1.6.1 tag

.gitattributes

@@ -18,9 +18,6 @@ doc/Doxyfile -text
 doc/H5X_File_Format.txt -text
 doc/Makefile.am -text
 doc/doxyfooter -text
-examples/core_vfd.c -text
-examples/fields.c -text
-examples/particles.c -text
 examples/simplef.F90 -text
 examples/stridedf.F90 -text
 examples/write_setview.c -text

NEWS

@@ -1,16 +1,3 @@
-#### H5PART 1.6.2 ############################################################
-
-Removed H5PartSetViewEmpty
---------------------------
-
-An empty view can now be selected with:
-H5PartSetNumParticles(file, 0);
-
-Bug Fixes to Attribute Calls in Fortran API
--------------------------------------------
-
-Fixed a problem where attribute values were reverting to zero.
-
 #### H5PART 1.6.1 ############################################################
 
 Chunking in the H5Part API

configure.ac

@@ -1,6 +1,6 @@
 # Every configure script must call AC_INIT before doing anything else.
 # AC_INIT (package, version, [bug-report], [tarname])
-AC_INIT([H5Part], [1.6.2], [h5part@lists.psi.ch], H5Part)
+AC_INIT([H5Part], [1.6.1], [h5part@lists.psi.ch], H5Part)
 
 
 # Ensure that a recent enough version of Autoconf is being used. 

examples/core_vfd.c

@@ -1,51 +0,0 @@
-#include <stdlib.h>
-#include <assert.h>
-#include <mpi.h>
-#include <H5Part.h>
-
-#define DATASIZE 32
-
-int main(int argc, char** argv)
-{
-    int i, rank, nprocs;
-    h5part_int32_t data[DATASIZE];
-    h5part_int64_t stat;
-    H5PartFile *file;
-
-    // initialize MPI
-    MPI_Init (&argc, &argv);
-    MPI_Comm_rank (MPI_COMM_WORLD, &rank);
-    MPI_Comm_size (MPI_COMM_WORLD, &nprocs);
-
-    H5PartSetVerbosityLevel(H5PART_VERB_DEBUG);
-
-    char filename[8];
-    sprintf (filename, "%d.h5", rank);
-
-    file = H5PartOpenFileParallel(
-            filename,
-            H5PART_WRITE | H5PART_VFD_CORE,
-            MPI_COMM_SELF);
-    assert (file != NULL);
-
-    stat = H5PartSetStep(file, 0);
-    assert (stat == H5PART_SUCCESS);
-
-    stat = H5PartSetNumParticles(file, DATASIZE);
-    assert (stat == H5PART_SUCCESS);
-
-    // create fake data
-    for (i=0; i<DATASIZE; i++) {
-        data[i] = i + rank * DATASIZE;
-    }
-
-    // write the data
-    stat = H5PartWriteDataInt32(file, "data", data);
-    assert (stat == H5PART_SUCCESS);
-
-    H5PartCloseFile(file);
-
-    MPI_Finalize();
-    return EXIT_SUCCESS;
-}
-

examples/fields.c

@@ -1,45 +0,0 @@
-#include <stdlib.h>
-#include <assert.h>
-#include <mpi.h>
-#include <H5Part.h>
-
-#define XSIZE 8
-#define YSIZE 8
-#define ZSIZE 8
-#define DATASIZE XSIZE*YSIZE*ZSIZE
-#define H5OpenFileParallel H5PartOpenFileParallel
-#define H5SetStep H5PartSetStep
-#define H5Block3dSetLayout H5BlockDefine3DFieldLayout
-#define H5CloseFile H5PartCloseFile
-
-int main(int argc, char** argv)
-{
-    int rank, nprocs;
-    h5part_float64_t ex[DATASIZE];
-    h5part_float64_t ey[DATASIZE];
-    h5part_float64_t ez[DATASIZE];
-    h5part_float64_t q[DATASIZE];
-    h5part_int64_t nparticles = DATASIZE;
-    H5PartFile *file;
-
-    // initialize MPI
-    MPI_Init (&argc, &argv);
-    MPI_Comm_rank (MPI_COMM_WORLD, &rank);
-    MPI_Comm_size (MPI_COMM_WORLD, &nprocs);
-
-    H5PartSetVerbosityLevel(H5PART_VERB_DEBUG);
-
-    file = H5OpenFileParallel("fields.h5", H5PART_WRITE, MPI_COMM_WORLD);
-    H5SetStep(file, 0);
-    H5Block3dSetLayout(file,
-            rank*XSIZE, (rank+1)*XSIZE - 1,
-            0, YSIZE - 1,
-            0, ZSIZE - 1);
-    H5Block3dWriteScalarFieldFloat64(file, "Q", q);
-    H5Block3dWrite3dVectorFieldFloat64(file, "E", ex, ez, ey);
-    H5CloseFile(file);
-
-    MPI_Finalize();
-    return EXIT_SUCCESS;
-}
-

