/*@
   PetscBagSetFromOptions - Allows setting options from a bag

   Collective on PetscBag

   Input Parameter:
.  bag - the bag of values

   Level: beginner

.seealso: PetscBag, PetscBagSetName(), PetscBagDestroy(), PetscBagLoad(), PetscBagGetData()
           PetscBagRegisterReal(), PetscBagRegisterInt(), PetscBagRegisterBool(), PetscBagRegisterScalar()
           PetscBagSetFromOptions(), PetscBagCreate(), PetscBagGetName(), PetscBagView(), PetscBagRegisterEnum()

@*/
PetscErrorCode  PetscBagSetFromOptions(PetscBag bag)
{
  PetscErrorCode ierr;
  PetscBagItem   nitem = bag->bagitems;
  char           name[PETSC_BAG_NAME_LENGTH+1],helpname[PETSC_BAG_NAME_LENGTH+PETSC_BAG_HELP_LENGTH+3];
  PetscInt       n;

  PetscFunctionBegin;
  ierr = PetscStrcpy(helpname,bag->bagname);CHKERRQ(ierr);
  ierr = PetscStrcat(helpname," ");CHKERRQ(ierr);
  ierr = PetscStrcat(helpname,bag->baghelp);CHKERRQ(ierr);
  ierr = PetscOptionsBegin(bag->bagcomm,bag->bagprefix,helpname,0);CHKERRQ(ierr);
  while (nitem) {
    name[0] = '-';
    name[1] = 0;
    ierr    = PetscStrcat(name,nitem->name);CHKERRQ(ierr);
    if (nitem->dtype == PETSC_CHAR) {   /* special handling for fortran required? [due to space padding vs null termination] */
      char *value = (char*)(((char*)bag) + nitem->offset);
      ierr = PetscOptionsString(name,nitem->help,"",value,value,nitem->msize,NULL);CHKERRQ(ierr);
    } else if (nitem->dtype == PETSC_REAL) {
      PetscReal *value = (PetscReal*)(((char*)bag) + nitem->offset);
      if (nitem->msize == 1) {
        ierr = PetscOptionsReal(name,nitem->help,"",*value,value,NULL);CHKERRQ(ierr);
      } else {
        n    = nitem->msize;
        ierr = PetscOptionsRealArray(name,nitem->help,"",value,&n,NULL);CHKERRQ(ierr);
      }
    } else if (nitem->dtype == PETSC_SCALAR) {
      PetscScalar *value = (PetscScalar*)(((char*)bag) + nitem->offset);
      ierr = PetscOptionsScalar(name,nitem->help,"",*value,value,NULL);CHKERRQ(ierr);
    } else if (nitem->dtype == PETSC_INT) {
      PetscInt *value = (PetscInt*)(((char*)bag) + nitem->offset);
      if (nitem->msize == 1) {
        ierr = PetscOptionsInt(name,nitem->help,"",*value,value,NULL);CHKERRQ(ierr);
      } else {
        n    = nitem->msize;
        ierr = PetscOptionsIntArray(name,nitem->help,"",value,&n,NULL);CHKERRQ(ierr);
      }
    } else if (nitem->dtype == PETSC_ENUM) {
      PetscEnum *value = (PetscEnum*)(((char*)bag) + nitem->offset);
      PetscInt  i      = 0;
      while (nitem->list[i++]) ;
      ierr = PetscOptionsEnum(name,nitem->help,nitem->list[i-3],(const char*const*)nitem->list,*value,value,NULL);CHKERRQ(ierr);
    } else if (nitem->dtype == PETSC_BOOL) {
      PetscBool *value = (PetscBool*)(((char*)bag) + nitem->offset);
      if (nitem->msize == 1) {
        ierr = PetscOptionsBool(name,nitem->help,"",*value,value,NULL);CHKERRQ(ierr);
      } else {
        n = nitem->msize;
        ierr = PetscOptionsBoolArray(name,nitem->help,"",value,&n,NULL);CHKERRQ(ierr);
      }
    }
    nitem = nitem->next;
  }
  PetscOptionsEnd();
  PetscFunctionReturn(0);
}

/**
 * output_singular
 * ------
 * Output the left and right singular vectors.
 */
PetscErrorCode output_singular(char *output_name, const Vec u, const Vec v)
{
	PetscFunctionBegin;
	PetscErrorCode ierr;

	char output_name_prefixed[PETSC_MAX_PATH_LEN];
	//const char *prefix = "/out/";
	const char *u_extension = ".U";
	const char *v_extension = ".V";

