine whether PetscFinalize() has been called yet

   Level: developer

.seealso: PetscInitialize(), PetscInitializeNoArguments(), PetscInitializeFortran()
@*/
PetscErrorCode PETSC_DLLEXPORT PetscFinalized(PetscTruth *isFinalized)
{
  PetscFunctionBegin;
  PetscValidPointer(isFinalized, 1);
  *isFinalized = PetscFinalizeCalled;
  PetscFunctionReturn(0);
}

EXTERN PetscErrorCode        PetscOptionsCheckInitial_Private(void);
extern PetscTruth PetscBeganMPI;

/*
       This function is the MPI reduction operation used to compute the sum of the
   first half of the datatype and the max of the second half.
*/
MPI_Op PetscMaxSum_Op = 0;

EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "PetscMaxSum_Local"
void PETSC_DLLEXPORT MPIAPI PetscMaxSum_Local(void *in,void *out,int *cnt,MPI_Datatype *datatype)
{
  PetscInt *xin = (PetscInt*)in,*xout = (PetscInt*)out,i,count = *cnt;

  PetscFunctionBegin;
  if (*datatype != MPIU_2INT) {
    (*PetscErrorPrintf)("Can only handle MPIU_2INT data types");
    MPI_Abort(MPI_COMM_WORLD,1);
  }

  for (i=0; i<count; i++) {
    xout[2*i]    = PetscMax(xout[2*i],xin[2*i]);
    xout[2*i+1] += xin[2*i+1];
  }
  PetscStackPop;
  return;
}
EXTERN_C_END

/*
    Returns the max of the first entry owned by this processor and the
sum of the second entry.

    The reason nprocs[2*i] contains lengths nprocs[2*i+1] contains flag of 1 if length is nonzero
is so that the PetscMaxSum_Op() can set TWO values, if we passed in only nprocs[i] with lengths
there would be no place to store the both needed results.
*/
#undef __FUNCT__
#define __FUNCT__ "PetscMaxSum"
PetscErrorCode PETSC_DLLEXPORT PetscMaxSum(MPI_Comm comm,const PetscInt nprocs[],PetscInt *max,PetscInt *sum)
{
  PetscMPIInt    size,rank;
  PetscInt       *work;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr   = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
  ierr   = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
  ierr   = PetscMalloc(2*size*sizeof(PetscInt),&work);CHKERRQ(ierr);
  ierr   = MPI_Allreduce((void*)nprocs,work,size,MPIU_2INT,PetscMaxSum_Op,comm);CHKERRQ(ierr);
  *max   = work[2*rank];
  *sum   = work[2*rank+1];
  ierr   = PetscFree(work);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/* ----------------------------------------------------------------------------*/
MPI_Op PETSC_DLLEXPORT PetscADMax_Op = 0;

EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "PetscADMax_Local"
void PETSC_DLLEXPORT MPIAPI PetscADMax_Local(void *in,void *out,PetscMPIInt *cnt,MPI_Datatype *datatype)
{
  PetscScalar *xin = (PetscScalar *)in,*xout = (PetscScalar*)out;
  PetscInt    i,count = *cnt;

  PetscFunctionBegin;
  if (*datatype != MPIU_2SCALAR) {
    (*PetscErrorPrintf)("Can only handle MPIU_2SCALAR data (i.e. double or complex) types");
    MPI_Abort(MPI_COMM_WORLD,1);
  }

  for (i=0; i<count; i++) {
    if (PetscRealPart(xout[2*i]) < PetscRealPart(xin[2*i])) {
      xout[2*i]   = xin[2*i];
      xout[2*i+1] = xin[2*i+1];
    }
  }

  PetscStackPop;
  return;
}
EXTERN_C_END

MPI_Op PETSC_DLLEXPORT PetscADMin_Op = 0;

EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "PetscADMin_Local"
void PETSC_DLLEXPORT MPIAPI PetscADMin_Local(void *in,void *out,PetscMPIInt *cnt,MPI_Datatype *datatype)
{
  PetscScalar *xin = (PetscScalar *)in,*xout = (PetscScalar*)out;
  PetscInt    i,count = *cnt;

