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HDFFV-10297 merge from develop

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This commit is contained in:
Allen Byrne 2017-10-10 14:46:59 -05:00
parent bd6de98d17
commit f92ccce1f9
40 changed files with 3725 additions and 3935 deletions
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30
config/cmake/jrunTest.cmake
View File

@ -122,7 +122,7 @@ if (TEST_MASK_ERROR)
endif ()
# if the return value is !=0 bail out
if (NOT ${TEST_RESULT} STREQUAL ${TEST_EXPECT})
if (NOT "${TEST_RESULT}" STREQUAL "${TEST_EXPECT}")
message (STATUS "ERROR OUTPUT: ${TEST_STREAM}")
message (FATAL_ERROR "Failed: Test program ${TEST_PROGRAM} exited != 0.\n${TEST_ERROR}")
endif ()
@ -141,13 +141,13 @@ if (NOT TEST_SKIP_COMPARE)
COMMAND ${CMAKE_COMMAND} -E compare_files ${TEST_FOLDER}/${TEST_OUTPUT} ${TEST_FOLDER}/${TEST_REFERENCE}
RESULT_VARIABLE TEST_RESULT
)
if (NOT ${TEST_RESULT} STREQUAL 0)
if (NOT "${TEST_RESULT}" STREQUAL "0")
set (TEST_RESULT 0)
file (STRINGS ${TEST_FOLDER}/${TEST_OUTPUT} test_act)
list (LENGTH test_act len_act)
file (STRINGS ${TEST_FOLDER}/${TEST_REFERENCE} test_ref)
list (LENGTH test_ref len_ref)
if (NOT ${len_act} STREQUAL "0" AND NOT ${len_ref} STREQUAL "0")
if (NOT "${len_act}" STREQUAL "0" AND NOT "${len_ref}" STREQUAL "0")
math (EXPR _FP_LEN "${len_ref} - 1")
foreach (line RANGE 0 ${_FP_LEN})
list (GET test_act ${line} str_act)
@ -160,14 +160,14 @@ if (NOT TEST_SKIP_COMPARE)
endif ()
endforeach ()
else ()
if (${len_act} STREQUAL "0")
if ("${len_act}" STREQUAL "0")
message (STATUS "COMPARE Failed: ${TEST_FOLDER}/${TEST_OUTPUT} is empty")
endif ()
if (${len_ref} STREQUAL "0")
if ("${len_ref}" STREQUAL "0")
message (STATUS "COMPARE Failed: ${TEST_FOLDER}/${TEST_REFERENCE} is empty")
endif ()
endif ()
if (NOT ${len_act} STREQUAL ${len_ref})
if (NOT "${len_act}" STREQUAL "${len_ref}")
set (TEST_RESULT 1)
endif ()
endif ()
@ -175,7 +175,7 @@ if (NOT TEST_SKIP_COMPARE)
message (STATUS "COMPARE Result: ${TEST_RESULT}")
# again, if return value is !=0 scream and shout
if (NOT ${TEST_RESULT} STREQUAL 0)
if (NOT "${TEST_RESULT}" STREQUAL "0")
message (FATAL_ERROR "Failed: The output of ${TEST_OUTPUT} did not match ${TEST_REFERENCE}")
endif ()
@ -191,14 +191,14 @@ if (NOT TEST_SKIP_COMPARE)
COMMAND ${CMAKE_COMMAND} -E compare_files ${TEST_FOLDER}/${TEST_OUTPUT}.err ${TEST_FOLDER}/${TEST_ERRREF}
RESULT_VARIABLE TEST_RESULT
)
if (NOT ${TEST_RESULT} STREQUAL 0)
if (NOT "${TEST_RESULT}" STREQUAL "0")
set (TEST_RESULT 0)
file (STRINGS ${TEST_FOLDER}/${TEST_OUTPUT}.err test_act)
list (LENGTH test_act len_act)
file (STRINGS ${TEST_FOLDER}/${TEST_ERRREF} test_ref)
list (LENGTH test_ref len_ref)
math (EXPR _FP_LEN "${len_ref} - 1")
if (NOT ${len_act} STREQUAL "0" AND NOT ${len_ref} STREQUAL "0")
if (NOT "${len_act}" STREQUAL "0" AND NOT "${len_ref}" STREQUAL "0")
math (EXPR _FP_LEN "${len_ref} - 1")
foreach (line RANGE 0 ${_FP_LEN})
list (GET test_act ${line} str_act)
@ -211,14 +211,14 @@ if (NOT TEST_SKIP_COMPARE)
endif ()
endforeach ()
else ()
if (${len_act} STREQUAL "0")
if ("${len_act}" STREQUAL "0")
message (STATUS "COMPARE Failed: ${TEST_FOLDER}/${TEST_OUTPUT}.err is empty")
endif ()
if (${len_ref} STREQUAL "0")
if ("${len_ref}" STREQUAL "0")
message (STATUS "COMPARE Failed: ${TEST_FOLDER}/${TEST_ERRREF} is empty")
endif ()
endif()
if (NOT ${len_act} STREQUAL ${len_ref})
if (NOT "${len_act}" STREQUAL "${len_ref}")
set (TEST_RESULT 1)
endif ()
endif ()
@ -239,15 +239,15 @@ if (TEST_GREP_COMPARE)
# TEST_REFERENCE should always be matched
string (REGEX MATCH "${TEST_REFERENCE}" TEST_MATCH ${TEST_STREAM})
string (COMPARE EQUAL "${TEST_REFERENCE}" "${TEST_MATCH}" TEST_RESULT)
if (${TEST_RESULT} STREQUAL "0")
if ("${TEST_RESULT}" STREQUAL "0")
message (FATAL_ERROR "Failed: The output of ${TEST_PROGRAM} did not contain ${TEST_REFERENCE}")
endif ()
string (REGEX MATCH "${TEST_FILTER}" TEST_MATCH ${TEST_STREAM})
if (${TEST_EXPECT} STREQUAL "1")
if ("${TEST_EXPECT}" STREQUAL "1")
# TEST_EXPECT (1) interperts TEST_FILTER as NOT to match
string (LENGTH "${TEST_MATCH}" TEST_RESULT)
if (NOT ${TEST_RESULT} STREQUAL "0")
if (NOT "${TEST_RESULT}" STREQUAL "0")
message (FATAL_ERROR "Failed: The output of ${TEST_PROGRAM} did contain ${TEST_FILTER}")
endif ()
endif ()

6
config/cmake/vfdTest.cmake
View File

@ -60,12 +60,12 @@ if (ERROR_APPEND AND EXISTS ${TEST_FOLDER}/${TEST_OUTPUT}_${TEST_VFD}.err)
endif ()
# if the return value is !=${TEST_EXPECT} bail out
if (NOT ${TEST_RESULT} STREQUAL ${TEST_EXPECT})
if (NOT "${TEST_RESULT}" STREQUAL "${TEST_EXPECT}")
if (NOT TEST_NOERRDISPLAY)
if (EXISTS ${TEST_FOLDER}/${TEST_OUTPUT}_${TEST_VFD}.out)
file (READ ${TEST_FOLDER}/${TEST_OUTPUT}_${TEST_VFD}.out TEST_STREAM)
message (STATUS "Output USING ${TEST_VFD}:\n${TEST_STREAM}")
endif ()
message (STATUS "Output USING ${TEST_VFD}:\n${TEST_STREAM}")
endif ()
endif ()
message (FATAL_ERROR "Failed: Test program ${TEST_PROGRAM} exited != ${TEST_EXPECT}.\n${TEST_ERROR}")
endif ()

6
config/cmake_ext_mod/grepTest.cmake
View File

@ -57,15 +57,15 @@ file (READ ${TEST_FOLDER}/${TEST_OUTPUT} TEST_STREAM)
# TEST_REFERENCE should always be matched
string (REGEX MATCH "${TEST_REFERENCE}" TEST_MATCH ${TEST_STREAM})
string (COMPARE EQUAL "${TEST_REFERENCE}" "${TEST_MATCH}" TEST_RESULT)
if (${TEST_RESULT} STREQUAL "0")
if ("${TEST_RESULT}" STREQUAL "0")
message (FATAL_ERROR "Failed: The output of ${TEST_PROGRAM} did not contain ${TEST_REFERENCE}")
endif ()
string (REGEX MATCH "${TEST_FILTER}" TEST_MATCH ${TEST_STREAM})
if (${TEST_EXPECT} STREQUAL "1")
if ("${TEST_EXPECT}" STREQUAL "1")
# TEST_EXPECT (1) interperts TEST_FILTER as NOT to match
string (LENGTH "${TEST_MATCH}" TEST_RESULT)
if (NOT ${TEST_RESULT} STREQUAL "0")
if (NOT "${TEST_RESULT}" STREQUAL "0")
message (FATAL_ERROR "Failed: The output of ${TEST_PROGRAM} did contain ${TEST_FILTER}")
endif ()
endif ()

28
config/cmake_ext_mod/runTest.cmake
View File

@ -87,7 +87,7 @@ if (TEST_REGEX)
file (READ ${TEST_FOLDER}/${TEST_OUTPUT} TEST_STREAM)
string (REGEX MATCH "${TEST_REGEX}" REGEX_MATCH ${TEST_STREAM})
string (COMPARE EQUAL "${REGEX_MATCH}" "${TEST_MATCH}" REGEX_RESULT)
if (${REGEX_RESULT} STREQUAL "0")
if ("${REGEX_RESULT}" STREQUAL "0")
message (STATUS "Failed: The output of ${TEST_PROGRAM} did not contain ${TEST_MATCH}")
endif ()
endif ()
@ -106,7 +106,7 @@ if (TEST_APPEND)
endif ()
# if the return value is !=${TEST_EXPECT} bail out
if (NOT ${TEST_RESULT} STREQUAL ${TEST_EXPECT})
if (NOT "${TEST_RESULT}" STREQUAL "${TEST_EXPECT}")
if (NOT TEST_NOERRDISPLAY)
if (EXISTS ${TEST_FOLDER}/${TEST_OUTPUT})
file (READ ${TEST_FOLDER}/${TEST_OUTPUT} TEST_STREAM)
@ -193,13 +193,13 @@ if (NOT TEST_SKIP_COMPARE)
endif ()
endif ()
if (NOT ${TEST_RESULT} STREQUAL 0)
if (NOT "${TEST_RESULT}" STREQUAL "0")
set (TEST_RESULT 0)
file (STRINGS ${TEST_FOLDER}/${TEST_OUTPUT} test_act)
list (LENGTH test_act len_act)
file (STRINGS ${TEST_FOLDER}/${TEST_REFERENCE} test_ref)
list (LENGTH test_ref len_ref)
if (NOT ${len_act} STREQUAL "0" AND NOT ${len_ref} STREQUAL "0")
if (NOT "${len_act}" STREQUAL "0" AND NOT "${len_ref}" STREQUAL "0")
math (EXPR _FP_LEN "${len_ref} - 1")
foreach (line RANGE 0 ${_FP_LEN})
list (GET test_act ${line} str_act)
@ -212,14 +212,14 @@ if (NOT TEST_SKIP_COMPARE)
endif ()
endforeach ()
else ()
if (${len_act} STREQUAL "0")
if ("${len_act}" STREQUAL "0")
message (STATUS "COMPARE Failed: ${TEST_FOLDER}/${TEST_OUTPUT} is empty")
endif ()
if (${len_ref} STREQUAL "0")
if ("${len_ref}" STREQUAL "0")
message (STATUS "COMPARE Failed: ${TEST_FOLDER}/${TEST_REFERENCE} is empty")
endif ()
endif ()
if (NOT ${len_act} STREQUAL ${len_ref})
if (NOT "${len_act}" STREQUAL "${len_ref}")
set (TEST_RESULT 1)
endif ()
endif ()
@ -227,7 +227,7 @@ if (NOT TEST_SKIP_COMPARE)
message (STATUS "COMPARE Result: ${TEST_RESULT}")
# again, if return value is !=0 scream and shout
if (NOT ${TEST_RESULT} STREQUAL 0)
if (NOT "${TEST_RESULT}" STREQUAL "0")
message (FATAL_ERROR "Failed: The output of ${TEST_OUTPUT} did not match ${TEST_REFERENCE}")
endif ()
@ -243,14 +243,14 @@ if (NOT TEST_SKIP_COMPARE)
COMMAND ${CMAKE_COMMAND} -E compare_files ${TEST_FOLDER}/${TEST_OUTPUT}.err ${TEST_FOLDER}/${TEST_ERRREF}
RESULT_VARIABLE TEST_RESULT
)
if (NOT ${TEST_RESULT} STREQUAL 0)
if (NOT "${TEST_RESULT}" STREQUAL "0")
set (TEST_RESULT 0)
file (STRINGS ${TEST_FOLDER}/${TEST_OUTPUT}.err test_act)
list (LENGTH test_act len_act)
file (STRINGS ${TEST_FOLDER}/${TEST_ERRREF} test_ref)
list (LENGTH test_ref len_ref)
math (EXPR _FP_LEN "${len_ref} - 1")
if (NOT ${len_act} STREQUAL "0" AND NOT ${len_ref} STREQUAL "0")
if (NOT "${len_act}" STREQUAL "0" AND NOT "${len_ref}" STREQUAL "0")
math (EXPR _FP_LEN "${len_ref} - 1")
foreach (line RANGE 0 ${_FP_LEN})
list (GET test_act ${line} str_act)
@ -263,14 +263,14 @@ if (NOT TEST_SKIP_COMPARE)
endif ()
endforeach ()
else ()
if (${len_act} STREQUAL "0")
if ("${len_act}" STREQUAL "0")
message (STATUS "COMPARE Failed: ${TEST_FOLDER}/${TEST_OUTPUT}.err is empty")
endif ()
if (${len_ref} STREQUAL "0")
if ("${len_ref}" STREQUAL "0")
message (STATUS "COMPARE Failed: ${TEST_FOLDER}/${TEST_ERRREF} is empty")
endif ()
endif ()
if (NOT ${len_act} STREQUAL ${len_ref})
if (NOT "${len_act}" STREQUAL "${len_ref}")
set (TEST_RESULT 1)
endif ()
endif ()
@ -278,7 +278,7 @@ if (NOT TEST_SKIP_COMPARE)
message (STATUS "COMPARE Result: ${TEST_RESULT}")
# again, if return value is !=0 scream and shout
if (NOT ${TEST_RESULT} STREQUAL 0)
if (NOT "${TEST_RESULT}" STREQUAL "0")
message (FATAL_ERROR "Failed: The error output of ${TEST_OUTPUT}.err did not match ${TEST_ERRREF}")
endif ()
endif ()

4
java/examples/datasets/CMakeLists.txt
View File

@ -101,7 +101,7 @@ if (BUILD_TESTING)
endif (H5_HAVE_FILTER_SZIP)
foreach (example ${HDF_JAVA_EXAMPLES})
if (${example} STREQUAL "H5Ex_D_External")
if ("${example}" STREQUAL "H5Ex_D_External")
add_test (
NAME JAVA_datasets-${example}-clear-objects
COMMAND ${CMAKE_COMMAND}
@ -129,7 +129,7 @@ if (BUILD_TESTING)
)
set_tests_properties (JAVA_datasets-${example}-copy-objects PROPERTIES DEPENDS JAVA_datasets-${example}-clear-objects)
set (last_test "JAVA_datasets-${example}-copy-objects")
if (${example} STREQUAL "H5Ex_D_Szip")
if ("${example}" STREQUAL "H5Ex_D_Szip")
if (USE_FILTER_SZIP)
ADD_H5_TEST (${example} 0)
endif ()

4
java/examples/groups/CMakeLists.txt
View File

@ -90,8 +90,8 @@ ENDMACRO ()
if (BUILD_TESTING)
foreach (example ${HDF_JAVA_EXAMPLES})
if (NOT ${example} STREQUAL "H5Ex_G_Iterate" AND NOT ${example} STREQUAL "H5Ex_G_Visit")
if (${example} STREQUAL "H5Ex_G_Compact")
if (NOT "${example}" STREQUAL "H5Ex_G_Iterate" AND NOT "${example}" STREQUAL "H5Ex_G_Visit")
if ("${example}" STREQUAL "H5Ex_G_Compact")
add_test (
NAME JAVA_groups-${example}-clear-h5s
COMMAND ${CMAKE_COMMAND}

23
release_docs/RELEASE.txt
View File

@ -206,6 +206,17 @@ Bug Fixes since HDF5-1.10.0-patch1 release
Library
-------
- H5Zfilter_avail in H5Z.c
The public function checked for plugins, while the private
function did not.
Modified H5Zfilter_avail and private function, H5Z_filter_avail.
Moved check for plugin from public to private function. Updated
H5P__set_filter due to change in H5Z_filter_avail. Updated tests.
(ADB - 2017/10/10, HDFFV-10297)
- Fix H5HL_offset_into()
(1) Fix H5HL_offset_into() to return error when offset exceeds heap data
@ -299,6 +310,18 @@ Bug Fixes since HDF5-1.10.0-patch1 release
Tools
-----
- h5repack
h5repack failed to copy a dataset with existing filter.
Reworked code for h5repack and h5diff code in tools library. Added
improved error handling, cleanup of resources and checks of calls.
Modified H5Zfilter_avail and private function, H5Z_filter_avail.
Moved check for plugin from public to private function. Updated
H5P__set_filter due to change in H5Z_filter_avail. Updated tests.
(ADB - 2017/10/10, HDFFV-10297)
- h5repack
h5repack always set the User Defined filter flag to H5Z_FLAG_MANDATORY.

