/*@C
  PFInitializePackage - This function initializes everything in the PF package. It is called
  from PetscDLLibraryRegister() when using dynamic libraries, and on the first call to PFCreate()
  when using static libraries.

  Input Parameter:
. path - The dynamic library path, or PETSC_NULL

  Level: developer

.keywords: Vec, initialize, package
.seealso: PetscInitialize()
@*/
PetscErrorCode  PFInitializePackage(const char path[]) 
{
  char              logList[256];
  char              *className;
  PetscBool         opt;
  PetscErrorCode    ierr;

  PetscFunctionBegin;
  if (PFPackageInitialized) PetscFunctionReturn(0);
  PFPackageInitialized = PETSC_TRUE;
  /* Register Classes */
  ierr = PetscClassIdRegister("PointFunction",&PF_CLASSID);CHKERRQ(ierr);
  /* Register Constructors */
  ierr = PFRegisterAll(path);CHKERRQ(ierr);
  /* Process info exclusions */
  ierr = PetscOptionsGetString(PETSC_NULL, "-info_exclude", logList, 256, &opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList, "pf", &className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscInfoDeactivateClass(PF_CLASSID);CHKERRQ(ierr);
    }
  }
  /* Process summary exclusions */
  ierr = PetscOptionsGetString(PETSC_NULL, "-log_summary_exclude", logList, 256, &opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList, "pf", &className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscLogEventDeactivateClass(PF_CLASSID);CHKERRQ(ierr);
    }
  }
  ierr = PetscRegisterFinalize(PFFinalizePackage);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
    PetscSetDebuggerFromString - Set the complete path for the
       debugger for PETSc to use.

   Not collective

   Level: developer

.seealso: PetscSetDebugger(), PetscSetDefaultDebugger()
@*/
PetscErrorCode  PetscSetDebuggerFromString(const char *string)
{
  const char     *debugger = NULL;
  PetscBool      xterm     = PETSC_TRUE;
  char           *f;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscStrstr(string, "noxterm", &f);CHKERRQ(ierr);
  if (f) xterm = PETSC_FALSE;
  ierr = PetscStrstr(string, "ddd", &f);CHKERRQ(ierr);
  if (f) xterm = PETSC_FALSE;
  ierr = PetscCheckDebugger_Private("xdb",      string, &debugger);CHKERRQ(ierr);
  ierr = PetscCheckDebugger_Private("dbx",      string, &debugger);CHKERRQ(ierr);
  ierr = PetscCheckDebugger_Private("xldb",     string, &debugger);CHKERRQ(ierr);
  ierr = PetscCheckDebugger_Private("gdb",      string, &debugger);CHKERRQ(ierr);
  ierr = PetscCheckDebugger_Private("idb",      string, &debugger);CHKERRQ(ierr);
  ierr = PetscCheckDebugger_Private("xxgdb",    string, &debugger);CHKERRQ(ierr);
  ierr = PetscCheckDebugger_Private("ddd",      string, &debugger);CHKERRQ(ierr);
  ierr = PetscCheckDebugger_Private("kdbg",     string, &debugger);CHKERRQ(ierr);
  ierr = PetscCheckDebugger_Private("ups",      string, &debugger);CHKERRQ(ierr);
  ierr = PetscCheckDebugger_Private("workshop", string, &debugger);CHKERRQ(ierr);
  ierr = PetscCheckDebugger_Private("pgdbg",    string, &debugger);CHKERRQ(ierr);
  ierr = PetscCheckDebugger_Private("pathdb",   string, &debugger);CHKERRQ(ierr);
  ierr = PetscCheckDebugger_Private("lldb",     string, &debugger);CHKERRQ(ierr);

  ierr = PetscSetDebugger(debugger, xterm);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
  RGInitializePackage - This function initializes everything in the RG package.
  It is called from PetscDLLibraryRegister() when using dynamic libraries, and
  on the first call to RGCreate() when using static libraries.

  Level: developer

.seealso: SlepcInitialize()
@*/
PetscErrorCode RGInitializePackage(void)
{
  char             logList[256];
  char             *className;
  PetscBool        opt;
  PetscErrorCode   ierr;

  PetscFunctionBegin;
  if (RGPackageInitialized) PetscFunctionReturn(0);
  RGPackageInitialized = PETSC_TRUE;
  /* Register Classes */
  ierr = PetscClassIdRegister("Region",&RG_CLASSID);CHKERRQ(ierr);
  /* Register Constructors */
  ierr = RGRegisterAll();CHKERRQ(ierr);
  /* Process info exclusions */
  ierr = PetscOptionsGetString(NULL,"-info_exclude",logList,256,&opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList,"rg",&className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscInfoDeactivateClass(RG_CLASSID);CHKERRQ(ierr);
    }
  }
  /* Process summary exclusions */
  ierr = PetscOptionsGetString(NULL,"-log_summary_exclude",logList,256,&opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList,"rg",&className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscLogEventDeactivateClass(RG_CLASSID);CHKERRQ(ierr);
    }
  }
  ierr = PetscRegisterFinalize(RGFinalizePackage);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
  DMInitializePackage - This function initializes everything in the DM package. It is called
  from PetscDLLibraryRegister() when using dynamic libraries, and on the first call to AOCreate()
  or DMDACreate() when using static libraries.