	//ierr = PetscStrcpy(output_name_prefixed, getenv("FD3D_ROOT")); CHKERRQ(ierr);
	//ierr = PetscStrcat(output_name_prefixed, prefix); CHKERRQ(ierr);
	//ierr = PetscStrcat(output_name_prefixed, output_name); CHKERRQ(ierr);
	ierr = PetscStrcpy(output_name_prefixed, output_name); CHKERRQ(ierr);

	char u_file[PETSC_MAX_PATH_LEN];
	char v_file[PETSC_MAX_PATH_LEN];

	ierr = PetscStrcpy(u_file, output_name_prefixed); CHKERRQ(ierr);
	ierr = PetscStrcat(u_file, u_extension); CHKERRQ(ierr);
	ierr = PetscStrcpy(v_file, output_name_prefixed); CHKERRQ(ierr);
	ierr = PetscStrcat(v_file, v_extension); CHKERRQ(ierr);

	PetscViewer viewer;

	//viewer = PETSC_VIEWER_STDOUT_WORLD;
	//ierr = PetscViewerHDF5Open(PETSC_COMM_WORLD, h_file, FILE_MODE_WRITE, &viewer); CHKERRQ(ierr);

	/** Write the left singular vector u. */
	ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer); CHKERRQ(ierr);
	ierr = PetscViewerSetType(viewer, PETSCVIEWERBINARY); CHKERRQ(ierr);
	ierr = PetscViewerFileSetMode(viewer, FILE_MODE_WRITE); CHKERRQ(ierr);
	ierr = PetscViewerBinarySkipInfo(viewer); CHKERRQ(ierr);
	ierr = PetscViewerFileSetName(viewer, u_file); CHKERRQ(ierr);
	/*
	   ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD, e_file, FILE_MODE_WRITE, &viewer); CHKERRQ(ierr);
	 */
	ierr = VecView(u, viewer); CHKERRQ(ierr);

	/** Write the right singular vector v. */
	ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr);

	ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer); CHKERRQ(ierr);
	ierr = PetscViewerSetType(viewer, PETSCVIEWERBINARY); CHKERRQ(ierr);
	ierr = PetscViewerFileSetMode(viewer, FILE_MODE_WRITE); CHKERRQ(ierr);
	ierr = PetscViewerBinarySkipInfo(viewer); CHKERRQ(ierr);
	ierr = PetscViewerFileSetName(viewer, v_file); CHKERRQ(ierr);
	/*
	   ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD, h_file, FILE_MODE_WRITE, &viewer); CHKERRQ(ierr);
	 */
	ierr = VecView(v, viewer); CHKERRQ(ierr);

	ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr);

	PetscFunctionReturn(0);
}

/*@C
  TSRegister - See TSRegisterDynamic()

  Level: advanced
@*/
PetscErrorCode  TSRegister(const char sname[], const char path[], const char name[], PetscErrorCode (*function)(TS))
{
  char           fullname[PETSC_MAX_PATH_LEN];
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscStrcpy(fullname, path);CHKERRQ(ierr);
  ierr = PetscStrcat(fullname, ":");CHKERRQ(ierr);
  ierr = PetscStrcat(fullname, name);CHKERRQ(ierr);
  ierr = PetscFunctionListAdd(PETSC_COMM_WORLD,&TSList, sname, fullname, (void (*)(void)) function);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscHTTPBuildRequest(const char type[],const char url[],const char header[],const char ctype[],const char body[],char **outrequest)
{
  char           *request=0;
  char           contentlength[40],contenttype[80],*path,*host;
  size_t         request_len,headlen,bodylen,contentlen,pathlen,hostlen,typelen,contenttypelen = 0;
  PetscErrorCode ierr;
  PetscBool      flg;

  PetscFunctionBegin;
  ierr = PetscStrallocpy(url,&host);CHKERRQ(ierr);
  ierr = PetscStrchr(host,'/',&path);CHKERRQ(ierr);
  if (!path) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"url must contain / it is %s",url);
  *path = 0;
  ierr  = PetscStrlen(host,&hostlen);CHKERRQ(ierr);

  ierr = PetscStrchr(url,'/',&path);CHKERRQ(ierr);
  ierr = PetscStrlen(path,&pathlen);CHKERRQ(ierr);

  if (header) {
    ierr = PetscStrendswith(header,"\r\n",&flg);CHKERRQ(ierr);
    if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"header must end with \\r\\n");
  }

  ierr = PetscStrlen(type,&typelen);CHKERRQ(ierr);
  if (ctype) {
    ierr = PetscSNPrintf(contenttype,80,"Content-Type: %s\r\n",ctype);CHKERRQ(ierr);
    ierr = PetscStrlen(contenttype,&contenttypelen);CHKERRQ(ierr);
  }
  ierr = PetscStrlen(header,&headlen);CHKERRQ(ierr);
  ierr = PetscStrlen(body,&bodylen);CHKERRQ(ierr);
  ierr = PetscSNPrintf(contentlength,40,"Content-Length: %d\r\n\r\n",(int)bodylen);CHKERRQ(ierr);
  ierr = PetscStrlen(contentlength,&contentlen);CHKERRQ(ierr);