4
src/H5PLextern.h
View File

@ -11,9 +11,9 @@
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Programmer: Raymond Lu <songyulu@hdfgroup.org>
* 13 February 2013
* Purpose: Header file for writing external HDF5 plugins.
*/
#ifndef _H5PLextern_H
#define _H5PLextern_H

10
src/H5PLmodule.h
View File

@ -11,13 +11,11 @@
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Programmer: Quincey Koziol <koziol@hdfgroup.org>
* Saturday, September 12, 2015
*
* Purpose: This file contains declarations which define macros for the
* H5PL package. Including this header means that the source file
* is part of the H5PL package.
* Purpose: This file contains declarations which define macros for the
* H5PL package. Including this header means that the source file
* is part of the H5PL package.
*/
#ifndef _H5PLmodule_H
#define _H5PLmodule_H

4
src/H5PLprivate.h
View File

@ -10,8 +10,8 @@
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/* Programmer: Raymond Lu <songyulu@hdfgroup.org>
* 13 February 2013
/*
* This file contains private information about the H5PL module
*/
#ifndef _H5PLprivate_H

412
src/H5Pocpl.c
View File

@ -13,11 +13,11 @@
/*-------------------------------------------------------------------------
*
* Created: H5Pocpl.c
* Nov 28 2006
* Quincey Koziol <koziol@hdfgroup.org>
* Created: H5Pocpl.c
* Nov 28 2006
* Quincey Koziol <koziol@hdfgroup.org>
*
* Purpose: Object creation property list class routines
* Purpose: Object creation property list class routines
*
*-------------------------------------------------------------------------
*/
@ -26,21 +26,21 @@
/* Module Setup */
/****************/
#define H5O_FRIEND /*suppress error about including H5Opkg */
#define H5O_FRIEND /*suppress error about including H5Opkg */
#include "H5Pmodule.h" /* This source code file is part of the H5P module */
/***********/
/* Headers */
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5Iprivate.h" /* IDs */
#include "H5MMprivate.h" /* Memory management */
#include "H5Opkg.h" /* Object headers */
#include "H5Ppkg.h" /* Property lists */
#include "H5PLprivate.h" /* Dynamic plugin */
#include "H5Zprivate.h" /* Filter pipeline */
#include "H5private.h" /* Generic Functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5Iprivate.h" /* IDs */
#include "H5MMprivate.h" /* Memory management */
#include "H5Opkg.h" /* Object headers */
#include "H5Ppkg.h" /* Property lists */
#include "H5PLprivate.h" /* Dynamic plugin */
#include "H5Zprivate.h" /* Filter pipeline */
/****************/
@ -100,7 +100,7 @@ static int H5P__ocrt_pipeline_cmp(const void *value1, const void *value2, size_t
static herr_t H5P__ocrt_pipeline_close(const char *name, size_t size, void *value);
/* Local routines */
static herr_t H5P__set_filter(H5P_genplist_t *plist, H5Z_filter_t filter,
static herr_t H5P__set_filter(H5P_genplist_t *plist, H5Z_filter_t filter,
unsigned int flags, size_t cd_nelmts, const unsigned int cd_values[/*cd_nelmts*/]);
/*********************/
@ -109,21 +109,21 @@ static herr_t H5P__set_filter(H5P_genplist_t *plist, H5Z_filter_t filter,
/* Object creation property list class library initialization object */
const H5P_libclass_t H5P_CLS_OCRT[1] = {{
"object create", /* Class name for debugging */
H5P_TYPE_OBJECT_CREATE, /* Class type */
"object create", /* Class name for debugging */
H5P_TYPE_OBJECT_CREATE, /* Class type */
&H5P_CLS_ROOT_g, /* Parent class */
&H5P_CLS_OBJECT_CREATE_g, /* Pointer to class */
&H5P_CLS_OBJECT_CREATE_ID_g, /* Pointer to class ID */
NULL, /* Pointer to default property list ID */
H5P__ocrt_reg_prop, /* Default property registration routine */
&H5P_CLS_ROOT_g, /* Parent class */
&H5P_CLS_OBJECT_CREATE_g, /* Pointer to class */
&H5P_CLS_OBJECT_CREATE_ID_g, /* Pointer to class ID */
NULL, /* Pointer to default property list ID */
H5P__ocrt_reg_prop, /* Default property registration routine */
NULL, /* Class creation callback */
NULL, /* Class creation callback info */
NULL, /* Class copy callback */
NULL, /* Class copy callback info */
NULL, /* Class close callback */
NULL /* Class close callback info */
NULL, /* Class creation callback */
NULL, /* Class creation callback info */
NULL, /* Class copy callback */
NULL, /* Class copy callback info */
NULL, /* Class close callback */
NULL /* Class close callback info */
}};
@ -165,25 +165,25 @@ H5P__ocrt_reg_prop(H5P_genclass_t *pclass)
FUNC_ENTER_STATIC
/* Register max. compact attribute storage property */
if(H5P_register_real(pclass, H5O_CRT_ATTR_MAX_COMPACT_NAME, H5O_CRT_ATTR_MAX_COMPACT_SIZE, &H5O_def_attr_max_compact_g,
if(H5P_register_real(pclass, H5O_CRT_ATTR_MAX_COMPACT_NAME, H5O_CRT_ATTR_MAX_COMPACT_SIZE, &H5O_def_attr_max_compact_g,
NULL, NULL, NULL, H5O_CRT_ATTR_MAX_COMPACT_ENC, H5O_CRT_ATTR_MAX_COMPACT_DEC,
NULL, NULL, NULL, NULL) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
/* Register min. dense attribute storage property */
if(H5P_register_real(pclass, H5O_CRT_ATTR_MIN_DENSE_NAME, H5O_CRT_ATTR_MIN_DENSE_SIZE, &H5O_def_attr_min_dense_g,
if(H5P_register_real(pclass, H5O_CRT_ATTR_MIN_DENSE_NAME, H5O_CRT_ATTR_MIN_DENSE_SIZE, &H5O_def_attr_min_dense_g,
NULL, NULL, NULL, H5O_CRT_ATTR_MIN_DENSE_ENC, H5O_CRT_ATTR_MIN_DENSE_DEC,
NULL, NULL, NULL, NULL) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
/* Register object header flags property */
if(H5P_register_real(pclass, H5O_CRT_OHDR_FLAGS_NAME, H5O_CRT_OHDR_FLAGS_SIZE, &H5O_def_ohdr_flags_g,
if(H5P_register_real(pclass, H5O_CRT_OHDR_FLAGS_NAME, H5O_CRT_OHDR_FLAGS_SIZE, &H5O_def_ohdr_flags_g,
NULL, NULL, NULL, H5O_CRT_OHDR_FLAGS_ENC, H5O_CRT_OHDR_FLAGS_DEC,
NULL, NULL, NULL, NULL) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
/* Register the pipeline property */
if(H5P_register_real(pclass, H5O_CRT_PIPELINE_NAME, H5O_CRT_PIPELINE_SIZE, &H5O_def_pline_g,
if(H5P_register_real(pclass, H5O_CRT_PIPELINE_NAME, H5O_CRT_PIPELINE_SIZE, &H5O_def_pline_g,
NULL, H5O_CRT_PIPELINE_SET, H5O_CRT_PIPELINE_GET, H5O_CRT_PIPELINE_ENC, H5O_CRT_PIPELINE_DEC,
H5O_CRT_PIPELINE_DEL, H5O_CRT_PIPELINE_COPY, H5O_CRT_PIPELINE_CMP, H5O_CRT_PIPELINE_CLOSE) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
@ -194,9 +194,9 @@ done:
/*-------------------------------------------------------------------------
* Function: H5Pset_attr_phase_change
* Function: H5Pset_attr_phase_change
*
* Purpose: Sets the cutoff values for indexes storing attributes
* Purpose: Sets the cutoff values for indexes storing attributes
* in object headers for this file. If more than max_compact
* attributes are in an object header, the attributes will be
* moved to a heap and indexed with a B-tree.
@ -208,10 +208,10 @@ done:
* never be stored in the object header but will be always be
* stored in a heap.
*
* Return: Non-negative on success/Negative on failure
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Tuesday, November 28, 2006
* Programmer: Quincey Koziol
* Tuesday, November 28, 2006
*
*-------------------------------------------------------------------------
*/
@ -248,14 +248,14 @@ done:
/*-------------------------------------------------------------------------
* Function: H5Pget_attr_phase_change
* Function: H5Pget_attr_phase_change
*
* Purpose: Gets the phase change values for attribute storage
* Purpose: Gets the phase change values for attribute storage
*
* Return: Non-negative on success/Negative on failure
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Tuesday, November 28, 2006
* Programmer: Quincey Koziol
* Tuesday, November 28, 2006
*
*-------------------------------------------------------------------------
*/
@ -486,37 +486,37 @@ done:
/*-------------------------------------------------------------------------
* Function: H5P_modify_filter
* Function: H5P_modify_filter
*
* Purpose: Modifies the specified FILTER in the
* transient or permanent output filter pipeline
* depending on whether PLIST is a dataset creation or dataset
* transfer property list. The FLAGS argument specifies certain
* general properties of the filter and is documented below.
* The CD_VALUES is an array of CD_NELMTS integers which are
* auxiliary data for the filter. The integer vlues will be
* stored in the dataset object header as part of the filter
* information.
* Purpose: Modifies the specified FILTER in the
* transient or permanent output filter pipeline
* depending on whether PLIST is a dataset creation or dataset
* transfer property list. The FLAGS argument specifies certain
* general properties of the filter and is documented below.
* The CD_VALUES is an array of CD_NELMTS integers which are
* auxiliary data for the filter. The integer vlues will be
* stored in the dataset object header as part of the filter
* information.
*
* The FLAGS argument is a bit vector of the following fields:
* The FLAGS argument is a bit vector of the following fields:
*
* H5Z_FLAG_OPTIONAL(0x0001)
* If this bit is set then the filter is optional. If the
* filter fails during an H5Dwrite() operation then the filter
* is just excluded from the pipeline for the chunk for which it
* failed; the filter will not participate in the pipeline
* during an H5Dread() of the chunk. If this bit is clear and
* the filter fails then the entire I/O operation fails.
* H5Z_FLAG_OPTIONAL(0x0001)
* If this bit is set then the filter is optional. If the
* filter fails during an H5Dwrite() operation then the filter
* is just excluded from the pipeline for the chunk for which it
* failed; the filter will not participate in the pipeline
* during an H5Dread() of the chunk. If this bit is clear and
* the filter fails then the entire I/O operation fails.
* If this bit is set but encoding is disabled for a filter,
* attempting to write will generate an error.
*
* Note: This function currently supports only the permanent filter
* pipeline. That is, PLIST_ID must be a dataset creation
* property list.
* Note: This function currently supports only the permanent filter
* pipeline. That is, PLIST_ID must be a dataset creation
* property list.
*
* Return: Non-negative on success/Negative on failure
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Programmer: Quincey Koziol
* Wednesday, October 17, 2007
*
*-------------------------------------------------------------------------
@ -623,33 +623,33 @@ done:
/*-------------------------------------------------------------------------
* Function: H5Pset_filter
* Function: H5Pset_filter
*
* Purpose: Adds the specified FILTER and corresponding properties to the
* end of the data or link output filter pipeline
* depending on whether PLIST is a dataset creation or group
* creation property list. The FLAGS argument specifies certain
* general properties of the filter and is documented below.
* The CD_VALUES is an array of CD_NELMTS integers which are
* auxiliary data for the filter. The integer vlues will be
* stored in the dataset object header as part of the filter
* information.
* Purpose: Adds the specified FILTER and corresponding properties to the
* end of the data or link output filter pipeline
* depending on whether PLIST is a dataset creation or group
* creation property list. The FLAGS argument specifies certain
* general properties of the filter and is documented below.
* The CD_VALUES is an array of CD_NELMTS integers which are
* auxiliary data for the filter. The integer vlues will be
* stored in the dataset object header as part of the filter
* information.
*
* The FLAGS argument is a bit vector of the following fields:
* The FLAGS argument is a bit vector of the following fields:
*
* H5Z_FLAG_OPTIONAL(0x0001)
* If this bit is set then the filter is optional. If the
* filter fails during an H5Dwrite() operation then the filter
* is just excluded from the pipeline for the chunk for which it
* failed; the filter will not participate in the pipeline
* during an H5Dread() of the chunk. If this bit is clear and
* the filter fails then the entire I/O operation fails.
* H5Z_FLAG_OPTIONAL(0x0001)
* If this bit is set then the filter is optional. If the
* filter fails during an H5Dwrite() operation then the filter
* is just excluded from the pipeline for the chunk for which it
* failed; the filter will not participate in the pipeline
* during an H5Dread() of the chunk. If this bit is clear and
* the filter fails then the entire I/O operation fails.
* If this bit is set but encoding is disabled for a filter,
* attempting to write will generate an error.
*
* Return: Non-negative on success/Negative on failure
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Programmer: Robb Matzke
* Wednesday, April 15, 1998
*
* Modifications:
@ -668,7 +668,7 @@ done:
*/
herr_t
H5Pset_filter(hid_t plist_id, H5Z_filter_t filter, unsigned int flags,
size_t cd_nelmts, const unsigned int cd_values[/*cd_nelmts*/])
size_t cd_nelmts, const unsigned int cd_values[/*cd_nelmts*/])
{
H5P_genplist_t *plist; /* Property list */
herr_t ret_value=SUCCEED; /* return value */
@ -698,43 +698,43 @@ done:
/*-------------------------------------------------------------------------
* Function: H5P__set_filter
* Function: H5P__set_filter
*
* Purpose: Adds the specified FILTER and corresponding properties to the
* end of the data or link output filter pipeline
* depending on whether PLIST is a dataset creation or group
* creation property list. The FLAGS argument specifies certain
* general properties of the filter and is documented below.
* The CD_VALUES is an array of CD_NELMTS integers which are
* auxiliary data for the filter. The integer vlues will be
* stored in the dataset object header as part of the filter
* information.
* Purpose: Adds the specified FILTER and corresponding properties to the
* end of the data or link output filter pipeline
* depending on whether PLIST is a dataset creation or group
* creation property list. The FLAGS argument specifies certain
* general properties of the filter and is documented below.
* The CD_VALUES is an array of CD_NELMTS integers which are
* auxiliary data for the filter. The integer vlues will be
* stored in the dataset object header as part of the filter
* information.
*
* The FLAGS argument is a bit vector of the following fields:
* The FLAGS argument is a bit vector of the following fields:
*
* H5Z_FLAG_OPTIONAL(0x0001)
* If this bit is set then the filter is optional. If the
* filter fails during an H5Dwrite() operation then the filter
* is just excluded from the pipeline for the chunk for which it
* failed; the filter will not participate in the pipeline
* during an H5Dread() of the chunk. If this bit is clear and
* the filter fails then the entire I/O operation fails.
* If this bit is set but encoding is disabled for a filter,
* attempting to write will generate an error.
* H5Z_FLAG_OPTIONAL(0x0001)
* If this bit is set then the filter is optional. If the
* filter fails during an H5Dwrite() operation then the filter
* is just excluded from the pipeline for the chunk for which it
* failed; the filter will not participate in the pipeline
* during an H5Dread() of the chunk. If this bit is clear and
* the filter fails then the entire I/O operation fails.
* If this bit is set but encoding is disabled for a filter,
* attempting to write will generate an error.
*
* If the filter is not registered, this function tries to load
* If the filter is not registered, this function tries to load
* it dynamically during run time.
*
* Return: Non-negative on success/Negative on failure
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Programmer: Robb Matzke
* Wednesday, April 15, 1998
*
*-------------------------------------------------------------------------
*/
static herr_t
H5P__set_filter(H5P_genplist_t *plist, H5Z_filter_t filter, unsigned int flags,
size_t cd_nelmts, const unsigned int cd_values[/*cd_nelmts*/])
size_t cd_nelmts, const unsigned int cd_values[/*cd_nelmts*/])
{
H5O_pline_t pline; /* Filter pipeline */
htri_t filter_avail; /* Filter availability */
@ -746,16 +746,6 @@ H5P__set_filter(H5P_genplist_t *plist, H5Z_filter_t filter, unsigned int flags,
if((filter_avail = H5Z_filter_avail(filter)) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't check filter availability")
/* If filter is not available, try to dynamically load it */
if(!filter_avail) {
const H5Z_class2_t *filter_info;
if(NULL == (filter_info = (const H5Z_class2_t *)H5PL_load(H5PL_TYPE_FILTER, (int)filter)))
HGOTO_ERROR(H5E_PLINE, H5E_CANTLOAD, FAIL, "failed to load dynamically loaded plugin")
if(H5Z_register(filter_info) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_CANTINIT, FAIL, "unable to register filter")
} /* end if */
/* Get the pipeline property to append to */
if(H5P_peek(plist, H5O_CRT_PIPELINE_NAME, &pline) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get pipeline")
@ -774,21 +764,21 @@ done:
/*-------------------------------------------------------------------------
* Function: H5Pget_nfilters
* Function: H5Pget_nfilters
*
* Purpose: Returns the number of filters in the data or link
* pipeline depending on whether PLIST_ID is a dataset creation
* or group creation property list. In each pipeline the
* filters are numbered from zero through N-1 where N is the
* value returned by this function. During output to the file
* the filters of a pipeline are applied in increasing order
* (the inverse is true for input).
* Purpose: Returns the number of filters in the data or link
* pipeline depending on whether PLIST_ID is a dataset creation
* or group creation property list. In each pipeline the
* filters are numbered from zero through N-1 where N is the
* value returned by this function. During output to the file
* the filters of a pipeline are applied in increasing order
* (the inverse is true for input).
*
* Return: Success: Number of filters or zero if there are none.
* Return: Success: Number of filters or zero if there are none.
*
* Failure: Negative
* Failure: Negative
*
* Programmer: Robb Matzke
* Programmer: Robb Matzke
* Tuesday, August 4, 1998
*
* Modifications:
@ -827,25 +817,25 @@ done:
/*-------------------------------------------------------------------------
* Function: H5Pget_filter2
* Function: H5Pget_filter2
*
* Purpose: This is the query counterpart of H5Pset_filter() and returns
* information about a particular filter number in a permanent
* or transient pipeline depending on whether PLIST_ID is a
* dataset creation or transfer property list. On input,
* CD_NELMTS indicates the number of entries in the CD_VALUES
* array allocated by the caller while on exit it contains the
* number of values defined by the filter. FILTER_CONFIG is a bit
* Purpose: This is the query counterpart of H5Pset_filter() and returns
* information about a particular filter number in a permanent
* or transient pipeline depending on whether PLIST_ID is a
* dataset creation or transfer property list. On input,
* CD_NELMTS indicates the number of entries in the CD_VALUES
* array allocated by the caller while on exit it contains the
* number of values defined by the filter. FILTER_CONFIG is a bit
* field contaning encode/decode flags from H5Zpublic.h. The IDX
* should be a value between zero and N-1 as described for
* H5Pget_nfilters() and the function will return failure if the
* filter number is out of range.
*
* Return: Success: Filter identification number.
* Return: Success: Filter identification number.
*
* Failure: H5Z_FILTER_ERROR (Negative)
* Failure: H5Z_FILTER_ERROR (Negative)
*
* Programmer: Robb Matzke
* Programmer: Robb Matzke
* Wednesday, April 15, 1998
*
* Modifications:
@ -859,8 +849,8 @@ done:
*/
H5Z_filter_t
H5Pget_filter2(hid_t plist_id, unsigned idx, unsigned int *flags/*out*/,
size_t *cd_nelmts/*in_out*/, unsigned cd_values[]/*out*/,
size_t namelen, char name[]/*out*/,
size_t *cd_nelmts/*in_out*/, unsigned cd_values[]/*out*/,
size_t namelen, char name[]/*out*/,
unsigned *filter_config /*out*/)
{
H5P_genplist_t *plist; /* Property list */
@ -921,23 +911,23 @@ done:
/*-------------------------------------------------------------------------
* Function: H5P_get_filter_by_id
* Function: H5P_get_filter_by_id
*
* Purpose: This is an additional query counterpart of H5Pset_filter() and
* Purpose: This is an additional query counterpart of H5Pset_filter() and
* returns information about a particular filter in a permanent
* or transient pipeline depending on whether PLIST_ID is a
* dataset creation or transfer property list. On input,
* CD_NELMTS indicates the number of entries in the CD_VALUES
* array allocated by the caller while on exit it contains the
* number of values defined by the filter. FILTER_CONFIG is a bit
* or transient pipeline depending on whether PLIST_ID is a
* dataset creation or transfer property list. On input,
* CD_NELMTS indicates the number of entries in the CD_VALUES
* array allocated by the caller while on exit it contains the
* number of values defined by the filter. FILTER_CONFIG is a bit
* field contaning encode/decode flags from H5Zpublic.h. The ID
* should be the filter ID to retrieve the parameters for. If the
* filter is not set for the property list, an error will be returned.
*
* Return: Success: Non-negative
* Failure: Negative
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Quincey Koziol
* Programmer: Quincey Koziol
* Wednesday, October 17, 2007
*
*-------------------------------------------------------------------------
@ -971,23 +961,23 @@ done:
/*-------------------------------------------------------------------------
* Function: H5Pget_filter_by_id2
* Function: H5Pget_filter_by_id2
*
* Purpose: This is an additional query counterpart of H5Pset_filter() and
* Purpose: This is an additional query counterpart of H5Pset_filter() and
* returns information about a particular filter in a permanent
* or transient pipeline depending on whether PLIST_ID is a
* dataset creation or transfer property list. On input,
* CD_NELMTS indicates the number of entries in the CD_VALUES
* array allocated by the caller while on exit it contains the
* number of values defined by the filter. FILTER_CONFIG is a bit
* or transient pipeline depending on whether PLIST_ID is a
* dataset creation or transfer property list. On input,
* CD_NELMTS indicates the number of entries in the CD_VALUES
* array allocated by the caller while on exit it contains the
* number of values defined by the filter. FILTER_CONFIG is a bit
* field contaning encode/decode flags from H5Zpublic.h. The ID
* should be the filter ID to retrieve the parameters for. If the
* filter is not set for the property list, an error will be returned.
*
* Return: Success: Non-negative
* Failure: Negative
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Quincey Koziol
* Programmer: Quincey Koziol
* Friday, April 5, 2003
*
* Modifications:
@ -1047,16 +1037,16 @@ done:
/*-------------------------------------------------------------------------
* Function: H5Pall_filters_avail
* Function: H5Pall_filters_avail
*
* Purpose: This is a query routine to verify that all the filters set
* Purpose: This is a query routine to verify that all the filters set
* in the dataset creation property list are available currently.
*
* Return: Success: TRUE if all filters available, FALSE if one or
* Return: Success: TRUE if all filters available, FALSE if one or
* more filters not currently available.
* Failure: FAIL on error
* Failure: FAIL on error
*
* Programmer: Quincey Koziol
* Programmer: Quincey Koziol
* Tuesday, April 8, 2003
*
* Modifications:
@ -1096,16 +1086,16 @@ done:
/*-------------------------------------------------------------------------
* Function: H5P_filter_in_pline
* Function: H5P_filter_in_pline
*
* Purpose: Check whether the filter is in the pipeline of the object
* creation property list.
* Purpose: Check whether the filter is in the pipeline of the object
* creation property list.
*
* Return: TRUE: found
* FALSE: not found
* FAIL: error
* Return: TRUE: found
* FALSE: not found
* FAIL: error
*
* Programmer: Raymond Lu
* Programmer: Raymond Lu
* 26 April 2013
*
*-------------------------------------------------------------------------
@ -1198,7 +1188,7 @@ done:
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Programmer: Robb Matzke
* Wednesday, April 15, 1998
*
* Modifications:
@ -1258,7 +1248,7 @@ done:
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* Programmer: Raymond Lu
* Dec 19, 2002
*
* Modifications:
@ -1302,13 +1292,13 @@ done:
/*-------------------------------------------------------------------------
* Function: H5P_get_filter
* Function: H5P_get_filter
*
* Purpose: Internal component of H5Pget_filter & H5Pget_filter_id
* Purpose: Internal component of H5Pget_filter & H5Pget_filter_id
*
* Return: Non-negative on success/Negative on failure
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Programmer: Quincey Koziol
* Monday, October 23, 2006
*
*-------------------------------------------------------------------------
@ -1330,7 +1320,7 @@ H5P_get_filter(const H5Z_filter_info_t *filter, unsigned int *flags/*out*/,
/* Filter parameters */
if(cd_values) {
size_t i; /* Local index variable */
size_t i; /* Local index variable */
for(i = 0; i < filter->cd_nelmts && i < *cd_nelmts; i++)
cd_values[i] = filter->cd_values[i];
@ -1460,8 +1450,8 @@ done:
* property in the dataset access property list is
* decoded.
*
* Return: Success: Non-negative
* Failure: Negative
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Mohamad Chaarawi
* Monday, October 10, 2011
@ -1553,15 +1543,15 @@ H5P__ocrt_pipeline_enc(const void *value, void **_pp, size_t *size)
* property in the dataset access property list is
* decoded.
*
* Return: Success: Non-negative
* Failure: Negative
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Mohamad Chaarawi
* Monday, October 10, 2011
*
*-------------------------------------------------------------------------
*/
static herr_t
static herr_t
H5P__ocrt_pipeline_dec(const void **_pp, void *_value)
{
H5O_pline_t *pline = (H5O_pline_t *)_value; /* Property to set */
@ -1637,7 +1627,7 @@ H5P__ocrt_pipeline_dec(const void **_pp, void *_value)
filter.cd_values = (unsigned *)H5MM_xfree(filter.cd_values);
} /* end for */
done:
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5P__ocrt_pipeline_dec() */
@ -1830,32 +1820,32 @@ done:
#ifndef H5_NO_DEPRECATED_SYMBOLS
/*-------------------------------------------------------------------------
* Function: H5Pget_filter1
* Function: H5Pget_filter1
*
* Purpose: This is the query counterpart of H5Pset_filter() and returns
* information about a particular filter number in a permanent
* or transient pipeline depending on whether PLIST_ID is a
* dataset creation or transfer property list. On input,
* CD_NELMTS indicates the number of entries in the CD_VALUES
* array allocated by the caller while on exit it contains the
* number of values defined by the filter. The IDX
* Purpose: This is the query counterpart of H5Pset_filter() and returns
* information about a particular filter number in a permanent
* or transient pipeline depending on whether PLIST_ID is a
* dataset creation or transfer property list. On input,
* CD_NELMTS indicates the number of entries in the CD_VALUES
* array allocated by the caller while on exit it contains the
* number of values defined by the filter. The IDX
* should be a value between zero and N-1 as described for
* H5Pget_nfilters() and the function will return failure if the
* filter number is out of range.
*
* Return: Success: Filter identification number.
* Return: Success: Filter identification number.
*
* Failure: H5Z_FILTER_ERROR (Negative)
* Failure: H5Z_FILTER_ERROR (Negative)
*
* Programmer: Robb Matzke
* Programmer: Robb Matzke
* Wednesday, April 15, 1998
*
*-------------------------------------------------------------------------
*/
H5Z_filter_t
H5Pget_filter1(hid_t plist_id, unsigned idx, unsigned int *flags/*out*/,
size_t *cd_nelmts/*in_out*/, unsigned cd_values[]/*out*/,
size_t namelen, char name[]/*out*/)
size_t *cd_nelmts/*in_out*/, unsigned cd_values[]/*out*/,
size_t namelen, char name[]/*out*/)
{
H5O_pline_t pline; /* Filter pipeline */
const H5Z_filter_info_t *filter; /* Pointer to filter information */
@ -1915,22 +1905,22 @@ done:
/*-------------------------------------------------------------------------
* Function: H5Pget_filter_by_id1
* Function: H5Pget_filter_by_id1
*
* Purpose: This is an additional query counterpart of H5Pset_filter() and
* Purpose: This is an additional query counterpart of H5Pset_filter() and
* returns information about a particular filter in a permanent
* or transient pipeline depending on whether PLIST_ID is a
* dataset creation or transfer property list. On input,
* CD_NELMTS indicates the number of entries in the CD_VALUES
* array allocated by the caller while on exit it contains the
* number of values defined by the filter. The ID
* or transient pipeline depending on whether PLIST_ID is a
* dataset creation or transfer property list. On input,
* CD_NELMTS indicates the number of entries in the CD_VALUES
* array allocated by the caller while on exit it contains the
* number of values defined by the filter. The ID
* should be the filter ID to retrieve the parameters for. If the
* filter is not set for the property list, an error will be returned.
*
* Return: Success: Non-negative
* Failure: Negative
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Quincey Koziol
* Programmer: Quincey Koziol
* Friday, April 5, 2003
*
*-------------------------------------------------------------------------

