| Commit message (Collapse) | Author | Age | Files | Lines |
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location set to be in a file. Only meant to be used by VOL connectors.
Implement H5VLpeek_connector_id() to support connectors querying their
own IDs. Fix app_ref with connector IDs in a couple places (external
VOLs registered as default through ENV should be visible to the
application). Modify vlen and reference interfaces to work with
arbitrary VOL connectors. Implement file "post open" specific
callback, to enable connectors to update their file structs after a
wrap context has been set.
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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
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naming convention for shared structs in rest of library data structures.
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pointer.
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- Added casts to quiet H5MM_memcpy warnings
- Removed char * casts from HDmemcpy
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cache. Fix issues involving datasets being "no allocated" when they
contain cached raw data.
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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.
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merge_hyperslab_updates
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Changes made so that raw data for dataset objects are copied from cached info when possible instead of flushing objects to file and read them back in again.
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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.
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improvements.
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Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1
autotools serial
autotools parallel (MPICH 3.1.4)
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(H5_DEBUG_BUILD)
tested on bb-8 with Serial and Parallel, debug and production builds.
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library.
Buffers that will be written to disk will now always be cleared since
not doing this has huge security implications.
Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0, x86_64) gcc 5.2.1
serial autotools
parallel autotools (MPICH 3.1.4)
serial CMake
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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.
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Also purged obsolete /*ARGSUSED*/ from the library.
Tested on:
Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
serial only
(these changes have been in revise_chunks for a long time)
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Refactor property list code to "deep copy" properties in the correct way,
retraining the rest of the library to copy & release things correctly. This
cleans up another batch of memory leaks, etc. within the library.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
Linux/32 2.6.x (jam) w/serial & parallel
(h5committest forthcoming)
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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
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Align w/vds branch: Move code for initializing contiguous datasets into
layout 'init' callback.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
(h5committest forthcoming)
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* H5_ATTR_FORMAT(X,Y,Z) __attribute__((format(X, Y, Z)))
- Rename UNUSED attribute characterstic to H5_ATTR_UNUSED.
- Rename NORETURN attribute characterstic to H5_ATTR_NORETURN
tested with h5committest.
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the arguments to be in a more logical order.
Tested on: h5committest
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Cache the dataset's rank & dimension sizes, instead of querying them
frequently, to speed up various checks & algorithms. Also, a few minor
cleanups.
Tested on:
MacOSX/64 10.10.2 (amazon) w/serial & parallel
Linux/32 2.6.18 (jam) w/serial & parallel
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- allocate sieve buffer with calloc instead of malloc
tested with h5committest
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Revert r25273, 25283 & 25439 (the hyperslab improvement changes). They
are buggy and it's taking me a long time to correct the problem. I'll check
in a revised form of the changes when I've got them straightened out.
Tested on:
Mac OSX 10.10.0 (amazon) w/gcc 4.9.x, C++, FORTRAN
Linux 2.6.x (jam) w/parallel
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Bring in Chao/Neil/my changes to optimize hyperslab selection operations
further, along with 3 new public API routines: H5Scombine_hyperslab(),
H5Sselect_select() and H5Scombine_select(), along with many minor cleanups to
the code and fixing a few compiler warnings.
Tested on:
Mac OSX/64 10.9.3 w/gcc 4.9.x and parallel w/OpenMPI
(h5commttest forthcoming)
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Check in Mohamad's changes to support collective I/O on point selections,
along with some other minor cleanups.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/parallel & serial
(h5committest forthcoming)
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project for
view objects. The addition of view objects in the fastforward project
is expected to be brough into the trunk sometimes in the future, which
is why we need to make this change.
Tested Manually on Jam and Ostrich.
Tested with h5commitest - Koala with intel compilers failed, but nothing had to do with those changes.
error on Koala: error while loading shared libraries: libirng.so
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Clean up more FUNC_ENTER/FUNC_LEAVE macros and move H5D & H5T code toward
the final design (as exemplified by the H5EA & H5FA code).
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug & parallel
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datasets in the file. It
could waste memory if any dataset size is smaller than the sieve buffer
size. Now the library picks the smaller one between the dataset size
and the sieve buffer size from the file access property.
Tested on jam, koala, and ostrich.
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Better fix for zero-sized dataset error (r22053).
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug & parallel
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Correct corner case for creating a contiguous dataset with a zero-sized
dataspace, when the allocation time is set to early.
Also clean up a few compiler warnings in the dataspace code.
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug & parallel
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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
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Clean up code a bit, move new "terminate" VFD callback to new position
in H5FD_class_t struct.
Tested on:
Mac OS X/32 10.6.7 (amazon) w/debug & production
(h5committest not required on this branch)
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Initial commit of John Biddescomb's VFD & MPI tweaks.
Tested on:
None (yet)
(h5committest not required for this branch)
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Bring Coverity revisions from branch back to trunk, and clean up some other
misc. compiler warnings also.
r19500:
Fix coverity items 1446 and 1447. Moved up calls to memset in test_cont in
ohdr.c so the test never tries to close uninitialized locations.
r19501:
Fix coverity items 1398-1445. Various uninitialized variable errors in fheap.c.
r19502:
Fixed coverity issue 579 and some additional warnings in the file as well.
r19503:
Bug fix: This fix addressed the "RESOURCE_LEAK" problems #789 and 790, run 26
r19504:
minor mods to try to keep coverity from flagging false positives.
r19505:
Fixed coverity issues 566 - 571. Declared variables that are passed to functions that use them as arrays to be arrays of size 1.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug, production & parallel
(h5committested on trunk)
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Optimize the vector-vector memcpy() routine even further, for a total
of ~2x speedup. :-)
Make a generic vector-vector operation routine and convert other
vector-vector read & write routines to use generic routine instead of multiple
copies of the basic algorithm.