  PetscFunctionBegin;
  if (*datatype != MPIU_2SCALAR) {
    (*PetscErrorPrintf)("Can only handle MPIU_2SCALAR data (i.e. double or complex) types");
    MPI_Abort(MPI_COMM_WORLD,1);
  }

  for (i=0; i<count; i++) {
    if (PetscRealPart(xout[2*i]) > PetscRealPart(xin[2*i])) {
      xout[2*i]   = xin[2*i];
      xout[2*i+1] = xin[2*i+1];
    }
  }

  PetscStackPop;
  return;
}
EXTERN_C_END
/* ---------------------------------------------------------------------------------------*/

#if defined(PETSC_USE_COMPLEX)
MPI_Op PetscSum_Op = 0;

EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "PetscSum_Local"
void PETSC_DLLEXPORT PetscSum_Local(void *in,void *out,PetscMPIInt *cnt,MPI_Datatype *datatype)
{
  PetscScalar *xin = (PetscScalar *)in,*xout = (PetscScalar*)out;
  PetscInt    i,count = *cnt;

  PetscFunctionBegin;
  if (*datatype != MPIU_SCALAR) {
    (*PetscErrorPrintf)("Can only handle MPIU_SCALAR data (i.e. double or complex) types");
    MPI_Abort(MPI_COMM_WORLD,1);
  }

  for (i=0; i<count; i++) {
    xout[i] += xin[i];
  }

  PetscStackPop;
  return;
}
EXTERN_C_END
#endif

#if defined(PETSC_USE_PETSC_MPI_EXTERNAL32)
#if !defined(PETSC_WORDS_BIGENDIAN)
EXTERN_C_BEGIN
extern PetscMPIInt PetscDataRep_extent_fn(MPI_Datatype,MPI_Aint*,void*);
extern PetscMPIInt PetscDataRep_read_conv_fn(void*, MPI_Datatype,PetscMPIInt,void*,MPI_Offset,void*);
extern PetscMPIInt PetscDataRep_write_conv_fn(void*, MPI_Datatype,PetscMPIInt,void*,MPI_Offset,void*);
EXTERN_C_END
#endif
#endif

static int  PetscGlobalArgc   = 0;
static char **PetscGlobalArgs = 0;

#undef __FUNCT__
#define __FUNCT__ "PetscGetArgs"
/*@C
   PetscGetArgs - Allows you to access the raw command line arguments anywhere
     after PetscInitialize() is called but before PetscFinalize().

   Not Collective

   Output Parameters:
+  argc - count of number of command line arguments
-  args - the command line arguments

   Level: intermediate

   Notes:
      This is usually used to pass the command line arguments into other libraries
   that are called internally deep in PETSc or the application.

   Concepts: command line arguments

.seealso: PetscFinalize(), PetscInitializeFortran(), PetscGetArguments()

@*/
PetscErrorCode PETSC_DLLEXPORT PetscGetArgs(int *argc,char ***args)
{
  PetscFunctionBegin;
  if (!PetscGlobalArgs) {
    SETERRQ(PETSC_ERR_ORDER,"You must call after PetscInitialize() but before PetscFinalize()");
  }
  *argc = PetscGlobalArgc;
  *args = PetscGlobalArgs;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscGetArguments"
/*@C
   PetscGetArguments - Allows you to access the  command line arguments anywhere
     after PetscInitialize() is called but before PetscFinalize().

   Not Collective

   Output Parameters:
.  args - the command line arguments

   Level: intermediate

   Notes:
      This does NOT start with the program name and IS null terminated (final arg is void)

   Concepts: command line arguments

.seealso: PetscFinalize(), PetscInitializeFortran(), PetscGetArgs(), PetscFreeArguments()

@*/
PetscErrorCode PETSC_DLLEXPORT PetscGetArguments(char ***args)
{
  PetscInt       i,argc = PetscGlobalArgc;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (!PetscGlobalArgs) {
    SETERRQ(PETSC_ERR_ORDER,"You must call after PetscInitialize() but before PetscFinalize()");
  }
  ierr = PetscMalloc(argc*sizeof(char*),args);CHKERRQ(ierr);
  for (i=0; i<argc-1; i++) {
    ierr = PetscStrallocpy(PetscGlobalArgs[i+1],&(*args)[i]);CHKERRQ(ierr);
  }
  (*args)[argc-1] = 0;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscFreeArguments"
/*@C
   PetscFreeArguments - Frees the memory obtained with PetscGetArguments()