  Level: developer

.keywords: AO, initialize, package
.seealso: PetscInitialize()
@*/
PetscErrorCode  DMInitializePackage(void)
{
  char           logList[256];
  char           *className;
  PetscBool      opt;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (DMPackageInitialized) PetscFunctionReturn(0);
  DMPackageInitialized = PETSC_TRUE;

  /* Register Classes */
  ierr = PetscClassIdRegister("Distributed Mesh",&DM_CLASSID);CHKERRQ(ierr);

#if defined(PETSC_HAVE_HYPRE)
  ierr = MatRegister(MATHYPRESTRUCT, MatCreate_HYPREStruct);CHKERRQ(ierr);
#endif

  /* Register Constructors */
  ierr = DMRegisterAll();CHKERRQ(ierr);
  /* Register Events */
  ierr = PetscLogEventRegister("DMConvert",              DM_CLASSID,&DM_Convert);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("DMGlobalToLocal",        DM_CLASSID,&DM_GlobalToLocal);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("DMLocalToGlobal",        DM_CLASSID,&DM_LocalToGlobal);CHKERRQ(ierr);

  ierr = PetscLogEventRegister("DMDALocalADFunc",        DM_CLASSID,&DMDA_LocalADFunction);CHKERRQ(ierr);

  ierr = PetscLogEventRegister("DMPlexInterpolate",      DM_CLASSID,&DMPLEX_Interpolate);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("DMPlexPartition",        DM_CLASSID,&DMPLEX_Partition);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("DMPlexDistribute",       DM_CLASSID,&DMPLEX_Distribute);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("DMPlexDistribCones",     DM_CLASSID,&DMPLEX_DistributeCones);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("DMPlexDistribLabels",    DM_CLASSID,&DMPLEX_DistributeLabels);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("DMPlexDistribSF",        DM_CLASSID,&DMPLEX_DistributeSF);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("DMPlexDistribField",     DM_CLASSID,&DMPLEX_DistributeField);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("DMPlexDistribData",      DM_CLASSID,&DMPLEX_DistributeData);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("DMPlexStratify",         DM_CLASSID,&DMPLEX_Stratify);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("DMPlexPreallocate",      DM_CLASSID,&DMPLEX_Preallocate);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("DMPlexResidualFEM",      DM_CLASSID,&DMPLEX_ResidualFEM);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("DMPlexJacobianFEM",      DM_CLASSID,&DMPLEX_JacobianFEM);CHKERRQ(ierr);
  /* Process info exclusions */
  ierr = PetscOptionsGetString(NULL, "-info_exclude", logList, 256, &opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList, "da", &className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscInfoDeactivateClass(DM_CLASSID);CHKERRQ(ierr);
    }
  }
  /* Process summary exclusions */
  ierr = PetscOptionsGetString(NULL, "-log_summary_exclude", logList, 256, &opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList, "da", &className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscLogEventDeactivateClass(DM_CLASSID);CHKERRQ(ierr);
    }
  }
  ierr = PetscRegisterFinalize(DMFinalizePackage);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
   PetscObjectsDump - Prints the currently existing objects.

   Logically Collective on PetscViewer

   Input Parameter:
+  fd - file pointer
-  all - by default only tries to display objects created explicitly by the user, if all is PETSC_TRUE then lists all outstanding objects

   Options Database:
.  -objects_dump <all>

   Level: advanced

   Concepts: options database^printing

@*/
PetscErrorCode  PetscObjectsDump(FILE *fd,PetscBool all)
{
  PetscErrorCode ierr;
  PetscInt       i;
#if defined(PETSC_USE_DEBUG)
  PetscInt       j,k=0;
#endif
  PetscObject    h;

  PetscFunctionBegin;
  if (PetscObjectsCounts) {
    ierr = PetscFPrintf(PETSC_COMM_WORLD,fd,"The following objects were never freed\n");CHKERRQ(ierr);
    ierr = PetscFPrintf(PETSC_COMM_WORLD,fd,"-----------------------------------------\n");CHKERRQ(ierr);
    for (i=0; i<PetscObjectsMaxCounts; i++) {
      if ((h = PetscObjects[i])) {
        ierr = PetscObjectName(h);CHKERRQ(ierr);
        {
#if defined(PETSC_USE_DEBUG)
        PetscStack *stack = 0;
        char       *create,*rclass;

