| Commit message (Collapse) | Author | Age | Files | Lines |
|
|
|
|
|
|
|
| |
Clean up warnings (from 2774 -> 1560, with my standard debug build)
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
(h5committest forthcoming)
|
|
|
|
|
|
|
|
|
| |
Clean up coding to increment/decrement underlying FAPL for multi/split
VFDs, to avoid copying property lists as much.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial & parallel
(h5committest forthcoming)
|
|
|
|
|
|
| |
(H5_DEBUG_BUILD)
tested on bb-8 with Serial and Parallel, debug and production builds.
|
|
|
|
|
|
|
| |
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)
|
|
|
|
|
|
| |
unsigned instead)
Tested on: Sun OS 5.11/64 (emu)
|
|
|
|
| |
Tested on: Sun OS 5.11/64 (emu)
|
|
|
|
|
|
|
|
|
|
|
|
| |
The H5F_ACC_DEBUG symbol remains but has been defined to zero and
has been listed as deprecated.
Fixes: HDFFV-1074
Tested on:
h5committest
32-bit Linux w/ C++ and Fortran and multi VFD
32-bit Linux w/ C++ and Fortran and multi VFD (no deprec symbols)
|
|
|
|
|
|
|
|
|
|
| |
Clean up EOF code within library and add 'mem_type' parameter to 'get_eof'
VFD callback, to avoid various ambiguous situations, particularly with the
multi VFD. (Supports changes for 'avoid_truncate' feature also)
Tested on:
MacOSX/64 10.10.1 (amazon) w/serial & parallel
h5committest forthcoming
|
|
|
|
|
|
|
|
| |
Minor code/comment cleanups, found while reviewing 'avoid truncate' code.
Tested on:
MacOSX/64 10.10.1 (amazon) w/serial & parallel
(Too minor to require h5committest)
|
|
|
|
|
|
|
|
| |
passes NULL to equally divide all the address space between all the members.
Before there was one chunk of the address space not being used.
tested h5committest, and multi vfd make check on jam.
|
|
|
|
|
|
|
|
|
|
| |
is passed
as NULL. The library is supposed in that case to equally divide the
address space among all members, but there was a bug causing an
overflow in the assignment.
tested with h5commitest
|
|
|
|
|
|
|
|
| |
Clean up more compiler warnings.
Tested on:
Mac OSX/64 10.8.4 (amazon) w/gcc, C++ & FORTRAN
(too minor to require h5committest)
|
|
|
|
|
|
|
|
|
|
|
| |
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
|
|
|
|
|
|
| |
Remove unused param (src) and unused var (hl) warnings
Tested on koala
|
|
|
|
|
|
|
|
|
|
|
| |
functions that
were removed in HDF5 1.8.11.
Tested on: jam w/ fortran & C++, tested with check-vfd
I did not test on other platforms (h5committest) since there is nothing
even remotely platform-specific here.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
from the
library. The intended functionality for them was never fully implemented
and they are fundamentally broken.
The functions were removed from the C and C++ interfaces. They were not
exported in the Fortran interface.
Tested on: jam(c++/fortran/hl)
I tested using check-vfd to ensure the multi VFD still works properly.
There is no reason to test this on other machines or on parallel.
|
|
|
|
|
|
|
|
|
| |
Revert use of snprintf() for sprintf(), as it is not supported on Windows.
(And file a bug, http://jira.hdfgroup.uiuc.edu/browse/HDFFV-8302, for the
general problem)
Tested:
Mac OSX/64 10.8.2 (amazon)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bring reviewed changes from Coverity branch back to trunk (QK & JK):
r20457:
Coverity issue 691: return of H5duo could be negative. Fixed by using
STDOUT_FILENO and redesign parse_command_line and main to cleanup file
allocations. The output_file var is null when using stdout. In cleanup do not
close output_file if NULL.
r20510:
Initialize ufid = -1 and predicate HDclose call on ufid != -1
r20511:
Purpose: Fix coverity issue 1715
Description: Free "file" and nested data on failure in H5FD_core_open.
r20512:
Initialize ifid = -1 and predicate HDclose call on ifid != -1
r20514:
Initialize h5fid = -1 and predicate HDclose call on h5fid != -1
r20516:
Added else branch to the if (ret_value < 0) check.