913
src/H5Z.c
View File

File diff suppressed because it is too large Load Diff

12
test/CMakeTests.cmake
View File

@ -660,7 +660,7 @@ foreach (test ${H5TEST_TESTS})
WORKING_DIRECTORY ${HDF5_TEST_BINARY_DIR}/H5TEST
)
else ()
if (${test} STREQUAL "big" AND CYGWIN)
if ("${test}" STREQUAL "big" AND CYGWIN)
add_test (NAME H5TEST-${test}
COMMAND ${CMAKE_COMMAND} -E echo "SKIP ${test}"
)
@ -701,7 +701,7 @@ if (BUILD_SHARED_LIBS)
)
foreach (test ${H5TEST_TESTS})
if (${test} STREQUAL "big" AND CYGWIN)
if ("${test}" STREQUAL "big" AND CYGWIN)
add_test (NAME H5TEST-shared-${test}
COMMAND ${CMAKE_COMMAND} -E echo "SKIP ${test}-shared"
)
@ -998,8 +998,10 @@ endif ()
##############################################################################
if (WIN32)
set (CMAKE_SEP "\;")
set (BIN_REL_PATH "../../")
else ()
set (CMAKE_SEP ":")
set (BIN_REL_PATH "../")
endif ()
add_test (NAME H5PLUGIN-plugin COMMAND $<TARGET_FILE:plugin>)
@ -1086,8 +1088,8 @@ if (HDF5_TEST_VFD)
# Windows only macro
macro (CHECK_VFD_TEST vfdtest vfdname resultcode)
if (${vfdtest} STREQUAL "flush1" OR ${vfdtest} STREQUAL "flush2")
if (${vfdname} STREQUAL "multi" OR ${vfdname} STREQUAL "split")
if ("${vfdtest}" STREQUAL "flush1" OR "${vfdtest}" STREQUAL "flush2")
if ("${vfdname}" STREQUAL "multi" OR "${vfdname}" STREQUAL "split")
if (NOT BUILD_SHARED_LIBS AND NOT CMAKE_BUILD_TYPE MATCHES Debug)
add_test (NAME VFD-${vfdname}-${vfdtest}
COMMAND "${CMAKE_COMMAND}"
@ -1176,7 +1178,7 @@ if (HDF5_TEST_VFD)
ENVIRONMENT "srcdir=${HDF5_TEST_BINARY_DIR}/${vfdname};HDF5TestExpress=${HDF_TEST_EXPRESS}"
WORKING_DIRECTORY ${HDF5_TEST_BINARY_DIR}/${vfdname}
)
if (BUILD_SHARED_LIBS AND NOT ${vfdtest} STREQUAL "cache")
if (BUILD_SHARED_LIBS AND NOT "${vfdtest}" STREQUAL "cache")
add_test (NAME VFD-${vfdname}-${vfdtest}-shared
COMMAND "${CMAKE_COMMAND}"
-D "TEST_PROGRAM=$<TARGET_FILE:${vfdtest}-shared>"

2737
test/dsets.c
View File

File diff suppressed because it is too large Load Diff

4
tools/lib/h5diff_attr.c
View File

@ -461,8 +461,8 @@ hsize_t diff_attr(hid_t loc1_id,
for(j = 0; j < rank1; j++)
nelmts1 *= dims1[j];
buf1 = (void *)HDmalloc((size_t)(nelmts1 * msize1));
buf2 = (void *)HDmalloc((size_t)(nelmts1 * msize2));
buf1 = (void *)HDcalloc((size_t)(nelmts1), msize1);
buf2 = (void *)HDcalloc((size_t)(nelmts1), msize2);
if(buf1 == NULL || buf2 == NULL) {
parallel_print("cannot read into memory\n");
goto error;

105
tools/lib/h5diff_dset.c
View File

@ -170,6 +170,7 @@ hsize_t diff_datasetid( hid_t did1,
const char *obj2_name,
diff_opt_t *options)
{
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
hid_t sid1=-1;
hid_t sid2=-1;
hid_t f_tid1=-1;
@ -211,30 +212,31 @@ hsize_t diff_datasetid( hid_t did1,
int i;
unsigned int vl_data = 0; /*contains VL datatypes */
options->err_stat = 1;
h5difftrace("diff_datasetid start\n");
/* Get the dataspace handle */
if((sid1 = H5Dget_space(did1)) < 0)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
/* Get rank */
if((rank1 = H5Sget_simple_extent_ndims(sid1)) < 0)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
/* Get the dataspace handle */
if((sid2 = H5Dget_space(did2)) < 0 )
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
/* Get rank */
if((rank2 = H5Sget_simple_extent_ndims(sid2)) < 0)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
/* Get dimensions */
if(H5Sget_simple_extent_dims(sid1, dims1, maxdim1) < 0)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
/* Get dimensions */
if(H5Sget_simple_extent_dims(sid2, dims2, maxdim2) < 0)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
h5diffdebug3("rank: %ld - %ld\n", rank1, rank2);
/*-------------------------------------------------------------------------
@ -244,25 +246,25 @@ hsize_t diff_datasetid( hid_t did1,
/* Get the data type */
if((f_tid1 = H5Dget_type(did1)) < 0)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed");
/* Get the data type */
if((f_tid2 = H5Dget_type(did2)) < 0)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed");
/*-------------------------------------------------------------------------
* get the storage layout type
*-------------------------------------------------------------------------
*/
if((dcpl1 = H5Dget_create_plist(did1)) < 0)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed");
if((dcpl2 = H5Dget_create_plist(did2)) < 0)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed");
if((stl1 = H5Pget_layout(dcpl1)) < 0)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_layout failed");
if((stl2 = H5Pget_layout(dcpl2)) < 0)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_layout failed");
/*-------------------------------------------------------------------------
* check for empty datasets
@ -303,10 +305,10 @@ hsize_t diff_datasetid( hid_t did1,
*/
h5difftrace("check for memory type and sizes\n");
if((m_tid1 = H5Tget_native_type(f_tid1, H5T_DIR_DEFAULT)) < 0)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_native_type failed");
if((m_tid2 = H5Tget_native_type(f_tid2, H5T_DIR_DEFAULT)) < 0)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_native_type failed");
m_size1 = H5Tget_size(m_tid1);
m_size2 = H5Tget_size(m_tid2);
@ -368,14 +370,14 @@ hsize_t diff_datasetid( hid_t did1,
if (FAIL == match_up_memsize (f_tid1, f_tid2,
&m_tid1, &m_tid2,
&m_size1, &m_size2))
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "match_up_memsize failed");
h5diffdebug3("m_size: %ld - %ld\n", m_size1, m_size2);
dadims = dims1;
dam_size = m_size1;
dam_tid = m_tid1;
danelmts = nelmts1;
need = (size_t)(nelmts1 * m_size1); /* bytes needed */
}
}
else {
h5diffdebug3("Array dims: %d - %d\n", dims1[0], dims2[0]);
/* Compare the smallest array, but create the largest buffer */
@ -413,10 +415,10 @@ hsize_t diff_datasetid( hid_t did1,
if(buf1 != NULL && buf2 != NULL) {
h5difftrace("buf1 != NULL && buf2 != NULL\n");
if(H5Dread(did1, m_tid1, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf1) < 0)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
h5difftrace("H5Dread did2\n");
if(H5Dread(did2, m_tid2, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf2) < 0)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
/* array diff */
nfound = diff_array(buf1, buf2, danelmts, (hsize_t)0, rank1, dadims,
@ -427,6 +429,14 @@ hsize_t diff_datasetid( hid_t did1,
H5Dvlen_reclaim(m_tid1, sid1, H5P_DEFAULT, buf1);
H5Dvlen_reclaim(m_tid2, sid2, H5P_DEFAULT, buf2);
} /* end if */
if(buf1 != NULL) {
HDfree(buf1);
buf1 = NULL;
}
if(buf2 != NULL) {
HDfree(buf2);
buf2 = NULL;
}
} /* end if */
else { /* possibly not enough memory, read/compare by hyperslabs */
size_t p_type_nbytes = dam_size; /*size of memory type */
@ -468,9 +478,9 @@ hsize_t diff_datasetid( hid_t did1,
* E.g., sm_space.
*/
if((sm_buf1 = HDmalloc((size_t)sm_nbytes)) == NULL)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
if((sm_buf2 = HDmalloc((size_t)sm_nbytes)) == NULL)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
sm_nelmts = sm_nbytes / p_type_nbytes;
sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
@ -487,19 +497,19 @@ hsize_t diff_datasetid( hid_t did1,
hs_nelmts *= hs_size[i];
} /* end for */
if(H5Sselect_hyperslab(sid1, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) < 0)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
if(H5Sselect_hyperslab(sid2, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) < 0)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
if(H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL) < 0)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
} /* end if */
else
hs_nelmts = 1;
if(H5Dread(did1, m_tid1, sm_space, sid1, H5P_DEFAULT, sm_buf1) < 0)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
if(H5Dread(did2, m_tid2, sm_space, sid2, H5P_DEFAULT, sm_buf2) < 0)
goto error;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
/* get array differences. in the case of hyperslab read, increment the number of differences
found in each hyperslab and pass the position at the beginning for printing */
@ -521,6 +531,14 @@ hsize_t diff_datasetid( hid_t did1,
carry = 0;
} /* i */
} /* elmtno */
if(sm_buf1 != NULL) {
HDfree(sm_buf1);
sm_buf1 = NULL;
}
if(sm_buf2 != NULL) {
HDfree(sm_buf2);
sm_buf2 = NULL;
}
H5Sclose(sm_space);
} /* hyperslab read */
@ -531,40 +549,11 @@ hsize_t diff_datasetid( hid_t did1,
* close
*-------------------------------------------------------------------------
*/
h5difftrace("compare attributes?\n");
h5difftrace("reclaim any VL memory\n");
/* free */
if(buf1 != NULL) {
HDfree(buf1);
buf1 = NULL;
} /* end if */
if(buf2 != NULL) {
HDfree(buf2);
buf2 = NULL;
} /* end if */
if(sm_buf1 != NULL) {
HDfree(sm_buf1);
sm_buf1 = NULL;
} /* end if */
if(sm_buf2 != NULL) {
HDfree(sm_buf2);
sm_buf2 = NULL;
} /* end if */
done:
H5E_BEGIN_TRY {
H5Sclose(sid1);
H5Sclose(sid2);
H5Tclose(f_tid1);
H5Tclose(f_tid2);
H5Tclose(m_tid1);
H5Tclose(m_tid2);
} H5E_END_TRY;
h5difftrace("diff_datasetid finish\n");
return nfound;
error:
options->err_stat=1;
options->err_stat = ret_value;
/* free */
if(buf1 != NULL) {
@ -606,7 +595,7 @@ error:
H5Tclose(m_tid2);
/* enable error reporting */
} H5E_END_TRY;
h5difftrace("diff_datasetid errored\n");
h5diffdebug3("diff_datasetid return:%d with nfound:%d\n", ret_value, nfound);
return nfound;
}