        /* if the PETSc function the user calls is not a create then this object was NOT directly created by them */
        ierr = PetscMallocGetStack(h,&stack);CHKERRQ(ierr);
        if (stack) {
          k = stack->currentsize-2;
          if (!all) {
            k = 0;
            while (!stack->petscroutine[k]) k++;
            ierr = PetscStrstr(stack->function[k],"Create",&create);CHKERRQ(ierr);
            if (!create) {
              ierr = PetscStrstr(stack->function[k],"Get",&create);CHKERRQ(ierr);
            }
            ierr = PetscStrstr(stack->function[k],h->class_name,&rclass);CHKERRQ(ierr);
            if (!create) continue;
            if (!rclass) continue;
          }
        }
#endif

        ierr = PetscFPrintf(PETSC_COMM_WORLD,fd,"[%d] %s %s %s\n",PetscGlobalRank,h->class_name,h->type_name,h->name);CHKERRQ(ierr);

#if defined(PETSC_USE_DEBUG)
        ierr = PetscMallocGetStack(h,&stack);CHKERRQ(ierr);
        if (stack) {
          for (j=k; j>=0; j--) {
            fprintf(fd,"      [%d]  %s() in %s\n",PetscGlobalRank,stack->function[j],stack->file[j]);
          }
        }
#endif
        }
      }
    }
  }
  PetscFunctionReturn(0);
}

/*@C
  PCInitializePackage - This function initializes everything in the PC package. It is called
  from PetscDLLibraryRegister() when using dynamic libraries, and on the first call to PCCreate()
  when using static libraries.

  Level: developer

.keywords: PC, initialize, package
.seealso: PetscInitialize()
@*/
PetscErrorCode  PCInitializePackage(void)
{
  char           logList[256];
  char           *className;
  PetscBool      opt;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (PCPackageInitialized) PetscFunctionReturn(0);
  PCPackageInitialized = PETSC_TRUE;
  /* Initialize subpackages */
  ierr = PCGAMGInitializePackage();CHKERRQ(ierr);
  /* Register Classes */
  ierr = PetscClassIdRegister("Preconditioner",&PC_CLASSID);CHKERRQ(ierr);
  /* Register Constructors */
  ierr = PCRegisterAll();CHKERRQ(ierr);
  /* Register Events */
  ierr = PetscLogEventRegister("PCSetUp",          PC_CLASSID,&PC_SetUp);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("PCSetUpOnBlocks",  PC_CLASSID,&PC_SetUpOnBlocks);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("PCApplyOnBlocks",  PC_CLASSID,&PC_ApplyOnBlocks);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("PCApplyOnMproc",   PC_CLASSID,&PC_ApplyOnMproc);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("PCApply",          PC_CLASSID,&PC_Apply);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("PCApplyCoarse",    PC_CLASSID,&PC_ApplyCoarse);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("PCApplyMultiple",  PC_CLASSID,&PC_ApplyMultiple);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("PCApplySymmLeft",  PC_CLASSID,&PC_ApplySymmetricLeft);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("PCApplySymmRight", PC_CLASSID,&PC_ApplySymmetricRight);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("PCModifySubMatri", PC_CLASSID,&PC_ModifySubMatrices);CHKERRQ(ierr);
  /* Process info exclusions */
  ierr = PetscOptionsGetString(NULL, "-info_exclude", logList, 256, &opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList, "pc", &className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscInfoDeactivateClass(PC_CLASSID);CHKERRQ(ierr);
    }
  }
  /* Process summary exclusions */
  ierr = PetscOptionsGetString(NULL, "-log_summary_exclude", logList, 256, &opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList, "pc", &className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscLogEventDeactivateClass(PC_CLASSID);CHKERRQ(ierr);
    }
  }
  /* Register data */
  ierr = PetscObjectComposedDataRegister(&PetscMGLevelId);CHKERRQ(ierr);
  ierr = PetscRegisterFinalize(PCFinalizePackage);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode PetscViewerFileSetName_MPIIO(PetscViewer viewer,const char name[])
{
  PetscMPIInt        rank;
  PetscErrorCode     ierr;
  size_t             len;
  PetscViewer_Binary *vbinary = (PetscViewer_Binary*)viewer->data;
  char               *gz;
  PetscBool          found;
  PetscFileMode      type = vbinary->btype;

  PetscFunctionBegin;
  if (type == (PetscFileMode) -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call PetscViewerFileSetMode() before PetscViewerFileSetName()");
  ierr = PetscViewerFileClose_MPIIO(viewer);CHKERRQ(ierr);
  ierr = PetscOptionsGetBool(((PetscObject)viewer)->prefix,"-viewer_binary_skip_info",&vbinary->skipinfo,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetBool(((PetscObject)viewer)->prefix,"-viewer_binary_skip_options",&vbinary->skipoptions,NULL);CHKERRQ(ierr);

  ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)viewer),&rank);CHKERRQ(ierr);
  ierr = PetscStrallocpy(name,&vbinary->filename);CHKERRQ(ierr);

  vbinary->storecompressed = PETSC_FALSE;

  /* only first processor opens file if writeable */
  if (type == FILE_MODE_READ) {
    MPI_File_open(PetscObjectComm((PetscObject)viewer),vbinary->filename,MPI_MODE_RDONLY,MPI_INFO_NULL,&vbinary->mfdes);CHKERRQ(ierr);
  } else if (type == FILE_MODE_WRITE) {
    MPI_File_open(PetscObjectComm((PetscObject)viewer),vbinary->filename,MPI_MODE_WRONLY | MPI_MODE_CREATE,MPI_INFO_NULL,&vbinary->mfdes);CHKERRQ(ierr);
  }

  /*
      try to open info file: all processors open this file if read only

      Below is identical code to the code for Binary above, should be put in seperate routine
  */
  if (!vbinary->skipinfo && (!rank || type == FILE_MODE_READ)) {
    char infoname[PETSC_MAX_PATH_LEN],iname[PETSC_MAX_PATH_LEN];

    ierr = PetscStrcpy(infoname,name);CHKERRQ(ierr);
    /* remove .gz if it ends library name */
    ierr = PetscStrstr(infoname,".gz",&gz);CHKERRQ(ierr);
    if (gz) {
      ierr = PetscStrlen(gz,&len);CHKERRQ(ierr);
      if (len == 3) *gz = 0;
    }

    ierr = PetscStrcat(infoname,".info");CHKERRQ(ierr);
    ierr = PetscFixFilename(infoname,iname);CHKERRQ(ierr);
    if (type == FILE_MODE_READ) {
      ierr = PetscFileRetrieve(PetscObjectComm((PetscObject)viewer),iname,infoname,PETSC_MAX_PATH_LEN,&found);CHKERRQ(ierr);
      ierr = PetscOptionsInsertFile(PetscObjectComm((PetscObject)viewer),infoname,PETSC_FALSE);CHKERRQ(ierr);
    } else {
      vbinary->fdes_info = fopen(infoname,"w");
      if (!vbinary->fdes_info) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Cannot open .info file %s for writing",infoname);
    }
  }

#if defined(PETSC_USE_LOG)
  PetscLogObjectState((PetscObject)viewer,"File: %s",name);
#endif
  PetscFunctionReturn(0);
}

/*@C
  SNESInitializePackage - This function initializes everything in the SNES package. It is called
  from PetscDLLibraryRegister() when using dynamic libraries, and on the first call to SNESCreate()
  when using static libraries.

  Level: developer

.keywords: SNES, initialize, package
.seealso: PetscInitialize()
@*/
PetscErrorCode  SNESInitializePackage(void)
{
  char           logList[256];
  char           *className;
  PetscBool      opt;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (SNESPackageInitialized) PetscFunctionReturn(0);
  SNESPackageInitialized = PETSC_TRUE;
  /* Initialize subpackages */
  ierr = SNESMSInitializePackage();CHKERRQ(ierr);
  /* Register Classes */
  ierr = PetscClassIdRegister("SNES",&SNES_CLASSID);CHKERRQ(ierr);
  ierr = PetscClassIdRegister("SNESLineSearch",&SNESLINESEARCH_CLASSID);CHKERRQ(ierr);
  ierr = PetscClassIdRegister("DMSNES",&DMSNES_CLASSID);CHKERRQ(ierr);
  /* Register Constructors */
  ierr = SNESRegisterAll();CHKERRQ(ierr);
  ierr = SNESLineSearchRegisterAll();CHKERRQ(ierr);
  /* Register Events */
  ierr = PetscLogEventRegister("SNESSolve",            SNES_CLASSID,&SNES_Solve);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("SNESFunctionEval",     SNES_CLASSID,&SNES_FunctionEval);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("SNESObjectiveEval",    SNES_CLASSID,&SNES_ObjectiveEval);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("SNESNGSEval",          SNES_CLASSID,&SNES_NGSEval);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("SNESNGSFuncEval",      SNES_CLASSID,&SNES_NGSFuncEval);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("SNESJacobianEval",     SNES_CLASSID,&SNES_JacobianEval);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("SNESLineSearch",       SNESLINESEARCH_CLASSID,&SNESLINESEARCH_Apply);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("SNESNPCSolve",         SNES_CLASSID,&SNES_NPCSolve);CHKERRQ(ierr);
  /* Process info exclusions */
  ierr = PetscOptionsGetString(NULL,NULL, "-info_exclude", logList, 256, &opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList, "snes", &className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscInfoDeactivateClass(SNES_CLASSID);CHKERRQ(ierr);
    }
  }
  /* Process summary exclusions */
  ierr = PetscOptionsGetString(NULL,NULL, "-log_exclude", logList, 256, &opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList, "snes", &className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscLogEventDeactivateClass(SNES_CLASSID);CHKERRQ(ierr);
    }
  }
  ierr = PetscRegisterFinalize(SNESFinalizePackage);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
   BVInitializePackage - This function initializes everything in the BV package.
   It is called from PetscDLLibraryRegister() when using dynamic libraries, and
   on the first call to BVCreate() when using static libraries.

