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Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_bmr_fixbug into develop

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This commit is contained in:
Binh-Minh Ribler 2019-01-26 11:59:45 -06:00
commit 55d1931dc6
7 changed files with 28 additions and 26 deletions
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8
config/cmake/HDF5_Examples.cmake.in
View File

@ -48,7 +48,11 @@ set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCTEST_CONFIGURATION_TYPE:STRING=${
##################################################################
if(NOT DEFINED INSTALLDIR)
set(INSTALLDIR "C:/Program Files/HDF_Group/@HDF5_PACKAGE_NAME@/@HDF5_PACKAGE_VERSION@")
if(WIN32)
set(INSTALLDIR "C:/Program Files/HDF_Group/@HDF5_PACKAGE_NAME@/@HDF5_PACKAGE_VERSION@")
else()
set(INSTALLDIR "@CMAKE_INSTALL_PREFIX@")
endif()
endif()
if(NOT DEFINED CTEST_SOURCE_NAME)
@ -70,7 +74,7 @@ set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DSITE:STRING=${CTEST_SITE} -DBUILDN
#TAR_SOURCE - name of tarfile
#if(NOT DEFINED TAR_SOURCE)
# set(CTEST_USE_TAR_SOURCE "HDF5Examples-1.10.10-Source")
# set(CTEST_USE_TAR_SOURCE "HDF5Examples-1.12.4-Source")
#endif()
###############################################################################################################

4
config/cmake/patch.xml
View File

@ -1,5 +1,5 @@
<CPackWiXPatch>
<CPackWiXFragment Id="CM_CP_libraries.bin.hdf5.dll">
<CPackWiXFragment Id="CM_CP_libraries.bin.hdf5.dll">
<Environment Id="PATH"
Name="PATH"
Value="[CM_DP_libraries.bin]"
@ -7,5 +7,5 @@
Part="last"
Action="set"
System="yes"/>
</CPackWiXFragment>
</CPackWiXFragment>
</CPackWiXPatch>

6
config/cmake_ext_mod/HDFMacros.cmake
View File

@ -14,7 +14,7 @@
macro (SET_HDF_BUILD_TYPE)
get_property(_isMultiConfig GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
if(_isMultiConfig)
set(HDF_CFG_NAME ${CTEST_CONFIGURATION_TYPE})
set(HDF_CFG_NAME \${CTEST_CONFIGURATION_TYPE})
set(HDF_BUILD_TYPE ${CMAKE_CFG_INTDIR})
set(HDF_CFG_BUILD_TYPE \${CMAKE_INSTALL_CONFIG_NAME})
else()
@ -170,7 +170,7 @@ macro (HDF_IMPORT_SET_LIB_OPTIONS libtarget libname libtype libversion)
if (${importtype} MATCHES "IMPORT")
set (importprefix "${CMAKE_STATIC_LIBRARY_PREFIX}")
endif ()
if (${CMAKE_BUILD_TYPE} MATCHES "Debug")
if (${HDF_CFG_NAME} MATCHES "Debug")
set (IMPORT_LIB_NAME ${LIB_DEBUG_NAME})
else ()
set (IMPORT_LIB_NAME ${LIB_RELEASE_NAME})
@ -273,7 +273,7 @@ macro (HDF_README_PROPERTIES target_fortran)
set (BINARY_PLATFORM "${BINARY_PLATFORM}, using VISUAL STUDIO 2015")
else ()
set (BINARY_PLATFORM "${BINARY_PLATFORM}, using VISUAL STUDIO 2017")
endif ()
endif ()
else ()
set (BINARY_PLATFORM "${BINARY_PLATFORM}, using VISUAL STUDIO ${CMAKE_C_COMPILER_VERSION}")
endif ()