examples/particles.c

@@ -1,41 +0,0 @@
-#include <stdlib.h>
-#include <assert.h>
-#include <mpi.h>
-#include <H5Part.h>
-
-#define DATASIZE 32
-
-int main(int argc, char** argv)
-{
-    int rank, nprocs;
-    h5part_float64_t x[DATASIZE];
-    h5part_float64_t y[DATASIZE];
-    h5part_float64_t z[DATASIZE];
-    h5part_float64_t px[DATASIZE];
-    h5part_float64_t py[DATASIZE];
-    h5part_float64_t pz[DATASIZE];
-    h5part_int64_t nparticles = DATASIZE;
-    H5PartFile *file;
-
-    // initialize MPI
-    MPI_Init (&argc, &argv);
-    MPI_Comm_rank (MPI_COMM_WORLD, &rank);
-    MPI_Comm_size (MPI_COMM_WORLD, &nprocs);
-
-    H5PartSetVerbosityLevel(H5PART_VERB_DEBUG);
-
-    file = H5PartOpenFileParallel("particles.h5", H5PART_WRITE, MPI_COMM_WORLD);
-    H5PartSetStep(file, 0);
-    H5PartSetNumParticles(file, nparticles);
-    H5PartWriteDataFloat64(file, "x", x);
-    H5PartWriteDataFloat64(file, "y", y);
-    H5PartWriteDataFloat64(file, "z", z);
-    H5PartWriteDataFloat64(file, "px", px);
-    H5PartWriteDataFloat64(file, "py", py);
-    H5PartWriteDataFloat64(file, "pz", pz);
-    H5PartCloseFile(file);
-
-    MPI_Finalize();
-    return EXIT_SUCCESS;
-}
-

examples/simplef.F90

@@ -8,15 +8,12 @@ program H5PartTest
   integer*8 :: file_id, status, npoints, i
   real*8, allocatable :: particles(:)
   integer*8, allocatable :: id(:)
-  real*8 :: r8val
-  integer*8 :: i8val
 
   comm = MPI_COMM_WORLD
   call mpi_init(ierr)
   call mpi_comm_rank(comm, rank, ierr)
 
   ! open the a file for parallel writing
-  file_id = h5pt_set_verbosity_level(5)
   file_id = h5pt_openw_par('test.h5', comm)
 
   ! in the Fortran API, time steps start at 1
@@ -25,10 +22,6 @@ program H5PartTest
   ! write an attribute to the file
   status = h5pt_writefileattrib_string(file_id, 'desc', 'This is a test.')
 
-  r8val = 0.5
-  i8val = 1
-  status = h5pt_writefileattrib_r8(file_id, 'double', r8val, i8val)
-
   ! create fake data
   npoints = 99
   allocate(particles(npoints), id(npoints))

src/H5Part.c

@@ -199,7 +199,7 @@ _H5Part_open_file (
 		{
 			/* extend the btree size so that metadata pieces are
 		 	* close to the alignment value */
-			if ( align > 16384 )
+			if ( align > 0 )
 			{
 				unsigned int btree_ik = (align - 4096) / 96;
 				unsigned int btree_bytes = 64 + 96*btree_ik;
@@ -252,7 +252,7 @@ _H5Part_open_file (
 			}
 		} else if (flags & H5PART_VFD_CORE) {
 			_H5Part_print_info ( "Selecting CORE VFD" );
-			if (H5Pset_fapl_core ( f->access_prop, align, 1 ) < 0) {
+			if (H5Pset_fapl_core ( f->access_prop, comm, 0 ) < 0) {
 				HANDLE_H5P_SET_FAPL_ERR;
 				goto error_cleanup;
 			}
@@ -713,11 +713,7 @@ _set_num_particles (
 	register int i;
 #endif
 