   Level: developer

.seealso: SlepcInitialize()
@*/
PetscErrorCode BVInitializePackage(void)
{
  char           logList[256];
  char           *className;
  PetscBool      opt;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (BVPackageInitialized) PetscFunctionReturn(0);
  BVPackageInitialized = PETSC_TRUE;
  /* Register Classes */
  ierr = PetscClassIdRegister("Basis Vectors",&BV_CLASSID);CHKERRQ(ierr);
  /* Register Constructors */
  ierr = BVRegisterAll();CHKERRQ(ierr);
  /* Register Events */
  ierr = PetscLogEventRegister("BVCreate",BV_CLASSID,&BV_Create);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("BVCopy",BV_CLASSID,&BV_Copy);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("BVMult",BV_CLASSID,&BV_Mult);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("BVDot",BV_CLASSID,&BV_Dot);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("BVOrthogonalize",BV_CLASSID,&BV_Orthogonalize);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("BVScale",BV_CLASSID,&BV_Scale);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("BVNorm",BV_CLASSID,&BV_Norm);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("BVSetRandom",BV_CLASSID,&BV_SetRandom);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("BVMatMult",BV_CLASSID,&BV_MatMult);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("BVMatProject",BV_CLASSID,&BV_MatProject);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("BVAXPY",BV_CLASSID,&BV_AXPY);CHKERRQ(ierr);
  /* Process info exclusions */
  ierr = PetscOptionsGetString(NULL,"-info_exclude",logList,256,&opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList,"bv",&className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscInfoDeactivateClass(BV_CLASSID);CHKERRQ(ierr);
    }
  }
  /* Process summary exclusions */
  ierr = PetscOptionsGetString(NULL,"-log_summary_exclude",logList,256,&opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList,"bv",&className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscLogEventDeactivateClass(BV_CLASSID);CHKERRQ(ierr);
    }
  }
  ierr = PetscRegisterFinalize(BVFinalizePackage);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
   NEPInitializePackage - This function initializes everything in the NEP package.
   It is called from PetscDLLibraryRegister() when using dynamic libraries, and
   on the first call to NEPCreate() when using static libraries.

   Level: developer

.seealso: SlepcInitialize()
@*/
PetscErrorCode NEPInitializePackage(void)
{
  char           logList[256];
  char           *className;
  PetscBool      opt;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (NEPPackageInitialized) PetscFunctionReturn(0);
  NEPPackageInitialized = PETSC_TRUE;
  /* Register Classes */
  ierr = PetscClassIdRegister("Nonlinear Eigenvalue Problem solver",&NEP_CLASSID);CHKERRQ(ierr);
  /* Register Constructors */
  ierr = NEPRegisterAll();CHKERRQ(ierr);
  /* Register Events */
  ierr = PetscLogEventRegister("NEPSetUp",NEP_CLASSID,&NEP_SetUp);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("NEPSolve",NEP_CLASSID,&NEP_Solve);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("NEPRefine",NEP_CLASSID,&NEP_Refine);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("NEPFunctionEval",NEP_CLASSID,&NEP_FunctionEval);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("NEPJacobianEval",NEP_CLASSID,&NEP_JacobianEval);CHKERRQ(ierr);
  /* Process info exclusions */
  ierr = PetscOptionsGetString(NULL,"-info_exclude",logList,256,&opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList,"nep",&className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscInfoDeactivateClass(NEP_CLASSID);CHKERRQ(ierr);
    }
  }
  /* Process summary exclusions */
  ierr = PetscOptionsGetString(NULL,"-log_summary_exclude",logList,256,&opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList,"nep",&className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscLogEventDeactivateClass(NEP_CLASSID);CHKERRQ(ierr);
    }
  }
  ierr = PetscRegisterFinalize(NEPFinalizePackage);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
     PetscPullJSONValue - Given a JSON response containing the substring with "key" : "value"  where there may or not be spaces around the : returns the value.