12
java/src/hdf/hdf5lib/H5.java
View File

@ -70,8 +70,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
* In general, arguments to the HDF Java API are straightforward translations from the 'C' API described in the HDF
* Reference Manual.
*
* <center>
* <table border=2 cellpadding=2>
* <table border=1>
* <caption><b>HDF-5 C types to Java types</b> </caption>
* <tr>
* <td><b>HDF-5</b></td>
@ -107,8 +106,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
* <td>Special -- see HDFArray</td>
* </tr>
* </table>
* </center>
* <center> <b>General Rules for Passing Arguments and Results</b> </center>
* <b>General Rules for Passing Arguments and Results</b>
* <p>
* In general, arguments passed <b>IN</b> to Java are the analogous basic types, as above. The exception is for arrays,
* which are discussed below.
@ -143,7 +141,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
* <p>
* All the routines where this convention is used will have specific documentation of the details, given below.
* <p>
* <a NAME="ARRAYS"> <b>Arrays</b> </a>
* <b>Arrays</b>
* <p>
* HDF5 needs to read and write multi-dimensional arrays of any number type (and records). The HDF5 API describes the
* layout of the source and destination, and the data for the array passed as a block of bytes, for instance,
@ -176,7 +174,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
* and the parameter <i>data</i> can be any multi-dimensional array of numbers, such as float[][], or int[][][], or
* Double[][].
* <p>
* <a NAME="CONSTANTS"> <b>HDF-5 Constants</b></a>
* <b>HDF-5 Constants</b>
* <p>
* The HDF-5 API defines a set of constants and enumerated values. Most of these values are available to Java programs
* via the class <a href="./hdf.hdf5lib.HDF5Constants.html"> <b>HDF5Constants</b></a>. For example, the parameters for
@ -196,7 +194,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
* The Java application uses both types of constants the same way, the only difference is that the
* <b><i>HDF5CDataTypes</i></b> may have different values on different platforms.
* <p>
* <a NAME="ERRORS"> <b>Error handling and Exceptions</b></a>
* <b>Error handling and Exceptions</b>
* <p>
* The HDF5 error API (H5E) manages the behavior of the error stack in the HDF-5 library. This API is omitted from the
* JHI5. Errors are converted into Java exceptions. This is totally different from the C interface, but is very natural

3
java/src/hdf/overview.html
View File

@ -90,8 +90,7 @@ like this:
The <i><b>H5</b> </i>class automatically loads the native method implementations
and the HDF5 library.
<h3>
<a NAME="DOWNLOAD"></a>To Obtain</h3>
<h3>To Obtain</h3>
The JHI5 is included with the <a href="https://portal.hdfgroup.org/display/support/Downloads">HDF5</a> library.
</body>

18
test/cork.c
View File

@ -286,19 +286,19 @@ static unsigned
verify_obj_dset_cork(hbool_t swmr)
{
/* Variable Declarations */
hid_t fid = -1; /* File ID */
hid_t fid = -1; /* File ID */
hid_t fapl = -1; /* File access property list */
hid_t aid = -1; /* Attribute ID */
hid_t sid = -1, sid2 = -1; /* Dataspace IDs */
hid_t did = -1, did2 = -1; /* Dataset IDs */
hid_t oid = -1; /* Object ID */
hid_t dcpl2; /* Dataset creation property list */
hid_t dcpl2; /* Dataset creation property list */
int i = 0; /* Local index variable */
hsize_t dim[1] = {100}; /* Dataset dimension size */
hsize_t dim[1] = {100}; /* Dataset dimension size */
hsize_t chunk_dim[1] = {7}; /* Dataset chunk dimension size */
H5O_info_t oinfo, oinfo2; /* Object metadata information */
char attrname[500]; /* Name of attribute */
unsigned flags; /* File access flags */
unsigned flags; /* File access flags */
if(swmr) {
TESTING("cork status for dataset objects with attributes (SWMR)");
@ -341,7 +341,7 @@ verify_obj_dset_cork(hbool_t swmr)
TEST_ERROR
/* Attach and write to an attribute to the dataset: DSET */
if((aid = H5Acreate2(did, ATTR, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
if((aid = H5Acreate2(did, ATTR, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
TEST_ERROR
/* Verify cork status of the dataset: DSET */
@ -380,11 +380,11 @@ verify_obj_dset_cork(hbool_t swmr)
TEST_ERROR
/* Attach 8 attributes to the dataset */
for(i = 0;i < 8; i++) {
sprintf(attrname, "attr %d", i);
if((aid = H5Acreate2(did2, attrname, H5T_NATIVE_UINT, sid2, H5P_DEFAULT, H5P_DEFAULT)) < 0)
for(i = 0; i < 8; i++) {
HDsprintf(attrname, "attr %d", i);
if((aid = H5Acreate2(did2, attrname, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
TEST_ERROR
if(H5Awrite(aid, H5T_NATIVE_UINT, &i) < 0)
if(H5Awrite(aid, H5T_NATIVE_INT, &i) < 0)
TEST_ERROR
if(H5Aclose(aid) < 0)
TEST_ERROR

3
tools/src/h5repack/h5repack_filters.c
View File

@ -338,9 +338,10 @@ int apply_filters(const char* name, /* object name from traverse list */
sm_nbytes = msize;
for (i = rank; i > 0; --i) {
hsize_t size = 0;
if(sm_nbytes == 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "number of bytes per stripmine must be > 0");
hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes;
size = H5TOOLS_BUFSIZE / sm_nbytes;
if (size == 0) /* datum size > H5TOOLS_BUFSIZE */
size = 1;
sm_size[i - 1] = MIN(dims[i - 1], size);