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Merge remote-tracking branch 'canonical/develop' into develop
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@derobins
derobins committed Mar 26, 2021
2 parents d242911 + da5aca2 commit bc70f95
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35 changes: 21 additions & 14 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,13 @@ mark_as_advanced (HDF5_EXTERNAL_LIB_PREFIX)
# If the parent project needs to install hdf libraries, but avoid
# name conflicts with system versions, then a prefix may be added
# to ensure that the correct versions configured are used.
set (HDF5_LIB_INFIX "" CACHE STRING "Use infix for custom library naming.")
mark_as_advanced (HDF5_LIB_INFIX)
# HDF5_LIB_INFIX :
# This infix is added to all library names after 'hdf5'.
# e.g. the infix '_openmpi' results in the library name 'libhdf5_openmpi.so'
# This name is used in packages on debian based systems.
# (see https://packages.debian.org/jessie/amd64/libhdf5-openmpi-8/filelist)
#
# HDF5_INSTALL_BIN_DIR, HDF5_INSTALL_LIB_DIR, HDF5_INSTALL_INCLUDE_DIR, HDF5_INSTALL_DATA_DIR :
# Customize the 'bin', 'lib', 'include', and 'share' installation directories.
Expand Down Expand Up @@ -130,20 +137,20 @@ mark_as_advanced (ALLOW_UNSUPPORTED)
#-----------------------------------------------------------------------------
# Set the core names of all the libraries
#-----------------------------------------------------------------------------
set (HDF5_LIB_CORENAME "hdf5")
set (HDF5_TEST_LIB_CORENAME "hdf5_test")
set (HDF5_CPP_LIB_CORENAME "hdf5_cpp")
set (HDF5_HL_LIB_CORENAME "hdf5_hl")
set (HDF5_HL_CPP_LIB_CORENAME "hdf5_hl_cpp")
set (HDF5_TOOLS_LIB_CORENAME "hdf5_tools")
set (HDF5_UTILS_LIB_CORENAME "hdf5_utils")
set (HDF5_F90_LIB_CORENAME "hdf5_fortran")
set (HDF5_F90_C_LIB_CORENAME "hdf5_f90cstub")
set (HDF5_F90_TEST_LIB_CORENAME "hdf5_test_fortran")
set (HDF5_F90_C_TEST_LIB_CORENAME "hdf5_test_f90cstub")
set (HDF5_HL_F90_LIB_CORENAME "hdf5_hl_fortran")
set (HDF5_HL_F90_C_LIB_CORENAME "hdf5_hl_f90cstub")
set (HDF5_JAVA_JNI_LIB_CORENAME "hdf5_java")
set (HDF5_LIB_CORENAME "hdf5${HDF5_LIB_INFIX}")
set (HDF5_TEST_LIB_CORENAME "hdf5${HDF5_LIB_INFIX}_test")
set (HDF5_CPP_LIB_CORENAME "hdf5${HDF5_LIB_INFIX}_cpp")
set (HDF5_HL_LIB_CORENAME "hdf5${HDF5_LIB_INFIX}_hl")
set (HDF5_HL_CPP_LIB_CORENAME "hdf5${HDF5_LIB_INFIX}_hl_cpp")
set (HDF5_TOOLS_LIB_CORENAME "hdf5${HDF5_LIB_INFIX}_tools")
set (HDF5_UTILS_LIB_CORENAME "hdf5${HDF5_LIB_INFIX}_utils")
set (HDF5_F90_LIB_CORENAME "hdf5${HDF5_LIB_INFIX}_fortran")
set (HDF5_F90_C_LIB_CORENAME "hdf5${HDF5_LIB_INFIX}_f90cstub")
set (HDF5_F90_TEST_LIB_CORENAME "hdf5${HDF5_LIB_INFIX}_test_fortran")
set (HDF5_F90_C_TEST_LIB_CORENAME "hdf5${HDF5_LIB_INFIX}_test_f90cstub")
set (HDF5_HL_F90_LIB_CORENAME "hdf5${HDF5_LIB_INFIX}_hl_fortran")
set (HDF5_HL_F90_C_LIB_CORENAME "hdf5${HDF5_LIB_INFIX}_hl_f90cstub")
set (HDF5_JAVA_JNI_LIB_CORENAME "hdf5${HDF5_LIB_INFIX}_java")
set (HDF5_JAVA_HDF5_LIB_CORENAME "jarhdf5")
set (HDF5_JAVA_TEST_LIB_CORENAME "jartest5")