    Input Parameters:
+    buff - the char array containing the possible values
.    key - the key of the requested value
-    valuelen - the length of the array to contain the value associated with the key

    Output Parameters:
+    value - the value obtained
-    found - flag indicating if the value was found in the buff

    Level: advanced

@*/
PetscErrorCode PetscPullJSONValue(const char buff[],const char key[],char value[],size_t valuelen,PetscBool *found)
{
  PetscErrorCode ierr;
  char           *v,*w;
  char           work[256];
  size_t         len;

  PetscFunctionBegin;
  ierr = PetscStrcpy(work,"\"");CHKERRQ(ierr);
  ierr = PetscStrlcat(work,key,sizeof(work));CHKERRQ(ierr);
  ierr = PetscStrcat(work,"\":");CHKERRQ(ierr);
  ierr = PetscStrstr(buff,work,&v);CHKERRQ(ierr);
  ierr = PetscStrlen(work,&len);CHKERRQ(ierr);
  if (v) {
    v += len;
  } else {
    work[len++-1] = 0;
    ierr = PetscStrcat(work," :");CHKERRQ(ierr);
    ierr = PetscStrstr(buff,work,&v);CHKERRQ(ierr);
    if (!v) {
      *found = PETSC_FALSE;
      PetscFunctionReturn(0);
    }
    v += len;
  }
  ierr = PetscStrchr(v,'\"',&v);CHKERRQ(ierr);
  if (!v) {
    *found = PETSC_FALSE;
    PetscFunctionReturn(0);
  }
  ierr = PetscStrchr(v+1,'\"',&w);CHKERRQ(ierr);
  if (!w) {
    *found = PETSC_FALSE;
    PetscFunctionReturn(0);
  }
  *found = PETSC_TRUE;
  ierr = PetscStrncpy(value,v+1,PetscMin((size_t)(w-v),valuelen));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
  PetscInitializeDrawPackage - This function initializes everything in the PetscDraw package. It is called
  from PetscDLLibraryRegister() when using dynamic libraries, and on the call to PetscInitialize()
  when using static libraries.

  Level: developer

.keywords: Petsc, initialize, package
.seealso: PetscInitialize()
@*/
PetscErrorCode  PetscDrawInitializePackage(void)
{
  char           logList[256];
  char           *className;
  PetscBool      opt;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (PetscDrawPackageInitialized) PetscFunctionReturn(0);
  PetscDrawPackageInitialized = PETSC_TRUE;
  /* Register Classes */
  ierr = PetscClassIdRegister("Draw",&PETSC_DRAW_CLASSID);CHKERRQ(ierr);
  ierr = PetscClassIdRegister("Axis",&PETSC_DRAWAXIS_CLASSID);CHKERRQ(ierr);
  ierr = PetscClassIdRegister("Line Graph",&PETSC_DRAWLG_CLASSID);CHKERRQ(ierr);
  ierr = PetscClassIdRegister("Histogram",&PETSC_DRAWHG_CLASSID);CHKERRQ(ierr);
  ierr = PetscClassIdRegister("Bar Grap",&PETSC_DRAWBAR_CLASSID);CHKERRQ(ierr);
  ierr = PetscClassIdRegister("Scatter Plot",&PETSC_DRAWSP_CLASSID);CHKERRQ(ierr);
  /* Register Constructors */
  ierr = PetscDrawRegisterAll();CHKERRQ(ierr);
  /* Process info exclusions */
  ierr = PetscOptionsGetString(NULL, "-info_exclude", logList, 256, &opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList, "draw", &className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscInfoDeactivateClass(0);CHKERRQ(ierr);
    }
  }
  /* Process summary exclusions */
  ierr = PetscOptionsGetString(NULL, "-log_summary_exclude", logList, 256, &opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList, "draw", &className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscLogEventDeactivateClass(0);CHKERRQ(ierr);
    }
  }
  ierr = PetscRegisterFinalize(PetscDrawFinalizePackage);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
  PetscViewerInitializePackage - This function initializes everything in the main PetscViewer package.

  Level: developer

.keywords: Petsc, initialize, package
.seealso: PetscInitialize()
@*/
PetscErrorCode  PetscViewerInitializePackage(void)
{
  char           logList[256];
  char           *className;
  PetscBool      opt;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (PetscViewerPackageInitialized) PetscFunctionReturn(0);
  PetscViewerPackageInitialized = PETSC_TRUE;
  /* Register Classes */
  ierr = PetscClassIdRegister("Viewer",&PETSC_VIEWER_CLASSID);CHKERRQ(ierr);

  /* Register Constructors */
  ierr = PetscViewerRegisterAll();CHKERRQ(ierr);

  /* Process info exclusions */
  ierr = PetscOptionsGetString(NULL,NULL, "-info_exclude", logList, 256, &opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList, "viewer", &className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscInfoDeactivateClass(0);CHKERRQ(ierr);
    }
  }
  /* Process summary exclusions */
  ierr = PetscOptionsGetString(NULL,NULL, "-log_exclude", logList, 256, &opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList, "viewer", &className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscLogEventDeactivateClass(0);CHKERRQ(ierr);
    }
  }
#if defined(PETSC_HAVE_MATHEMATICA)
  ierr = PetscViewerMathematicaInitializePackage();CHKERRQ(ierr);
#endif
  ierr = PetscRegisterFinalize(PetscViewerFinalizePackage);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*
    Removes all zeros but one from .0000
*/
PetscErrorCode PetscStripe0(char *buf)
{
  PetscErrorCode ierr;
  size_t         n;
  PetscBool      flg;
  char           *str;