192
tools/lib/h5tools_filters.c
View File

@ -20,9 +20,9 @@
*/
static void print_warning(const char *dname, const char *fname)
{
fprintf(stderr,
"warning: dataset <%s> cannot be read, %s filter is not available\n",
dname, fname);
fprintf(stderr,
"warning: dataset <%s> cannot be read, %s filter is not available\n",
dname, fname);
}
/*-------------------------------------------------------------------------
@ -34,100 +34,97 @@ static void print_warning(const char *dname, const char *fname)
* 2) the internal filters might be turned off
*
* Return: 1, can read, 0, cannot, -1 error
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: March 1, 2004
*
*-------------------------------------------------------------------------
*/
int h5tools_canreadf(const char* name, /* object name, serves also as boolean print */
hid_t dcpl_id) /* dataset creation property list */
{
int ret_value = 1; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
int nfilters; /* number of filters */
H5Z_filter_t filtn; /* filter identification number */
int i; /* index */
int udfilter_avail; /* index */
int nfilters; /* number of filters */
H5Z_filter_t filtn; /* filter identification number */
int i; /* index */
int udfilter_avail; /* index */
/* get information about filters */
if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_nfilters failed");
/* get information about filters */
if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
return -1;
/* if we do not have filters, we can read the dataset safely */
if (!nfilters)
HGOTO_DONE(1);
/* if we do not have filters, we can read the dataset safely */
if (!nfilters)
return 1;
/* check availability of filters */
for (i = 0; i < nfilters; i++) {
if ((filtn = H5Pget_filter2(dcpl_id, (unsigned) i, 0, 0, 0, (size_t) 0, 0, NULL)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_filter2 failed");
/* check availability of filters */
for (i = 0; i < nfilters; i++) {
if ((filtn = H5Pget_filter2(dcpl_id, (unsigned) i, 0, 0, 0, (size_t) 0, 0, NULL)) < 0)
return -1;
switch (filtn) {
/*-------------------------------------------------------------------------
* user defined filter
*-------------------------------------------------------------------------
*/
default:
if ((udfilter_avail = H5Zfilter_avail(filtn)) < 0) {
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Zfilter_avail failed");
}
else if (!udfilter_avail) {
if (name)
print_warning(name, "user defined");
ret_value = 0;
}
break;
switch (filtn) {
/*-------------------------------------------------------------------------
* user defined filter
*-------------------------------------------------------------------------
*/
default:
if ((udfilter_avail = H5Zfilter_avail(filtn)) < 0)
return -1;
else if (udfilter_avail == 0) {
if (name)
print_warning(name, "user defined");
return 0;
}
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_DEFLATE 1 , deflation like gzip
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_DEFLATE:
/*-------------------------------------------------------------------------
* H5Z_FILTER_DEFLATE 1 , deflation like gzip
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_DEFLATE:
#ifndef H5_HAVE_FILTER_DEFLATE
if (name)
print_warning(name,"deflate");
return 0;
if (name)
print_warning(name,"deflate");
ret_value = 0;
#endif
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_SZIP 4 , szip compression
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_SZIP:
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_SZIP 4 , szip compression
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_SZIP:
#ifndef H5_HAVE_FILTER_SZIP
if (name)
print_warning(name,"SZIP");
return 0;
if (name)
print_warning(name,"SZIP");
ret_value = 0;
#endif
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_SHUFFLE 2 , shuffle the data
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_SHUFFLE:
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_FLETCHER32 3 , fletcher32 checksum of EDC
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_FLETCHER32:
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_NBIT
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_NBIT:
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_SCALEOFFSET
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_SCALEOFFSET:
break;
}/*switch*/
}/*for*/
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_SHUFFLE 2 , shuffle the data
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_SHUFFLE:
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_FLETCHER32 3 , fletcher32 checksum of EDC
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_FLETCHER32:
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_NBIT
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_NBIT:
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_SCALEOFFSET
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_SCALEOFFSET:
break;
}/*switch*/
}/*for*/
return 1;
done:
return ret_value;
}
/*-------------------------------------------------------------------------
@ -138,31 +135,26 @@ int h5tools_canreadf(const char* name, /* object name, serves also as boolean pr
* except SZIP, which may be configured decoder-only.
*
* Return: 1, can write, 0, cannot, -1 error
*
* Programmer:
*
* Date: October 5, 2004
*
*-------------------------------------------------------------------------
*/
H5_ATTR_CONST int
h5tools_can_encode(H5Z_filter_t filtn) {
switch (filtn) {
/* user defined filter */
default:
/* user defined filter */
default:
return 0;
case H5Z_FILTER_DEFLATE:
case H5Z_FILTER_DEFLATE:
#ifndef H5_HAVE_FILTER_DEFLATE
return 0;
#endif
break;
case H5Z_FILTER_SZIP:
case H5Z_FILTER_SZIP:
#ifndef H5_HAVE_FILTER_SZIP
return 0;
#else
{
{
unsigned int filter_config_flags;
if (H5Zget_filter_info(filtn, &filter_config_flags) < 0)
@ -171,36 +163,36 @@ h5tools_can_encode(H5Z_filter_t filtn) {
& (H5Z_FILTER_CONFIG_ENCODE_ENABLED | H5Z_FILTER_CONFIG_DECODE_ENABLED)) == 0) {
/* filter present but neither encode nor decode is supported (???) */
return -1;
}
}
else if ((filter_config_flags
& (H5Z_FILTER_CONFIG_ENCODE_ENABLED | H5Z_FILTER_CONFIG_DECODE_ENABLED)) == H5Z_FILTER_CONFIG_DECODE_ENABLED) {
/* decoder only: read but not write */
return 0;
}
}
else if ((filter_config_flags
& (H5Z_FILTER_CONFIG_ENCODE_ENABLED | H5Z_FILTER_CONFIG_DECODE_ENABLED)) == H5Z_FILTER_CONFIG_ENCODE_ENABLED) {
/* encoder only: write but not read (???) */
return -1;
}
}
else if ((filter_config_flags
& (H5Z_FILTER_CONFIG_ENCODE_ENABLED | H5Z_FILTER_CONFIG_DECODE_ENABLED))
== (H5Z_FILTER_CONFIG_ENCODE_ENABLED | H5Z_FILTER_CONFIG_DECODE_ENABLED)) {
return 1;
}
}
}
#endif
break;
case H5Z_FILTER_SHUFFLE:
case H5Z_FILTER_SHUFFLE:
break;
case H5Z_FILTER_FLETCHER32:
case H5Z_FILTER_FLETCHER32:
break;
case H5Z_FILTER_NBIT:
case H5Z_FILTER_NBIT:
break;
case H5Z_FILTER_SCALEOFFSET:
case H5Z_FILTER_SCALEOFFSET:
break;
}/*switch*/

197
tools/src/h5repack/h5repack.c
View File

@ -284,8 +284,7 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
/* Set return value */
ret_value = dt_ret->id_out;
/* Increment the ref count on id_out, because the calling function will try
* to close it */
/* Increment the ref count on id_out, because the calling function will try to close it */
if(H5Iinc_ref(ret_value) < 0)
ret_value = -1;
@ -482,24 +481,8 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
if (options->verbose)
printf(FORMAT_OBJ_ATTR, "attr", name);
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
if (H5Tclose(ftype_id) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
if (H5Tclose(wtype_id) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
if (H5Sclose(space_id) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
if (H5Aclose(attr_id) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed");
} /* u */
return 0;
done:
H5E_BEGIN_TRY {
if (buf) {
@ -541,8 +524,8 @@ static int check_options(pack_opt_t *options) {
*-------------------------------------------------------------------------
*/
if (options->verbose && have_request(options) /* only print if requested */) {
printf("Objects to modify layout are...\n");
if (options->all_layout == 1) {
printf("All objects to modify layout are...\n");
switch (options->layout_g) {
case H5D_COMPACT:
strcpy(slayout, "compact");
@ -563,14 +546,17 @@ static int check_options(pack_opt_t *options) {
strcpy(slayout, "invalid layout\n");
HGOTO_DONE(FAIL);
}
printf(" Apply %s layout to all\n", slayout);
printf(" Apply %s layout to all", slayout);
if (H5D_CHUNKED == options->layout_g) {
printf("with dimension [");
printf("with dimension [ ");
for (j = 0; j < options->chunk_g.rank; j++)
printf("%d ", (int) options->chunk_g.chunk_lengths[j]);
printf("]\n");
printf("]");
}
printf("\n");
}
else
printf("No all objects to modify layout\n");
}/* verbose */
for (i = 0; i < options->op_tbl->nelems; i++) {
@ -601,10 +587,14 @@ static int check_options(pack_opt_t *options) {
*/
if (options->verbose && have_request(options) /* only print if requested */) {
printf("Objects to apply filter are...\n");
if (options->all_filter == 1) {
printf("All objects to apply filter are...\n");
for (k = 0; k < options->n_filter_g; k++) {
H5Z_filter_t filtn = options->filter_g[k].filtn;
if (filtn < 0) {
printf(" Unknown\n");
continue;
}
switch (filtn) {
case H5Z_FILTER_NONE:
printf(" Uncompress all\n");
@ -623,6 +613,8 @@ static int check_options(pack_opt_t *options) {
} /* k */
};
}
else
printf("No all objects to apply filter\n");
} /* verbose */
for (i = 0; i < options->op_tbl->nelems; i++) {
@ -631,7 +623,12 @@ static int check_options(pack_opt_t *options) {
for (j = 0; j < pack.nfilters; j++) {
if (options->verbose) {
printf(" <%s> with %s filter\n", name, get_sfilter(pack.filter[j].filtn));
if(pack.filter[j].filtn >= 0) {
if(pack.filter[j].filtn > H5Z_FILTER_SCALEOFFSET)
printf(" <%s> with %s filter %d\n", name, get_sfilter(pack.filter[j].filtn), pack.filter[j].filtn);
else
printf(" <%s> with %s filter\n", name, get_sfilter(pack.filter[j].filtn));
}
}
has_cp = 1;
} /* j */
@ -661,8 +658,7 @@ static int check_options(pack_opt_t *options) {
*/
if (options->ublock_filename != NULL && options->ublock_size == 0) {
if (options->verbose) {
printf("Warning: user block size missing for file %s. Assigning a default size of 1024...\n",
options->ublock_filename);
printf("Warning: user block size missing for file %s. Assigning a default size of 1024...\n", options->ublock_filename);
options->ublock_size = 1024;
}
}
@ -692,27 +688,29 @@ done:
*-------------------------------------------------------------------------
*/
static int check_objects(const char* fname, pack_opt_t *options) {
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
hid_t fid;
hid_t did;
hid_t sid;
unsigned int i;
unsigned int uf;
trav_table_t *travt = NULL;
/* nothing to do */
if (options->op_tbl->nelems == 0)
return 0;
HGOTO_DONE(0);
/*-------------------------------------------------------------------------
* open the file
*-------------------------------------------------------------------------
*/
if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0)) < 0) {
printf("<%s>: %s\n", fname, H5FOPENERROR);
return -1;
}
* open the file
*-------------------------------------------------------------------------
*/
if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_fopen failed <%s>: %s", fname, H5FOPENERROR);
/*-------------------------------------------------------------------------
* get the list of objects in the file
*-------------------------------------------------------------------------
*/
* get the list of objects in the file
*-------------------------------------------------------------------------
*/
/* Initialize indexing options */
h5trav_set_index(sort_by, sort_order);
@ -721,15 +719,15 @@ static int check_objects(const char* fname, pack_opt_t *options) {
/* get the list of objects in the file */
if (h5trav_gettable(fid, travt) < 0)
goto done;
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed");
/*-------------------------------------------------------------------------
* compare with user supplied list
*-------------------------------------------------------------------------
*/
* compare with user supplied list
*-------------------------------------------------------------------------
*/
if (options->verbose)
printf("Opening file <%s>. Searching for objects to modify...\n", fname);
printf("Opening file. Searching %d objects to modify ...\n", travt->nobjs);
for (i = 0; i < options->op_tbl->nelems; i++) {
char* name = options->op_tbl->objs[i].path;
@ -737,73 +735,70 @@ static int check_objects(const char* fname, pack_opt_t *options) {
printf(" <%s>", name);
/* the input object names are present in the file and are valid */
if (h5trav_getindext(name, travt) < 0) {
error_msg("%s Could not find <%s> in file <%s>. Exiting...\n",
if (h5trav_getindext(name, travt) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "%s Could not find <%s> in file <%s>. Exiting...\n",
(options->verbose ? "\n" : ""), name, fname);
goto done;
}
if (options->verbose)
printf("...Found\n");
/* check for extra filter conditions */
switch (options->op_tbl->objs[i].filter->filtn) {
/* chunk size must be smaller than pixels per block */
case H5Z_FILTER_SZIP:
{
int j;
hsize_t csize = 1;
unsigned ppb = options->op_tbl->objs[i].filter->cd_values[0];
hsize_t dims[H5S_MAX_RANK];
int rank;
hid_t did;
hid_t sid;
for (uf = 0; uf < options->op_tbl->objs[i].nfilters; uf++) {
if (options->op_tbl->objs[i].filter[uf].filtn < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid filter");
/* check for extra filter conditions */
switch (options->op_tbl->objs[i].filter[uf].filtn) {
/* chunk size must be smaller than pixels per block */
case H5Z_FILTER_SZIP:
{
int j;
hsize_t csize = 1;
unsigned ppb = options->op_tbl->objs[i].filter[uf].cd_values[0];
hsize_t dims[H5S_MAX_RANK];
int rank;
if (options->op_tbl->objs[i].chunk.rank > 0) {
rank = options->op_tbl->objs[i].chunk.rank;
for (j = 0; j < rank; j++)
csize *= options->op_tbl->objs[i].chunk.chunk_lengths[j];
}
else {
if ((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
goto done;
if ((sid = H5Dget_space(did)) < 0)
goto done;
if ((rank = H5Sget_simple_extent_ndims(sid)) < 0)
goto done;
HDmemset(dims, 0, sizeof dims);
if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
goto done;
for (j = 0; j < rank; j++)
csize *= dims[j];
if (H5Sclose(sid) < 0)
goto done;
if (H5Dclose(did) < 0)
goto done;
}
if (options->op_tbl->objs[i].chunk.rank > 0) {
rank = options->op_tbl->objs[i].chunk.rank;
for (j = 0; j < rank; j++)
csize *= options->op_tbl->objs[i].chunk.chunk_lengths[j];
}
else {
if ((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
if ((sid = H5Dget_space(did)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
if ((rank = H5Sget_simple_extent_ndims(sid)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
HDmemset(dims, 0, sizeof dims);
if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
for (j = 0; j < rank; j++)
csize *= dims[j];
if (H5Sclose(sid) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
if (H5Dclose(did) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
}
if (csize < ppb) {
printf(" <warning: SZIP settins, chunk size is smaller than pixels per block>\n");
goto done;
if (csize < ppb) {
printf(" <warning: SZIP settings, chunk size is smaller than pixels per block>\n");
HGOTO_DONE(0);
}
}
break;
default:
break;
}
break;
default:
break;
}
} /* i */
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
H5Fclose(fid);
trav_table_free(travt);
return 0;
} /* for uf */
} /* for i */
done:
H5Fclose(fid);
trav_table_free(travt);
return -1;
H5E_BEGIN_TRY {
H5Fclose(fid);
H5Sclose(sid);
H5Dclose(did);
} H5E_END_TRY;
if (travt)
trav_table_free(travt);
return ret_value;
}
/*-------------------------------------------------------------------------
@ -833,7 +828,9 @@ static int have_request(pack_opt_t *options) {
*/
static const char* get_sfilter(H5Z_filter_t filtn) {
if (filtn == H5Z_FILTER_NONE)
if (filtn < 0)
return NULL;
else if (filtn == H5Z_FILTER_NONE)
return "NONE";
else if (filtn == H5Z_FILTER_DEFLATE)
return "GZIP";

