Modify h5repack to integrate with VOL connectors
Update tools library to accomodate VOL connectors
Update logic in h5tools_fopen for VOL connectors
Add command-line options to h5repack for specifying in/out VOL
connectors
Implement h5tools_set_vol_fapl
Fix library shutdown issue
Integrate ROS3 and HDFS VFDs into new h5tools_get_fapl() scheme
Avoid H5Ocopy in h5repack when using different VOL connectors
Update h5tools_test_utils.c for ROS3 and HDFS integration
* commit 'f19e06b59ee53f17465a7b5974c25c3245a40d9a':
testpar/t_2Gio.c: Fix a typo that I think was introduced by a previous warnings PR. An array element was assigned to itself---shape[2]Â =Â shape[2];---instead of being assigned to chunk[2].
previous warnings PR. An array element was assigned to
itself---shape[2]Â =Â shape[2];---instead of being assigned to
chunk[2].
fortran/src/H5Pf.c: move conditional compilation controlled by
H5_NO_DEPRECATED_SYMBOLS outside of a function for readability.
fortran/src/H5match_types.c: put a variable's declaration under the same
conditional compilation (H5_FORTRAN_HAVE_C_LONG_DOUBLE) as its
use.
For now, skip compilation of some unused debug dump routines in the JNI.
While I'm in the JNI, delete a set-but-unused variable.
src/H5Z.c: condition a variable declaration on H5_NO_DEPRECATED_SYMBOLS
so that it's not declared but unused or vice versa.
test/cache_common.h: add an #include in to get some symbols we need to
avoid implicit declaration warnings.
test/dsets.c: use a more conventional conditional-compilation syntax.
test/dt_arith.c, test/fillval.c: initialize a bunch of uninitialized
variables before use.
test/vfd.c: pass the expected type of `void **` to posix_memalign(3)
instead of `int **`.
testpar/t_bigio.c: explicitly compare with 0 instead of using ! when
"equal to 0?" is the question not "is false?" Repair some
indentation while I'm here.
testpar/testpar.h: repair misaligned line-continuation backslashes in a
macro that probably should be a function so that we don't have
to fiddle with the line continuation to begin with.
tools/src/h5repack/h5repack_main.c: fix some compiler fussing about
enums.
tools/test/perform/pio_engine.c: the compiler fusses if you cast a
function call returning double directly to off_t. It's ok if
you cast a variable that's a double to off_t, however. Write
and use a new function, sqrto(), to avoid the cast warnings.
Reduce gratuitous casts---e.g., (size_t)1.
Use the right format string for a pointer.
In the H5C sanity checks, change a "size increase" variable from ssize_t
(too narrow) to int64_t (wide enough).
Parenthesize every appearance of `storage` in the macro
`H5D_CHUNK_STORAGE_INDEX_CHK(storage)` so that you can pass in an
expression like &sc and it works properly.
Disallow re-assignment of the `dset` parameter to H5D__chunk_init()
because it helped assure me that it's safe to replace the repeating
expression `&dset->shared->layout.storage.u.chunk` with `sc` throughout.
Replace lengthy expressions such as
`&dset->shared->layout.storage.u.chunk` with `sc` throughout several
functions in H5Dchunk.c ISTR that the compiler warned that `sc` was
declared but unused in a couple of functions, and then I found that `sc`
could be used in many places. Maybe the disused `sc` appeared because a
bunch of code was copied and pasted, I don't know. Anyway, it's a lot
tighter code now that I use `sc`.
In H5D__chunk_update_old_edge_chunks() and H5D__chunk_delete()
I actually expand `sc` and another temporary variable, `pline`,
because they're used only in !defined(NDEBUG) code. This squashes
unused-variable warnings in the defined(NDEBUG) configuration.
Don't drop the `volatile` qualification with a cast in
tools/src/h5import/h5import.c.
* commit '44739ccd4715cc9e15595575700e945341fcdbcc':
Tidying from code review.
Fixed stack and frame size warnings. Not complete, but fixes most of the easier cases.
* commit '0a2bb11b248df6841daabca3970df5d8504adfc7':
address problems from comments
fix and address comments
change according to previous comments
add missing piece
remove unnecessary check macro
fix intel compile warnings
Revert "fix warnings from Intel compiler"
Revert "fix warnings and some text alignment"
Revert "let hdf5 pick up the right compiler in Intel environment"
Revert "fix issues from previous PR comments"
Revert "using a different MACRO"
using a different MACRO
fix issues from previous PR comments
let hdf5 pick up the right compiler in Intel environment
fix warnings and some text alignment
fix warnings from Intel compiler
* commit 'b55a584fd5b3aac6f2514fba41a6182030b497ae':
In portable shell scripts (using #!/bin/sh) we have to use single square brackets, [ ], instead of the bash-ism double square brackets, [[ ]].
