| Commit message (Collapse) | Author | Age | Files | Lines |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
This brings the H5VL code in line with the H5I code regarding
naming, parameter order, etc.
Several public API calls were affected by this change.
These changed names to reflect their use with VOL drivers:
H5VLregister() --> H5VLregister_driver()
H5VLregister_by_name() --> H5VLregister_driver_by_name()
H5VLunregister() --> H5VLunregister_driver()
H5VLis_registered() --> H5VLis_driver_registered()
This call was renamed to match H5Iregister(). The order of the first
two parameters also reversed and the object pointer is now const.
H5VLobject_register() --> H5VLregister()
|
| |
|
| |
|
|
|
|
| |
other misc).
|
|
|
|
| |
orginally intended to support the full SWMR feature.
|
| |
|
| |
|
| |
|
|
|
|
|
|
|
|
|
|
| |
hdf5_1_10
* commit '54957d37f5aa73912763dbb6e308555e863c43f4':
Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes.
Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh.
Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1
Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
|
|\ |
|
| |
| |
| |
| |
| |
| |
| |
| | |
Bring over missing flush+refresh routines, to address Java failures.
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
Linux/64 2.6.18 (jam) w/Java
|
| | |
|
| | |
|
|/
|
|
|
| |
flush flag up the function call stack and not setting
it during H5Dclose().
|
|
|
|
|
|
|
|
| |
metadata optimizations.
- rename H5AC_dxpl_id to H5AC_ind_read_dxpl_id and update all usage in the library
tested on bb-8 with parallel and serial.
|
|
|
|
|
|
|
|
|
|
| |
checks from metadata dxpls
- remove H5AC_ind_dxpl_id and use only H5AC_dxpl_id everywhere instead.
- remove flush_me_collectively flag from cache entries
- add a collective sanity check (MPI_Barrier) for every HDF5 API routine that could possibly touch the file. This is trigerred when the environment variable H5_COLL_API_SANITY_CHECK is set to a non 0 digit.
tested on BB-8 with serial and parallel.
|
|
|
|
|
|
|
|
| |
Normalize against incoming changes from the phdf5_metadata_opt branch.
Tested on:
MacOSX/64 10.11.2 (amazon) w/serial & parallel
(h5committest forthcoming)
|
|
|
|
|
|
|
|
| |
Normalize against changes on phdf5_metadata_opt branch to trunk
Tested on:
MacoSX/64 10.11.2 (amazon) w/serial & parallel
(h5committest forthcoming)
|
|
|
|
| |
internal one.
|
|
|
|
|
|
|
|
| |
Clean up memory leak when generating group creation property list for user.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & valgrind
Linux/64 4.1.8 (Jerome's laptop) w/serial & valgrind
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Complete revamp of package initialization/shutdown mechanism in the library.
Each package now has a single init/term routine.
This new way should avoid packages being re-initialized during library
shutdown and is also be _much_ more proactive about giving feedback for
resource leaks internal to the library.
Introduces a new "module" header file for packages in the library
(e.g src/H5Fmodule.h) which sets up some necessary package configuration macros
for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly
modified version of this header, src/H5FDdrvr_module.h)
Also cleaned up a bunch of resources leaks all across the library and tests,
along with addressing many warnings, as I encountered them.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
Linux/64 3.10.x (kituo) w/serial & parallel
Linux/64 2.6.x (ostrich) w/serial
|
|
|
|
|
|
| |
- allocate sieve buffer with calloc instead of malloc
tested with h5committest
|
|
|
|
|
|
|
|
|
| |
Merge 64-bit ID changes from branch to trunk. (Plus a few minor cleanups
that aren't on the branch)
Tested on:
Mac OSX/64 10.9.4 (amazon) w/C++ & FORTRAN
(h5committested on branch already for a week)
|
|
|
|
|
|
|
|
|
| |
Begin process of migrating from using property list IDs internally to the
library to using the internal generic property list data structure.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel
(h5committest forthcoming)
|
|
|
|
|
|
|
|
| |
Check in Neil's changes for correctly handling case where library is
reinitialized through a deprecated routine.
Tested on:
Linux 2.4.x/32 (jam)
|
|
|
|
|
|
|
|
| |
Switch H5I internal data structure from using hash table to skip lists.