106
tools/src/h5repack/h5repack.h
View File

@ -29,7 +29,7 @@
#define MAX_COMPACT_DSIZE 64512 /* max data size for compact layout. -1k for header size */
/* File space default information */
#define FS_PAGESIZE_DEF 4096
#define FS_PAGESIZE_DEF 4096
#define FS_STRATEGY_DEF H5F_FSPACE_STRATEGY_FSM_AGGR
#define FS_PERSIST_DEF FALSE
#define FS_THRESHOLD_DEF 1
@ -42,7 +42,7 @@
/* a list of names */
typedef struct {
char obj[MAX_NC_NAME];
char obj[MAX_NC_NAME];
} obj_list_t;
/*
@ -60,16 +60,16 @@ typedef struct {
#define CD_VALUES 20
typedef struct {
H5Z_filter_t filtn; /* filter identification number */
unsigned filt_flag; /* filter definition flag */
unsigned cd_values[CD_VALUES]; /* filter client data values */
size_t cd_nelmts; /* filter client number of values */
H5Z_filter_t filtn; /* filter identification number */
unsigned filt_flag; /* filter definition flag */
unsigned cd_values[CD_VALUES]; /* filter client data values */
size_t cd_nelmts; /* filter client number of values */
} filter_info_t;
/* chunk lengths along each dimension and rank */
typedef struct {
hsize_t chunk_lengths[MAX_VAR_DIMS];
int rank;
hsize_t chunk_lengths[MAX_VAR_DIMS];
int rank;
} chunk_info_t;
/* we currently define a maximum value for the filters array,
@ -78,19 +78,19 @@ typedef struct {
/* information for one object, contains PATH, CHUNK info and FILTER info */
typedef struct {
char path[MAX_NC_NAME]; /* name of object */
filter_info_t filter[H5_REPACK_MAX_NFILTERS]; /* filter array */
int nfilters; /* current number of filters */
H5D_layout_t layout; /* layout information */
chunk_info_t chunk; /* chunk information */
hid_t refobj_id; /* object ID, references */
char path[MAX_NC_NAME]; /* name of object */
filter_info_t filter[H5_REPACK_MAX_NFILTERS]; /* filter array */
int nfilters; /* current number of filters */
H5D_layout_t layout; /* layout information */
chunk_info_t chunk; /* chunk information */
hid_t refobj_id; /* object ID, references */
} pack_info_t;
/* store a table of all objects */
typedef struct {
unsigned int size;
unsigned int nelems;
pack_info_t *objs;
unsigned int size;
unsigned int nelems;
pack_info_t *objs;
} pack_opttbl_t;
@ -101,30 +101,30 @@ typedef struct {
/* all the above, ready to go to the hrepack call */
typedef struct {
pack_opttbl_t *op_tbl; /*table with all -c and -f options */
int all_layout; /*apply the layout to all objects */
int all_filter; /*apply the filter to all objects */
filter_info_t filter_g[H5_REPACK_MAX_NFILTERS]; /*global filter array for the ALL case */
int n_filter_g; /*number of global filters */
chunk_info_t chunk_g; /*global chunk INFO for the ALL case */
H5D_layout_t layout_g; /*global layout information for the ALL case */
int verbose; /*verbose mode */
hsize_t min_comp; /*minimum size to compress, in bytes */
int use_native; /*use a native type in write */
hbool_t latest; /*pack file with the latest file format */
int grp_compact; /* Set the maximum number of links to store as header messages in the group */
int grp_indexed; /* Set the minimum number of links to store in the indexed format */
int msg_size[8]; /* Minimum size of shared messages: dataspace,
datatype, fill value, filter pipleline, attribute */
const char *ublock_filename; /* user block file name */
hsize_t ublock_size; /* user block size */
hsize_t meta_block_size; /* metadata aggregation block size (for H5Pset_meta_block_size) */
hsize_t threshold; /* alignment threshold for H5Pset_alignment */
hsize_t alignment; /* alignment for H5Pset_alignment */
H5F_fspace_strategy_t fs_strategy; /* File space handling strategy */
int fs_persist; /* Free space section threshold */
long fs_threshold; /* Free space section threshold */
long long fs_pagesize; /* File space page size */
pack_opttbl_t *op_tbl; /*table with all -c and -f options */
int all_layout; /*apply the layout to all objects */
int all_filter; /*apply the filter to all objects */
filter_info_t filter_g[H5_REPACK_MAX_NFILTERS]; /*global filter array for the ALL case */
int n_filter_g; /*number of global filters */
chunk_info_t chunk_g; /*global chunk INFO for the ALL case */
H5D_layout_t layout_g; /*global layout information for the ALL case */
int verbose; /*verbose mode */
hsize_t min_comp; /*minimum size to compress, in bytes */
int use_native; /*use a native type in write */
hbool_t latest; /*pack file with the latest file format */
int grp_compact; /* Set the maximum number of links to store as header messages in the group */
int grp_indexed; /* Set the minimum number of links to store in the indexed format */
int msg_size[8]; /* Minimum size of shared messages: dataspace,
datatype, fill value, filter pipleline, attribute */
const char *ublock_filename; /* user block file name */
hsize_t ublock_size; /* user block size */
hsize_t meta_block_size; /* metadata aggregation block size (for H5Pset_meta_block_size) */
hsize_t threshold; /* alignment threshold for H5Pset_alignment */
hsize_t alignment; /* alignment for H5Pset_alignment */
H5F_fspace_strategy_t fs_strategy; /* File space handling strategy */
int fs_persist; /* Free space section threshold */
long fs_threshold; /* Free space section threshold */
long long fs_pagesize; /* File space page size */
} pack_opt_t;
@ -214,18 +214,18 @@ int apply_filters(const char* name, /* object name from traverse list */
* options table
*-------------------------------------------------------------------------
*/
int options_table_init( pack_opttbl_t **tbl );
int options_table_free( pack_opttbl_t *table );
int options_add_layout( obj_list_t *obj_list,
unsigned n_objs,
pack_info_t *pack,
pack_opttbl_t *table );
int options_add_filter ( obj_list_t *obj_list,
unsigned n_objs,
filter_info_t filt,
pack_opttbl_t *table );
pack_info_t* options_get_object( const char *path,
pack_opttbl_t *table);
int options_table_init(pack_opttbl_t **tbl);
int options_table_free(pack_opttbl_t *table);
int options_add_layout(obj_list_t *obj_list,
unsigned n_objs,
pack_info_t *pack,
pack_opttbl_t *table);
int options_add_filter(obj_list_t *obj_list,
unsigned n_objs,
filter_info_t filt,
pack_opttbl_t *table);
pack_info_t* options_get_object(const char *path,
pack_opttbl_t *table);
/*-------------------------------------------------------------------------
* parse functions

185
tools/src/h5repack/h5repack_copy.c
View File

@ -109,9 +109,8 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
* open input file
*-------------------------------------------------------------------------
*/
if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t) 0)) < 0) {
if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t) 0)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_fopen failed <%s>: %s", fnamein, H5FOPENERROR);
}
/* get user block size and file space strategy/persist/threshold */
{
@ -119,23 +118,20 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
hid_t grp_in = -1; /* group ID */
hid_t gcpl_in = -1; /* group creation property list */
if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) {
if ((fcpl_in = H5Fget_create_plist(fidin)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fget_create_plist failed to retrieve file creation property list");
}
if (H5Pget_userblock(fcpl_in, &ub_size) < 0) {
if (H5Pget_userblock(fcpl_in, &ub_size) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_userblock failed to retrieve userblock size");
}
/* If the -S option is not set, get "strategy" from the input file */
if(H5Pget_file_space_strategy(fcpl_in, &in_strategy, &in_persist, &in_threshold) < 0) {
if(H5Pget_file_space_strategy(fcpl_in, &in_strategy, &in_persist, &in_threshold) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space_strategy failed to retrieve file space strategy");
}
/* If the -G option is not set, get "pagesize" from the input file */
if(H5Pget_file_space_page_size(fcpl_in, &in_pagesize) < 0) {
if(H5Pget_file_space_page_size(fcpl_in, &in_pagesize) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space_page_size failed to retrieve file space threshold");
}
/* open root group */
if ((grp_in = H5Gopen2(fidin, "/", H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
@ -148,23 +144,19 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed");
if (H5Pclose(fcpl_in) < 0) {
if (H5Pclose(fcpl_in) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed to close property list");
}
}
/* Check if we need to create a non-default file creation property list */
if (options->latest || ub_size > 0) {
/* Create file creation property list */
if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create a file creation property list");
}
if (ub_size > 0) {
if (H5Pset_userblock(fcpl, ub_size) < 0) {
if (ub_size > 0)
if (H5Pset_userblock(fcpl, ub_size) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_userblock failed to set non-default userblock size");
}
}
if (options->latest) {
unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5];
@ -172,9 +164,8 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
/* Adjust group creation parameters for root group */
/* (So that it is created in "dense storage" form) */
if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact,
(unsigned) options->grp_indexed) < 0) {
(unsigned) options->grp_indexed) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_phase_change failed to adjust group creation parameters for root group");
}
for (i = 0; i < 5; i++) {
if (options->msg_size[i] > 0) {
@ -209,26 +200,21 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
} /* end for */
if (nindex > 0) {
if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) {
if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_shared_mesg_nindexes failed to set the number of shared object header message indexes");
}
/* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */
for (i = 0; i < (nindex - 1); i++) {
if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i]) < 0) {
for (i = 0; i < (nindex - 1); i++)
if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i]) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_shared_mesg_index failed to configure the specified shared object header message index");
} /* end if */
} /* end for */
} /* if (nindex>0) */
/* Create file access property list */
if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create file access property list");
} /* end if */
if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) {
if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_libver_bounds failed to set property for using latest version of the format");
} /* end if */
} /* end if */
} /* end if */
#if defined (H5REPACK_DEBUG_USER_BLOCK)
@ -241,17 +227,14 @@ print_user_block(fnamein, fidin);
*/
if (options->ublock_size > 0) {
/* either use the FCPL already created or create a new one */
if (fcpl == H5P_DEFAULT) {
if (fcpl == H5P_DEFAULT)
/* create a file creation property list */
if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create a file creation property list");
}
}
/* set user block size */
if (H5Pset_userblock(fcpl, options->ublock_size) < 0) {
if (H5Pset_userblock(fcpl, options->ublock_size) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_userblock failed to set userblock size");
}
}
/*-------------------------------------------------------------------------
@ -260,16 +243,13 @@ print_user_block(fnamein, fidin);
*/
if (options->alignment > 0) {
/* either use the FAPL already created or create a new one */
if (fapl == H5P_DEFAULT) {
if (fapl == H5P_DEFAULT)
/* create a file access property list */
if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create file access property list");
}
}
if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) {
if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_alignment failed to set alignment");
}
}
/*-------------------------------------------------------------------------
@ -278,16 +258,13 @@ print_user_block(fnamein, fidin);
*/
if (options->meta_block_size > 0) {
/* either use the FAPL already created or create a new one */
if (fapl == H5P_DEFAULT) {
if (fapl == H5P_DEFAULT)
/* create a file access property list */
if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create file access property list");
}
}
if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) {
if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_meta_block_size failed to set metadata block size");
}
}
/*-------------------------------------------------------------------------
@ -296,12 +273,10 @@ print_user_block(fnamein, fidin);
*/
/* either use the FCPL already created or create a new one */
if (fcpl == H5P_DEFAULT) {
if (fcpl == H5P_DEFAULT)
/* create a file creation property list */
if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create a file creation property list");
}
}
if(H5Pset_link_creation_order(fcpl, crt_order_flags ) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_creation_order failed");
@ -328,9 +303,8 @@ print_user_block(fnamein, fidin);
set_threshold = (hsize_t)options->fs_threshold;
/* Set file space information as specified */
if(H5Pset_file_space_strategy(fcpl, set_strategy, set_persist, set_threshold) < 0) {
if(H5Pset_file_space_strategy(fcpl, set_strategy, set_persist, set_threshold) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_file_space_strategy failed to set file space strategy");
}
if(options->fs_pagesize == -1) /* A "0" file space page size is specified by user */
set_pagesize = (hsize_t)0;
@ -338,30 +312,26 @@ print_user_block(fnamein, fidin);
set_pagesize = (hsize_t)options->fs_pagesize;
if(set_pagesize != FS_PAGESIZE_DEF) /* Set non-default file space page size as specified */
if(H5Pset_file_space_page_size(fcpl, set_pagesize) < 0) {
if(H5Pset_file_space_page_size(fcpl, set_pagesize) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_file_space_page_size failed to set file space page size");
}
/*-------------------------------------------------------------------------
* create the output file
*-------------------------------------------------------------------------
*/
if (options->verbose)
printf("Making file <%s>...\n", fnameout);
printf("Making new file ...\n");
if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0) {
if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fcreate could not create file <%s>:", fnameout);
}
/*-------------------------------------------------------------------------
* write a new user block if requested
*-------------------------------------------------------------------------
*/
if (options->ublock_size > 0) {
if (copy_user_block(options->ublock_filename, fnameout, options->ublock_size) < 0) {
if (options->ublock_size > 0)
if (copy_user_block(options->ublock_filename, fnameout, options->ublock_size) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not copy user block. Exiting...");
}
}
/*-------------------------------------------------------------------------
* get list of objects
@ -381,18 +351,16 @@ print_user_block(fnamein, fidin);
* do the copy
*-------------------------------------------------------------------------
*/
if (do_copy_objects(fidin, fidout, travt, options) < 0) {
if (do_copy_objects(fidin, fidout, travt, options) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "do_copy_objects from <%s> could not copy data to <%s>", fnamein, fnameout);
} /* end if */
/*-------------------------------------------------------------------------
* do the copy of referenced objects
* and create hard links
*-------------------------------------------------------------------------
*/
if (do_copy_refobjs(fidin, fidout, travt, options) < 0) {
if (do_copy_refobjs(fidin, fidout, travt, options) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "do_copy_refobjs from <%s> could not copy data to <%s>", fnamein, fnameout);
}
/*-------------------------------------------------------------------------
* close
@ -417,11 +385,9 @@ print_user_block(fnamein, fidin);
*-------------------------------------------------------------------------
*/
if (ub_size > 0 && options->ublock_size == 0) {
if (copy_user_block(fnamein, fnameout, ub_size) < 0) {
if (ub_size > 0 && options->ublock_size == 0)
if (copy_user_block(fnamein, fnameout, ub_size) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not copy user block. Exiting...");
}
}
return 0;
@ -732,13 +698,14 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
unsigned crt_order_flags; /* group creation order flag */
unsigned i;
unsigned u;
unsigned uf;
int is_ref = 0;
htri_t is_named;
hbool_t limit_maxdims;
hsize_t size_dset;
/*-------------------------------------------------------------------------
* copy the suppplied object list
* copy the supplied object list
*-------------------------------------------------------------------------
*/
@ -748,12 +715,13 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
printf("-----------------------------------------\n");
}
for (i = 0; i < travt->nobjs; i++) {
/* init variables per obj */
buf = NULL;
limit_maxdims = FALSE;
if (travt->objs) {
for (i = 0; i < travt->nobjs; i++) {
/* init variables per obj */
buf = NULL;
limit_maxdims = FALSE;
switch (travt->objs[i].type) {
switch (travt->objs[i].type) {
case H5TRAV_TYPE_UNKNOWN:
break;
@ -833,10 +801,15 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
req_filter = 1;
/* check if filters were requested for individual objects */
for (u = 0; u < options->op_tbl->nelems; u++)
if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0)
if (options->op_tbl->objs[u].filter->filtn > 0)
req_filter = 1;
if (options->op_tbl->objs) {
for (u = 0; u < options->op_tbl->nelems; u++) {
if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0)
for (uf = 0; uf < options->op_tbl->objs[uf].nfilters; uf++) {
if (options->op_tbl->objs[u].filter[uf].filtn > 0)
req_filter = 1;
}
}
}
/* check if layout change requested individual object */
if (options->layout_g != H5D_LAYOUT_ERROR) {
@ -1012,9 +985,10 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
buf = HDmalloc(need);
if (buf != NULL) {
/* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
CHECK_H5DRW_ERROR(H5Dread, FAIL, dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
CHECK_H5DRW_ERROR(H5Dwrite, FAIL, dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
if(H5Dread(dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
if(H5Dwrite(dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
/* Check if we have VL data in the dataset's
* datatype that must be reclaimed */
@ -1097,9 +1071,10 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
hs_select_nelmts = 1;
} /* rank */
/* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
CHECK_H5DRW_ERROR(H5Dread, FAIL, dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
CHECK_H5DRW_ERROR(H5Dwrite, FAIL, dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
if(H5Dread(dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
if(H5Dwrite(dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
/* reclaim any VL memory, if necessary */
if (vl_data)
@ -1293,19 +1268,9 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
default:
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Object type not found");
} /* switch */
/* free */
if (buf != NULL) {
HDfree(buf);
buf = NULL;
}
} /* i */
/* Finalize (link) the stack of named datatypes (if any) */
named_datatype_free(&named_dt_head, 0);
return ret_value;
} /* switch */
} /* end for */
} /* end if */
done:
H5E_BEGIN_TRY
@ -1322,8 +1287,7 @@ done:
H5Tclose(wtype_id);
H5Tclose(type_in);
H5Tclose(type_out);
named_datatype_free(&named_dt_head, 1);
}H5E_END_TRY;
} H5E_END_TRY;
/* free */
if (buf != NULL)
@ -1331,6 +1295,14 @@ done:
if (hslab_buf != NULL)
HDfree(hslab_buf);
/* Finalize (link) the stack of named datatypes (if any) */
if (0 == ret_value && named_dt_head != NULL)
named_datatype_free(&named_dt_head, 0);
else
H5E_BEGIN_TRY {
named_datatype_free(&named_dt_head, 1);
} H5E_END_TRY;
return ret_value;
}
@ -1364,8 +1336,11 @@ static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int p
for (i = 0; i < nfilters; i++) {
cd_nelmts = NELMTS(cd_values);
filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts,
cd_values, sizeof(f_objname), f_objname, NULL);
if ((filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts,
cd_values, sizeof(f_objname), f_objname, NULL)) < 0) {
HDstrcat(strfilter, "ERROR ");
continue;
}
switch (filtn) {
case H5Z_FILTER_NONE:
@ -1551,7 +1526,7 @@ void print_user_block(const char *filename, hid_t fid)
}
/* open file */
if((fh = HDopen(filename, O_RDONLY, 0)) < 0) {
if((fh = HDopen(filename, O_RDONLY)) < 0) {
HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDopen failed to open file <%s>", filename);
}