Make this script work on hosts where PERL is not installed at /usr/bin/perl.
* commit '0772b975d1d2bfa15aedeb4b6e2c2aac78c61a2f':
Fix missing free in H5T__ref_mem_read()
Fix bugs in H5VL file comparison code. Add short circuit success to H5VL_cmp_connector_cls().
Implement file comparison VOL callback. Other changes to allow references to work with non-native connectors. There is a bug somewhere.
Add support for point selections to H5S_select_project_intersection.
Remove H5VL_NATIVE_FILE_GET_FILE_ID and add H5VL_OBJECT_GET_FILE
Revert "Make a squash commit of 'Quiet some warnings by adjusting warnings level and fixing some code.' (commit 5c911d8baf)"
Revert "Oops, remove more C99 designated initializers for VS 2010 compatibility."
H5R: fix H5Tconv to check for null references
Trivial parameter renaming in VOL API calls.
Move checking for zero offset in selection adjust calls to the selection callbacks. This makes the procedure for checking it consistent across selection types and between _s and _u, ensures it is always is performed even when called within the H5S package, and removes the redundant check that would occur when callins H5S_select_adjust_s() from outside the H5S package.
Replace H5Sselect_adjust_u() and H5Shyper_adjust_s() with H5Sselect_adjust. Implement "adjust_s" callback for all selection types. Add range checking to H5Sselect_adjust().
* commit 'a8892bb42d6f6e4fbc30fae0eb2b957f81c938b9': (45 commits)
Oops, remove more C99 designated initializers for VS 2010 compatibility.
Add an #include to get a function declaration.
Don't use C99 designated initializers, they're not compatible with Visual Studio 2010.
Quiet some more maybe-uninitialized warnings---each is a false positive, *sigh*. This is more code that may not compile with VS2010, *sigh sigh*.
Always warn on maybe-uninitialized. -Wincompatible-pointer-types was not available until GCC 5, so enable it only if that's the GCC version we're using.
Only promote maybe-uninitialized warnings to errors on GCC 8. Even on GCC 8, there may be false positives at low optimization levels? I need to check.
Only use -Werror=cast-function-type with GCC 8 and later.
Put all of the -W options back into the order I found them in so that it's easier to compare old and new config/gnu-flags.
Add new source files to CMakeLists.txt.
Mention the -Werror= flags in libhdf5.settings.in.
free -> HDfree
Promote decleration-after-statement warnings to errors.
Quiet decleration-after-statement warnings.
Move a statement under some declarations since some vintages of Visual Studio don't like declarations after statements.
Document H5D__chunk_mem_xfree_wrapper().
Undo accidental test deletion.
Oops, delete a debug printf that snuck in here.
Undo my changes to the HD macros, hadn't really intended those to be on this branch....
Make errors of some more warnings. Move disabled warnings to DEVELOPER_WARNING_CFLAGS. Put just one warning option on a line, and sort some of the options.
Cast to the parameter type, H5VL_token_t *, instead of to unsigned char *.
...
* 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 `==`.
* commit '4c558700ab33934e7358483c5d20fea4823baf9e':
Update RELEASE.txt for reference changes
Fix reference type comparison in h5dump
Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim()
Add new H5R API that abstracts object, region and attribute reference types
Remove ability to loc by ref from H5VL layer
Add support for retrieving object name by token
Add H5VL_OBJECT_GET_TYPE to get object type
Add H5VL_MAX_TOKEN_SIZE and H5VL_token_t
Adapt Jerome's "file info" H5VL 'get' query to retrieve container token info.
Fix H5VL_blob_get to return size of blob
Add 'blob' callbacks to VOL, along with a native implementation to store them in the global heap, and changed the VL datatype conversion code to use blobs.
Remove debugging logic from the new t_bigio test
Expanded t_bigio.c to include Jordan's test from HDFFV-10539
Another cleanup pass as suggested by the reviewers.
Fix some typos and remove an unused prototype from H5Sprivate.h
At the suggestion of the PR reviewers, moved the mpio_create_large_type to H5mpi.c and renamed the function appropriately. Also moved some support functions to set and get the vvalue where we transistion to using derived datatypes.
Made code review edit suggested by Jerome, plus various code updates to files that I touched to eliminate compile warnings (on my Linux box).
No functional changes, just removed some tab characters
Make the initial bug fixes to allow >2GB writes with Independent IO
* commit 'a6930a2bcfd37ea3610baafb608faec883286315':
Renamed get/set_time() calls in the tools library to avoid name clash when building static parallel HDF5 w/ static linking to OpenMPI.