Tested on:
Mac OSX 10.8.4 (amazon) w/C++ & FORTRAN
FreeBSD, Linux, etc. forthcoming
|
|
|
|
|
|
|
|
|
|
|
| |
Tested: jam, koala, ostrich (h5committest)
Log from r23939:
Fix unused variables warnings in trunk
Rename static functions in H5Adense.c, H5B2cache.c, H5Bcache.c
Switch these functions to use FUNC_ENTER_STATIC* macros
Tested: koala
|
|
|
|
|
|
|
|
|
| |
protection measures:
1. If any opened object uses the filter, let it fail.
2. Flush all opened files to push any cached data to files.
Tested with h5committest.
|
|
|
|
|
|
|
|
|
| |
Refactor ID class registration to be more like how other "class"s in the
library are registered, and clean up compiler warnings.
Tested on:
Mac OSX/64 10.7.4 (amazon) w/debug
(Too minor to require h5comittest)
|
|
|
|
|
|
|
|
|
| |
Add FUNC_ENTER macros for package-private routines and begin process of
switching package routines to use them. All H5G routines are currently
finished.
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug, production & parallel
|
|
|
|
|
|
|
|
| |
Refactor function name macros and simplify the FUNC_ENTER macros, to clear
away the cruft and prepare for further cleanups.
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug, production & parallel
|
|
|
|
|
|
|
|
|
|
| |
Bring [spirit of] r20393 from coverity branch back to trunk:
Move initialization ocrt_info.new_obj = NULL; before FUNC_ENTER_NOAPI -- gh
Tested on:
Mac OS X/64 10.7.3 (amazon) w/debug, production & parallel
(too minor to require h5commitest)
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Description:
Added new H5SL_TYPE_GENERIC skip list type, which uses void *'s as keys and a
client-supplied callback for key comparison. This was added to support the
upcoming "merge named datatype" feature for H5Ocopy, but may be used in other
places as well. Also added testing.
Also fixed a potential bug with the H5SL_TYPE_OBJ implementation, and added
testing for that.
Tested: jam, koala, heiwa (h5committest), durandal
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Clean up some compiler warnings, but mainly an interim checkin on the
path of reducing code coupling in the library by removing most of the places
which were accessing H5F package definitions.
Tested on:
Mac OS X/32 10.6.8 (amazon) w/debug
FreeBSD/32 8.2 (loyalty) w/debug
FreeBSD/64 8.2 (freedom) w/debug
Linux/64 2.6 (heiwa) w/debug
Linux/64 2.6 (ember) w/parallel
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring Coverity changes back to trunk:
r20340:
Address coverity issue 248. Set freed pointer to NULL if realloc fails, then check for NULL before attempting to close array of handles stored in memory addressed by pointer.
r20341:
Added initialization udata.path = NULL; udata.visited = NULL; to prevent unintialized use after done: label.
Do C-style initialization AFTER all variable definitions.
r20342:
Fix valgrind error in H5DUMP-XML-tall.h5
r20343:
Addressed Coverity issue 591 - check the return value of H5S_SELECT_ITER_RELEASE.
r20344:
Added initialization udata.path = NULL; to prevent uninitialized used after done: label
r20347:
Purpose: Fix memory leak in overhead.c
Description: Fixed leak in test() in overhead.c where array "had" was never
freed.
r20348:
Addressed Coverity issue 705 - added prototype for resize_configs_are_equal to cache_common.h.
r20392:
Purpose: Fix coverity issues 1677 and 1678
Description: Added return value checking for 4 funciton calls in
H5tools_get_symlink_info().
r20394:
Purpose: Fix coverity issues 1674 and 1675
Description: Modified H5Epush2() and H5E_printf_stack() to keep track of whether
va_start() has been called, and to call va_end() at the end if so.
r20395:
Should be H5MM_calloc(count * sizeof(void*)). Fixed --gh
r20396:
Should be H5MM_calloc(count * sizeof(void*)). Fixed. --gh
Tested on:
Mac OSX/32 10.6.7 (amazon) w/debug & production
(h5committested on branch)
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Description:
When closing an object that had two open id's, the library would previously fail
to account for the status of the "holding_file" field, potentially causing the
file's "nopen_objs" field to become inconsistent. This caused problems when
opening the same object twice through an external link using th external file
cache. Modified the library to properly account for the status of the
"holding_file" field when closing an object id, even when the underlying
"shared" object isn't closed.