268
tools/src/h5repack/h5repack_filters.c
View File

@ -24,24 +24,72 @@
#undef MIN
#define MIN(a,b) (((a)<(b)) ? (a) : (b))
/*-------------------------------------------------------------------------
* Function: aux_copy_obj
*
* Purpose: copy the object filters for object copy
*
* Return: 0 success, -1 failure
*-------------------------------------------------------------------------
*/
static int aux_copy_obj(hid_t dcpl_id, /* dataset creation property list */
const char* name, /* object name from traverse list */
pack_info_t *objout /*OUT*/) /* info about object to filter */
{
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
int nfilters; /* number of filters in DCPL */
char f_objname[256]; /* filter objname */
H5D_layout_t layout;
int rank; /* rank of dataset */
hsize_t chsize[64]; /* chunk size in elements */
unsigned int i, j;
/* get information about input filters */
if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_nfilters failed");
/* copy filter_info_t structure */
for (i = 0; i < nfilters; i++) {
if ((objout->filter[i].filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &objout->filter[i].filt_flag, &objout->filter[i].cd_nelmts,
objout->filter[i].cd_values, sizeof(f_objname), f_objname, NULL)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_filter2 failed");
}
objout->nfilters = nfilters;
HDstrcpy(objout->path, name);
if ((layout = H5Pget_layout(dcpl_id)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_layout failed");
objout->layout = layout;
if (layout == H5D_CHUNKED) {
if ((rank = H5Pget_chunk(dcpl_id, NELMTS(chsize), chsize/*out*/)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_chunk failed");
objout->chunk.rank = rank;
for (i = 0; i < rank; i++)
objout->chunk.chunk_lengths[i] = chsize[i];
}
done:
return ret_value;
}
/*-------------------------------------------------------------------------
* Function: aux_find_obj
*
* Purpose: find the object name NAME (got from the traverse list)
* in the repack options list
*
*-------------------------------------------------------------------------
*/
static int aux_find_obj(const char* name, /* object name from traverse list */
pack_opt_t *options, /* repack options */
pack_info_t *obj /*OUT*/) /* info about object to filter */
pack_opt_t *options, /* repack options */
pack_info_t *obj /*OUT*/) /* info about object to filter */
{
char *pdest;
int result;
unsigned int i;
for (i = 0; i < options->op_tbl->nelems; i++) {
if (HDstrcmp(options->op_tbl->objs[i].path,name) == 0) {
if (HDstrcmp(options->op_tbl->objs[i].path, name) == 0) {
*obj = options->op_tbl->objs[i];
return (int) i;
}
@ -66,14 +114,12 @@ static int aux_find_obj(const char* name, /* object name from traverse list */
* in the repack options list; assign the filter information OBJ
*
* Return: 0 not found, 1 found
*
*-------------------------------------------------------------------------
*/
static int aux_assign_obj(const char* name, /* object name from traverse list */
pack_opt_t *options, /* repack options */
pack_info_t *obj /*OUT*/) /* info about object to filter */
pack_opt_t *options, /* repack options */
pack_info_t *obj /*OUT*/) /* info about object to filter */
{
int idx, i;
pack_info_t tmp;
@ -83,7 +129,6 @@ static int aux_assign_obj(const char* name, /* object name from traverse list */
/* name was on input */
if (idx >= 0) {
/* applying to all objects */
if (options->all_layout) {
/* assign the global layout info to the OBJ info */
@ -92,8 +137,7 @@ static int aux_assign_obj(const char* name, /* object name from traverse list */
case H5D_CHUNKED:
tmp.chunk.rank = options->chunk_g.rank;
for (i = 0; i < tmp.chunk.rank; i++)
tmp.chunk.chunk_lengths[i] =
options->chunk_g.chunk_lengths[i];
tmp.chunk.chunk_lengths[i] = options->chunk_g.chunk_lengths[i];
break;
case H5D_LAYOUT_ERROR:
case H5D_COMPACT:
@ -111,8 +155,7 @@ static int aux_assign_obj(const char* name, /* object name from traverse list */
case H5D_CHUNKED:
tmp.chunk.rank = options->op_tbl->objs[idx].chunk.rank;
for (i = 0; i < tmp.chunk.rank; i++)
tmp.chunk.chunk_lengths[i] =
options->op_tbl->objs[idx].chunk.chunk_lengths[i];
tmp.chunk.chunk_lengths[i] = options->op_tbl->objs[idx].chunk.chunk_lengths[i];
break;
case H5D_LAYOUT_ERROR:
case H5D_COMPACT:
@ -123,7 +166,6 @@ static int aux_assign_obj(const char* name, /* object name from traverse list */
default:
break;
}/*switch*/
}
/* applying to all objects */
@ -183,28 +225,24 @@ static int aux_assign_obj(const char* name, /* object name from traverse list */
* of H5Z_FILTER_NONE present in the PACK_INFO_T filter array
*
* Return: 0 success, -1 an error occured
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: December 19, 2003
*
*-------------------------------------------------------------------------
*/
int apply_filters(const char* name, /* object name from traverse list */
int rank, /* rank of dataset */
hsize_t *dims, /* dimensions of dataset */
size_t msize, /* size of type */
hid_t dcpl_id, /* dataset creation property list */
pack_opt_t *options, /* repack options */
int *has_filter) /* (OUT) object NAME has a filter */
int rank, /* rank of dataset */
hsize_t *dims, /* dimensions of dataset */
size_t msize, /* size of type */
hid_t dcpl_id, /* dataset creation property list */
pack_opt_t *options, /* repack options */
int *has_filter) /* (OUT) object NAME has a filter */
{
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
int nfilters; /* number of filters in DCPL */
hsize_t chsize[64]; /* chunk size in elements */
int nfilters; /* number of filters in DCPL */
hsize_t chsize[64]; /* chunk size in elements */
H5D_layout_t layout;
int i;
int i, j;
pack_info_t obj;
pack_info_t filtobj;
*has_filter = 0;
@ -212,15 +250,16 @@ int apply_filters(const char* name, /* object name from traverse list */
HGOTO_DONE(0);
/*-------------------------------------------------------------------------
* initialize the assigment object
*-------------------------------------------------------------------------
*/
* initialize the assigment object
*-------------------------------------------------------------------------
*/
init_packobject(&obj);
init_packobject(&filtobj);
/*-------------------------------------------------------------------------
* find options
*-------------------------------------------------------------------------
*/
* find options
*-------------------------------------------------------------------------
*/
if (aux_assign_obj(name, options, &obj) == 0)
HGOTO_DONE(0);
@ -228,55 +267,61 @@ int apply_filters(const char* name, /* object name from traverse list */
if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_nfilters failed");
/*-------------------------------------------------------------------------
* check if we have filters in the pipeline
* we want to replace them with the input filters
* only remove if we are inserting new ones
*-------------------------------------------------------------------------
*/
* check if we have filters in the pipeline
* we want to replace them with the input filters
* only remove if we are inserting new ones
*-------------------------------------------------------------------------
*/
if (nfilters && obj.nfilters) {
*has_filter = 1;
if (H5Premove_filter(dcpl_id, H5Z_FILTER_ALL) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Premove_filter failed");
}
/*-------------------------------------------------------------------------
* check if there is an existent chunk
* read it only if there is not a requested layout
*-------------------------------------------------------------------------
*/
if (obj.layout == -1) {
if ((layout = H5Pget_layout(dcpl_id)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_layout failed");
/*-------------------------------------------------------------------------
* check if there is an existent chunk
* read it only if there is not a requested layout
*-------------------------------------------------------------------------
*/
if (obj.layout == -1) {
if ((layout = H5Pget_layout(dcpl_id)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_layout failed");
if (layout == H5D_CHUNKED) {
if ((rank = H5Pget_chunk(dcpl_id, NELMTS(chsize), chsize/*out*/)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_chunk failed");
obj.layout = H5D_CHUNKED;
obj.chunk.rank = rank;
for (i = 0; i < rank; i++)
obj.chunk.chunk_lengths[i] = chsize[i];
if (layout == H5D_CHUNKED) {
if ((rank = H5Pget_chunk(dcpl_id, NELMTS(chsize), chsize/*out*/)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_chunk failed");
obj.layout = H5D_CHUNKED;
obj.chunk.rank = rank;
for (i = 0; i < rank; i++)
obj.chunk.chunk_lengths[i] = chsize[i];
}
}
}
else if(nfilters) {
*has_filter = 1;
if (aux_copy_obj(dcpl_id, name, &filtobj) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "aux_copy_obj failed");
}
/*-------------------------------------------------------------------------
* the type of filter and additional parameter
* type can be one of the filters
* H5Z_FILTER_NONE 0 , uncompress if compressed
* H5Z_FILTER_DEFLATE 1 , deflation like gzip
* H5Z_FILTER_SHUFFLE 2 , shuffle the data
* H5Z_FILTER_FLETCHER32 3 , fletcher32 checksum of EDC
* H5Z_FILTER_SZIP 4 , szip compression
* H5Z_FILTER_NBIT 5 , nbit compression
* H5Z_FILTER_SCALEOFFSET 6 , scaleoffset compression
*-------------------------------------------------------------------------
*/
* the type of filter and additional parameter
* type can be one of the filters
* H5Z_FILTER_NONE 0 , uncompress if compressed
* H5Z_FILTER_DEFLATE 1 , deflation like gzip
* H5Z_FILTER_SHUFFLE 2 , shuffle the data
* H5Z_FILTER_FLETCHER32 3 , fletcher32 checksum of EDC
* H5Z_FILTER_SZIP 4 , szip compression
* H5Z_FILTER_NBIT 5 , nbit compression
* H5Z_FILTER_SCALEOFFSET 6 , scaleoffset compression
*-------------------------------------------------------------------------
*/
if (obj.nfilters) {
/*-------------------------------------------------------------------------
* filters require CHUNK layout; if we do not have one define a default
*-------------------------------------------------------------------------
*/
* filters require CHUNK layout; if we do not have one define a default
*-------------------------------------------------------------------------
*/
if (obj.layout == -1) {
/* stripmine info */
hsize_t sm_size[H5S_MAX_RANK]; /*stripmine size */
@ -285,9 +330,9 @@ int apply_filters(const char* name, /* object name from traverse list */
obj.chunk.rank = rank;
/*
* determine the strip mine size. The strip mine is
* a hyperslab whose size is manageable.
*/
* determine the strip mine size. The strip mine is
* a hyperslab whose size is manageable.
*/
sm_nbytes = msize;
for (i = rank; i > 0; --i) {
@ -305,18 +350,21 @@ int apply_filters(const char* name, /* object name from traverse list */
}
for (i = 0; i < obj.nfilters; i++) {
if (obj.filter[i].filtn < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid filter");
switch (obj.filter[i].filtn) {
/*-------------------------------------------------------------------------
* H5Z_FILTER_NONE 0 , uncompress if compressed
*-------------------------------------------------------------------------
*/
* H5Z_FILTER_NONE 0 , uncompress if compressed
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_NONE:
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_DEFLATE 1 , deflation like gzip
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* H5Z_FILTER_DEFLATE 1 , deflation like gzip
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_DEFLATE:
{
unsigned aggression; /* the deflate level */
@ -330,10 +378,10 @@ int apply_filters(const char* name, /* object name from traverse list */
}
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_SZIP 4 , szip compression
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* H5Z_FILTER_SZIP 4 , szip compression
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_SZIP:
{
unsigned options_mask;
@ -350,10 +398,10 @@ int apply_filters(const char* name, /* object name from traverse list */
}
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_SHUFFLE 2 , shuffle the data
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* H5Z_FILTER_SHUFFLE 2 , shuffle the data
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_SHUFFLE:
if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed");
@ -361,31 +409,30 @@ int apply_filters(const char* name, /* object name from traverse list */
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_shuffle failed");
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_FLETCHER32 3 , fletcher32 checksum of EDC
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* H5Z_FILTER_FLETCHER32 3 , fletcher32 checksum of EDC
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_FLETCHER32:
if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed");
if (H5Pset_fletcher32(dcpl_id) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_fletcher32 failed");
break;
/*----------- -------------------------------------------------------------
* H5Z_FILTER_NBIT , NBIT compression
*-------------------------------------------------------------------------
*/
/*----------- -------------------------------------------------------------
* H5Z_FILTER_NBIT , NBIT compression
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_NBIT:
if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed");
if (H5Pset_nbit(dcpl_id) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_nbit failed");
break;
/*----------- -------------------------------------------------------------
* H5Z_FILTER_SCALEOFFSET , scale+offset compression
*-------------------------------------------------------------------------
*/
/*----------- -------------------------------------------------------------
* H5Z_FILTER_SCALEOFFSET , scale+offset compression
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_SCALEOFFSET:
{
H5Z_SO_scale_type_t scale_type;
@ -402,12 +449,12 @@ int apply_filters(const char* name, /* object name from traverse list */
break;
default:
{
if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed");
if (H5Pset_filter(dcpl_id, obj.filter[i].filtn,
obj.filter[i].filt_flag, obj.filter[i].cd_nelmts,
obj.filter[i].cd_values) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_filter failed");
if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed");
}
break;
} /* switch */
@ -415,10 +462,20 @@ int apply_filters(const char* name, /* object name from traverse list */
}
/*obj.nfilters*/
if (filtobj.nfilters) {
for (i = 0; i < filtobj.nfilters; i++) {
if (filtobj.filter[i].filtn < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid filter");
if (H5Zfilter_avail(filtobj.filter[i].filtn) <= 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "%d filter unavailable", filtobj.filter[i].filtn);
} /* for */
} /* nfilters */
/*-------------------------------------------------------------------------
* layout
*-------------------------------------------------------------------------
*/
* layout
*-------------------------------------------------------------------------
*/
if (obj.layout >= 0) {
/* a layout was defined */
@ -438,7 +495,6 @@ int apply_filters(const char* name, /* object name from traverse list */
if (H5Premove_filter(dcpl_id, H5Z_FILTER_ALL) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Premove_filter failed");
}
}
done:

10
tools/src/h5repack/h5repack_main.c
View File

@ -428,13 +428,13 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
switch ((char) opt) {
/* -i for backward compability */
/* -i for backward compatibility */
case 'i':
infile = opt_arg;
has_i_o = 1;
break;
/* -o for backward compability */
/* -o for backward compatibility */
case 'o':
outfile = opt_arg;
has_i_o = 1;
@ -695,8 +695,10 @@ int main(int argc, const char **argv)
}
/* initialize options */
h5repack_init(&options, 0, FALSE);
if (h5repack_init(&options, 0, FALSE) < 0) {
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
/* Initialize default indexing options */
sort_by = H5_INDEX_CRT_ORDER;

3
tools/src/h5repack/h5repack_opttable.c
View File

@ -30,6 +30,7 @@ void init_packobject(pack_info_t *obj) {
HDstrcpy(obj->path, "\0");
for (j = 0; j < H5_REPACK_MAX_NFILTERS; j++) {
obj->filter[j].filtn = -1;
obj->filter[j].cd_nelmts = CD_VALUES;
for (k = 0; k < CD_VALUES; k++)
obj->filter[j].cd_values[k] = 0;
}
@ -261,7 +262,7 @@ options_add_filter(obj_list_t *obj_list, unsigned n_objs, filter_info_t filt, pa
/* search if this object is already in the table; "path" is the key */
if (table->nelems > 0) {
/* go tru the supplied list of names */
/* go through the supplied list of names */
for (j = 0; j < n_objs; j++) {
/* linear table search */
for (i = 0; i < table->nelems; i++) {

13
tools/src/h5repack/h5repack_parse.c
View File

@ -58,26 +58,30 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt,
/* check for the end of object list and number of objects */
for (i = 0, n = 0; i < len; i++) {
c = str[i];
if (c == ':')
if (c == ':') {
end_obj = (int) i;
break;
}
if (c == ',')
n++;
}
n++;
/* Check for missing : */
if (end_obj == -1) {
/* apply to all objects */
options->all_filter = 1;
*is_glb = 1;
*n_objs = 1;
}
else
*n_objs = n;
n++;
obj_list = (obj_list_t *) HDmalloc(n * sizeof(obj_list_t));
if (obj_list == NULL) {
error_msg("could not allocate object list\n");
return NULL;
}
*n_objs = n;
/* get object list */
if (end_obj > 0)
@ -89,6 +93,7 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt,
sobj[k] = '\0';
else
sobj[k + 1] = '\0';
HDstrcpy(obj_list[n].obj, sobj);
HDmemset(sobj, 0, sizeof(sobj));
n++;
@ -142,7 +147,6 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt,
if (l == 2) {
smask[l] = '\0';
i = len - 1; /* end */
(*n_objs)--; /* we counted an extra ',' */
if (HDstrcmp(smask,"NN") == 0)
filt->cd_values[j++] = H5_SZIP_NN_OPTION_MASK;
else if (HDstrcmp(smask,"EC") == 0)
@ -193,7 +197,6 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt,
if (l == 2) {
smask[l] = '\0';
i = len - 1; /* end */
(*n_objs)--; /* we counted an extra ',' */
if (HDstrcmp(smask,"IN") == 0)
filt->cd_values[j++] = H5Z_SO_INT;
else if (HDstrcmp(smask, "DS") == H5Z_SO_FLOAT_DSCALE)