   Not Collective

   Output Parameters:
.  args - the command line arguments

   Level: intermediate

   Concepts: command line arguments

.seealso: PetscFinalize(), PetscInitializeFortran(), PetscGetArgs(), PetscGetArguments()

@*/
PetscErrorCode PETSC_DLLEXPORT PetscFreeArguments(char **args)
{
  PetscInt       i = 0;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  while (args[i]) {
    ierr = PetscFree(args[i]);CHKERRQ(ierr);
    i++;
  }
  ierr = PetscFree(args);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscInitialize"
/*@C
   PetscInitialize - Initializes the PETSc database and MPI.
   PetscInitialize() calls MPI_Init() if that has yet to be called,
   so this routine should always be called near the beginning of
   your program -- usually the very first line!

   Collective on MPI_COMM_WORLD or PETSC_COMM_WORLD if it has been set

   Input Parameters:
+  argc - count of number of command line arguments
.  args - the command line arguments
.  file - [optional] PETSc database file, also checks ~username/.petscrc and .petscrc use PETSC_NULL to not check for
          code specific file. Use -skip_petscrc in the code specific file to skip the .petscrc files
-  help - [optional] Help message to print, use PETSC_NULL for no message

   If you wish PETSc to run on a subcommunicator of MPI_COMM_WORLD, create that
   communicator first and assign it to PETSC_COMM_WORLD BEFORE calling PetscInitialize()

   Options Database Keys:
+  -start_in_debugger [noxterm,dbx,xdb,gdb,...] - Starts program in debugger
.  -on_error_attach_debugger [noxterm,dbx,xdb,gdb,...] - Starts debugger when error detected
.  -on_error_emacs <machinename> causes emacsclient to jump to error file
.  -on_error_abort calls abort() when error detected (no traceback)
.  -on_error_mpiabort calls MPI_abort() when error detected
.  -error_output_stderr prints error messages to stderr instead of the default stdout
.  -error_output_none does not print the error messages (but handles errors in the same way as if this was not called)
.  -debugger_nodes [node1,node2,...] - Indicates nodes to start in debugger
.  -debugger_pause [sleeptime] (in seconds) - Pauses debugger
.  -stop_for_debugger - Print message on how to attach debugger manually to
                        process and wait (-debugger_pause) seconds for attachment
.  -malloc - Indicates use of PETSc error-checking malloc (on by default for debug version of libraries)
.  -malloc no - Indicates not to use error-checking malloc
.  -malloc_debug - check for memory corruption at EVERY malloc or free
.  -fp_trap - Stops on floating point exceptions (Note that on the
              IBM RS6000 this slows code by at least a factor of 10.)
.  -no_signal_handler - Indicates not to trap error signals
.  -shared_tmp - indicates /tmp directory is shared by all processors
.  -not_shared_tmp - each processor has own /tmp
.  -tmp - alternative name of /tmp directory
.  -get_total_flops - returns total flops done by all processors
-  -memory_info - Print memory usage at end of run

   Options Database Keys for Profiling:
   See the Profiling chapter of the users manual for details.
+  -log_trace [filename] - Print traces of all PETSc calls
        to the screen (useful to determine where a program
        hangs without running in the debugger).  See PetscLogTraceBegin().
.  -info <optional filename> - Prints verbose information to the screen
-  -info_exclude <null,vec,mat,pc,ksp,snes,ts> - Excludes some of the verbose messages

   Environmental Variables:
+   PETSC_TMP - alternative tmp directory
.   PETSC_SHARED_TMP - tmp is shared by all processes
.   PETSC_NOT_SHARED_TMP - each process has its own private tmp
.   PETSC_VIEWER_SOCKET_PORT - socket number to use for socket viewer
-   PETSC_VIEWER_SOCKET_MACHINE - machine to use for socket viewer to connect to


   Level: beginner

   Notes:
   If for some reason you must call MPI_Init() separately, call
   it before PetscInitialize().