-#ifdef PARALLEL_IO
-	if ( nparticles < 0 )
-#else
 	if ( nparticles <= 0 )
-#endif
 		return HANDLE_H5PART_INVALID_ERR ( "nparticles", nparticles );
 
 	/* prevent invalid stride value */	
@@ -730,8 +726,6 @@ _set_num_particles (
 		stride = (hsize_t) _stride;
 	}
 
-	if ( nparticles == 0 ) stride = 1;
-
 #ifndef PARALLEL_IO
 	/*
 	  if we are not using parallel-IO, there is enough information
@@ -757,14 +751,11 @@ _set_num_particles (
 
 	f->nparticles = (hsize_t) nparticles;
 
-	if ( f->nparticles > 0 )
-	{
-		/* declare local memory datasize with striding */
-		count = f->nparticles * stride;
-		f->memshape = H5Screate_simple ( 1, &count, &dmax );
-		if ( f->memshape < 0 )
-			return HANDLE_H5S_CREATE_SIMPLE_ERR ( f->nparticles );
-	}
+	/* declare local memory datasize with striding */
+	count = f->nparticles * stride;
+	f->memshape = H5Screate_simple ( 1, &count, &dmax );
+	if ( f->memshape < 0 )
+		return HANDLE_H5S_CREATE_SIMPLE_ERR ( f->nparticles );
 
 	/* we need a hyperslab selection if there is striding
 	 * (otherwise, the default H5S_ALL selection is ok)
@@ -805,7 +796,7 @@ _set_num_particles (
 	*/
 
 	ret = MPI_Allgather (
-		(void*)&nparticles, 1, MPI_LONG_LONG,
+		&nparticles, 1, MPI_LONG_LONG,
 		f->pnparticles, 1, MPI_LONG_LONG,
 		f->comm );
 	if ( ret != MPI_SUCCESS) return HANDLE_MPI_ALLGATHER_ERR;
@@ -842,16 +833,12 @@ _set_num_particles (
 
 	count = nparticles;
 	stride = 1;
-	if ( count > 0 ) {
-		herr = H5Sselect_hyperslab (
-			f->diskshape,
-			H5S_SELECT_SET,
-			&start,
-			&stride,
-			&count, NULL );
-	} else {
-		herr = H5Sselect_none ( f->diskshape );
-	}
+	herr = H5Sselect_hyperslab (
+		f->diskshape,
+		H5S_SELECT_SET,
+		&start,
+		&stride,
+		&count, NULL );
 	if ( herr < 0 ) return HANDLE_H5S_SELECT_HYPERSLAB_ERR;
 #endif
 
@@ -1647,9 +1634,9 @@ H5PartWriteStepAttrib (
 	h5part_int64_t herr = _H5Part_write_step_attrib (
 		f,
 		name,
-		(hid_t)type,
+		(const hid_t)type,
 		data,
-		(hsize_t)nelem );
+		nelem );
 	if ( herr < 0 ) return herr;
 
 	return H5PART_SUCCESS;
@@ -1691,9 +1678,9 @@ H5PartWriteFileAttrib (
 	h5part_int64_t herr = _H5Part_write_file_attrib (
 		f,
 		name,
-		(hid_t)type,
+		(const hid_t)type,
 		data,
-		(hsize_t)nelem );
+		nelem );
 	if ( herr < 0 ) return herr;
 
 	return H5PART_SUCCESS;
@@ -2282,12 +2269,7 @@ _H5Part_get_num_objects_matching_pattern (
 	data.pattern = pattern;
 
