* commit 'b42325e8f5ff3b6bfa2ce446af5b6dc5cbbff666':
More fixes for previous committed PR #2079 dated Dec 5 2019. (1) H5O_dtype_ver_bounds[] for V112 should be H5O_DTYPE_VRESION_4 (2) The tests for the new reference types should work for V112 and beyond
* commit '7b03a1c03633d695b487642e54f897c715f8622e':
Fix H5VL_token_t type and fix H5VL_loc_by_token to use H5VL_token_t *
Change hdset_reg_ref_t and H5R_ref_t from arrays of unsigned char to structs containing those arrays. Encapsulating the arrays in this way makes it easier to write and think about pointers to these types, casts to/from these types, etc.
structs containing those arrays. Encapsulating the arrays in this way
makes it easier to write and think about pointers to these types, casts
to/from these types, etc.
An interesting side-effect that we probably should *not* rely on is
that the struct-encapsulation changes the alignment so that some GCC
warnings about casts that increase the alignment requirement of the
operand go away. Warnings like that have to be taken seriously: I will
add -Werror=cast-align to the default compiler flags so that they stop
the build quickly.
GCC warnings led me to some surprising casts in test/trefer.c. I found
that it was possible to make many simplifications after introducing the
struct-encapsulation that I described, above.
In test objcopy_ref `same_file` is assigned but never used. Delete it.
* commit '4d834adba4aeb1a0174bddb83212b7073b64e269':
Use HD prefix.
Fix HDFFV-10937: use a more reliable (and probably faster) scheme for visiting all elements of a matrix in an arbitrary order.
* commit '0b721858e46a317c370a24115032d5be41688f67':
Make these scripts relocatable again: derive a relative path for the original installation prefix from the examples prefix. Use that relative path to locate the current installation prefix, always. Fall back to an absolute installation prefix if the relative path cannot be derived.
Get the path to prefix right: needs a ../ to back out of subdirectory c/.
Make this script relocatable again: derive a relative path for the original installation prefix from the examples prefix. Use that relative path to locate the current installation prefix, always. Fall back to an absolute installation prefix if the relative path cannot be derived.
Let us override the examples directory using --with-examplesdir=DIR. This is handy for NetBSD where HDF5 examples are installed by convention in $prefix/share/examples/hdf5/ rather than in ${prefix}/share/hdf5_examples/, which is the HDF5 default.
Follow longstanding execv convention for compatibility with NetBSD.
Under the examples directories, always find the installed HDF5 executables and scripts using @prefix@ instead of a relative path, because the number of ../ in the relative path will be different on NetBSD than on other systems.
Make the HDF5 configure script grok NetBSD.
For portability, insulate the HDF5 library from some system macros.
Not every system has perl installed in /usr/bin/, so change the shebang (#!) line to `/usr/bin/env perl` to locate perl on the PATH.
For portability, use the POSIX sh(1) string-comparison operator `=` instead of `==`.
Also support references to external files
Add new H5T_REF type and type conversion routines
Support conversion from H5T_REF_OBJ/DSET_REG to H5T_REF
Add H5Treclaim() API to reclaim memory of vlen/reference types
Deprecate H5Dvlen_reclaim()
Fix H5T_vlen_reclaim() and H5T_reclaim() to use private callback
Add H5T_ref_reclaim()
Move previous H5R APIs to H5Rdeprec.c
Clean up H5Ocopy
Separate H5O_copy_expand_ref() to H5Ocopy_ref()
Add support for copying new reference types
Clean up deprecated routines to go through VOL and same code path
Fix return codes in existing trefer.c test
Rename trefer.c to trefer_deprec.c
trefer.c is for new references
Add performance test for trefer
Add additional obj_copy_ref test
Make use of tokens and blobs to store references
Skip blob encoding for object references
Start adding new reference examples
H5Gget_objinfo() call had changed and passing in a non-existing
soft link with a statbuf of NULL passed instead of failed (as
it should as per the RM). The HDF5 1.8 and 1.10 behavior was
restored and H5Gget_objinfo() will now fail and return -1 as
before.
* commit '7924eee0e5ee0745b784c635042b8633886fb799':
(1) Address the feedback from the PR review (2) Add release notes
Fix for HDFFV-10585 investigate hyperslab slowness: 1) Improve hyperslab performance when doing I/O from 1-d disjoint file dataspace to 1-d contiguous memory dataspace. 2) Move coding in H5D__chunk_io_init() that is constructing the chunk mappings to a separate routine.
* commit '0ea77179d507bd2c29f3b9b357a0c35d4077b29c': (39 commits)
Fix the errors when updating the versions in the new 1.13 develop branch.
add missing version to list
Add new versioned filename to list
Update N_FSINFO_VERSION_BOUNDS to H5F_LIBVER_NBOUND.
Remove file script
Update versioning to next major version
Update develop branch version to 1.13.0 after creation of hdf5_1_12 branch.
Merge Binh-Minh's changes for code improvement to chunk_info.c (PR #1942) to develop branch.
Update to current external file population.
Revert else-if to single line.
Fix missing option and incorrect close
Revert "Moved NDEBUG guards to H5EA_DEBUG in H5EA package."
Revert "Fix for H5EA debug package when built in release mode."
Change print calls to HD-wrapped. Minor formatting tweaks (inc. regressions and in-file style-matching).
Refactor h5repackgentest to have more modular internals, for easier addition of new tests. Update manifest and test script for new hdf5 external-storage .h5 files.
Remove obsolete symbol
small syntax changes
Renamed get/set_time() calls in the tools library to avoid name clash when building static parallel HDF5 w/ static linking to OpenMPI.
Change unused variable to generic form
Whitespace cleanup
...
1) Improve hyperslab performance when doing I/O from 1-d disjoint file dataspace
to 1-d contiguous memory dataspace.
2) Move coding in H5D__chunk_io_init() that is constructing the chunk mappings to
a separate routine.
Description:
Fixed tests to handle the case when a requested compression filter
is not available.
Platform tested
Linux/64 (jelly)
Darwin (osx1011test)
- Added new chunk query functions: H5Dget_num_chunks(), H5Dget_chunk_info(), and H5Dget_chunk_info_by_coord()
- Fixed iterator issue in H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate()
* commit '96dab622e3bbe75d85b0cef3ca2bd5288cf4ac32':
Fixed error code and error messages Tested on Jelly (very minor)
Changed H5VL_NATIVE_DATASET_GET_CHUNK_INFO_BY_COOR to H5VL_NATIVE_DATASET_GET_CHUNK_INFO_BY_COORD per a review comment.
Updated comments
Updated based on reviews and refactored test code
Code cleanup and refactor
Re-ordered items w.r.t. date.
Fixed typo
Added notes about HDFFV-10677 and HDFFV-10661
HDFFV-10677 and HDFFV-10661