   Fortran Version:
   In Fortran this routine has the format
$       call PetscInitialize(file,ierr)

+   ierr - error return code
-  file - [optional] PETSc database file, also checks ~username/.petscrc and .petscrc use PETSC_NULL_CHARACTER to not check for
          code specific file. Use -skip_petscrc in the code specific file to skip the .petscrc files

   Important Fortran Note:
   In Fortran, you MUST use PETSC_NULL_CHARACTER to indicate a
   null character string; you CANNOT just use PETSC_NULL as
   in the C version.  See the users manual for details.


   Concepts: initializing PETSc

.seealso: PetscFinalize(), PetscInitializeFortran(), PetscGetArgs()

@*/
PetscErrorCode PETSC_DLLEXPORT PetscInitialize(int *argc,char ***args,const char file[],const char help[])
{
  PetscErrorCode ierr;
  PetscMPIInt    flag, size;
  PetscInt       nodesize;
  PetscTruth     flg;
  char           hostname[256];

  PetscFunctionBegin;
  if (PetscInitializeCalled) PetscFunctionReturn(0);
  if (PetscFinalizeCalled)
    SETERRQ(1,"You can not initialize PETSc a second time")

  /* these must be initialized in a routine, not as a constant declaration*/
  PETSC_STDOUT = stdout;
  PETSC_STDERR = stderr;

  ierr = PetscOptionsCreate();CHKERRQ(ierr);

  /*
     We initialize the program name here (before MPI_Init()) because MPICH has a bug in
     it that it sets args[0] on all processors to be args[0] on the first processor.
  */
  if (argc && *argc) {
    ierr = PetscSetProgramName(**args);CHKERRQ(ierr);
  } else {
    ierr = PetscSetProgramName("Unknown Name");CHKERRQ(ierr);
  }

  ierr = MPI_Initialized(&flag);CHKERRQ(ierr);
  if (!flag) {
    if (PETSC_COMM_WORLD) SETERRQ(PETSC_ERR_SUP,"You cannot set PETSC_COMM_WORLD if you have not initialized MPI first");
    ierr          = MPI_Init(argc,args);CHKERRQ(ierr);
    PetscBeganMPI = PETSC_TRUE;
  }
  if (argc && args) {
    PetscGlobalArgc = *argc;
    PetscGlobalArgs = *args;
  }
  PetscInitializeCalled = PETSC_TRUE;
  PetscFinalizeCalled   = PETSC_FALSE;

  if (!PETSC_COMM_WORLD) {
    PETSC_COMM_WORLD = MPI_COMM_WORLD;
  }

  /* Done after init due to a bug in MPICH-GM? */
  ierr = PetscErrorPrintfInitialize();CHKERRQ(ierr);

  ierr = MPI_Comm_rank(MPI_COMM_WORLD,&PetscGlobalRank);CHKERRQ(ierr);
  ierr = MPI_Comm_size(MPI_COMM_WORLD,&PetscGlobalSize);CHKERRQ(ierr);

#if defined(PETSC_USE_COMPLEX)
  /*
     Initialized the global complex variable; this is because with
     shared libraries the constructors for global variables
     are not called; at least on IRIX.
  */
  {
#if defined(PETSC_CLANGUAGE_CXX)
    PetscScalar ic(0.0,1.0);
    PETSC_i = ic;
#else
    PETSC_i = I;
#endif
  }

  ierr = MPI_Type_contiguous(2,MPIU_REAL,&MPIU_COMPLEX);CHKERRQ(ierr);
  ierr = MPI_Type_commit(&MPIU_COMPLEX);CHKERRQ(ierr);
  ierr = MPI_Op_create(PetscSum_Local,1,&PetscSum_Op);CHKERRQ(ierr);
#endif

  /*
     Create the PETSc MPI reduction operator that sums of the first
     half of the entries and maxes the second half.
  */
  ierr = MPI_Op_create(PetscMaxSum_Local,1,&PetscMaxSum_Op);CHKERRQ(ierr);

  ierr = MPI_Type_contiguous(2,MPIU_SCALAR,&MPIU_2SCALAR);CHKERRQ(ierr);
  ierr = MPI_Type_commit(&MPIU_2SCALAR);CHKERRQ(ierr);
  ierr = MPI_Op_create(PetscADMax_Local,1,&PetscADMax_Op);CHKERRQ(ierr);
  ierr = MPI_Op_create(PetscADMin_Local,1,&PetscADMin_Op);CHKERRQ(ierr);

  ierr = MPI_Type_contiguous(2,MPIU_INT,&MPIU_2INT);CHKERRQ(ierr);
  ierr = MPI_Type_commit(&MPIU_2INT);CHKERRQ(ierr);