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
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Polish the vectorized memory <-> memory and memory <-> file I/O
routines to speed them up a little bit (~10%)
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
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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
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couldn't close (bug 1260). The fix releases all resources and closes
the dataset but returns a failure.
Tested with h5committest - jam, heiwa, amani.
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with non-default VL
fill values.
Description:
Previously, H5D_chunk_allocate would, if a dataset were filtered and had a non-default VL fill value, allocate a new buffer for every chunk. Changed
H5D_chunk_allocate to reuse the existing buffer if possible. Also other
miscellaneous cleanup.
Tested: jam, linew, amani (h5committest)
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Bring back various minor tweaks & cleanups from the revise_chunks
branch.
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-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
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Clean up compiler warnings
Tested on:
Mac OS X/32 10.6.3 (amazon) w/debug
(too minor to require h5committest)
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Bring r18356 from metadata journaling merge branch to trunk:
Converge metadata journaling branch with trunk with a bunch of v1 B-tree
changes:
- Remove H5ACprivate.h header from H5Bprivate.h header
- Revise v1 B-tree client callbacks
- Get rid of H5B_serialize() by bringing it into H5B_flush()
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-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
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Bring revisions from Coverity fixing branch to trunk:
r18184:
Fixed Coverity issue 373. Allocated memory freed in line 762 in case of error.
r18185:
Fixed Coverity issues 357 & 358. Added check for NULL pointer before use.
r18186:
Fix coverity item 65. Added code to h5unjam to correctly handle failures in
read() and write, and also to correctly handle writes that write less than
requested.
r18187:
Fix coverity items 115 and 116. Added code to H5Tenum.c to correctly close
opened datatypes in case of failure.
r18188:
Fixed Coverity issue 46. Check that dataset->shared is not null when freeing
memory after error.
r18190:
Fix coverity item 95. Added code to H5T_create_vlen to correctly close
allocated datatype in case of failure.
r18191:
Fixed Coverity error 59. Checked sfirst for -1 value before use in line 10533.
r18192:
Fix Coverity items 121 and 28
Added Asserts:
121: assert that all dimensions of count have values greater than zero.
28: assert curr_span pointer is not null before dereference.
Note: still need too add checks in hyperslab APIs that fail
when count values are zero, and appropriate tests.
r18194:
Fixed Coverity issues 61 & 62. Checked variable snpoints for value < 0 in line
218.
Tested on:
Mac OS X/32 10.6.2 (amazon) w/debug & production
(already daily tested on coverity branch)
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Bring Coverity changes into the trunk: (also other minor cleanups)
r17991:
Fix Coverity items 175 and 176. Fixed memory leak on error in print_enum in
H5LT.c.
r17993: (r17992 was not a Coverity change)
Close Coverity issue #206: inconsistently checking whether dt->shared was
non-NULL after H5T_alloc() returned a valid 'dt' value (which should guarantee
that dt->shared is valid).
r17994:
Fix Coverity item 149. Fixed file handle leak on error in H5FD_stdio_open.
r17995:
Fixed Coverity issues 154 to 161:
Added H5MP_close routine to error handling in the event *mp has not been
freed before error.
r17996:
Close Coverity issue #126: potentially leaking merged_spans on routine failure.
r17997:
Fix Coverity items 147 and 148. Fixed resource leaks on error in H5FDloc.c.
r17998:
Coverity issue 269-272:
Added integer result variable to functions that could return negative.
Assigned to unsigned after checking.
Added H5E_BEGIN_TRY block around H5Tclose and removed H5E_THROW in the
catch block.
Checked buffer is NULL before free. Changed HGOTO_ERROR outside of the if
block to H5E_THROW.
r17999:
Close Coverity issue #127: release temporary spans in more generic manner.
(Also add error checking to previous fix)
r18000:
Resolved Coverity issues 211 and 212 in H5T.c. Added comments to ignore
Coverity warning regarding not checking pointer for NULL, as we are using
an assert which catches the issue.
r18001:
Fix Coverity item 146. Fixed resource leak on error in H5O_layout_copy.
r18002:
Fix Coverity items 143 and 145. Fixed resource leaks on error in
H5D_compact_copy and H5D_contig_copy.
r18003:
Close Coverity issue #192: close file on error
r18004:
Fix Coverity issue #125: release temporary spans on error
r18005:
Resolved Coverity issues 5, 25, and 83 (in H5T.c):
Separated embedded functions in order to check for NULL on return of
H5I_object before passing into H5T_copy.
Check to see if new_dt is NULL within error handling before
dereferencing it.
Ignore Coverity's dead code warnings as the checks that lead to the code
are machine dependent.
r18006:
Coverity 63,70,73: Checked result of function before assigning to an unsigned
variable.
r18007:
Coverity 78,79: added continue statement if H5Pget_filter2 returns negative.
r18008:
Fixed Coverity issue # 138:
Added support in error handling to free dst pointer (if allocated) on error.
r18009:
Whitespace & coding style cleanup
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