MPIPOSIX removed, this has been removed in hdf5 1.8.13, so we cannot use it any more

- fix early return in  _select_hyperslab_for_writing()

.gitignore

@@ -1,3 +1,11 @@
+*.o
+*.lo
+*.la
+*~
+*.h5
+*.vtk
+.deps
+.libs
 /H5hut
 /INSTALL
 /Makefile
@@ -5,6 +13,7 @@
 /aclocal.m4
 /autom4te.cache
 /build
+/compile
 /config.guess
 /config.h
 /config.h.in

configure.ac

@@ -1,4 +1,4 @@
-AC_INIT([H5hut], [1.99.11], [h5part@lists.psi.ch], H5hut)
+AC_INIT([H5hut], [1.99.14], [h5part@lists.psi.ch], H5hut)
 AC_PREREQ(2.60)
 AC_CONFIG_HEADERS(config.h)
 AC_CONFIG_MACRO_DIR([m4])
@@ -62,7 +62,7 @@ AC_ARG_WITH(
 	[hdf5],
 	[AS_HELP_STRING([--with-hdf5],
 	[path to HDF5 installation [default=""]])],
-	[HDF5_PREFIX=$withval], [HDF5_PREFIX=""])
+	[HDF5_PREFIX=$withval], [])
 
 AC_ARG_WITH(
 	[mpi],
@@ -259,13 +259,13 @@ fi
 AC_MSG_CHECKING([if parallel interface enabled])
 if test "X$ENABLE_PARALLEL" = "Xyes"; then
 	AC_MSG_RESULT([yes])
-	AM_CPPFLAGS="${AM_CPPFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
+	CPPFLAGS="${CPPFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
 
         if test "X$ENABLE_EXPERIMENTAL" = "Xyes"; then
         	AC_MSG_CHECKING([for ParMETIS])
                 if test "X$PARMETISPATH" != "X"; then
-                        AM_CPPFLAGS="$AM_CPPFLAGS -I$PARMETISPATH/include"
-	                AM_LDFLAGS="$AM_LDFLAGS -L$PARMETISPATH/lib"
+                        CPPFLAGS="$CPPFLAGS -I$PARMETISPATH/include"
+	                LDFLAGS="$LDFLAGS -L$PARMETISPATH/lib"
 	        fi
 
                 LIBS="$LIBS -lparmetis -lmetis"
@@ -284,9 +284,15 @@ fi
 
 ###############################################################################
 # LIBRARY PATHS
-if test -n "${HDF5_PREFIX}" ; then
-        AM_CPPFLAGS="$AM_CPPFLAGS -I$HDF5_PREFIX/include"
-        AM_LDFLAGS="$AM_LDFLAGS -L$HDF5_PREFIX/lib"
+if test -z "${HDF5_PREFIX}"; then
+	# alternatives to HDF5_PREFIX
+	if test -n "${HDF5_DIR}"; then
+		HDF5_PREFIX=${HDF5_DIR}
+	fi
+fi
+if test -n "${HDF5_PREFIX}"; then
+        CPPFLAGS="$CPPFLAGS -I$HDF5_PREFIX/include"
+        LDFLAGS="$LDFLAGS -L$HDF5_PREFIX/lib"
 fi
 AC_CHECK_LIB([z], [compress2])
 AC_CHECK_LIB([hdf5], [H5open])
@@ -317,8 +323,8 @@ if test -z "$LUSTREROOT"; then
 	AC_MSG_WARN([Couldn't locate the lustre API... building without support for lustre striping!])
 else
         CFLAGS="$CFLAGS -DH5_USE_LUSTRE"
-        AM_CPPFLAGS="$AM_CPPFLAGS -I$LUSTREROOT/usr/include"
-        AM_LDFLAGS="$AM_LDFLAGS -L$LUSTREROOT/usr/lib"
+        CPPFLAGS="$CPPFLAGS -I$LUSTREROOT/usr/include"
+        LDFLAGS="$LDFLAGS -L$LUSTREROOT/usr/lib"
         LIBS="$LIBS -llustreapi"
 fi
 