  /*
     Build the options database
  */
  ierr = PetscOptionsInsert(argc,args,file);CHKERRQ(ierr);


  /*
     Print main application help message
  */
  ierr = PetscOptionsHasName(PETSC_NULL,"-help",&flg);CHKERRQ(ierr);
  if (help && flg) {
    ierr = PetscPrintf(PETSC_COMM_WORLD,help);CHKERRQ(ierr);
  }
  ierr = PetscOptionsCheckInitial_Private();CHKERRQ(ierr);

  /* SHOULD PUT IN GUARDS: Make sure logging is initialized, even if we do not print it out */
#if defined(PETSC_USE_LOG)
  ierr = PetscLogBegin_Private();CHKERRQ(ierr);
#endif

  /*
     Load the dynamic libraries (on machines that support them), this registers all
     the solvers etc. (On non-dynamic machines this initializes the PetscDraw and PetscViewer classes)
  */
  ierr = PetscInitialize_DynamicLibraries();CHKERRQ(ierr);

  ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
  ierr = PetscInfo1(0,"PETSc successfully started: number of processors = %d\n",size);CHKERRQ(ierr);
  ierr = PetscGetHostName(hostname,256);CHKERRQ(ierr);
  ierr = PetscInfo1(0,"Running on machine: %s\n",hostname);CHKERRQ(ierr);

  ierr = PetscOptionsCheckInitial_Components();CHKERRQ(ierr);
  /* Check the options database for options related to the options database itself */
  ierr = PetscOptionsSetFromOptions(); CHKERRQ(ierr);

#if defined(PETSC_USE_PETSC_MPI_EXTERNAL32)
  /*
      Tell MPI about our own data representation converter, this would/should be used if extern32 is not supported by the MPI

      Currently not used because it is not supported by MPICH.
  */
#if !defined(PETSC_WORDS_BIGENDIAN)
  ierr = MPI_Register_datarep((char *)"petsc",PetscDataRep_read_conv_fn,PetscDataRep_write_conv_fn,PetscDataRep_extent_fn,PETSC_NULL);CHKERRQ(ierr);
#endif
#endif

  ierr = PetscOptionsGetInt(PETSC_NULL,"-openmp_spawn_size",&nodesize,&flg);CHKERRQ(ierr);
  if (flg) {
#if defined(PETSC_HAVE_MPI_COMM_SPAWN)
    ierr = PetscOpenMPSpawn((PetscMPIInt) nodesize);CHKERRQ(ierr);
#else
    SETERRQ(PETSC_ERR_SUP,"PETSc built without MPI 2 (MPI_Comm_spawn) support, use -openmp_merge_size instead");
#endif
  } else {
    ierr = PetscOptionsGetInt(PETSC_NULL,"-openmp_merge_size",&nodesize,&flg);CHKERRQ(ierr);
    if (flg) {
      ierr = PetscOpenMPMerge((PetscMPIInt) nodesize);CHKERRQ(ierr);
    }
  }
  ierr = PetscOptionsHasName(PETSC_NULL,"-python",&flg);CHKERRQ(ierr);
  if (flg) {ierr = PetscPythonInitialize(PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);}

  PetscFunctionReturn(ierr);
}


#undef __FUNCT__
#define __FUNCT__ "PetscFinalize"
/*@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 PetscOptionsPrint()
.  -options_left - Prints unused options that remain in the database
.  -options_left no - Does not print unused options that remain in the database
.  -mpidump - Calls PetscMPIDump()
.  -malloc_dump - Calls PetscMallocDump()
.  -malloc_info - Prints total memory usage
-  -malloc_log - Prints summary of memory usage