 #ifdef H5PART_HAVE_HDF5_18
-	hid_t child_id = H5Gopen( group_id, group_name
-#ifndef H5_USE_16_API
-		, H5P_DEFAULT
-#endif
-		);
-
+	hid_t child_id = H5Gopen( group_id, group_name, H5P_DEFAULT );
 	if ( child_id < 0 ) return child_id;
  	herr = H5Literate( child_id, H5_INDEX_NAME, H5_ITER_INC, 0,
  			_H5Part_iteration_operator2, &data );
@@ -2790,7 +2772,10 @@ _set_view (
 	  end==-1 to mean end of file
 	*/
 	total = (hsize_t) _H5Part_get_num_particles ( f );
-	if ( total == 0 ) {
+	if ( total < 0 ) {
+		return HANDLE_H5PART_GET_NUM_PARTICLES_ERR ( total );
+	}
+	else if ( total == 0 ) {
 		/* No datasets have been created yet and no veiws are set.
 		 * We have to leave the view empty because we don't know how
 		 * many particles there should be! */
@@ -2869,7 +2854,10 @@ _set_view_indices (
 	  end==-1 to mean end of file
 	*/
 	total = (hsize_t) _H5Part_get_num_particles ( f );
-	if ( total == 0 ) {
+	if ( total < 0 ) {
+		return HANDLE_H5PART_GET_NUM_PARTICLES_ERR ( total );
+	}
+	else if ( total == 0 ) {
 		/* No datasets have been created yet and no veiws are set.
 		 * We have to leave the view empty because we don't know how
 		 * many particles there should be! */
@@ -2994,6 +2982,34 @@ H5PartSetViewIndices (
 	return _set_view_indices ( f, indices, nelems );
 }
 
+/*!
+  \ingroup h5part_model
+
+  In MPI-IO collective mode, all MPI tasks must participate in I/O
+  operations. \c H5PartSetViewEmpty() allows a task to participate
+  but with an empty view of the file, so that it contributes no data
+  to the I/O operation.
+
+  \return	\c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5PartSetViewEmpty (
+	H5PartFile *f			/*!< [in]  Handle to open file */
+	) {
+
+	SET_FNAME ( "H5PartSetViewEmpty" );
+
+	CHECK_FILEHANDLE( f );
+
+	if ( f->timegroup < 0 ) {
+		h5part_int64_t herr = _H5Part_set_step ( f, 0 );
+		if ( herr < 0 ) return herr;
+	}
+
+        /* using a null indices list will set an empty view */
+	return _set_view_indices ( f, NULL, 0 );
+}
+
 /*!
   \ingroup h5part_model
 
@@ -3141,7 +3157,7 @@ _read_data (
 	) {
 
 	h5part_int64_t herr;
-	hssize_t ndisk, nread, nmem;
+	hsize_t ndisk, nread, nmem;
 	hid_t dataset_id;
 	hid_t space_id;
 	hid_t memspace_id;

src/H5Part.f90

@@ -265,6 +265,14 @@ INTEGER*8 FUNCTION h5pt_setview_indices (filehandle,indices,nelem)
     INTEGER*8, INTENT(IN) :: nelem      !< number of particles in the list
 END FUNCTION
 
+!> \ingroup h5partf_model
+!! See \ref H5PartSetViewEmpty
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5pt_setview_empty (filehandle)
+    INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open
+END FUNCTION
+
 !> \ingroup h5partf_model
 !! See \ref H5PartResetView
 !! \return 0 on success or error code

src/H5Part.h

@@ -220,6 +220,11 @@ H5PartSetViewIndices (
 	h5part_int64_t nelems		/*!< [in]  Size of list */
 	);
 
+h5part_int64_t
+H5PartSetViewEmpty (
+	H5PartFile *f
+	);
+
 h5part_int64_t
 H5PartGetView (
 	H5PartFile *f,

src/H5PartAttribF.c

@@ -23,7 +23,7 @@ h5pt_writefileattrib_r8 (
 	h5part_int64_t *f,
 	const char *name,
 	const h5part_float64_t *data,
-	const h5part_int64_t *nelem,
+	const h5part_float64_t *nelem,
 	const int l_name
 	) {
 