@@ -336,6 +342,9 @@ fi
 
 ###############################################################################
 # EXPORTING VARIABLES & CREATING OUTPUT FILES
+AM_CPPFLAGS=$CPPFLAGS
+AM_LDFLAGS=$LDFLAGS
+
 AC_SUBST(HDF5_PREFIX)
 AC_SUBST(CFLAGS)
 AC_SUBST(FFLAGS)

src/h5core/h5_hdf5_private.h

@@ -925,6 +925,7 @@ hdf5_set_fapl_mpio_property (
 	HDF5_WRAPPER_RETURN (H5_SUCCESS);
 }
 
+#if H5_VERSION_LE(1,8,12)
 static inline h5_err_t
 hdf5_set_fapl_mpiposix_property (
 	hid_t fapl_id,
@@ -942,6 +943,7 @@ hdf5_set_fapl_mpiposix_property (
 				" the file access property list."));
 	HDF5_WRAPPER_RETURN (H5_SUCCESS);
 }
+#endif
 
 static inline h5_err_t
 hdf5_set_dxpl_mpio_property (

src/h5core/h5_openclose.c

@@ -139,11 +139,14 @@ h5_err_t mpi_init (
 	TRY (f->access_prop = hdf5_create_property(H5P_FILE_ACCESS));
 
 	/* select the HDF5 VFD */
+#if H5_VERSION_LE(1,8,12)
 	if (f->mode & H5_VFD_MPIPOSIX) {
 		h5_info("Selecting MPI-POSIX VFD");
 		hbool_t use_gpfs = 0; // TODO autodetect GPFS?
 		TRY (hdf5_set_fapl_mpiposix_property(f->access_prop, comm, use_gpfs));
-	} else {
+	} else
+#endif
+	{
 		h5_info("Selecting MPI-IO VFD");
 		TRY (hdf5_set_fapl_mpio_property(f->access_prop, comm, MPI_INFO_NULL));
 		if (f->mode & H5_VFD_INDEPENDENT) {

src/h5core/h5_readwrite.c

@@ -292,7 +292,11 @@ h5_set_throttle (
 	const int factor
 	) {
 	H5_CORE_API_ENTER (h5_err_t, "f=%p, factor=%d", f, factor);
+#if H5_VERSION_LE(1,8,12)
 	if ( (f->mode & H5_VFD_INDEPENDENT) || (f->mode & H5_VFD_MPIPOSIX) ) {
+#else
+	if (f->mode & H5_VFD_INDEPENDENT) {
+#endif
 		f->throttle = factor;
 		h5_info ("Throttling enabled with factor = %d", f->throttle );
 	} else {

src/h5core/h5b_model.c

@@ -547,8 +547,8 @@ h5b_3d_set_view (
 	p->k_end =   k_end;
 	_normalize_partition(p);
 
-#ifdef PARALLEL_IO
 	h5b_fdata_t *b = f->b;
+#ifdef PARALLEL_IO
 	h5b_partition_t *user_layout;
 	h5b_partition_t *write_layout;
 
@@ -565,7 +565,6 @@ h5b_3d_set_view (
 	TRY( _dissolve_ghostzones(f, user_layout, write_layout) );
 	b->user_layout[0] = user_layout[f->myproc];
 	b->write_layout[0] = write_layout[f->myproc];
-	b->have_layout = 1;
 
 	p = b->user_layout;
 	h5_debug (
@@ -587,9 +586,9 @@ h5b_3d_set_view (
 
 	h5_free(user_layout);
 	h5_free(write_layout);
-
-	TRY( h5bpriv_release_hyperslab(f) );
 #endif
+	TRY( h5bpriv_release_hyperslab(f) );
+	b->have_layout = 1;
 