Tested: jam, koala, heiwa (h5committest)
|
|
|
|
|
|
|
|
|
|
|
| |
Remove global variable for the path name in the group traversal code. Also
clean up a bunch of compiler warnings.
Tested on:
Mac OS X/32 10.6.7 (amazon) w/debug & production
FreeBSD/32 6.3 (duty) w/debug
FreeBSD/64 6.3 (liberty) w/debug
Solaris/32 2.7 (linew) w/debug
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Refactor root group routines to centralize and simplify them some.
Also patch root group's file pointer when it doesn't match the querying
file, from H5G_rootof.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Mac OS X/32 10.6.6 (amazon) in debug mode
Mac OS X/32 10.6.6 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.6 (amazon) w/parallel, in debug mode
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Address issue with object headers being created getting evicted from
the metadata cache cache before they are completely initialized. This is
done by pinning the object header in the cache until it is completely
initialized and attached to a group.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
|
|
|
|
|
|
|
|
|
|
|
| |
Description:
Library versions 1.6.3 and earlier contain a bug which causes them to be unable
to perform certain operations on a group if that group's symbol table
information is not cached in the parent group's symbol table. Versions 1.8.0
to 1.8.5 did not cache this information. Modified library to cache this
information.
Tested: jam, amani, heiwa (h5committest)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Clean up the internal usage H5I_dec_ref() to eliminate the sequence of
flags that has been creeping in.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
|
|
|
|
|
|
|
| |
couldn't close (bug 1260). The fix releases all resources and closes
the dataset but returns a failure.
Tested with h5committest - jam, heiwa, amani.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r18672 from metadata journaling "merging" branch to trunk:
Mostly changes to move to only using one 'user data' parameter for
calls to H5AC_protect(), along with some minor reformatting code cleanups.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.3 (amazon) in debug mode
Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
|
|
|
|
|
|
|
|
| |
Clean up compiler warnings
Tested on:
Mac OS X/32 10.6.3 (amazon) w/debug
(too minor to require h5committest)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring r18542 from metadata journaling "merging" branch to trunk:
Bring new object header pin/unpin & protect/unprotect routines and
split-out object header chunk proxy changes from metadata_journaling branch to
"merging" branch, along with some other minor tweaks to clean up compiler
warnings, etc.
Also: clean up chunk protect/unprotect calls when allocating or freeing
space in a chunk, optimize metadata accumulator code to avoid some re-reading
of information from the file, refactor H5O_pin/H5O_unpin from way they are done
on the merging branch back to way they were previously done on trunk, other
minor code cleanups, etc.
Tested on
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.3 (amazon) in debug mode
Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring "compress group's fractal heap" feature from branch back to
trunk.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers, w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.1 (amazon) in debug mode
Mac OS X/32 10.6.1 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Description:
Versions of the library between 1.3.0 and 1.6.3 have a bug which prevents them
from opening any file that does not have the root group's symbol table
information cached in the root group's entry in the superblock. Prior to 1.8
this was not an issue as this information was always cached. However, 1.8.0
stopped writing this information (which is not required by the file format
specification), and these older versions can therefore not read files created or
last written by versions 1.8.0 to 1.8.2. This fix modifies the library to once
again add this information to the superblock (when using the old file format).
Tested: jam, linew, smirom (h5committest)
|
|
|
|
|
|
|
|
|
| |
Description:
Changed Skip list package to use a deterministic skip list. This allows the
skip list package to avoid calling rand() and srand(), even on machines without
rand_r(). There is no longer a p-value or maximum level for skip lists.
Tested: jam, smirom, linew (h5committest)
|
|
|
|
|
|
|
|
|
|
|
| |
Description:
Some files apparently exist in the wild which have corrupt symbol table messages
on the root group. These files can be opened by 1.6 (which uses the cached
information in the superblock) but not by 1.8. This patch fixes 1.8 and 1.9 so
they can now open these files, and will correct them if necessary. Also fix
some potential (rare) problems with array datatype versions.
Tested: jam (parallel; h5committest not working on linew or smirom)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring file free space branch changes through r15795 into trunk, which
includes a fair bit of code cleanup & rearrangement along with a couple of
bug fixes also.
Tested on:
Mac OS X/32 10.5.5 (amazon) in debug mode
Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
|