@@ -39,9 +39,9 @@ h5pt_writefileattrib_r8 (
 }
 
 #if ! defined(F77_NO_UNDERSCORE)
-#define h5pt_readfileattrib_r8 F77NAME ( \
-	h5pt_readfileattrib_r8_, \
-	H5PT_READFILEATTRIB_R8 )
+#define h5pt_writefileattrib_r8 F77NAME ( \
+	h5pt_writefileattrib_r8_, \
+	H5PT_WRITEFILEATTRIB_R8 )
 #endif
 
 h5part_int64_t
@@ -74,7 +74,7 @@ h5pt_writefileattrib_r4 (
 	h5part_int64_t *f,
 	const char *name,
 	const h5part_float32_t *data,
-	const h5part_int64_t *nelem,
+	const h5part_float32_t *nelem,
 	const int l_name
 	) {
 
@@ -90,9 +90,9 @@ h5pt_writefileattrib_r4 (
 }
 
 #if ! defined(F77_NO_UNDERSCORE)
-#define h5pt_readfileattrib_r4 F77NAME ( \
-	h5pt_readfileattrib_r4_, \
-	H5PT_READFILEATTRIB_R4 )
+#define h5pt_writefileattrib_r4 F77NAME ( \
+	h5pt_writefileattrib_r4_, \
+	H5PT_WRITEFILEATTRIB_R4 )
 #endif
 
 h5part_int64_t
@@ -141,9 +141,9 @@ h5pt_writefileattrib_i8 (
 }
 
 #if ! defined(F77_NO_UNDERSCORE)
-#define h5pt_readfileattrib_i8 F77NAME ( \
-	h5pt_readfileattrib_i8_, \
-	H5PT_READFILEATTRIB_I8 )
+#define h5pt_writefileattrib_i8 F77NAME ( \
+	h5pt_writefileattrib_i8_, \
+	H5PT_WRITEFILEATTRIB_I8 )
 #endif
 
 h5part_int64_t
@@ -176,7 +176,7 @@ h5pt_writefileattrib_i4 (
 	h5part_int64_t *f,
 	const char *name,
 	const h5part_int32_t *data,
-	const h5part_int64_t *nelem,
+	const h5part_int32_t *nelem,
 	const int l_name
 	) {
 
@@ -192,9 +192,9 @@ h5pt_writefileattrib_i4 (
 }
 
 #if ! defined(F77_NO_UNDERSCORE)
-#define h5pt_readfileattrib_i4 F77NAME ( \
-	h5pt_readfileattrib_i4_, \
-	H5PT_READFILEATTRIB_I4 )
+#define h5pt_writefileattrib_i4 F77NAME ( \
+	h5pt_writefileattrib_i4_, \
+	H5PT_WRITEFILEATTRIB_I4 )
 #endif
 
 h5part_int64_t
@@ -227,7 +227,7 @@ h5pt_writestepattrib_r8 (
 	h5part_int64_t *f,
 	const char *name,
 	const h5part_float64_t *data,
-	const h5part_int64_t *nelem,
+	const h5part_float64_t *nelem,
 	const int l_name
 	) {
 
@@ -243,9 +243,9 @@ h5pt_writestepattrib_r8 (
 }
 
 #if ! defined(F77_NO_UNDERSCORE)
-#define h5pt_readstepattrib_r8 F77NAME ( \
-	h5pt_readstepattrib_r8_, \
-	H5PT_READSTEPATTRIB_R8 )
+#define h5pt_writestepattrib_r8 F77NAME ( \
+	h5pt_writestepattrib_r8_, \
+	H5PT_WRITESTEPATTRIB_R8 )
 #endif
 
 h5part_int64_t
@@ -278,7 +278,7 @@ h5pt_writestepattrib_r4 (
 	h5part_int64_t *f,
 	const char *name,
 	const h5part_float32_t *data,
-	const h5part_int64_t *nelem,
+	const h5part_float32_t *nelem,
 	const int l_name
 	) {
 