  PetscFunctionBegin;
  ierr = PetscStrlen(buf,&n);CHKERRQ(ierr);
  ierr = PetscStrendswith(buf,"e00",&flg);CHKERRQ(ierr);
  if (flg) buf[n-3] = 0;
  ierr = PetscStrstr(buf,"e0",&str);CHKERRQ(ierr);
  if (str) {
    buf[n-2] = buf[n-1];
    buf[n-1] = 0;
  }
  ierr = PetscStrstr(buf,"e-0",&str);CHKERRQ(ierr);
  if (str) {
    buf[n-2] = buf[n-1];
    buf[n-1] = 0;
  }
  PetscFunctionReturn(0);
}

PetscErrorCode PetscP4estInitialize(void)
{
  PetscBool      psc_catch_signals    = PETSC_FALSE;
  PetscBool      psc_print_backtrace  = PETSC_TRUE;
  int            psc_log_threshold    = SC_LP_DEFAULT;
  int            pp4est_log_threshold = SC_LP_DEFAULT;
  char           logList[256], *className;
  PetscBool      opt;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (PetscP4estInitialized) PetscFunctionReturn(0);
  PetscP4estInitialized = PETSC_TRUE;

  ierr = PetscClassIdRegister("p4est logging",&P4ESTLOGGING_CLASSID);CHKERRQ(ierr);
  ierr = PetscOptionsGetString(NULL,NULL, "-info_exclude", logList, 256, &opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList, "p4est", &className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscInfoDeactivateClass(P4ESTLOGGING_CLASSID);CHKERRQ(ierr);
    }
  }
  ierr = PetscHeaderCreate(P4estLoggingObject,P4ESTLOGGING_CLASSID,"p4est","p4est logging","DM",PETSC_COMM_WORLD,NULL,PetscObjectView);CHKERRQ(ierr);
  if (sc_package_id == -1) {
    int       log_threshold_shifted = psc_log_threshold + 1;
    PetscBool set;

    PetscBeganSc = PETSC_TRUE;
    ierr         = PetscOptionsGetBool(NULL,NULL,"-petsc_sc_catch_signals",&psc_catch_signals,NULL);CHKERRQ(ierr);
    ierr         = PetscOptionsGetBool(NULL,NULL,"-petsc_sc_print_backtrace",&psc_print_backtrace,NULL);CHKERRQ(ierr);
    ierr         = PetscOptionsGetEnum(NULL,NULL,"-petsc_sc_log_threshold",SCLogTypes,(PetscEnum*)&log_threshold_shifted,&set);CHKERRQ(ierr);
    if (set) psc_log_threshold = log_threshold_shifted - 1;
    sc_init(PETSC_COMM_WORLD,(int)psc_catch_signals,(int)psc_print_backtrace,PetscScLogHandler,psc_log_threshold);
    if (sc_package_id == -1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_LIB,"Could not initialize libsc package used by p4est");
    sc_set_abort_handler(PetscScAbort);
  }
  if (p4est_package_id == -1) {
    int       log_threshold_shifted = pp4est_log_threshold + 1;
    PetscBool set;

    ierr = PetscOptionsGetEnum(NULL,NULL,"-petsc_p4est_log_threshold",SCLogTypes,(PetscEnum*)&log_threshold_shifted,&set);CHKERRQ(ierr);
    if (set) pp4est_log_threshold = log_threshold_shifted - 1;
    PetscStackCallP4est(p4est_init,(PetscScLogHandler,pp4est_log_threshold));
    if (p4est_package_id == -1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_LIB,"Could not initialize p4est");
  }
  ierr = DMForestRegisterType(DMP4EST);CHKERRQ(ierr);
  ierr = DMForestRegisterType(DMP8EST);CHKERRQ(ierr);
  ierr = PetscRegisterFinalize(PetscP4estFinalize);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscCheckDebugger_Private(const char defaultDbg[], const char string[], const char *debugger[])
{
  PetscBool      exists;
  char           *f;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscStrstr(string, defaultDbg, &f);CHKERRQ(ierr);
  if (f) {
    ierr = PetscTestFile(string, 'x', &exists);CHKERRQ(ierr);
    if (exists) *debugger = string;
    else        *debugger = defaultDbg;
  }
  PetscFunctionReturn(0);
}

/*@C
  AOInitializePackage - This function initializes everything in the AO package. It is called
  from PetscDLLibraryRegister() when using dynamic libraries, and on the first call to AOCreate().