  /* Now construct our HTTP request */
  request_len = typelen + 1 + pathlen + hostlen + 100 + headlen + contenttypelen + contentlen + bodylen + 1;
  ierr = PetscMalloc1(request_len,&request);CHKERRQ(ierr);
  ierr = PetscStrcpy(request,type);CHKERRQ(ierr);
  ierr = PetscStrcat(request," ");CHKERRQ(ierr);
  ierr = PetscStrcat(request,path);CHKERRQ(ierr);
  ierr = PetscStrcat(request," HTTP/1.1\r\nHost: ");CHKERRQ(ierr);
  ierr = PetscStrcat(request,host);CHKERRQ(ierr);
  ierr = PetscFree(host);CHKERRQ(ierr);
  ierr = PetscStrcat(request,"\r\nUser-Agent:PETScClient\r\n");CHKERRQ(ierr);
  ierr = PetscStrcat(request,header);CHKERRQ(ierr);
  if (ctype) {
    ierr = PetscStrcat(request,contenttype);CHKERRQ(ierr);
  }
  ierr = PetscStrcat(request,contentlength);CHKERRQ(ierr);
  ierr = PetscStrcat(request,body);CHKERRQ(ierr);
  ierr = PetscStrlen(request,&request_len);CHKERRQ(ierr);
  ierr = PetscInfo1(NULL,"HTTPS request follows: \n%s\n",request);CHKERRQ(ierr);

  *outrequest = request;
  PetscFunctionReturn(0);
}

/*@C
    PetscSSLInitializeContext - Set up an SSL context suitable for initiating HTTPS requests.

    Output Parameter:
.   octx - the SSL_CTX to be passed to PetscHTTPSConnect

    Level: advanced

    If PETSc was ./configure -with-ssl-certificate requires the user have created a self-signed certificate with
$    saws/CA.pl  -newcert  (using the passphrase of password)
$    cat newkey.pem newcert.pem > sslclient.pem

    and put the resulting file in either the current directory (with the application) or in the home directory. This seems kind of
    silly but it was all I could figure out.

.seealso: PetscSSLDestroyContext(), PetscHTTPSConnect(), PetscHTTPSRequest()

@*/
PetscErrorCode PetscSSLInitializeContext(SSL_CTX **octx)
{
    SSL_CTX        *ctx;
#if defined(PETSC_USE_SSL_CERTIFICATE)
    char           keyfile[PETSC_MAX_PATH_LEN];
    PetscBool      exists;
    PetscErrorCode ierr;
#endif

    PetscFunctionBegin;
    if (!bio_err){
      SSL_library_init();
      SSL_load_error_strings();
      bio_err = BIO_new_fp(stderr,BIO_NOCLOSE);
    }

    /* Set up a SIGPIPE handler */
    signal(SIGPIPE,sigpipe_handle);

/* suggested at https://mta.openssl.org/pipermail/openssl-dev/2015-May/001449.html */
#if (OPENSSL_VERSION_NUMBER >= 0x10100000L)
    ctx  = SSL_CTX_new(TLS_client_method());
#else
    ctx  = SSL_CTX_new(SSLv23_client_method());
#endif
    SSL_CTX_set_mode(ctx,SSL_MODE_AUTO_RETRY);

#if defined(PETSC_USE_SSL_CERTIFICATE)
    /* Locate keyfile */
    ierr = PetscStrcpy(keyfile,"sslclient.pem");CHKERRQ(ierr);
    ierr = PetscTestFile(keyfile,'r',&exists);CHKERRQ(ierr);
    if (!exists) {
      ierr = PetscGetHomeDirectory(keyfile,PETSC_MAX_PATH_LEN);CHKERRQ(ierr);
      ierr = PetscStrcat(keyfile,"/");CHKERRQ(ierr);
      ierr = PetscStrcat(keyfile,"sslclient.pem");CHKERRQ(ierr);
      ierr = PetscTestFile(keyfile,'r',&exists);CHKERRQ(ierr);
      if (!exists) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Unable to locate sslclient.pem file in current directory or home directory");
    }

    /* Load our keys and certificates*/
    if (!(SSL_CTX_use_certificate_chain_file(ctx,keyfile))) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Cannot read certificate file");

    SSL_CTX_set_default_passwd_cb(ctx,password_cb);
    if (!(SSL_CTX_use_PrivateKey_file(ctx,keyfile,SSL_FILETYPE_PEM))) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Cannot read key file");
#endif