 	H5_CORE_API_RETURN (H5_SUCCESS);
 }

src/h5core/h5b_readwrite.c

@@ -9,7 +9,8 @@ _select_hyperslab_for_writing (
 	/*
 	  re-use existing hyperslab
 	*/
-	if ( f->b->shape >= 0 ) return H5_SUCCESS;
+	if ( f->b->shape >= 0 )
+		H5_PRIV_FUNC_LEAVE (H5_SUCCESS);
 
 	h5b_fdata_t *b = f->b;
 	h5b_partition_t *p = b->write_layout;

src/include/H5.h

@@ -28,7 +28,8 @@ extern "C" {
 
   You can also select a "virtual file driver" in the HDF5 layer using:
   - H5_VFD_INDEPENDENT: MPI-IO in independent (asynchronous) mode
-  - H5_VFD_MPIPOSIX: parallel I/O implemented directly by HDF5, bypassing MPI-IO
+  - H5_VFD_MPIPOSIX: parallel I/O implemented directly by HDF5, bypassing
+    MPI-IO (only for hdf5 <= 1.8.12)
 
   \return File handle.
   \return NULL on error.

tools/vtk2h5grid/Makefile.am

@@ -1,10 +1,10 @@
-AM_CPPFLAGS = -I${abs_top_builddir}/src/include -Wno-deprecated
+AM_CPPFLAGS = -I${abs_top_srcdir}/src/include -Wno-deprecated
 FFLAGS += -cpp $(AM_CPPFLAGS)
 LDFLAGS += -L${abs_top_builddir}/src/lib
 
 LDADD = 
 
-LDADD += -lH5hut -lvtkIO -lvtkFiltering -lvtkCommon -lvtksys
+LDADD += -lH5hut -lvtkIO -lvtkFiltering -lvtkCommon -lvtksys -lpthread -ldl
 
 
 bin_PROGRAMS = 

tools/vtk2h5grid/vtk2h5grid.cc

@@ -14,9 +14,21 @@
 
 #include "H5hut.h"
 
+#if !defined (PARALLEL_IO)
+#define MPI_Init(argc, argv)
+#define MPI_Comm_size(comm, nprocs) { *nprocs = 1; }
+#define MPI_Comm_rank(comm, myproc) { *myproc = 0; }
+#define MPI_Finalize()
+#define MPI_COMM_WORLD (0)
+#endif
+
 const char* version = "0.1.0";
 int convert_boundary = 1;
 int convert_volume = 0;
+double x_shift = 0.0;
+double y_shift = 0.0;
+double z_shift = 0.0;
+
 const struct option longopts[] = {
         {"version",     no_argument, 0,                 'v'},
         {"help",        no_argument, 0,                 'h'},
@@ -24,6 +36,7 @@ const struct option longopts[] = {
         {"volume",      no_argument, &convert_volume,   1},
         {"no-boundary", no_argument, &convert_boundary, 0},
         {"no-volume",   no_argument, &convert_volume,   0},
+        {"shift",       required_argument,  0,          's'},
         {0,0,0,0},
 };
 
@@ -75,6 +88,10 @@ init (
                 case 'v':
                         print_version (argv[0]);
                         break;
+                case 's':
+                        sscanf (optarg, "%lf,%lf,%lf", &x_shift, &y_shift, &z_shift);
+                        cout << "shift = (" << x_shift << ", " << y_shift << ", " << z_shift << ")" << endl;
+                        break;
                 }
         }
         return argc - optind;
@@ -106,6 +123,9 @@ convert_vtk2h5grid (
                                 // add point to H5hut mesh
                                 double pt[3];
                                 vtk_grid->GetPoint (pts[i], pt);
+                                pt[0] += x_shift;
+                                pt[1] += y_shift;
+                                pt[2] += z_shift;
                                 H5FedStoreVertex (h5_grid, -1, pt);
                                 // map pt index in vtk file to pt index in H5hut file
                                 idmap.insert (IdMap::value_type (pts[i], h5_vertex_idx));
@@ -145,6 +165,10 @@ main (
         int argc,
         char* argv[]
         ) {
+        MPI_Init (&argc, &argv);
+        MPI_Comm comm = MPI_COMM_WORLD;
+        int comm_size;
+        MPI_Comm_size (comm,&comm_size);
 
         argc = init (argc, argv);
         if (argc == 0) {
@@ -200,5 +224,6 @@ main (
                 }
                 H5CloseFile (f);
         }
+        MPI_Finalize ();
         return 0;
 }