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Integrated H5Part regression test and fixed numerous errors that it discovered.

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Finished integrating H5Block and the Fortran interface (untested).
Started adding an H5Block regression test with a few simple tests (all pass).
Added automatic detection of stripe information on lustre, and config option to compile against lustre API.
Moved buffers for H5Block ghost zone disolving out of the file handle and into the h5b_3d_set_view function.
Fixed bug with pointers in the H5Fed file data not being initialized to NULL.
This commit is contained in:
Marc Howison
2010-07-15 19:44:48 +00:00
parent 2c267f173a
commit 7ea00c38f8
50 changed files with 1404 additions and 747 deletions
Download Patch File Download Diff File Expand all files Collapse all files
src/C/H5.c
+65 -3
View File
@@ -94,13 +94,13 @@ H5CheckFile (
Define format of the step names.
Example: ==H5FedDefineStepNameFormat( f, "Step", 6 )== defines step names
Example: ==H5SetStepNameFormat( f, "Step", 6 )== defines step names
like ==Step#000042==.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5DefineStepNameFormat (
H5SetStepNameFormat (
h5_file_t* const f, /*!< Handle to file */
const char* name, /*!< Prefix */
const h5_int64_t width /*!< Width of the number */
@@ -140,7 +140,7 @@ H5GetStepNameFormat (
h5_err_t
H5SetStep (
h5_file_t* const f, /*!< [in] Handle to open file */
const h5_int64_t step /*!< [in] Step to set. */
const h5_id_t step /*!< [in] Step to set. */
) {
SET_FNAME (f, __func__);
@@ -163,6 +163,68 @@ H5GetStep (
return h5_get_step (f);
}
/*!
\ingroup h5_inquiry
Get the number of processors.
\param[in] f File handle.
\return Number of processors.
\return \c -1 on error.
*/
int
H5GetNumProcs (
h5_file_t* const f
) {
SET_FNAME (f, __func__);
return h5_get_num_procs(f);
}
/*!
\ingroup h5part_c_api_read
Get the number of time-steps that are currently stored in the file
\c f.
It works for both reading and writing of files, but is probably
only typically used when you are reading.
\param[in] f File handle.
\return number of time-steps or error code
*/
h5_size_t
H5GetNumSteps (
h5_file_t* const f
) {
SET_FNAME (f, __func__);
return h5_get_num_steps(f);
}
/*!
\ingroup h5_inquiry
Query whether a particular step already exists in the file.
\param[in] f File handle.
\param[in] stepno Step number to query for existence
\return true or false
*/
h5_err_t
H5HasStep (
h5_file_t* const f,
h5_id_t stepno
) {
SET_FNAME (f, __func__);
return h5_has_step (f, stepno);
}
/*!
\ingroup h5_c_api_general
src/C/H5Block.c
+13 -9
View File
@@ -226,6 +226,9 @@ H5BlockGetNumFields (
Get the name, rank and dimensions of the field specified by the
index \c idx.
\c elem_rank reports the rank of the elements in the field
(e.g. scalar or vector).
This function can be used to retrieve all fields bound to the
current time-step by looping from \c 0 to the number of fields
minus one. The number of fields bound to the current time-step
@@ -239,22 +242,23 @@ H5BlockGetFieldInfo (
const h5_size_t idx, /*!< IN: index of field */
char *name, /*!< OUT: field name */
const h5_size_t len_name, /*!< IN: buffer size */
h5_size_t *grid_rank, /*!< OUT: grid rank */
h5_size_t *grid_dims, /*!< OUT: grid dimensions */
h5_size_t *field_rank, /*!< OUT: field rank */
h5_size_t *field_dims, /*!< OUT: field dimensions */
h5_size_t *elem_rank, /*!< OUT: element rank */
h5_int64_t *type /*!< OUT: datatype */
) {
SET_FNAME( f, __func__ );
return h5b_get_field_info (
f, idx, name, len_name, grid_rank, grid_dims, field_rank, type);
return h5b_get_field_info (f,
idx, name, len_name, field_rank, field_dims, elem_rank, type);
}
/*!
\ingroup h5block_model
Get the rank and dimensions of the field specified by its name.
See \ref H5BlockGetFieldInfo.