    *octx = ctx;
    PetscFunctionReturn(0);
}

static PetscErrorCode PetscDrawSave_SAWs(PetscDraw draw)
{
  PetscImageList image;
  char           body[4096];
  size_t         len = 0;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (!draw->savefilename) PetscFunctionReturn(0);
  ierr = PetscImageListAdd(draw->savefilename,draw->saveimageext,draw->savefilecount-1);CHKERRQ(ierr);
  image = SAWs_images;
  while (image) {
    const char *name = image->filename;
    const char *ext  = image->ext;
    if (draw->savesinglefile) {
      ierr = PetscSNPrintf(body+len,4086-len,"<img src=\"%s%s\" alt=\"None\">",name,ext);CHKERRQ(ierr);
    } else {
      ierr = PetscSNPrintf(body+len,4086-len,"<img src=\"%s/%s_%d%s\" alt=\"None\">",name,name,image->count,ext);CHKERRQ(ierr);
    }
    ierr = PetscStrlen(body,&len);CHKERRQ(ierr);
    image = image->next;
  }
  ierr = PetscStrcat(body,"<br>\n");CHKERRQ(ierr);
  if (draw->savefilecount > 0) PetscStackCallSAWs(SAWs_Pop_Body,("index.html",1));
  PetscStackCallSAWs(SAWs_Push_Body,("index.html",1,body));
  PetscFunctionReturn(0);
}

/*@C
   PetscDrawAppendTitle - Appends to the title of a PetscDraw context.

   Not collective (any processor or all can call this)

   Input Parameters:
+  draw - the graphics context
-  title - the title

   Note:
   A copy of the string is made, so you may destroy the
   title string after calling this routine.

   Level: advanced

.seealso: PetscDrawSetTitle(), PetscDrawGetTitle()
@*/
PetscErrorCode  PetscDrawAppendTitle(PetscDraw draw,const char title[])
{
  PetscErrorCode ierr;
  size_t         len1,len2,len;
  char           *newtitle;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(draw,PETSC_DRAW_CLASSID,1);
  if (!title) PetscFunctionReturn(0);

  if (draw->title) {
    ierr = PetscStrlen(title,&len1);CHKERRQ(ierr);
    ierr = PetscStrlen(draw->title,&len2);CHKERRQ(ierr);
    len  = len1 + len2;
    ierr = PetscMalloc1((len + 1),&newtitle);CHKERRQ(ierr);
    ierr = PetscStrcpy(newtitle,draw->title);CHKERRQ(ierr);
    ierr = PetscStrcat(newtitle,title);CHKERRQ(ierr);
    ierr = PetscFree(draw->title);CHKERRQ(ierr);

    draw->title = newtitle;
  } else {
    ierr = PetscStrallocpy(title,&draw->title);CHKERRQ(ierr);
  }
  if (draw->ops->settitle) {
    ierr = (*draw->ops->settitle)(draw,draw->title);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

static PetscErrorCode PetscViewerFileClose_ASCII(PetscViewer viewer)
{
  PetscErrorCode    ierr;
  PetscMPIInt       rank;
  PetscViewer_ASCII *vascii = (PetscViewer_ASCII *)viewer->data;
  int               err;

  PetscFunctionBegin;
  ierr = MPI_Comm_rank(((PetscObject)viewer)->comm,&rank);CHKERRQ(ierr);
  if (!rank && vascii->fd != stderr && vascii->fd != PETSC_STDOUT) {
    if (vascii->fd && vascii->closefile) {
      err = fclose(vascii->fd);
      if (err) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SYS,"fclose() failed on file");    
    }
    if (vascii->storecompressed) {
      char par[PETSC_MAX_PATH_LEN],buf[PETSC_MAX_PATH_LEN];
      FILE *fp;
      ierr = PetscStrcpy(par,"gzip ");CHKERRQ(ierr);
      ierr = PetscStrcat(par,vascii->filename);CHKERRQ(ierr);
#if defined(PETSC_HAVE_POPEN)
      ierr = PetscPOpen(PETSC_COMM_SELF,PETSC_NULL,par,"r",&fp);CHKERRQ(ierr);
      if (fgets(buf,1024,fp)) {
        SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error from compression command %s\n%s",par,buf);
      }
      ierr = PetscPClose(PETSC_COMM_SELF,fp);CHKERRQ(ierr);
#else
      SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP_SYS,"Cannot run external programs on this machine");
#endif
    }
  }
  ierr = PetscFree(vascii->filename);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode 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);
}

static PetscErrorCode PetscViewerFileClose_Binary(PetscViewer v)
{
  PetscViewer_Binary *vbinary = (PetscViewer_Binary*)v->data;
  PetscErrorCode     ierr;
  PetscMPIInt        rank;
  int                err;