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6 changes: 6 additions & 0 deletions examples/testh5cc.sh.in
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Expand Up @@ -91,6 +91,8 @@ temp_FILES="a.out $applib"
cat > $appmain <<EOF
#include "hdf5.h"
#define H5FILE_NAME "tmp.h5"
extern void sub1(void);
extern void sub2(void);
int
main (void)
{
Expand All @@ -115,6 +117,8 @@ EOF

# generate prog1
cat > $prog1 <<EOF
#include <stdio.h>
void
sub1(void)
{
printf("in sub1\n");
Expand All @@ -123,6 +127,8 @@ EOF

# generate prog2
cat > $prog2 <<EOF
#include <stdio.h>
void
sub2(void)
{
printf("in sub2\n");
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2 changes: 2 additions & 0 deletions java/src/hdf/hdf5lib/exceptions/HDF5LibraryException.java
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Expand Up @@ -30,7 +30,9 @@

@SuppressWarnings("serial")
public class HDF5LibraryException extends HDF5Exception {
/** major error number of the first error on the HDF5 library error stack. */
private final long majorErrorNumber;
/** minor error number of the first error on the HDF5 library error stack. */
private final long minorErrorNumber;

/**
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243 changes: 236 additions & 7 deletions java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java
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Expand Up @@ -20,41 +20,270 @@
*/
public class H5AC_cache_config_t implements Serializable{
private static final long serialVersionUID = -6748085696476149972L;
// general configuration fields:
// general configuration fields
/**
* version: Integer field containing the version number of this version
* of the H5AC_cache_config_t structure. Any instance of
* H5AC_cache_config_t passed to the cache must have a known
* version number, or an error will be flagged.
*/
public int version;
/**
* rpt_fcn_enabled: Boolean field used to enable and disable the default
* reporting function. This function is invoked every time the
* automatic cache resize code is run, and reports on its activities.
*
* This is a debugging function, and should normally be turned off.
*/
public boolean rpt_fcn_enabled;
/**
* open_trace_file: Boolean field indicating whether the trace_file_name
* field should be used to open a trace file for the cache.
*
* *** DEPRECATED *** Use H5Fstart/stop logging functions instead
*/
public boolean open_trace_file;
/**
* close_trace_file: Boolean field indicating whether the current trace
* file (if any) should be closed.
*
* *** DEPRECATED *** Use H5Fstart/stop logging functions instead
*/
public boolean close_trace_file;
/**
* trace_file_name: Full path of the trace file to be opened if the
* open_trace_file field is TRUE.
*
* *** DEPRECATED *** Use H5Fstart/stop logging functions instead
*/
public String trace_file_name;
/**
* evictions_enabled: Boolean field used to either report the current
* evictions enabled status of the cache, or to set the cache's
* evictions enabled status.
*/
public boolean evictions_enabled;
/**
* set_initial_size: Boolean flag indicating whether the size of the
* initial size of the cache is to be set to the value given in
* the initial_size field. If set_initial_size is FALSE, the
* initial_size field is ignored.
*/
public boolean set_initial_size;
/**
* initial_size: If enabled, this field contain the size the cache is
* to be set to upon receipt of this structure. Needless to say,
* initial_size must lie in the closed interval [min_size, max_size].
*/
public long initial_size;
/**
* min_clean_fraction: double in the range 0 to 1 indicating the fraction
* of the cache that is to be kept clean. This field is only used
* in parallel mode. Typical values are 0.1 to 0.5.
*/
public double min_clean_fraction;
/**
* max_size: Maximum size to which the cache can be adjusted. The
* supplied value must fall in the closed interval
* [MIN_MAX_CACHE_SIZE, MAX_MAX_CACHE_SIZE]. Also, max_size must
* be greater than or equal to min_size.
*/
public long max_size;
/**
* min_size: Minimum size to which the cache can be adjusted. The
* supplied value must fall in the closed interval
* [H5C__MIN_MAX_CACHE_SIZE, H5C__MAX_MAX_CACHE_SIZE]. Also, min_size
* must be less than or equal to max_size.
*/
public long min_size;
/**
* epoch_length: Number of accesses on the cache over which to collect
* hit rate stats before running the automatic cache resize code,
* if it is enabled.
*/
public long epoch_length;
// size increase control fields:
public int incr_mode; // H5C_cache_incr_mode
// size increase control fields
/**
* incr_mode: Instance of the H5C_cache_incr_mode enumerated type whose
* value indicates how we determine whether the cache size should be
* increased. At present there are two possible values.
*/
public int incr_mode;
/**
* lower_hr_threshold: Lower hit rate threshold. If the increment mode
* (incr_mode) is H5C_incr__threshold and the hit rate drops below the
* value supplied in this field in an epoch, increment the cache size by
* size_increment. Note that cache size may not be incremented above
* max_size, and that the increment may be further restricted by the
* max_increment field if it is enabled.
*/
public double lower_hr_threshold;
/**
* increment: Double containing the multiplier used to derive the new
* cache size from the old if a cache size increment is triggered.
* The increment must be greater than 1.0, and should not exceed 2.0.
*/
public double increment;
/**
* apply_max_increment: Boolean flag indicating whether the max_increment
* field should be used to limit the maximum cache size increment.
*/
public boolean apply_max_increment;
/**
* max_increment: If enabled by the apply_max_increment field described
* above, this field contains the maximum number of bytes by which the
* cache size can be increased in a single re-size.
*/
public long max_increment;
public int flash_incr_mode; // H5C_cache_flash_incr_mode
/**
* flash_incr_mode: Instance of the H5C_cache_flash_incr_mode enumerated
* type whose value indicates whether and by which algorithm we should
* make flash increases in the size of the cache to accommodate insertion
* of large entries and large increases in the size of a single entry.
*/
public int flash_incr_mode;
/**
* flash_multiple: Double containing the multiple described above in the
* H5C_flash_incr__add_space section of the discussion of the
* flash_incr_mode section. This field is ignored unless flash_incr_mode
* is H5C_flash_incr__add_space.
*/
public double flash_multiple;
/**
* flash_threshold: Double containing the factor by which current max cache
* size is multiplied to obtain the size threshold for the add_space flash
* increment algorithm. The field is ignored unless flash_incr_mode is
* H5C_flash_incr__add_space.
*/
public double flash_threshold;
// size decrease control fields:
public int decr_mode; // H5C_cache_decr_mode
// size decrease control fields
/**
* decr_mode: Instance of the H5C_cache_decr_mode enumerated type whose
* value indicates how we determine whether the cache size should be
* decreased. At present there are four possibilities.
*/
public int decr_mode;
/**
* upper_hr_threshold: Upper hit rate threshold. The use of this field
* varies according to the current decr_mode.
*/
public double upper_hr_threshold;
/**
* decrement: This field is only used when the decr_mode is
* H5C_decr__threshold.
*/
public double decrement;
/**
* apply_max_decrement: Boolean flag used to determine whether decrements
* in cache size are to be limited by the max_decrement field.
*/
public boolean apply_max_decrement;
/**
* max_decrement: Maximum number of bytes by which the cache size can be
* decreased in a single re-size. Note that decrements may also be
* restricted by the min_size of the cache, and (in age out modes) by
* the empty_reserve field.
*/
public long max_decrement;
/**
* epochs_before_eviction: Integer field used in H5C_decr__age_out and
* H5C_decr__age_out_with_threshold decrement modes.
*/
public int epochs_before_eviction;
/**
* apply_empty_reserve: Boolean field controlling whether the empty_reserve
* field is to be used in computing the new cache size when the
* decr_mode is H5C_decr__age_out or H5C_decr__age_out_with_threshold.
*/
public boolean apply_empty_reserve;
/**
* empty_reserve: To avoid a constant racheting down of cache size by small
* amounts in the H5C_decr__age_out and H5C_decr__age_out_with_threshold
* modes, this field allows one to require that any cache size
* reductions leave the specified fraction of unused space in the cache.
*/
public double empty_reserve;
// parallel configuration fields:
// parallel configuration fields
/**
* dirty_bytes_threshold: Threshold of dirty byte creation used to
* synchronize updates between caches.
*/
public long dirty_bytes_threshold;
/**
* metadata_write_strategy: Integer field containing a code indicating the
* desired metadata write strategy.
*/
public int metadata_write_strategy;