\return \c H5_SUCCESS or error code
*/
@@ -262,16 +266,16 @@ h5_err_t
H5BlockGetFieldInfoByName (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: field name */
h5_size_t *grid_rank, /*!< OUT: grid rank */
h5_size_t *grid_dims, /*!< OUT: grid dimensions */
h5_size_t *field_rank, /*!< OUT: field rank */
h5_size_t *field_rank, /*!< OUT: field rank */
h5_size_t *field_dims, /*!< OUT: field dimensions */
h5_size_t *elem_rank, /*!< OUT: element rank */
h5_int64_t *type /*!< OUT: datatype */
) {
SET_FNAME( f, __func__ );
return h5b_get_field_info_by_name (
f, name, grid_rank, grid_dims, field_rank, type );
return h5b_get_field_info_by_name (f,
name, field_rank, field_dims, elem_rank, type );
}
/********************** reading and writing attribute ************************/
src/C/H5Part.c
+38 -44
View File
@@ -109,12 +109,12 @@ For further information contact: <a href="mailto:h5part@lists.psi.ch">h5part</a>
h5_err_t
H5PartSetNumParticles (
h5_file_t *f, /*!< [in] Handle to open file */
h5_int64_t nparticles /*!< [in] Number of particles */
h5_size_t nparticles /*!< [in] Number of particles */
) {
SET_FNAME( f, __func__ );
h5_int64_t stride = 1;
h5_size_t stride = 1;
return h5u_set_num_particles( f, nparticles, stride );
}
@@ -148,8 +148,8 @@ H5PartSetNumParticles (
h5_err_t
H5PartSetNumParticlesStrided (
h5_file_t *f, /*!< [in] Handle to open file */
h5_int64_t nparticles, /*!< [in] Number of particles */
h5_int64_t stride /*!< [in] Stride value (e.g. number of fields in the particle array) */
h5_size_t nparticles, /*!< [in] Number of particles */
h5_size_t stride /*!< [in] Stride value (e.g. number of fields in the particle array) */
) {
SET_FNAME( f, __func__ );
@@ -171,9 +171,9 @@ H5PartSetNumParticlesStrided (
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5PartSetChunkSize (
H5PartSetChunk (
h5_file_t *f,
h5_int64_t size
h5_size_t size
) {
SET_FNAME( f, __func__ );
@@ -437,15 +437,13 @@ H5PartReadDataInt32 (
\return number of datasets in current timestep or error code
*/
h5_int64_t
h5_ssize_t
H5PartGetNumDatasets (
h5_file_t *f /*!< [in] Handle to open file */
) {
SET_FNAME( f, __func__ );
CHECK_FILEHANDLE( f );
return h5u_get_num_datasets(f);
}
@@ -459,19 +457,16 @@ H5PartGetNumDatasets (
\result \c H5_SUCCESS
*/
h5_int64_t
h5_err_t
H5PartGetDatasetName (
h5_file_t *f, /*!< [in] Handle to open file */
const h5_int64_t idx, /*!< [in] Index of the dataset */
const h5_id_t idx, /*!< [in] Index of the dataset */
char *name, /*!< [out] Name of dataset */
const h5_int64_t len /*!< [in] Size of buffer \c name */
const h5_size_t len /*!< [in] Size of buffer \c name */
) {
SET_FNAME( f, __func__ );
CHECK_FILEHANDLE ( f );
//CHECK_TIMEGROUP ( f );
return h5u_get_dataset_info(f, idx, name, len, NULL, NULL);
}
@@ -481,54 +476,53 @@ H5PartGetDatasetName (
Gets the name, type and number of elements of a dataset based on its
index in the current timestep.
Type is one of the following macros:
Type is one of the following values:
- \c h5_float64 (for \c h5part_float64_t)
- \c h5_float32 (for \c h5part_float32_t)
- \c h5_int64 (for \c h5part_int64_t)
- \c h5_int32 (for \c h5part_int32_t)
- \c H5PART_CHAR (for \c char)
- \c H5PART_STRING (for \c char*)
- \c H5_FLOAT64_T (for \c h5_float64_t)
- \c H5_FLOAT32_T (for \c h5_float32_t)
- \c H5_INT64_T (for \c h5_int64_t)
- \c H5_INT32_T (for \c h5_int32_t)
\return \c H5_SUCCESS
*/
h5_int64_t
h5_err_t
H5PartGetDatasetInfo (
h5_file_t *f, /*!< [in] Handle to open file */
const h5_int64_t idx,/*!< [in] Index of the dataset */
const h5_id_t idx, /*!< [in] Index of the dataset */
char *dataset_name, /*!< [out] Name of dataset */
const h5_int64_t len_dataset_name,
const h5_size_t len_dataset_name,
/*!< [in] Size of buffer \c dataset_name */
h5_int64_t *type, /*!< [out] Type of data in dataset */
h5_int64_t *nelem /*!< [out] Number of elements. */
h5_size_t *nelem /*!< [out] Number of elements. */
) {
SET_FNAME( f, __func__ );
CHECK_FILEHANDLE ( f );
//CHECK_TIMEGROUP ( f );
return h5u_get_dataset_info(f, idx, dataset_name, len_dataset_name, type, nelem);
}
/*!
\ingroup h5part_model
This function returns the number of particles in the first dataset of
the current timestep (or in the first timestep if none has been set).
This function returns the number of particles in this processor's view,
if a view has been set.
If you have neither set the number of particles (read or write)
nor set a view (read-only), then this returns the total number of
elements on disk of the first dataset if is exists. Otherwise,
it returns 0.