  PetscFunctionBegin;
  ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)v),&rank);CHKERRQ(ierr);
  if ((!rank || vbinary->btype == FILE_MODE_READ) && vbinary->fdes) {
    close(vbinary->fdes);
    if (!rank && vbinary->storecompressed) {
      char par[PETSC_MAX_PATH_LEN],buf[PETSC_MAX_PATH_LEN];
      FILE *fp;
      /* compress the file */
      ierr = PetscStrcpy(par,"gzip -f ");CHKERRQ(ierr);
      ierr = PetscStrcat(par,vbinary->filename);CHKERRQ(ierr);
#if defined(PETSC_HAVE_POPEN)
      ierr = PetscPOpen(PETSC_COMM_SELF,NULL,par,"r",&fp);CHKERRQ(ierr);
      if (fgets(buf,1024,fp)) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error from command %s\n%s",par,buf);
      ierr = PetscPClose(PETSC_COMM_SELF,fp,NULL);CHKERRQ(ierr);
#else
      SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP_SYS,"Cannot run external programs on this machine");
#endif
    }
  }
  if (vbinary->fdes_info) {
    err = fclose(vbinary->fdes_info);
    if (err) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SYS,"fclose() failed on file");
  }
  ierr = PetscFree(vbinary->filename);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode  PetscLs(MPI_Comm comm,const char libname[],char found[],size_t tlen,PetscBool  *flg)
{
  PetscErrorCode ierr;
  size_t         len;
  char           *f,program[PETSC_MAX_PATH_LEN];
  FILE           *fp;

  PetscFunctionBegin;
  ierr   = PetscStrcpy(program,"ls ");CHKERRQ(ierr);
  ierr   = PetscStrcat(program,libname);CHKERRQ(ierr); 
#if defined(PETSC_HAVE_POPEN)
  ierr   = PetscPOpen(comm,PETSC_NULL,program,"r",&fp);CHKERRQ(ierr);
#else
  SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP_SYS,"Cannot run external programs on this machine");
#endif
  f      = fgets(found,tlen,fp);
  if (f) *flg = PETSC_TRUE; else *flg = PETSC_FALSE;
  while (f) {
    ierr  = PetscStrlen(found,&len);CHKERRQ(ierr);
    f     = fgets(found+len,tlen-len,fp);
  }
  if (*flg) {ierr = PetscInfo2(0,"ls on %s gives \n%s\n",libname,found);CHKERRQ(ierr);}
#if defined(PETSC_HAVE_POPEN)
  ierr   = PetscPClose(comm,fp);CHKERRQ(ierr);
#else
  SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP_SYS,"Cannot run external programs on this machine");
#endif
  PetscFunctionReturn(0);
}

/*@C
     PetscURLShorten - Uses Google's service to get a short url for a long url

    Input Parameters:
+    url - long URL you want shortened
-    lenshorturl - length of buffer to contain short URL

    Output Parameter:
.    shorturl - the shortened URL

.seealso: PetscGoogleDriveRefresh(), PetscGoogleDriveUpload(), PetscGoogleDriveAuthorize()
@*/
PetscErrorCode PetscURLShorten(const char url[],char shorturl[],size_t lenshorturl)
{
    SSL_CTX        *ctx;
    SSL            *ssl;
    int            sock;
    PetscErrorCode ierr;
    char           buff[1024],body[512];
    PetscBool      found;

    PetscFunctionBegin;
    ierr = PetscSSLInitializeContext(&ctx);
    CHKERRQ(ierr);
    ierr = PetscHTTPSConnect("www.googleapis.com",443,ctx,&sock,&ssl);
    CHKERRQ(ierr);
    ierr = PetscStrcpy(body,"{");
    CHKERRQ(ierr);
    ierr = PetscPushJSONValue(body,"longUrl",url,sizeof(body)-2);
    CHKERRQ(ierr);
    ierr = PetscStrcat(body,"}");
    CHKERRQ(ierr);
    ierr = PetscHTTPSRequest("POST","www.googleapis.com/urlshortener/v1/url",NULL,"application/json",body,ssl,buff,sizeof(buff));
    CHKERRQ(ierr);
    ierr = PetscSSLDestroyContext(ctx);
    CHKERRQ(ierr);
    close(sock);

    ierr   = PetscPullJSONValue(buff,"id",shorturl,lenshorturl,&found);
    CHKERRQ(ierr);
    if (!found) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Google drive did not return short URL");
    PetscFunctionReturn(0);
}

static PetscErrorCode PCBDDCScalingSetUp_Deluxe_Private(PC pc)
{
  PC_BDDC                *pcbddc=(PC_BDDC*)pc->data;
  PCBDDCDeluxeScaling    deluxe_ctx=pcbddc->deluxe_ctx;
  PCBDDCSubSchurs        sub_schurs = pcbddc->sub_schurs;
  PetscErrorCode         ierr;