   Options Database Keys for Profiling:
   See the Profiling chapter of the users manual for details.
+  -log_summary [filename] - Prints summary of flop and timing
        information to screen. If the filename is specified the
        summary is written to the file. (for code compiled with
        PETSC_USE_LOG).  See PetscLogPrintSummary().
.  -log_all [filename] - Logs extensive profiling information
        (for code compiled with PETSC_USE_LOG). See PetscLogDump().
.  -log [filename] - Logs basic profiline information (for
        code compiled with PETSC_USE_LOG).  See PetscLogDump().
.  -log_sync - Log the synchronization in scatters, inner products
        and norms
-  -log_mpe [filename] - Creates a logfile viewable by the
      utility Upshot/Nupshot (in MPICH distribution)

   Level: beginner

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

.seealso: PetscInitialize(), PetscOptionsPrint(), PetscMallocDump(), PetscMPIDump(), PetscEnd()
@*/
PetscErrorCode PETSC_DLLEXPORT PetscFinalize(void)
{
  PetscErrorCode ierr;
  PetscMPIInt    rank;
  int            nopt;
  PetscTruth     flg1,flg2,flg3;
  extern FILE   *PETSC_ZOPEFD;

  PetscFunctionBegin;

  if (!PetscInitializeCalled) {
    (*PetscErrorPrintf)("PetscInitialize() must be called before PetscFinalize()\n");
    PetscFunctionReturn(0);
  }
  ierr = PetscOpenMPFinalize();CHKERRQ(ierr);

  ierr = PetscOptionsHasName(PETSC_NULL,"-python",&flg1);CHKERRQ(ierr);
  if (flg1) {ierr = PetscPythonFinalize();CHKERRQ(ierr);}

  ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
  ierr = PetscOptionsHasName(PETSC_NULL,"-malloc_info",&flg2);CHKERRQ(ierr);
  if (!flg2) {
    ierr = PetscOptionsHasName(PETSC_NULL,"-memory_info",&flg2);CHKERRQ(ierr);
  }
  if (flg2) {
    ierr = PetscMemoryShowUsage(PETSC_VIEWER_STDOUT_WORLD,"Summary of Memory Usage in PETSc\n");CHKERRQ(ierr);
  }

  /*
     Free all objects registered with PetscObjectRegisterDestroy() such as PETSC_VIEWER_XXX_().
  */
  ierr = PetscObjectRegisterDestroyAll();CHKERRQ(ierr);

  /*
       Free all the registered create functions, such as KSPList, VecList, SNESList, etc
  */
  ierr = PetscFListDestroyAll();CHKERRQ(ierr);

  /*
     Destroy any packages that registered a finalize
  */
  ierr = PetscRegisterFinalizeAll();CHKERRQ(ierr);

  /*
     Destroy all the function registration lists created
  */
  ierr = PetscFinalize_DynamicLibraries();CHKERRQ(ierr);

#if defined(PETSC_USE_LOG)
  ierr = PetscOptionsHasName(PETSC_NULL,"-get_total_flops",&flg1);CHKERRQ(ierr);
  if (flg1) {
    PetscLogDouble flops = 0;
    ierr = MPI_Reduce(&_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

  ierr = PetscOptionsHelpDestroyList();CHKERRQ(ierr);

#if defined(PETSC_USE_DEBUG)
  if (PetscStackActive) {
    ierr = PetscStackDestroy();CHKERRQ(ierr);
  }
#endif

#if defined(PETSC_USE_LOG)
  {
    char mname[PETSC_MAX_PATH_LEN];
#if defined(PETSC_HAVE_MPE)
    mname[0] = 0;
    ierr = PetscOptionsGetString(PETSC_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(PETSC_NULL,"-log_summary",mname,PETSC_MAX_PATH_LEN,&flg1);CHKERRQ(ierr);
    if (flg1) {
      if (mname[0])  {ierr = PetscLogPrintSummary(PETSC_COMM_WORLD,mname);CHKERRQ(ierr);}
      else           {ierr = PetscLogPrintSummary(PETSC_COMM_WORLD,0);CHKERRQ(ierr);}
    }