259
tools/src/h5repack/h5repack_refs.c
View File

@ -30,15 +30,10 @@ static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
/*-------------------------------------------------------------------------
* Function: do_copy_refobjs
*
* Purpose: duplicate all referenced HDF5 objects in the file
* and create hard links
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: December, 10, 2003
* Purpose: duplicate all referenced HDF5 objects in the file
* and create hard links
*
* Return: 0, ok, -1 no
*-------------------------------------------------------------------------
*/
@ -47,41 +42,39 @@ int do_copy_refobjs(hid_t fidin,
trav_table_t *travt,
pack_opt_t *options) /* repack options */
{
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
hid_t grp_in = (-1); /* read group ID */
hid_t grp_out = (-1); /* write group ID */
hid_t dset_in = (-1); /* read dataset ID */
hid_t dset_out = (-1); /* write dataset ID */
hid_t type_in = (-1); /* named type ID */
hid_t dcpl_id = (-1); /* dataset creation property list ID */
hid_t space_id = (-1); /* space ID */
hid_t ftype_id = (-1); /* file data type ID */
hid_t mtype_id = (-1); /* memory data type ID */
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
hid_t grp_in = -1; /* read group ID */
hid_t grp_out = -1; /* write group ID */
hid_t dset_in = -1; /* read dataset ID */
hid_t dset_out = -1; /* write dataset ID */
hid_t type_in = -1; /* named type ID */
hid_t dcpl_id = -1; /* dataset creation property list ID */
hid_t space_id = -1; /* space ID */
hid_t ftype_id = -1; /* file data type ID */
hid_t mtype_id = -1; /* memory data type ID */
size_t msize; /* memory size of memory type */
hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */
unsigned int i, j;
int k;
named_dt_t *named_dt_head=NULL; /* Pointer to the stack of named datatypes
copied */
named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */
/*-------------------------------------------------------------------------
* browse
*-------------------------------------------------------------------------
*/
for(i = 0; i < travt->nobjs; i++) {
switch(travt->objs[i].type)
{
switch(travt->objs[i].type) {
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_GROUP
*-------------------------------------------------------------------------
*/
* H5TRAV_TYPE_GROUP
*-------------------------------------------------------------------------
*/
case H5TRAV_TYPE_GROUP:
/*-------------------------------------------------------------------------
* copy referenced objects in attributes
*-------------------------------------------------------------------------
*/
* copy referenced objects in attributes
*-------------------------------------------------------------------------
*/
if((grp_out = H5Gopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
@ -97,18 +90,18 @@ int do_copy_refobjs(hid_t fidin,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed");
/*-------------------------------------------------------------------------
* check for hard links
*-------------------------------------------------------------------------
*/
* check for hard links
*-------------------------------------------------------------------------
*/
if(travt->objs[i].nlinks)
for(j = 0; j < travt->objs[i].nlinks; j++)
H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT);
break;
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_DATASET
*-------------------------------------------------------------------------
*/
* H5TRAV_TYPE_DATASET
*-------------------------------------------------------------------------
*/
case H5TRAV_TYPE_DATASET:
if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
@ -141,16 +134,16 @@ int do_copy_refobjs(hid_t fidin,
*/
if(h5tools_canreadf(NULL, dcpl_id) == 1) {
/*-------------------------------------------------------------------------
* test for a valid output dataset
*-------------------------------------------------------------------------
*/
* test for a valid output dataset
*-------------------------------------------------------------------------
*/
dset_out = FAIL;
/*-------------------------------------------------------------------------
* object references are a special case
* we cannot just copy the buffers, but instead we recreate the reference
*-------------------------------------------------------------------------
*/
* object references are a special case
* we cannot just copy the buffers, but instead we recreate the reference
*-------------------------------------------------------------------------
*/
if(H5Tequal(mtype_id, H5T_STD_REF_OBJ)) {
hid_t refobj_id;
hobj_ref_t *refbuf = NULL; /* buffer for object references */
@ -159,9 +152,9 @@ int do_copy_refobjs(hid_t fidin,
unsigned u;
/*-------------------------------------------------------------------------
* read to memory
*-------------------------------------------------------------------------
*/
* read to memory
*-------------------------------------------------------------------------
*/
if(nelmts) {
buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize));
if(buf==NULL) {
@ -201,9 +194,9 @@ int do_copy_refobjs(hid_t fidin,
} /*nelmts*/
/*-------------------------------------------------------------------------
* create/write dataset/close
*-------------------------------------------------------------------------
*/
* create/write dataset/close
*-------------------------------------------------------------------------
*/
if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed");
if(nelmts)
@ -223,11 +216,10 @@ int do_copy_refobjs(hid_t fidin,
} /*H5T_STD_REF_OBJ*/
/*-------------------------------------------------------------------------
* dataset region references
*-------------------------------------------------------------------------
*/
else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG))
{
* dataset region references
*-------------------------------------------------------------------------
*/
else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) {
hid_t refobj_id;
hdset_reg_ref_t *refbuf = NULL; /* input buffer for region references */
hdset_reg_ref_t *buf = NULL; /* output buffer */
@ -235,9 +227,9 @@ int do_copy_refobjs(hid_t fidin,
unsigned u;
/*-------------------------------------------------------------------------
* read input to memory
*-------------------------------------------------------------------------
*/
* read input to memory
*-------------------------------------------------------------------------
*/
if(nelmts) {
buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize));
if(buf == NULL) {
@ -248,9 +240,9 @@ int do_copy_refobjs(hid_t fidin,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
/*-------------------------------------------------------------------------
* create output
*-------------------------------------------------------------------------
*/
* create output
*-------------------------------------------------------------------------
*/
refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */
if(refbuf == NULL) {
printf("cannot allocate memory\n");
@ -289,9 +281,9 @@ int do_copy_refobjs(hid_t fidin,
} /*nelmts*/
/*-------------------------------------------------------------------------
* create/write dataset/close
*-------------------------------------------------------------------------
*/
* create/write dataset/close
*-------------------------------------------------------------------------
*/
if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed");
if(nelmts)
@ -310,25 +302,25 @@ int do_copy_refobjs(hid_t fidin,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
} /* H5T_STD_REF_DSETREG */
/*-------------------------------------------------------------------------
* not references, open previously created object in 1st traversal
*-------------------------------------------------------------------------
*/
* not references, open previously created object in 1st traversal
*-------------------------------------------------------------------------
*/
else {
if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
} /* end else */
/*-------------------------------------------------------------------------
* copy referenced objects in attributes
*-------------------------------------------------------------------------
*/
* copy referenced objects in attributes
*-------------------------------------------------------------------------
*/
if(copy_refs_attr(dset_in, dset_out, options, travt, fidout) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_refs_attr failed");
/*-------------------------------------------------------------------------
* check for hard links
*-------------------------------------------------------------------------
*/
* check for hard links
*-------------------------------------------------------------------------
*/
if(travt->objs[i].nlinks)
for(j = 0; j < travt->objs[i].nlinks; j++)
H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT);
@ -338,9 +330,9 @@ int do_copy_refobjs(hid_t fidin,
} /*can_read*/
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
* close
*-------------------------------------------------------------------------
*/
if(H5Tclose(ftype_id) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
if(H5Tclose(mtype_id) < 0)
@ -354,9 +346,9 @@ int do_copy_refobjs(hid_t fidin,
break;
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_NAMED_DATATYPE
*-------------------------------------------------------------------------
*/
* H5TRAV_TYPE_NAMED_DATATYPE
*-------------------------------------------------------------------------
*/
case H5TRAV_TYPE_NAMED_DATATYPE:
if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Topen2 failed");
@ -365,9 +357,9 @@ int do_copy_refobjs(hid_t fidin,
break;
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_LINK
*-------------------------------------------------------------------------
*/
* H5TRAV_TYPE_LINK
*-------------------------------------------------------------------------
*/
case H5TRAV_TYPE_LINK:
/*nothing to do */
break;
@ -410,27 +402,22 @@ done:
/*-------------------------------------------------------------------------
* Function: copy_refs_attr
*
* Purpose: duplicate all referenced HDF5 located in attributes
* relative to LOC_IN, which is obtained either from
* loc_id = H5Gopen2(fid, name, H5P_DEFAULT);
* loc_id = H5Dopen2(fid, name, H5P_DEFAULT);
* loc_id = H5Topen2(fid, name, H5P_DEFAULT);
* Purpose: duplicate all referenced HDF5 located in attributes
* relative to LOC_IN, which is obtained either from
* loc_id = H5Gopen2(fid, name, H5P_DEFAULT);
* loc_id = H5Dopen2(fid, name, H5P_DEFAULT);
* loc_id = H5Topen2(fid, name, H5P_DEFAULT);
*
* Return: 0, ok, -1 no
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Modifier: xcao@hdfgroup.org, 9/12/2011
* Update values of references(object and region) for the following types:
* Modified:
* Update values of references(object and region) for the following types:
* 1) References,
* 2) ARRAY of reference,
* 3) VLEN of references.
* 4) COMPOUND of references.
* This function does not handle references in other complicated structures,
* such as references in nested compound datatypes.
*
* Date: October, 28, 2003
*
* This function does not handle references in other complicated structures,
* such as references in nested compound datatypes.
*-------------------------------------------------------------------------
*/
@ -438,30 +425,32 @@ static int copy_refs_attr(hid_t loc_in,
hid_t loc_out,
pack_opt_t *options,
trav_table_t *travt,
hid_t fidout /* for saving references */
)
hid_t fidout) /* for saving references */
{
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
hid_t attr_id = -1; /* attr ID */
hid_t attr_out = -1; /* attr ID */
hid_t space_id = -1; /* space ID */
hid_t ftype_id = -1; /* file data type ID */
hid_t mtype_id = -1; /* memory data type ID */
size_t msize; /* memory size of type */
hsize_t nelmts; /* number of elements in dataset */
hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
char name[255];
H5O_info_t oinfo; /* Object info */
unsigned u, i, j;
int rank;
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
hid_t attr_id = -1; /* attr ID */
hid_t attr_out = -1; /* attr ID */
hid_t space_id = -1; /* space ID */
hid_t ftype_id = -1; /* file data type ID */
hid_t mtype_id = -1; /* memory data type ID */
size_t msize; /* memory size of type */
hsize_t nelmts; /* number of elements in dataset */
hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
char name[255];
H5O_info_t oinfo; /* Object info */
unsigned u, i, j;
int rank;
H5T_class_t type_class = -1;
hbool_t is_ref=0, is_ref_vlen=0, is_ref_array=0, is_ref_comp=0;
void *refbuf = NULL;
void *buf = NULL;
const char* refname = NULL;
unsigned *ref_comp_index = NULL;
size_t *ref_comp_size = NULL;
int ref_comp_field_n = 0;
hbool_t is_ref = 0,
is_ref_vlen = 0,
is_ref_array = 0,
is_ref_comp = 0;
void *refbuf = NULL;
void *buf = NULL;
const char *refname = NULL;
unsigned *ref_comp_index = NULL;
size_t *ref_comp_size = NULL;
int ref_comp_field_n = 0;
if(H5Oget_info(loc_in, &oinfo) < 0)
@ -492,7 +481,7 @@ static int copy_refs_attr(hid_t loc_in,
hid_t base_type;
base_type = H5Tget_super(ftype_id);
is_ref_vlen = (H5Tget_class(base_type)==H5T_REFERENCE);
is_ref_vlen = (H5Tget_class(base_type) == H5T_REFERENCE);
msize = H5Tget_size(base_type);
H5Tclose(base_type);
}
@ -500,7 +489,7 @@ static int copy_refs_attr(hid_t loc_in,
hid_t base_type;
base_type = H5Tget_super(ftype_id);
is_ref_array = (H5Tget_class(base_type)==H5T_REFERENCE);
is_ref_array = (H5Tget_class(base_type) == H5T_REFERENCE);
msize = H5Tget_size(base_type);
H5Tclose(base_type);
}
@ -515,9 +504,9 @@ static int copy_refs_attr(hid_t loc_in,
ref_comp_field_n = 0;
for (i=0; i<(unsigned)nmembers; i++) {
hid_t mtid = H5Tget_member_type( ftype_id, i );
hid_t mtid = H5Tget_member_type(ftype_id, i);
if ((H5Tget_class(mtid)==H5T_REFERENCE)) {
if ((H5Tget_class(mtid) == H5T_REFERENCE)) {
ref_comp_index[ref_comp_field_n] = i;
ref_comp_size[ref_comp_field_n] = H5Tget_size(mtid);
ref_comp_field_n++;
@ -627,9 +616,9 @@ static int copy_refs_attr(hid_t loc_in,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed");
/*-------------------------------------------------------------------------
* create output
*-------------------------------------------------------------------------
*/
* create output
*-------------------------------------------------------------------------
*/
refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */
if(refbuf == NULL) {
printf( "cannot allocate memory\n" );
@ -669,7 +658,8 @@ static int copy_refs_attr(hid_t loc_in,
HDmemcpy(&(ptr[j]), &ref_out, msize);
}
} /* for (i=0; i<nelems; i++) */
} else if (H5R_DSET_REG_REF_BUF_SIZE == msize) {
}
else if (H5R_DSET_REG_REF_BUF_SIZE == msize) {
hdset_reg_ref_t ref_out;
for (i=0; i<(unsigned)nelmts; i++) {
@ -689,8 +679,7 @@ static int copy_refs_attr(hid_t loc_in,
buf = HDmalloc((unsigned)(nelmts * msize));
refbuf = buf; /* reuse the read buffer for write */
if(buf == NULL)
{
if(buf == NULL) {
printf( "cannot read into memory\n" );
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
} /* end if */
@ -767,8 +756,6 @@ static int copy_refs_attr(hid_t loc_in,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed");
} /* for(u = 0; u < (unsigned)oinfo.num_attrs; u++) */
return ret_value;
done:
if(refbuf)
HDfree(refbuf);
@ -795,7 +782,7 @@ done:
/*-------------------------------------------------------------------------
* Function: MapIdToName
*
* Purpose: map a ID from a reference to a dataset name
* Purpose: map a ID from a reference to a dataset name
*
*-------------------------------------------------------------------------
*/
@ -803,7 +790,7 @@ static const char*
MapIdToName(hid_t refobj_id, trav_table_t *travt)
{
unsigned int u;
const char* ret = NULL;
const char *ret = NULL;
/* linear search */
for(u = 0; u < travt->nobjs; u++) {
@ -830,18 +817,16 @@ out:
/*-------------------------------------------------------------------------
* Function: Update_Ref_value
*
* Purpose: Update a reference value
*
* Programmer: xcao@hdfgroup.org 9/12/2011
*
* Purpose: Update a reference value
*-------------------------------------------------------------------------
*/
static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
hid_t fid_out, void *ref_out, trav_table_t *travt)
{
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
const char* ref_obj_name;
hid_t space_id=-1, ref_obj_id=-1;
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
const char *ref_obj_name;
hid_t space_id = -1;
hid_t ref_obj_id = -1;
ref_obj_id = H5Rdereference2(obj_id, H5P_DEFAULT, ref_type, ref_in);
if (ref_obj_id < 0)

205
tools/src/h5repack/h5repack_verify.c
View File

@ -39,22 +39,22 @@ static int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *fil
int
h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options)
{
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
hid_t fidin = -1; /* file ID for input file*/
hid_t fidout = -1; /* file ID for output file*/
hid_t did = -1; /* dataset ID */
hid_t pid = -1; /* dataset creation property list ID */
hid_t sid = -1; /* space ID */
hid_t tid = -1; /* type ID */
int ok = 1; /* step results */
unsigned int i;
trav_table_t *travt = NULL;
int ok = 1;
hid_t fcpl_in = -1; /* file creation property for input file */
hid_t fcpl_out = -1; /* file creation property for output file */
hid_t fcpl_in = -1; /* file creation property for input file */
hid_t fcpl_out = -1; /* file creation property for output file */
H5F_fspace_strategy_t in_strategy, out_strategy; /* file space handling strategy for in/output file */
hbool_t in_persist, out_persist; /* free-space persist status for in/output file */
hsize_t in_threshold, out_threshold; /* free-space section threshold for in/output file */
hsize_t in_pagesize, out_pagesize; /* file space page size for input/output file */
hbool_t in_persist, out_persist; /* free-space persist status for in/output file */
hsize_t in_threshold, out_threshold; /* free-space section threshold for in/output file */
hsize_t in_pagesize, out_pagesize; /* file space page size for input/output file */
/* open the output file */
if((fidout = H5Fopen(out_fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0 )
@ -84,7 +84,6 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
if(verify_filters(pid, tid, obj->nfilters, obj->filter) <= 0)
ok = 0;
/*-------------------------------------------------------------------------
* layout check
*-------------------------------------------------------------------------
@ -104,10 +103,8 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
if (H5Tclose(tid) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
}
/*-------------------------------------------------------------------------
* check for the "all" objects option
*-------------------------------------------------------------------------
@ -163,7 +160,6 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
ok = 0;
}
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
@ -177,11 +173,11 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
if (H5Tclose(tid) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
} /* if */
} /* i */
/* free table */
trav_table_free(travt);
travt = NULL;
}
/*-------------------------------------------------------------------------
@ -190,39 +186,33 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
*/
/* open the input file */
if((fidin = H5Fopen(in_fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0 )
if((fidin = H5Fopen(in_fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fopen failed on file <%s>", in_fname);
/* Get file creation property list for input file */
if((fcpl_in = H5Fget_create_plist(fidin)) < 0) {
if((fcpl_in = H5Fget_create_plist(fidin)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fget_create_plist failed to retrieve file creation property list");
}
/* Get file space info for input file */
if(H5Pget_file_space_strategy(fcpl_in, &in_strategy, &in_persist, &in_threshold) < 0) {
if(H5Pget_file_space_strategy(fcpl_in, &in_strategy, &in_persist, &in_threshold) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space_strategy failed to retrieve file space strategy & threshold");
}
/* Get file space page size for input file */
if(H5Pget_file_space_page_size(fcpl_in, &in_pagesize) < 0) {
if(H5Pget_file_space_page_size(fcpl_in, &in_pagesize) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space_page_size failed to retrieve file space page size");
}
/* Output file is already opened */
/* Get file creation property list for output file */
if((fcpl_out = H5Fget_create_plist(fidout)) < 0) {
if((fcpl_out = H5Fget_create_plist(fidout)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fget_create_plist failed to retrieve file creation property list");
}
/* Get file space info for output file */
if(H5Pget_file_space_strategy(fcpl_out, &out_strategy, &out_persist, &out_threshold) < 0) {
if(H5Pget_file_space_strategy(fcpl_out, &out_strategy, &out_persist, &out_threshold) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space_strategy failed to retrieve file space strategy & threshold");
}
/* Get file space page size for output file */
if(H5Pget_file_space_page_size(fcpl_out, &out_pagesize) < 0) {
if(H5Pget_file_space_page_size(fcpl_out, &out_pagesize) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space_page_size failed to retrieve file space page size");
}
/*
* If -S option is set, the file space handling strategy should be set as specified.
@ -230,14 +220,12 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
* the same as the input file's strategy.
*/
if(options->fs_strategy) {
if(out_strategy != (options->fs_strategy == (H5F_fspace_strategy_t)-1 ? 0 : options->fs_strategy)) {
if(out_strategy != (options->fs_strategy == (H5F_fspace_strategy_t)-1 ? 0 : options->fs_strategy))
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space strategy not set as unexpected");
}
}
else {
if(out_strategy != in_strategy) {
if(out_strategy != in_strategy)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space strategy not set as unexpected");
}
}
/*
@ -246,14 +234,12 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
* the same as the input file's free-space persist status
*/
if(options->fs_persist) {
if(out_persist != (hbool_t)(options->fs_persist == (-1) ? FALSE : options->fs_persist)) {
if(out_persist != (hbool_t)(options->fs_persist == (-1) ? FALSE : options->fs_persist))
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "free-space persist status not set as unexpected");
}
}
else {
if(out_persist != in_persist) {
if(out_persist != in_persist)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "free-space persist status not set as unexpected");
}
}
/*
@ -262,14 +248,12 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
* input file's threshold size.
*/
if(options->fs_threshold) {
if(out_threshold != (hsize_t)(options->fs_threshold == (-1) ? 0 : options->fs_threshold)) {
if(out_threshold != (hsize_t)(options->fs_threshold == (-1) ? 0 : options->fs_threshold))
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "threshold not set as unexpected");
}
}
else {
if(out_threshold != in_threshold) {
if(out_threshold != in_threshold)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "threshold not set as unexpected");
}
}
/*
@ -278,27 +262,16 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
* the same as the input file's file space page size.
*/
if(options->fs_pagesize) {
if(out_pagesize != (hsize_t)(options->fs_pagesize == (-1) ? 0 : options->fs_pagesize)) {
if(out_pagesize != (hsize_t)(options->fs_pagesize == (-1) ? 0 : options->fs_pagesize))
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space page size not set as unexpected");
}
}
else { /* "-G" is not set */
if(out_pagesize != in_pagesize) {
if(out_pagesize != in_pagesize)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space page size not set as unexpected");
}
}
/* Closing */
if (H5Pclose(fcpl_in) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
if (H5Pclose(fcpl_out) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
if (H5Fclose(fidin) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fclose failed");
if (H5Fclose(fidout) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fclose failed");
return ok;
ret_value = ok;
done:
H5E_BEGIN_TRY {
@ -307,6 +280,7 @@ done:
H5Pclose(pid);
H5Sclose(sid);
H5Dclose(did);
H5Tclose(tid);
H5Fclose(fidin);
H5Fclose(fidout);
if (travt)
@ -319,13 +293,15 @@ done:
/*-------------------------------------------------------------------------
* Function: verify_layout
*
* Purpose: verify which layout is present in the property list DCPL_ID
* Purpose: verify which layout is present in the property list DCPL_ID
* H5D_COMPACT = 0
* H5D_CONTIGUOUS = 1
* H5D_CHUNKED = 2
*
* H5D_COMPACT = 0
* H5D_CONTIGUOUS = 1
* H5D_CHUNKED = 2
*
* Return: 1 has, 0 does not, -1 error
* Return:
* 1 has,
* 0 does not,
* -1 error
*-------------------------------------------------------------------------
*/
@ -342,7 +318,7 @@ int verify_layout(hid_t pid, pack_info_t *obj)
return -1;
/* a non chunked layout was requested on a filtered object */
if (nfilters && obj->layout!=H5D_CHUNKED)
if (nfilters && obj->layout != H5D_CHUNKED)
return 0;
/* get layout */
@ -353,11 +329,11 @@ int verify_layout(hid_t pid, pack_info_t *obj)
return 0;
if (layout==H5D_CHUNKED) {
if ((rank = H5Pget_chunk(pid,NELMTS(chsize),chsize/*out*/)) < 0)
if ((rank = H5Pget_chunk(pid, NELMTS(chsize), chsize/*out*/)) < 0)
return -1;
if (obj->chunk.rank != rank)
return 0;
for ( i=0; i<rank; i++)
for (i = 0; i < rank; i++)
if (chsize[i] != obj->chunk.chunk_lengths[i])
return 0;
}
@ -368,50 +344,40 @@ int verify_layout(hid_t pid, pack_info_t *obj)
/*-------------------------------------------------------------------------
* Function: h5repack_cmp_pl
*
* Purpose: compare 2 files for identical property lists of all objects
* Purpose: compare 2 files for identical property lists of all objects
*
* Return: 1=identical, 0=not identical, -1=error
* Return:
* 1 = identical,
* 0 = not identical,
* -1 = error
*-------------------------------------------------------------------------
*/
int h5repack_cmp_pl(const char *fname1, const char *fname2)
{
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
hid_t fid1=-1; /* file ID */
hid_t fid2=-1; /* file ID */
hid_t dset1=-1; /* dataset ID */
hid_t dset2=-1; /* dataset ID */
hid_t gid=-1; /* group ID */
hid_t dcpl1=-1; /* dataset creation property list ID */
hid_t dcpl2=-1; /* dataset creation property list ID */
hid_t gcplid=-1; /* group creation property list */
unsigned crt_order_flag1; /* group creation order flag */
unsigned crt_order_flag2; /* group creation order flag */
trav_table_t *trav=NULL;
int ret=1;
int ret_value = 1; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
hid_t fid1 =-1; /* file ID */
hid_t fid2 =-1; /* file ID */
hid_t dset1 =-1; /* dataset ID */
hid_t dset2 =-1; /* dataset ID */
hid_t gid =-1; /* group ID */
hid_t dcpl1 =-1; /* dataset creation property list ID */
hid_t dcpl2 =-1; /* dataset creation property list ID */
hid_t gcplid =-1; /* group creation property list */
unsigned crt_order_flag1; /* group creation order flag */
unsigned crt_order_flag2; /* group creation order flag */
trav_table_t *trav = NULL;
unsigned int i;
/*-------------------------------------------------------------------------
* open the files
*-------------------------------------------------------------------------
*/
/* disable error reporting */
H5E_BEGIN_TRY
{
/* Open the files */
if ((fid1 = H5Fopen(fname1,H5F_ACC_RDONLY,H5P_DEFAULT)) < 0 ) {
error_msg("<%s>: %s\n", fname1, H5FOPENERROR );
return -1;
}
if ((fid2 = H5Fopen(fname2,H5F_ACC_RDONLY,H5P_DEFAULT)) < 0 ) {
error_msg("<%s>: %s\n", fname2, H5FOPENERROR );
H5Fclose(fid1);
return -1;
}
/* enable error reporting */
} H5E_END_TRY;
/* Open the files */
if ((fid1 = H5Fopen(fname1, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_fopen failed <%s>: %s", fname1, H5FOPENERROR);
if ((fid2 = H5Fopen(fname2, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_fopen failed <%s>: %s", fname2, H5FOPENERROR);
/*-------------------------------------------------------------------------
* get file table list of objects
@ -452,9 +418,8 @@ int h5repack_cmp_pl(const char *fname1, const char *fname2)
if (H5Gclose(gid) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed");
if (crt_order_flag1 != crt_order_flag2) {
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "property lists failed for <%s> are different", trav->objs[i].name);
}
if (crt_order_flag1 != crt_order_flag2)
HGOTO_ERROR(0, H5E_tools_min_id_g, "property lists failed for <%s> are different", trav->objs[i].name);
}
else if(trav->objs[i].type == H5TRAV_TYPE_DATASET) {
if((dset1 = H5Dopen2(fid1, trav->objs[i].name, H5P_DEFAULT)) < 0)
@ -470,12 +435,11 @@ int h5repack_cmp_pl(const char *fname1, const char *fname2)
* compare the property lists
*-------------------------------------------------------------------------
*/
if((ret = H5Pequal(dcpl1, dcpl2)) < 0)
if((ret_value = H5Pequal(dcpl1, dcpl2)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pequal failed");
if(ret == 0) {
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "property lists failed for <%s> are different",trav->objs[i].name);
}
if(ret_value == 0)
HGOTO_ERROR(0, H5E_tools_min_id_g, "property lists failed for <%s> are different", trav->objs[i].name);
/*-------------------------------------------------------------------------
* close
@ -490,29 +454,8 @@ int h5repack_cmp_pl(const char *fname1, const char *fname2)
if(H5Dclose(dset2) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
} /*if*/
} /*i*/
} /*for*/
/*-------------------------------------------------------------------------
* free
*-------------------------------------------------------------------------
*/
trav_table_free(trav);
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
H5Fclose(fid1);
H5Fclose(fid2);
return ret;
/*-------------------------------------------------------------------------
* error
*-------------------------------------------------------------------------
*/
done:
H5E_BEGIN_TRY
{
@ -524,7 +467,8 @@ done:
H5Fclose(fid2);
H5Pclose(gcplid);
H5Gclose(gid);
trav_table_free(trav);
if(trav)
trav_table_free(trav);
} H5E_END_TRY;
return ret_value;
@ -534,14 +478,14 @@ done:
/*-------------------------------------------------------------------------
* Function: verify_filters
*
* Purpose: verify if all requested filters in the array FILTER obtained
* from user input are present in the property list PID obtained from
* the output file
* Purpose: verify if all requested filters in the array FILTER obtained
* from user input are present in the property list PID obtained from
* the output file
*
* Return:
* 1 match
* 0 do not match
* -1 error
* 1 match
* 0 do not match
* -1 error
*-------------------------------------------------------------------------
*/
@ -583,6 +527,8 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter)
cd_values, sizeof(f_name), f_name, NULL);
/* filter ID */
if (filtn < 0)
return -1;
if (filtn != filter[i].filtn)
return 0;
@ -657,4 +603,3 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter)
return 1;
}