* commit 'f97e11e7635a0cd8728d4604ca5dceb3925ba44c':
Update comment and check for strtoumax.
Modify CMakeLists.txt file for renamed h5tools_test_utils files.
Add HD to string functions. Switched strtoul to strtoumax in H5FDs3comms.c. Removed unused functions and variables in s3 and hdfs TestH5Pfapl*.java. Update Copyright headers.
Squashed commit of the following:
* commit '35fd0ec8ceffe96cee352187154da15c967fb990':
Updated H5Tcopy() to get the dataset's datatype through the VOL when that is passed in as the object ID.
Fix fortran test and test library linking
Update GCC 6 & 7 flags for CMake builds
Move -Wnormalized down into GCC 6.x flags
Put the memcpy overlap check back into H5MM.
Fixed the heap overflow in t_filters_parallel
Fixed some low-hanging fruit from -fsanitize in t_filters_parallel.
Add lib dir for testing plugins
Add support for GCC 7.x warnings, update warnhist script to account for them, clean up warnings.
Add H5_HLDLL prefix for windows link
HDFFV-10805 cleanup examples and test code
Fix minor typo in H5S_select_iter_release
Add missing fortran mods
HDFFV-10805 Fix test of library libinfo
Cleanup possible CMake target conflicts
Correct CMake issues
should always be built and installed whether tools are enabled or
disabled. Also added Makefile.am to bin to build h5redeploy and
to install and uninstall them. h5cc is created from h5cc.in by
configure.
disabling tests.
Moved h5cc.in from tools/src/misc to src directory to always create h5cc
whether or not tools are enabled.
Added configuration status of tools and tests to libhdf5.settings.
* commit '844f38c6462f42a9a3a6002de6a4acb0520b8fb7':
Correct entry
Snapshot version 1.11 release 4. Update version to 1.11.5.
Allow option to select NAMESPACE
Correct examples for packaging
This implicitly adds support for changing the VOL connector for command-line
tools or any application linked with the library.
Also, add 'make check-vol' support for all directories, clearing up necessary
issues in testing scripts, etc.
HDFFV-10586 and HDFFV-10588
* commit '25cd1ab02b9ddaf58a4f5422f4ab4fde411e050a':
Added test for HDFFV-10588
Fixed HDFFV-10684
Fixed HDFFV-10586 and HDFFV-10588 Description: HDFFV-10586 CVE-2018-17434 Divide by zero inh5repack_filters Added a check for zero value HDFFV-10588 CVE-2018-17437 Memory leak in H5O_dtype_decode_helper This is actually an Invalid read issue. It was found that the attribute name length in an attribute message was corrupted, which caused the buffer pointer to be advanced too far and later caused an invalid read. Added a check to detect attribute name and its length mismatch. The fix is not perfect, but it'll reduce the chance of this issue when a name length is corrupted or the attribute name is corrupted. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
Description:
HDFFV-10586 CVE-2018-17434 Divide by zero inh5repack_filters
Added a check for zero value
HDFFV-10588 CVE-2018-17437 Memory leak in H5O_dtype_decode_helper
This is actually an Invalid read issue. It was found that the
attribute name length in an attribute message was corrupted,
which caused the buffer pointer to be advanced too far and later
caused an invalid read.
Added a check to detect attribute name and its length mismatch. The
fix is not perfect, but it'll reduce the chance of this issue when a
name length is corrupted or the attribute name is corrupted.
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1010test)
* commit '90d13bef33f9e2e80b23996a0c39f16f7c34ecf8':
Fixed typo Platforms tested: Darwin (osx1010test)
Refixed HDFFV-10578 Description: Applied Neil's fix for this issue after removing previous attempt. The resources are now released in init_objs() when failure occurs there. Neil will fix HDFFV-10676 separately. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
Removed previous change in H5O__chunk_deserialize().
Removed the previous change in H5O__chunk_deserialize()
Removed previous change in table_list_add().
Removed the previous change in table_list_add()
Updated per review Description: HDFFV-10676 - CVE-2018-13873 Changed the new assert to if statement, per Dana's comment. Platforms tested: Linux/64 (jelly)
HDFFV-10578 and HDFFV-10676 Description: HDFFV-10578 - CVE-2018-17234 The file has some issue, however, there was a bug in h5dump that caused memory leaks after the problem in the file was encountered. The bug was that an if statement was missing in the function table_list_add() resulting in the memory not being freed at a later time. After the fix had been applied, there were no more leaks after h5dump detected the issue in the file and reported the error.
Description:
Applied Neil's fix for this issue after removing previous
attempt. The resources are now released in init_objs() when
failure occurs there.
Neil will fix HDFFV-10676 separately.
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1010test)