  PetscFunctionBegin;
  if (!sub_schurs->n_subs) {
    PetscFunctionReturn(0);
  }

  /* Create work vectors for sequential part of deluxe */
  ierr = MatCreateVecs(sub_schurs->S_Ej_all,&deluxe_ctx->seq_work1,&deluxe_ctx->seq_work2);CHKERRQ(ierr);

  /* Compute deluxe sequential scatter */
  if (sub_schurs->reuse_mumps && !sub_schurs->is_dir) {
    PCBDDCReuseMumps reuse_mumps = sub_schurs->reuse_mumps;
    ierr = PetscObjectReference((PetscObject)reuse_mumps->correction_scatter_B);CHKERRQ(ierr);
    deluxe_ctx->seq_scctx = reuse_mumps->correction_scatter_B;
  } else {
    ierr = VecScatterCreate(pcbddc->work_scaling,sub_schurs->is_Ej_all,deluxe_ctx->seq_work1,NULL,&deluxe_ctx->seq_scctx);CHKERRQ(ierr);
  }

  /* Create Mat object for deluxe scaling */
  ierr = PetscObjectReference((PetscObject)sub_schurs->S_Ej_all);CHKERRQ(ierr);
  deluxe_ctx->seq_mat = sub_schurs->S_Ej_all;
  if (sub_schurs->sum_S_Ej_all) { /* if this matrix is present, then we need to create the KSP object to invert it */
    PC               pc_temp;
    MatSolverPackage solver=NULL;
    char             ksp_prefix[256];
    size_t           len;

    ierr = KSPCreate(PETSC_COMM_SELF,&deluxe_ctx->seq_ksp);CHKERRQ(ierr);
    ierr = KSPSetOperators(deluxe_ctx->seq_ksp,sub_schurs->sum_S_Ej_all,sub_schurs->sum_S_Ej_all);CHKERRQ(ierr);
    ierr = KSPSetType(deluxe_ctx->seq_ksp,KSPPREONLY);CHKERRQ(ierr);
    ierr = KSPGetPC(deluxe_ctx->seq_ksp,&pc_temp);CHKERRQ(ierr);
    ierr = PCSetType(pc_temp,PCLU);CHKERRQ(ierr);
    ierr = KSPGetPC(pcbddc->ksp_D,&pc_temp);CHKERRQ(ierr);
    ierr = PCFactorGetMatSolverPackage(pc_temp,(const MatSolverPackage*)&solver);CHKERRQ(ierr);
    if (solver) {
      PC     new_pc;
      PCType type;

      ierr = PCGetType(pc_temp,&type);CHKERRQ(ierr);
      ierr = KSPGetPC(deluxe_ctx->seq_ksp,&new_pc);CHKERRQ(ierr);
      ierr = PCSetType(new_pc,type);CHKERRQ(ierr);
      ierr = PCFactorSetMatSolverPackage(new_pc,solver);CHKERRQ(ierr);
    }
    ierr = PetscStrlen(((PetscObject)(pcbddc->ksp_D))->prefix,&len);CHKERRQ(ierr);
    len -= 10; /* remove "dirichlet_" */
    ierr = PetscStrncpy(ksp_prefix,((PetscObject)(pcbddc->ksp_D))->prefix,len+1);CHKERRQ(ierr);
    ierr = PetscStrcat(ksp_prefix,"deluxe_");CHKERRQ(ierr);
    ierr = KSPSetOptionsPrefix(deluxe_ctx->seq_ksp,ksp_prefix);CHKERRQ(ierr);
    ierr = KSPSetFromOptions(deluxe_ctx->seq_ksp);CHKERRQ(ierr);
    ierr = KSPSetUp(deluxe_ctx->seq_ksp);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

static PetscErrorCode TestFieldProjection(DM dm, DM auxdm, DMLabel label, Vec la, const char name[], AppCtx *user)
{
  PetscErrorCode (**afuncs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *);
  void           (**funcs)(PetscInt, PetscInt, PetscInt,
                           const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
                           const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
                           PetscReal, const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]);
  Vec               lx, lu;
  PetscInt          Nf, f;
  PetscInt          val[1] = {1};
  char              lname[PETSC_MAX_PATH_LEN];
  PetscErrorCode    ierr;