    ierr = PetscOptionsGetString(PETSC_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(PETSC_NULL,"-log_all",mname,PETSC_MAX_PATH_LEN,&flg1);CHKERRQ(ierr);
    ierr = PetscOptionsGetString(PETSC_NULL,"-log",mname,PETSC_MAX_PATH_LEN,&flg2);CHKERRQ(ierr);
    if (flg1 || flg2){
      if (mname[0]) PetscLogDump(mname);
      else          PetscLogDump(0);
    }
    ierr = PetscLogDestroy();CHKERRQ(ierr);
  }
#endif
  ierr = PetscOptionsHasName(PETSC_NULL,"-no_signal_handler",&flg1);CHKERRQ(ierr);
  if (!flg1) { ierr = PetscPopSignalHandler();CHKERRQ(ierr);}
  ierr = PetscOptionsHasName(PETSC_NULL,"-mpidump",&flg1);CHKERRQ(ierr);
  if (flg1) {
    ierr = PetscMPIDump(stdout);CHKERRQ(ierr);
  }
  ierr = PetscOptionsHasName(PETSC_NULL,"-malloc_dump",&flg1);CHKERRQ(ierr);
  ierr = PetscOptionsHasName(PETSC_NULL,"-options_table",&flg2);CHKERRQ(ierr);
  if (flg2) {
    if (!rank) {ierr = PetscOptionsPrint(stdout);CHKERRQ(ierr);}
  }

  /* to prevent PETSc -options_left from warning */
  ierr = PetscOptionsHasName(PETSC_NULL,"-nox",&flg1);CHKERRQ(ierr)
  ierr = PetscOptionsHasName(PETSC_NULL,"-nox_warning",&flg1);CHKERRQ(ierr)

  if (!PetscOpenMPWorker) { /* worker processes skip this because they do not usually process options */
    flg3 = PETSC_FALSE; /* default value is required */
    ierr = PetscOptionsGetTruth(PETSC_NULL,"-options_left",&flg3,&flg1);CHKERRQ(ierr);
    ierr = PetscOptionsAllUsed(&nopt);CHKERRQ(ierr);
    if (flg3) {
      if (!flg2) { /* have not yet printed the options */
	ierr = PetscOptionsPrint(stdout);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);
    }
  }

  ierr = PetscOptionsHasName(PETSC_NULL,"-log_history",&flg1);CHKERRQ(ierr);
  if (flg1) {
    ierr = PetscLogCloseHistoryFile(&petsc_history);CHKERRQ(ierr);
    petsc_history = 0;
  }

  ierr = PetscInfoAllow(PETSC_FALSE,PETSC_NULL);CHKERRQ(ierr);

  ierr = PetscOptionsHasName(PETSC_NULL,"-malloc_dump",&flg1);CHKERRQ(ierr);
  ierr = PetscOptionsHasName(PETSC_NULL,"-malloc_log",&flg3);CHKERRQ(ierr);
  if (flg1) {
    char fname[PETSC_MAX_PATH_LEN];
    FILE *fd;
    int  err;

    fname[0] = 0;
    ierr = PetscOptionsGetString(PETSC_NULL,"-malloc_dump",fname,250,&flg1);CHKERRQ(ierr);
    if (flg1 && fname[0]) {
      char sname[PETSC_MAX_PATH_LEN];

      sprintf(sname,"%s_%d",fname,rank);
      fd   = fopen(sname,"w"); if (!fd) SETERRQ1(PETSC_ERR_FILE_OPEN,"Cannot open log file: %s",sname);
      ierr = PetscMallocDump(fd);CHKERRQ(ierr);
      err = fclose(fd);
      if (err) SETERRQ(PETSC_ERR_SYS,"fclose() failed on file");
    } else {
      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);
    }
  }
  if (flg3) {
    char fname[PETSC_MAX_PATH_LEN];
    FILE *fd;

    fname[0] = 0;
    ierr = PetscOptionsGetString(PETSC_NULL,"-malloc_log",fname,250,&flg1);CHKERRQ(ierr);
    if (flg1 && fname[0]) {
      char sname[PETSC_MAX_PATH_LEN];
      int  err;