  Input Parameter:
  path - The dynamic library path, or PETSC_NULL

  Level: developer

.keywords: AO, initialize, package
.seealso: PetscInitialize()
@*/
PetscErrorCode  AOInitializePackage(const char path[])
{
  char              logList[256];
  char              *className;
  PetscBool         opt;
  PetscErrorCode    ierr;

  PetscFunctionBegin;
  if (AOPackageInitialized) PetscFunctionReturn(0);
  AOPackageInitialized = PETSC_TRUE;
  /* Register Classes */
  ierr = PetscClassIdRegister("Application Order",&AO_CLASSID);CHKERRQ(ierr);
  /* Register Constructors */
  ierr = AORegisterAll(path);CHKERRQ(ierr);
  /* Register Events */
  ierr = PetscLogEventRegister("AOPetscToApplication", AO_CLASSID,&AO_PetscToApplication);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("AOApplicationToPetsc", AO_CLASSID,&AO_ApplicationToPetsc);CHKERRQ(ierr);
  /* Process info exclusions */
  ierr = PetscOptionsGetString(PETSC_NULL, "-info_exclude", logList, 256, &opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList, "ao", &className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscInfoDeactivateClass(AO_CLASSID);CHKERRQ(ierr);
    }
  }
  /* Process summary exclusions */
  ierr = PetscOptionsGetString(PETSC_NULL, "-log_summary_exclude", logList, 256, &opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList, "ao", &className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscLogEventDeactivateClass(AO_CLASSID);CHKERRQ(ierr);
    }
  }
  ierr = PetscRegisterFinalize(AOFinalizePackage);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
  MFNInitializePackage - This function initializes everything in the MFN package.
  It is called from PetscDLLibraryRegister() when using dynamic libraries, and
  on the first call to MFNCreate() when using static libraries.

  Level: developer

.seealso: SlepcInitialize()
@*/
PetscErrorCode MFNInitializePackage(void)
{
  char           logList[256];
  char           *className;
  PetscBool      opt;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (MFNPackageInitialized) PetscFunctionReturn(0);
  MFNPackageInitialized = PETSC_TRUE;
  /* Register Classes */
  ierr = PetscClassIdRegister("Matrix Function",&MFN_CLASSID);CHKERRQ(ierr);
  /* Register Constructors */
  ierr = MFNRegisterAll();CHKERRQ(ierr);
  /* Register Events */
  ierr = PetscLogEventRegister("MFNSetUp",MFN_CLASSID,&MFN_SetUp);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("MFNSolve",MFN_CLASSID,&MFN_Solve);CHKERRQ(ierr);
  /* Process info exclusions */
  ierr = PetscOptionsGetString(NULL,"-info_exclude",logList,256,&opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList,"mfn",&className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscInfoDeactivateClass(MFN_CLASSID);CHKERRQ(ierr);
    }
  }
  /* Process summary exclusions */
  ierr = PetscOptionsGetString(NULL,"-log_summary_exclude",logList,256,&opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList,"mfn",&className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscLogEventDeactivateClass(MFN_CLASSID);CHKERRQ(ierr);
    }
  }
  ierr = PetscRegisterFinalize(MFNFinalizePackage);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
  EPSInitializePackage - This function initializes everything in the EPS package.
  It is called from PetscDLLibraryRegister() when using dynamic libraries, and
  on the first call to EPSCreate() when using static libraries.

  Level: developer

.seealso: SlepcInitialize()
@*/
PetscErrorCode EPSInitializePackage()
{
  char           logList[256];
  char           *className;
  PetscBool      opt;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (EPSPackageInitialized) PetscFunctionReturn(0);
  EPSPackageInitialized = PETSC_TRUE;
  /* Register Classes */
  ierr = PetscClassIdRegister("Eigenvalue Problem Solver",&EPS_CLASSID);CHKERRQ(ierr);
  /* Register Constructors */
  ierr = EPSRegisterAll();CHKERRQ(ierr);
  /* Register Events */
  ierr = PetscLogEventRegister("EPSSetUp",EPS_CLASSID,&EPS_SetUp);CHKERRQ(ierr);
  ierr = PetscLogEventRegister("EPSSolve",EPS_CLASSID,&EPS_Solve);CHKERRQ(ierr);
  /* Process info exclusions */
  ierr = PetscOptionsGetString(NULL,"-info_exclude",logList,256,&opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList,"eps",&className);CHKERRQ(ierr);
    if (className) {
      ierr = PetscInfoDeactivateClass(EPS_CLASSID);CHKERRQ(ierr);
    }
  }
  /* Process summary exclusions */
  ierr = PetscOptionsGetString(NULL,"-log_summary_exclude",logList,256,&opt);CHKERRQ(ierr);
  if (opt) {
    ierr = PetscStrstr(logList,"eps