  PetscFunctionBeginUser;
  if (auxdm) {
    ierr = PetscObjectCompose((PetscObject) dm, "dmAux", (PetscObject) auxdm);CHKERRQ(ierr);
    ierr = PetscObjectCompose((PetscObject) dm, "A", (PetscObject) la);CHKERRQ(ierr);
  }
  ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr);
  ierr = PetscMalloc2(Nf, &funcs, Nf, &afuncs);CHKERRQ(ierr);
  for (f = 0; f < Nf; ++f) afuncs[f]  = linear;
  funcs[0] = linear_vector;
  funcs[1] = linear_scalar;
  ierr = DMGetLocalVector(dm, &lu);CHKERRQ(ierr);
  ierr = PetscStrcpy(lname, "Local Field Input ");CHKERRQ(ierr);
  ierr = PetscStrcat(lname, name);CHKERRQ(ierr);
  ierr = PetscObjectSetName((PetscObject) lu, lname);CHKERRQ(ierr);
  if (!label) {ierr = DMProjectFunctionLocal(dm, 0.0, afuncs, NULL, INSERT_VALUES, lu);CHKERRQ(ierr);}
  else        {ierr = DMProjectFunctionLabelLocal(dm, 0.0, label, 1, val, 0, NULL, afuncs, NULL, INSERT_VALUES, lu);CHKERRQ(ierr);}
  ierr = VecViewFromOptions(lu, NULL, "-local_input_view");CHKERRQ(ierr);
  ierr = DMGetLocalVector(dm, &lx);CHKERRQ(ierr);
  ierr = PetscStrcpy(lname, "Local Field ");CHKERRQ(ierr);
  ierr = PetscStrcat(lname, name);CHKERRQ(ierr);
  ierr = PetscObjectSetName((PetscObject) lx, lname);CHKERRQ(ierr);
  if (!label) {ierr = DMProjectFieldLocal(dm, 0.0, lu, funcs, INSERT_VALUES, lx);CHKERRQ(ierr);}
  else        {ierr = DMProjectFieldLabelLocal(dm, 0.0, label, 1, val, 0, NULL, lu, funcs, INSERT_VALUES, lx);CHKERRQ(ierr);}
  ierr = VecViewFromOptions(lx, NULL, "-local_field_view");CHKERRQ(ierr);
  ierr = DMRestoreLocalVector(dm, &lx);CHKERRQ(ierr);
  ierr = DMRestoreLocalVector(dm, &lu);CHKERRQ(ierr);
  ierr = PetscFree2(funcs, afuncs);CHKERRQ(ierr);
  if (auxdm) {
    ierr = PetscObjectCompose((PetscObject) dm, "dmAux", NULL);CHKERRQ(ierr);
    ierr = PetscObjectCompose((PetscObject) dm, "A", NULL);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

/*@C
      PetscPOpen - Runs a program on processor zero and sends either its input or output to
          a file.

     Logically Collective on MPI_Comm, but only process 0 runs the command

   Input Parameters:
+   comm - MPI communicator, only processor zero runs the program
.   machine - machine to run command on or NULL, or string with 0 in first location
.   program - name of program to run
-   mode - either r or w

   Output Parameter:
.   fp - the file pointer where program input or output may be read or NULL if don't care

   Level: intermediate

   Notes:
       Use PetscPClose() to close the file pointer when you are finished with it
       Does not work under Windows

       If machine is not provided will use the value set with PetsPOpenSetMachine() if that was provided, otherwise
       will use the machine running node zero of the communicator

       The program string may contain ${DISPLAY}, ${HOMEDIRECTORY} or ${WORKINGDIRECTORY}; these
    will be replaced with relevent values.

.seealso: PetscFOpen(), PetscFClose(), PetscPClose(), PetscPOpenSetMachine()

@*/
PetscErrorCode  PetscPOpen(MPI_Comm comm,const char machine[],const char program[],const char mode[],FILE **fp)
{
  PetscErrorCode ierr;
  PetscMPIInt    rank;
  size_t         i,len,cnt;
  char           commandt[PETSC_MAX_PATH_LEN],command[PETSC_MAX_PATH_LEN];
  FILE           *fd;

  PetscFunctionBegin;
  /* all processors have to do the string manipulation because PetscStrreplace() is a collective operation */
  if (PetscPOpenMachine[0] || (machine && machine[0])) {
    ierr = PetscStrcpy(command,"ssh ");CHKERRQ(ierr);
    if (PetscPOpenMachine[0]) {
      ierr = PetscStrcat(command,PetscPOpenMachine);CHKERRQ(ierr);
    } else {
      ierr = PetscStrcat(command,machine);CHKERRQ(ierr);
    }
    ierr = PetscStrcat(command," \" export DISPLAY=${DISPLAY}; ");CHKERRQ(ierr);
    /*
        Copy program into command but protect the " with a \ in front of it
    */
    ierr = PetscStrlen(command,&cnt);CHKERRQ(ierr);
    ierr = PetscStrlen(program,&len);CHKERRQ(ierr);
    for (i=0; i<len; i++) {
      if (program[i] == '\"') command[cnt++] = '\\';
      command[cnt++] = program[i];
    }
    command[cnt] = 0;

    ierr = PetscStrcat(command,"\"");CHKERRQ(ierr);
  } else {
    ierr = PetscStrcpy(command,program);CHKERRQ(ierr);
  }

  ierr = PetscStrreplace(comm,command,commandt,1024);CHKERRQ(ierr);

  ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
  if (!rank) {
    ierr = PetscInfo1(0,"Running command :%s\n",commandt);CHKERRQ(ierr);
    if (!(fd = popen(commandt,mode))) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot run command %s",commandt);
    if (fp) *fp = fd;
  }
  PetscFunctionReturn(0);
}

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;

        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 = 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);
}

static PetscErrorCode  PetscLoadDynamicLibrary(const char *name,PetscBool  *found)
{
  char           libs[PETSC_MAX_PATH_LEN],dlib[PETSC_MAX_PATH_LEN];
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscStrcpy(libs,"${PETSC_LIB_DIR}/libpetsc");CHKERRQ(ierr);
  ierr = PetscStrcat(libs,name);CHKERRQ(ierr);
  ierr = PetscDLLibraryRetrieve(PETSC_COMM_WORLD,libs,dlib,1024,found);CHKERRQ(ierr);
  if (*found) {
    ierr = PetscDLLibraryAppend(PETSC_COMM_WORLD,&PetscDLLibrariesLoaded,dlib);CHKERRQ(ierr);
  } else {
    ierr = PetscStrcpy(libs,"${PETSC_DIR}/${PETSC_ARCH}/lib/libpetsc");CHKERRQ(ierr);
    ierr = PetscStrcat(libs,name);CHKERRQ(ierr);
    ierr = PetscDLLibraryRetrieve(PETSC_COMM_WORLD,libs,dlib,1024,found);CHKERRQ(ierr);
    if (*found) {
      ierr = PetscDLLibraryAppend(PETSC_COMM_WORLD,&PetscDLLibrariesLoaded,dlib);CHKERRQ(ierr);
    }
  }
  PetscFunctionReturn(0);
}

static PetscErrorCode TestFunctionProjection(DM dm, DM auxdm, DMLabel label, Vec la, const char name[], AppCtx *user)
{
  PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *);
  Vec               x, lx;
  PetscInt          Nf, f;
  PetscInt          val[1] = {1};
  char              lname[PETSC_MAX_PATH_LEN];
  PetscErrorCode    ierr;

  PetscFunctionBeginUser;
  if (auxdm) {
    ierr = PetscObjectCompose((PetscObject) dm, "dmAux", (PetscObject) auxdm);CHKERRQ(ierr);
    ierr = PetscObjectCompose((PetscObject) dm, "A", (PetscObject) la);CHKERRQ(ierr);
  }
  ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr);
  ierr = PetscMalloc1(Nf, &funcs);CHKERRQ(ierr);
  for (f = 0; f < Nf; ++f) funcs[f] = linear;
  ierr = DMGetGlobalVector(dm, &x);CHKERRQ(ierr);
  ierr = PetscStrcpy(lname, "Function ");CHKERRQ(ierr);
  ierr = PetscStrcat(lname, name);CHKERRQ(ierr);
  ierr = PetscObjectSetName((PetscObject) x, lname);CHKERRQ(ierr);
  if (!label) {ierr = DMProjectFunction(dm, 0.0, funcs, NULL, INSERT_VALUES, x);CHKERRQ(ierr);}
  else        {ierr = DMProjectFunctionLabel(dm, 0.0, label, 1, val, 0, NULL, funcs, NULL, INSERT_VALUES, x);CHKERRQ(ierr);}
  ierr = VecViewFromOptions(x, NULL, "-func_view");CHKERRQ(ierr);
  ierr = DMRestoreGlobalVector(dm, &x);CHKERRQ(ierr);
  ierr = DMGetLocalVector(dm, &lx);CHKERRQ(ierr);
  ierr = PetscStrcpy(lname, "Local Function ");CHKERRQ(ierr);
  ierr = PetscStrcat(lname, name);CHKERRQ(ierr);
  ierr = PetscObjectSetName((PetscObject) lx, lname);CHKERRQ(ierr);
  if (!label) {ierr = DMProjectFunctionLocal(dm, 0.0, funcs, NULL, INSERT_VALUES, lx);CHKERRQ(ierr);}
  else        {ierr = DMProjectFunctionLabelLocal(dm, 0.0, label, 1, val, 0, NULL, funcs, NULL, INSERT_VALUES, lx);CHKERRQ(ierr);}
  ierr = VecViewFromOptions(lx, NULL, "-local_func_view");CHKERRQ(ierr);
  ierr = DMRestoreLocalVector(dm, &lx);CHKERRQ(ierr);
  ierr = PetscFree(funcs);CHKERRQ(ierr);
  if (auxdm) {
    ierr = PetscObjectCompose((PetscObject) dm, "dmAux", NULL);CHKERRQ(ierr);
    ierr = PetscObjectCompose((PetscObject) dm, "A", NULL);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);
}