@@ -294,9 +294,9 @@ h5pt_writestepattrib_r4 (
 }
 
 #if ! defined(F77_NO_UNDERSCORE)
-#define h5pt_readstepattrib_r4 F77NAME ( \
-	h5pt_readstepattrib_r4_, \
-	H5PT_READSTEPATTRIB_R4 )
+#define h5pt_writestepattrib_r4 F77NAME ( \
+	h5pt_writestepattrib_r4_, \
+	H5PT_WRITESTEPATTRIB_R4 )
 #endif
 
 h5part_int64_t
@@ -345,9 +345,9 @@ h5pt_writestepattrib_i8 (
 }
 
 #if ! defined(F77_NO_UNDERSCORE)
-#define h5pt_readstepattrib_i8 F77NAME ( \
-	h5pt_readstepattrib_i8_, \
-	H5PT_READSTEPATTRIB_I8 )
+#define h5pt_writestepattrib_i8 F77NAME ( \
+	h5pt_writestepattrib_i8_, \
+	H5PT_WRITESTEPATTRIB_I8 )
 #endif
 
 h5part_int64_t
@@ -380,7 +380,7 @@ h5pt_writestepattrib_i4 (
 	h5part_int64_t *f,
 	const char *name,
 	const h5part_int32_t *data,
-	const h5part_int64_t *nelem,
+	const h5part_int32_t *nelem,
 	const int l_name
 	) {
 
@@ -396,9 +396,9 @@ h5pt_writestepattrib_i4 (
 }
 
 #if ! defined(F77_NO_UNDERSCORE)
-#define h5pt_readstepattrib_i4 F77NAME ( \
-	h5pt_readstepattrib_i4_, \
-	H5PT_READSTEPATTRIB_I4 )
+#define h5pt_writestepattrib_i4 F77NAME ( \
+	h5pt_writestepattrib_i4_, \
+	H5PT_WRITESTEPATTRIB_I4 )
 #endif
 
 h5part_int64_t

src/H5PartF.c

@@ -100,6 +100,9 @@
 #define h5pt_setview_indices F77NAME (					\
 					h5pt_setview_indices_,		\
 					H5PT_SETVIEW_INDICES )
+#define h5pt_setview_empty F77NAME (					\
+					h5pt_setview_empty_,		\
+					H5PT_SETVIEW_EMPTY )
 #define h5pt_resetview F77NAME (					\
 					h5pt_resetview_,		\
 					H5PT_RESETVIEW )
@@ -638,6 +641,16 @@ h5pt_setview_indices (
 	return H5PartSetViewIndices ( filehandle, indices, *nelem );
 }
 
+h5part_int64_t
+h5pt_setview_empty (
+	const h5part_int64_t *f
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	return H5PartSetViewEmpty ( filehandle );
+}
+
 h5part_int64_t
 h5pt_resetview (
 	const h5part_int64_t *f

src/H5PartTypes.h

@@ -19,9 +19,11 @@ __attribute__ ((format (printf, 3, 4)))
 #endif
  ;
 
-#ifndef PARALLEL_IO
+#ifndef MPI_INCLUDED
+#ifndef OPEN_MPI
 typedef unsigned long		MPI_Comm;
 #endif
+#endif
 
 #define H5PART_STEPNAME_LEN	64
 #define H5PART_DATANAME_LEN	64

src/generate-attr.py

@@ -113,7 +113,7 @@ h5pt_write#LEVELLC#attrib_#TYPE_F90_ABV# (
 	h5part_int64_t *f,
 	const char *name,
 	const h5part_#TYPE_H5P#_t *data,
-	const h5part_int64_t *nelem,
+	const h5part_#TYPE_H5P#_t *nelem,
 	const int l_name
 	) {
 
@@ -143,9 +143,9 @@ END FUNCTION
 
 read_attr_fc = """
 #if ! defined(F77_NO_UNDERSCORE)
-#define h5pt_read#LEVELLC#attrib_#TYPE_F90_ABV# F77NAME ( \\
-	h5pt_read#LEVELLC#attrib_#TYPE_F90_ABV#_, \\
-	H5PT_READ#LEVELUC#ATTRIB_#TYPE_F90_ABVC# )
+#define h5pt_write#LEVELLC#attrib_#TYPE_F90_ABV# F77NAME ( \\
+	h5pt_write#LEVELLC#attrib_#TYPE_F90_ABV#_, \\
+	H5PT_WRITE#LEVELUC#ATTRIB_#TYPE_F90_ABVC# )
 #endif
 
 h5part_int64_t