If not, it returns the total number of particles across all processors
from the last \ref H5PartSetNumParticles call.
If you have set a view, this return the number of particles
in the view.
If you have neither set the number of particles
nor set a view, then this returns the total number of
particles in the first data set of the current time step.
Note that H5Part assumes that all data sets within a given time step
have the same number of particles (although the number particles can
vary across time steps).
If none of these conditions are met, an error is thrown.
\return number of particles in current timestep or an error
code.
*/
h5_int64_t
h5_ssize_t
H5PartGetNumParticles (
h5_file_t *f /*!< [in] Handle to open file */
) {
@@ -556,7 +550,7 @@ H5PartResetView (
/*!
\ingroup h5part_model
*/
h5_int64_t
h5_err_t
H5PartHasView (
h5_file_t *f /*!< [in] Handle to open file */
) {
@@ -569,15 +563,15 @@ H5PartHasView (
/*!
\ingroup h5part_model
For parallel I/O or for subsetting operations on the datafile, the
\c H5PartSetView() function allows you to define a subset of the total
For parallel I/O or for subsetting operations on the datafile,
this function allows you to define a subset of the total
particle dataset to operate on.
The concept of "view" works for both serial
and for parallel I/O. The "view" will remain in effect until a new view
is set, or the number of particles in a dataset changes, or the view is
"unset" by calling \c H5PartSetView(file,-1,-1);
Before you set a view, the \c H5PartGetNumParticles() will return the
Before you set a view, \ref H5PartGetNumParticles will return the
total number of particles in the current time-step (even for the parallel
reads). However, after you set a view, it will return the number of
particles contained in the view.
@@ -620,8 +614,8 @@ H5PartSetView (
h5_err_t
H5PartSetViewIndices (
h5_file_t *f, /*!< [in] Handle to open file */
const h5_int64_t *indices, /*!< [in] List of indices */
h5_int64_t nelems /*!< [in] Size of list */
const h5_id_t *indices, /*!< [in] List of indices */
h5_size_t nelems /*!< [in] Size of list */
) {
SET_FNAME( f, __func__ );
src/C/H5_attribs.c
+1 -1
View File
@@ -161,7 +161,7 @@ H5WriteStepAttribFloat64 (
f,
H5_ATTRIB_STEP,
name,
H5T_NATIVE_FLOAT,
H5T_NATIVE_DOUBLE,
values,
nelems );
}
src/C/H5_inquiry.c
-89
View File
@@ -1,89 +0,0 @@
/*
Copyright 2007-2008
Paul Scherrer Institut, Villigen, Switzerland;
Benedikt Oswald;
Achim Gsell
All rights reserved.
Authors
Achim Gsell
Warning
This code is under development.
*/
/*!
\ingroup h5f_c_api
\defgroup h5_inquiry
*/
#include "h5core/h5_core.h"
#include "H5.h"
/*!
\ingroup h5_inquiry
Get the number of compute nodes.
\param[in] f File handle.
\return Number of compute notes.
\return \c -1 on error.
*/
int
H5GetNumNodes (
h5_file_t* const f
) {
SET_FNAME (f, __func__);
CHECK_FILEHANDLE (f);
return h5_get_num_procs(f);
}
/*!
\ingroup h5part_c_api_read
Get the number of time-steps that are currently stored in the file
\c f.
It works for both reading and writing of files, but is probably
only typically used when you are reading.
\param[in] f File handle.
\return number of time-steps or error code
*/
h5_size_t
H5GetNumSteps (
h5_file_t* const f
) {
SET_FNAME (f, __func__);
CHECK_FILEHANDLE (f);
return h5_get_num_steps(f);
}
/*!
\ingroup h5_inquiry
Query whether a particular step already exists in the file.
\param[in] f File handle.
\param[in] stepno Step number to query for existence
\return true or false
*/
h5_err_t
H5HasStep (
h5_file_t* const f,
h5_id_t stepno
) {
SET_FNAME (f, __func__);
CHECK_FILEHANDLE (f);
return h5_has_step (f, stepno);
}
src/C/Makefile.am
-2
View File
@@ -17,7 +17,6 @@ EXTRA_LIBRARIES = libH5hutC.a
include_HEADERS = \
../include/H5hut.h \
../include/H5.h \
../include/H5_inquiry.h \
../include/H5_attribs.h \
../include/H5Part.h \
../include/H5Block.h \
@@ -35,7 +34,6 @@ EXTRA_HEADERS =
libH5hutC_a_SOURCES = \
H5.c \
H5_attribs.c \
H5_inquiry.c \
H5Part.c \
H5Block.c \
H5Block_readwrite.c \
src/C/generate-h5b-readwrite.py
+2
View File
@@ -14,6 +14,8 @@ h_tail = """
"""
fc_head = """
#include <stdlib.h>
#include "H5hut.h"
#include "Underscore.h"