      sprintf(sname,"%s_%d",fname,rank);
      fd   = fopen(sname,"w"); if (!fd) SETERRQ1(PETSC_ERR_FILE_OPEN,"Cannot open log file: %s",sname);
      ierr = PetscMallocDumpLog(fd);CHKERRQ(ierr);
      err = fclose(fd);
      if (err) SETERRQ(PETSC_ERR_SYS,"fclose() failed on file");
    } else {
      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_COMPLEX)
  ierr = MPI_Op_free(&PetscSum_Op);CHKERRQ(ierr);
  ierr = MPI_Type_free(&MPIU_COMPLEX);CHKERRQ(ierr);
#endif
  ierr = MPI_Type_free(&MPIU_2SCALAR);CHKERRQ(ierr);
  ierr = MPI_Type_free(&MPIU_2INT);CHKERRQ(ierr);
  ierr = MPI_Op_free(&PetscMaxSum_Op);CHKERRQ(ierr);
  ierr = MPI_Op_free(&PetscADMax_Op);CHKERRQ(ierr);
  ierr = MPI_Op_free(&PetscADMin_Op);CHKERRQ(ierr);

  ierr = PetscInfo(0,"PETSc successfully ended!\n");CHKERRQ(ierr);
  if (PetscBeganMPI) {
#if defined(PETSC_HAVE_MPI_FINALIZED)
    PetscMPIInt flag;
    ierr = MPI_Finalized(&flag);CHKERRQ(ierr);
    if (flag) SETERRQ(PETSC_ERR_LIB,"MPI_Finalize() has already been called, even though MPI_Init() was called by PetscInitialize()");
#endif
    ierr = MPI_Finalize();CHKERRQ(ierr);
  }

  if(PETSC_ZOPEFD != NULL){
    if (PETSC_ZOPEFD != PETSC_STDOUT) fprintf(PETSC_ZOPEFD, "<<<end>>>");
    else fprintf(PETSC_STDOUT, "<<<end>>>");}

/*

     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);
}

/*
     These may be used in code that ADIC is to be used on
*/

#undef __FUNCT__
#define __FUNCT__ "PetscGlobalMax"
/*@C
      PetscGlobalMax - Computes the maximum value over several processors

     Collective on MPI_Comm

   Input Parameters:
+   local - the local value
-   comm - the processors that find the maximum

   Output Parameter:
.   result - the maximum value

   Level: intermediate

   Notes:
     These functions are to be used inside user functions that are to be processed with
   ADIC. PETSc will automatically provide differentiated versions of these functions

.seealso: PetscGlobalMin(), PetscGlobalSum()
@*/
PetscErrorCode PETSC_DLLEXPORT PetscGlobalMax(PetscReal* local,PetscReal* result,MPI_Comm comm)
{
  return MPI_Allreduce(local,result,1,MPIU_REAL,MPI_MAX,comm);
}

#undef __FUNCT__
#define __FUNCT__ "PetscGlobalMin"
/*@C
      PetscGlobalMin - Computes the minimum value over several processors

     Collective on MPI_Comm

   Input Parameters:
+   local - the local value
-   comm - the processors that find the minimum

   Output Parameter:
.   result - the minimum value

   Level: intermediate

   Notes:
     These functions are to be used inside user functions that are to be processed with
   ADIC. PETSc will automatically provide differentiated versions of these functions

.seealso: PetscGlobalMax(), PetscGlobalSum()
@*/
PetscErrorCode PETSC_DLLEXPORT PetscGlobalMin(PetscReal* local,PetscReal* result,MPI_Comm comm)
{
  return MPI_Allreduce(local,result,1,MPIU_REAL,MPI_MIN,comm);
}

#undef __FUNCT__
#define __FUNCT__ "PetscGlobalSum"
/*@C
      PetscGlobalSum - Computes the sum over sever processors

     Collective on MPI_Comm

   Input Parameters:
+   local - the local value
-   comm - the processors that find the sum

   Output Parameter:
.   result - the sum

   Level: intermediate

   Notes:
     These functions are to be used inside user functions that are to be processed with
   ADIC. PETSc will automatically provide differentiated versions of these functions

.seealso: PetscGlobalMin(), PetscGlobalMax()
@*/
PetscErrorCode PETSC_DLLEXPORT PetscGlobalSum(PetscScalar* local,PetscScalar* result,MPI_Comm comm)
{
  return MPI_Allreduce(local,result,1,MPIU_SCALAR,PetscSum_Op,comm);
}