10
tools/test/h5diff/CMakeLists.txt
View File

@ -19,9 +19,10 @@ INCLUDE_DIRECTORIES (${HDF5_TOOLS_DIR}/lib)
#add_test (NAME h5diffgentest COMMAND $<TARGET_FILE:h5diffgentest>)
endif ()
#-----------------------------------------------------------------------------
# If plugin library tests can be tested
#-----------------------------------------------------------------------------
#-----------------------------------------------------------------------------
# If plugin library tests can be tested
#-----------------------------------------------------------------------------
if (BUILD_SHARED_LIBS)
set (HDF5_TOOL_PLUGIN_LIB_CORENAME "dynlibdiff")
set (HDF5_TOOL_PLUGIN_LIB_NAME "${HDF5_EXTERNAL_LIB_PREFIX}${HDF5_TOOL_PLUGIN_LIB_CORENAME}")
set (HDF5_TOOL_PLUGIN_LIB_TARGET ${HDF5_TOOL_PLUGIN_LIB_CORENAME})
@ -46,5 +47,6 @@ INCLUDE_DIRECTORIES (${HDF5_TOOLS_DIR}/lib)
"$<TARGET_FILE:${HDF5_TOOL_PLUGIN_LIB_TARGET}>"
"${CMAKE_BINARY_DIR}/plugins/$<TARGET_FILE_NAME:${HDF5_TOOL_PLUGIN_LIB_TARGET}>"
)
endif ()
include (CMakeTests.cmake)
include (CMakeTests.cmake)

14
tools/test/h5diff/CMakeTests.cmake
View File

@ -501,7 +501,7 @@
add_test (
NAME H5DIFF_UD-${testname}
COMMAND "${CMAKE_COMMAND}"
-D "TEST_PROGRAM=$<TARGET_FILE:h5diff>"
-D "TEST_PROGRAM=$<TARGET_FILE:h5diff-shared>"
-D "TEST_ARGS:STRING=${ARGN}"
-D "TEST_FOLDER=${PROJECT_BINARY_DIR}/testfiles"
-D "TEST_OUTPUT=${resultfile}.out"
@ -516,7 +516,7 @@
add_test (
NAME H5DIFF_UD-${testname}
COMMAND "${CMAKE_COMMAND}"
-D "TEST_PROGRAM=$<TARGET_FILE:h5diff>"
-D "TEST_PROGRAM=$<TARGET_FILE:h5diff-shared>"
-D "TEST_ARGS:STRING=${ARGN}"
-D "TEST_FOLDER=${PROJECT_BINARY_DIR}/testfiles"
-D "TEST_OUTPUT=${resultfile}.out"
@ -546,7 +546,7 @@
add_test (
NAME H5DIFF_UD_ERR-${testname}
COMMAND "${CMAKE_COMMAND}"
-D "TEST_PROGRAM=$<TARGET_FILE:h5diff>"
-D "TEST_PROGRAM=$<TARGET_FILE:h5diff-shared>"
-D "TEST_ARGS:STRING=--enable-error-stack;${ARGN}"
-D "TEST_FOLDER=${PROJECT_BINARY_DIR}/testfiles"
-D "TEST_OUTPUT=${resultfile}_ERR.out"
@ -562,7 +562,7 @@
add_test (
NAME H5DIFF_UD_ERR-${testname}
COMMAND "${CMAKE_COMMAND}"
-D "TEST_PROGRAM=$<TARGET_FILE:h5diff>"
-D "TEST_PROGRAM=$<TARGET_FILE:h5diff-shared>"
-D "TEST_ARGS:STRING=--enable-error-stack;${ARGN}"
-D "TEST_FOLDER=${PROJECT_BINARY_DIR}/testfiles"
-D "TEST_OUTPUT=${resultfile}_ERR.out"
@ -1653,8 +1653,10 @@ ADD_H5_TEST (h5diff_v3 0 -c ${FILEV1} ${FILEV2})
##############################################################################
### P L U G I N T E S T S
##############################################################################
ADD_H5_UD_TEST (h5diff_plugin_test 0 h5diff_ud -v tudfilter.h5 tudfilter2.h5)
ADD_H5_UD_TEST (h5diff_plugin_fail 2 h5diff_udfail -v tudfilter.h5 tudfilter2.h5)
if (BUILD_SHARED_LIBS)
ADD_H5_UD_TEST (h5diff_plugin_test 0 h5diff_ud -v tudfilter.h5 tudfilter2.h5)
ADD_H5_UD_TEST (h5diff_plugin_fail 2 h5diff_udfail -v tudfilter.h5 tudfilter2.h5)
endif ()
# ##############################################################################
# # END

6
tools/test/h5dump/h5dumpgentest.c
View File

@ -287,9 +287,9 @@ typedef struct s1_t {
#define F64_DIM1 (F64_ARRAY_BUF_LEN / sizeof(int) + 1)
/* File 65 macros */
#define STRATEGY H5F_FSPACE_STRATEGY_NONE /* File space handling strategy */
#define THRESHOLD10 10 /* Free-space section threshold */
#define FSPACE_PAGE_SIZE 8192 /* File space page size */
#define STRATEGY H5F_FSPACE_STRATEGY_NONE /* File space handling strategy */
#define THRESHOLD10 10 /* Free-space section threshold */
#define FSPACE_PAGE_SIZE 8192 /* File space page size */
/* "FILE66" macros and for FILE69 */
#define F66_XDIM 8

6
tools/test/h5repack/CMakeTests.cmake
View File

@ -1377,11 +1377,7 @@
ADD_H5_UD_TEST (plugin_test 0 h5repack_layout.h5 -v -f UD=257,0,1,9)
ADD_H5_UD_TEST (plugin_none 0 h5repack_layout.UD.h5 -v -f NONE)
# check for no parameters
set (TESTRETVAL 255)
if (WIN32)
set (TESTRETVAL -1)
endif ()
ADD_H5_UD_TEST (plugin_zero ${TESTRETVAL} h5repack_layout.h5 -v -f UD=250,0,0)
ADD_H5_UD_TEST (plugin_zero 0 h5repack_layout.h5 -v -f UD=250,0,0)
if (HDF5_TEST_VFD)
# Run test with different Virtual File Driver

1692
tools/test/h5repack/h5repacktst.c
View File

File diff suppressed because it is too large Load Diff

4
tools/test/h5repack/testfiles/deflate_limit.h5repack_layout.h5.ddl
View File

@ -76,8 +76,8 @@ GROUP "/" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
STORAGE_LAYOUT {
CHUNKED ( 20, 10 )
SIZE 1283 (2.494:1 COMPRESSION)
CHUNKED ( 40, 20 )
SIZE 1150 (2.783:1 COMPRESSION)
}
FILTERS {
COMPRESSION DEFLATE { LEVEL 1 }

5
tools/test/h5repack/testfiles/h5repack_filters.h5-gzip_verbose_filters.tst
View File

@ -1,7 +1,8 @@
Objects to modify layout are...
Objects to apply filter are...
No all objects to modify layout
No all objects to apply filter
</dset_deflate> with GZIP filter
</dset_deflate>...Found
Making new file ...
-----------------------------------------
Type Filter (Compression) Name
-----------------------------------------

2
tools/test/h5repack/testfiles/h5repack_layout.h5-plugin_test.ddl
View File

@ -92,7 +92,7 @@ GROUP "/" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
STORAGE_LAYOUT {
CHUNKED ( 20, 10 )
CHUNKED ( 40, 20 )
SIZE 3200 (1.000:1 COMPRESSION)
}
FILTERS {

16
tools/test/h5repack/testfiles/h5repack_layout.h5-plugin_version_test.ddl
View File

@ -11,7 +11,7 @@ GROUP "/" {
USER_DEFINED_FILTER {
FILTER_ID 260
COMMENT dynlib4
PARAMS { 9 1 10 2 }
PARAMS { 9 1 11 0 }
}
}
FILLVALUE {
@ -33,7 +33,7 @@ GROUP "/" {
USER_DEFINED_FILTER {
FILTER_ID 260
COMMENT dynlib4
PARAMS { 9 1 10 2 }
PARAMS { 9 1 11 0 }
}
}
FILLVALUE {
@ -55,7 +55,7 @@ GROUP "/" {
USER_DEFINED_FILTER {
FILTER_ID 260
COMMENT dynlib4
PARAMS { 9 1 10 2 }
PARAMS { 9 1 11 0 }
}
}
FILLVALUE {
@ -77,7 +77,7 @@ GROUP "/" {
USER_DEFINED_FILTER {
FILTER_ID 260
COMMENT dynlib4
PARAMS { 9 1 10 2 }
PARAMS { 9 1 11 0 }
}
}
FILLVALUE {
@ -92,14 +92,14 @@ GROUP "/" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
STORAGE_LAYOUT {
CHUNKED ( 20, 10 )
CHUNKED ( 40, 20 )
SIZE 3200 (1.000:1 COMPRESSION)
}
FILTERS {
USER_DEFINED_FILTER {
FILTER_ID 260
COMMENT dynlib4
PARAMS { 9 1 10 2 }
PARAMS { 9 1 11 0 }
}
}
FILLVALUE {
@ -121,7 +121,7 @@ GROUP "/" {
USER_DEFINED_FILTER {
FILTER_ID 260
COMMENT dynlib4
PARAMS { 9 1 10 2 }
PARAMS { 9 1 11 0 }
}
}
FILLVALUE {
@ -143,7 +143,7 @@ GROUP "/" {
USER_DEFINED_FILTER {
FILTER_ID 260
COMMENT dynlib4
PARAMS { 9 1 10 2 }
PARAMS { 9 1 11 0 }
}
}
FILLVALUE {

131
tools/test/h5repack/testfiles/h5repack_layout.h5-plugin_zero.ddl
View File

@ -1,4 +1,135 @@
HDF5 "out-plugin_zero.h5repack_layout.h5" {
GROUP "/" {
DATASET "dset1" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
STORAGE_LAYOUT {
CONTIGUOUS
SIZE 3200
OFFSET 2048
}
FILTERS {
NONE
}
FILLVALUE {
FILL_TIME H5D_FILL_TIME_IFSET
VALUE H5D_FILL_VALUE_DEFAULT
}
ALLOCATION_TIME {
H5D_ALLOC_TIME_LATE
}
}
DATASET "dset2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
STORAGE_LAYOUT {
CONTIGUOUS
SIZE 3200
OFFSET 5248
}
FILTERS {
NONE
}
FILLVALUE {
FILL_TIME H5D_FILL_TIME_IFSET
VALUE H5D_FILL_VALUE_DEFAULT
}
ALLOCATION_TIME {
H5D_ALLOC_TIME_LATE
}
}
DATASET "dset3" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
STORAGE_LAYOUT {
CONTIGUOUS
SIZE 3200
OFFSET 8448
}
FILTERS {
NONE
}
FILLVALUE {
FILL_TIME H5D_FILL_TIME_IFSET
VALUE H5D_FILL_VALUE_DEFAULT
}
ALLOCATION_TIME {
H5D_ALLOC_TIME_LATE
}
}
DATASET "dset4" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
STORAGE_LAYOUT {
CONTIGUOUS
SIZE 3200
OFFSET 13696
}
FILTERS {
NONE
}
FILLVALUE {
FILL_TIME H5D_FILL_TIME_IFSET
VALUE H5D_FILL_VALUE_DEFAULT
}
ALLOCATION_TIME {
H5D_ALLOC_TIME_LATE
}
}
DATASET "dset_chunk" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
STORAGE_LAYOUT {
CHUNKED ( 20, 10 )
SIZE 3200
}
FILTERS {
NONE
}
FILLVALUE {
FILL_TIME H5D_FILL_TIME_IFSET
VALUE H5D_FILL_VALUE_DEFAULT
}
ALLOCATION_TIME {
H5D_ALLOC_TIME_INCR
}
}
DATASET "dset_compact" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
STORAGE_LAYOUT {
COMPACT
SIZE 3200
}
FILTERS {
NONE
}
FILLVALUE {
FILL_TIME H5D_FILL_TIME_IFSET
VALUE H5D_FILL_VALUE_DEFAULT
}
ALLOCATION_TIME {
H5D_ALLOC_TIME_EARLY
}
}
DATASET "dset_contiguous" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
STORAGE_LAYOUT {
CONTIGUOUS
SIZE 3200
OFFSET 26184
}
FILTERS {
NONE
}
FILLVALUE {
FILL_TIME H5D_FILL_TIME_IFSET
VALUE H5D_FILL_VALUE_DEFAULT
}
ALLOCATION_TIME {
H5D_ALLOC_TIME_LATE
}
}
}
}

5
tools/test/h5repack/testfiles/plugin_none.h5repack_layout.UD.h5.tst
View File

@ -1,6 +1,7 @@
Objects to modify layout are...
Objects to apply filter are...
No all objects to modify layout
All objects to apply filter are...
Uncompress all
Making new file ...
-----------------------------------------
Type Filter (Compression) Name
-----------------------------------------

5
tools/test/h5repack/testfiles/plugin_test.h5repack_layout.h5.tst
View File

@ -1,6 +1,7 @@
Objects to modify layout are...
Objects to apply filter are...
No all objects to modify layout
All objects to apply filter are...
User Defined 257
Making new file ...
-----------------------------------------
Type Filter (Compression) Name
-----------------------------------------

5
tools/test/h5repack/testfiles/plugin_version_test.h5repack_layout.h5.tst
View File

@ -1,6 +1,7 @@
Objects to modify layout are...
Objects to apply filter are...
No all objects to modify layout
All objects to apply filter are...
User Defined 260
Making new file ...
-----------------------------------------
Type Filter (Compression) Name
-----------------------------------------

19
tools/test/h5repack/testfiles/plugin_zero.h5repack_layout.h5.tst
View File

@ -1,7 +1,22 @@
Objects to modify layout are...
Objects to apply filter are...
No all objects to modify layout
All objects to apply filter are...
User Defined 250
Making new file ...
-----------------------------------------
Type Filter (Compression) Name
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group /
warning: could not create dataset </dset1>. Applying original settings
dset /dset1
warning: could not create dataset </dset2>. Applying original settings
dset /dset2
warning: could not create dataset </dset3>. Applying original settings
dset /dset3
warning: could not create dataset </dset4>. Applying original settings
dset /dset4
warning: could not create dataset </dset_chunk>. Applying original settings
dset /dset_chunk
warning: could not create dataset </dset_compact>. Applying original settings
dset /dset_compact
warning: could not create dataset </dset_contiguous>. Applying original settings
dset /dset_contiguous