/** H5AC_cache_config_t is a public structure intended for use in public APIs.
* At least in its initial incarnation, it is basically a copy of struct
* H5C_auto_size_ctl_t, minus the report_fcn field, and plus the
* dirty_bytes_threshold field.
*
* @param version: Integer field containing the version number of this version
* @param rpt_fcn_enabled: Boolean field used to enable and disable the default reporting function.
* @param open_trace_file: Boolean field indicating whether the trace_file_name
* field should be used to open a trace file for the cache.
* @param close_trace_file: Boolean field indicating whether the current trace
* file (if any) should be closed.
* @param trace_file_name: Full path of the trace file to be opened if the
* open_trace_file field is TRUE.
* @param evictions_enabled: Boolean field used to either report or set the current
* evictions enabled status of the cache.
* @param set_initial_size: Boolean flag indicating whether the size of the
* initial size of the cache is to be set to the value given in
* the initial_size field.
* @param initial_size: If enabled, this field contain the size the cache is
* to be set to upon receipt of this structure.
* @param min_clean_fraction: double in the range 0 to 1 indicating the fraction
* of the cache that is to be kept clean.
* @param max_size: Maximum size to which the cache can be adjusted.
* @param min_size: Minimum size to which the cache can be adjusted.
* @param epoch_length: Number of accesses on the cache over which to collect
* hit rate stats before running the automatic cache resize code.
* @param incr_mode: Instance of the H5C_cache_incr_mode enumerated type.
* @param lower_hr_threshold: Lower hit rate threshold.
* @param increment: Double containing the multiplier used to derive the new
* cache size from the old if a cache size increment is triggered.
* @param apply_max_increment: Boolean flag indicating whether the max_increment
* field should be used to limit the maximum cache size increment.
* @param max_increment: If enabled by the apply_max_increment field described
* above, this field contains the maximum number of bytes by which the
* cache size can be increased in a single re-size.
* @param flash_incr_mode: Instance of the H5C_cache_flash_incr_mode enumerated
* type whose value indicates whether and by which algorithm we should
* make flash increases in the size of the cache to accommodate insertion
* of large entries and large increases in the size of a single entry.
* @param flash_multiple: Double containing the multiple described above in the
* H5C_flash_incr__add_space section of the discussion of the
* flash_incr_mode section.
* @param flash_threshold: Double containing the factor by which current max cache
* size is multiplied to obtain the size threshold for the add_space flash
* increment algorithm.
* @param decr_mode: Instance of the H5C_cache_decr_mode enumerated type whose
* value indicates how we determine whether the cache size should be
* decreased.
* @param upper_hr_threshold: Upper hit rate threshold. The use of this field
* varies according to the current decr_mode.
* @param decrement: This field is only used when the decr_mode is
* H5C_decr__threshold.
* @param apply_max_decrement: Boolean flag used to determine whether decrements
* in cache size are to be limited by the max_decrement field.
* @param max_decrement: Maximum number of bytes by which the cache size can be
* decreased in a single re-size.
* @param epochs_before_eviction: Integer field used in H5C_decr__age_out and
* H5C_decr__age_out_with_threshold decrement modes.
* @param apply_empty_reserve: Boolean field controlling whether the empty_reserve
* field is to be used in computing the new cache size when the
* decr_mode is H5C_decr__age_out or H5C_decr__age_out_with_threshold.
* @param empty_reserve: To avoid a constant racheting down of cache size by small
* amounts in the H5C_decr__age_out and H5C_decr__age_out_with_threshold
* modes.
* @param dirty_bytes_threshold: Threshold of dirty byte creation used to
* synchronize updates between caches.
* @param metadata_write_strategy: Integer field containing a code indicating the
* desired metadata write strategy.
*/
public H5AC_cache_config_t (int version, boolean rpt_fcn_enabled, boolean open_trace_file,
boolean close_trace_file, String trace_file_name, boolean evictions_enabled,
boolean set_initial_size, long initial_size, double min_clean_fraction, long max_size,
Expand Down
22 changes: 14 additions & 8 deletions java/src/hdf/hdf5lib/structs/H5E_error2_t.java
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Expand Up @@ -20,14 +20,20 @@
*/
public class H5E_error2_t implements Serializable{
private static final long serialVersionUID = 279144359041667613L;

public long cls_id; //class ID
public long maj_num; //major error ID
public long min_num; //minor error number
public int line; //line in file where error occurs
public String func_name; //function in which error occurred
public String file_name; //file in which error occurred
public String desc; //optional supplied description
/** class ID */
public long cls_id;
/** major error ID */
public long maj_num;
/** minor error number */
public long min_num;
/** line in file where error occurs */
public int line;
/** function in which error occurred */
public String func_name;
/** file in which error occurred */
public String file_name;
/** optional supplied description */
public String desc;

H5E_error2_t(long cls_id, long maj_num, long min_num, int line, String func_name, String file_name, String desc) {
this.cls_id = cls_id;
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