r20522:
Addressed coverity issues 930-933, 850, 836, 835, 1307. All minor
potential buffer overwrite bugs, or coverity errors. Fixed by replacing
strcpy and sprintf with strncpy and snprintf.
r20523:
fixed coverity issues 68, 1120, 1116i
r20524:
Check H5Z_SZIP->encoder_present < 1 assuming 0 represents absence.
r20601:
Purpose: Fix coverity issues 1703-1705
Description: Modified the cleanup code in test_free in accum.c to reset
allocated buffers to NULL after they are freed, and modified the error cleanup
code to check if these buffers are NULL before freeing them. Also fixed some
unrelated warnings in accum.c.
r20602:
Use HDsnprintf and HDstrncat
r20603:
Purpose: Fix coverity issues 808-809
Description: Modified test_core in vfd.c to check the returns from malloc, and
keep track of whether points and check are allocated by setting them to NULL
when they are not. Added code to free points and check on error if they are
not NULL. Also fixed unrelated warnings in vfd.c.
r20604:
Use HDstrncpy.
r20605:
Use HDstrncpy and HDstrncat.
r20606:
Purpose: Fix coverity issue 807
Description: Modified long_compact in stab.c to keep track of whether objname is
allocated by setting it to NULL when it is not. Added code to free objname on
error if it is not NULL.
r20607:
Changed string function calls to use versions that specify the string length
to fix coverity issues 832 and 839.
Tested on:
Mac OSX/64 10.8.2 (amazon)
(Too minor to require h5committest)
|
|
|
|
|
|
|
|
|
|
| |
Bring back some more cleanups from the plist_encode_decode branch, clean up
some formatting and compiler errors, and add a few more property comparison
routines that we've skipped implementing in the past.
Tested on:
Mac OSX/64 10.7.4 (amazon) w/debug
(Too minor to require h5committest)
|
|
|
|
|
|
|
|
| |
Clean up file driver property handling, along with some misc. warnings.
Tested on:
Mac OSX/64 10.7.4 (amazon) w/debug, gcc 4.7.1, C++, FORTRAN & threadsafe
(h5committest upcoming)
|
|
|
|
|
|
|
| |
(2) fix to extend into the aggregator based on threshold
(3) fix for the "flavor" logging problem
(4) fix for test failures due to the above fixes
(5) bug fix for h5stat when h5stat against a non-existing file
|
|
|
|
|
|
| |
2594). According to Quincey's suggestion, I moved the EOAs for individual files from H5FD_multi_fapl_t to H5FD_multi_t struct. It's a more proper place.
Tested on jam, koala, and heiwa.
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
whole MULTI file saved in the
super block. We took it out in v1.8 library because it's meaningless
for the MULTI file. v1.8 library saves the EOA for the metadata file,
instead. But this caused some backward compatibility problem.
v1.8 library couldn't open the file created with v1.6 library. I
fixed the problem by checking the EOA value to detect the file
created with v1.6 library.
Tested on jam, koala, and heiwa.
|
|
|
|
|
|
|
|
|
| |
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)
|
|
|
|
|
|
|
|
| |
Initial commit of John Biddescomb's VFD & MPI tweaks.
Tested on:
None (yet)
(h5committest not required for this branch)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Final merge of changes from sblock_mdc branch back to trunk. The superblock is now managed by the metadata cache.
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 (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
Mac OS X/32 10.5.8 (amazon) in debug mode
Mac OS X/32 10.5.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
|
|
|
|
|
|
|
|
|
|
|
| |
replacing all instances with long long.
Tested:
h5comittest
fedora 10 x64
Vista 32, VS2005, IVF101
XP32, Cygwin
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Various bug fixes & cleanups with VFDs and file free space changes,
along with cleaning up compiler warnings.
Enable more VFDs (for 'make check-vfd' testing) for many tests.
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
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Remove trailing whitespace from C/C++ source files, with the following
script:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Tested on:
Mac OS X/32 10.5.5 (amazon)
No need for h5committest, just whitespace changes...
|
|
|
|
|
|
|
|
| |
Clean up warnings & formatting
Tested on:
Mac OS X/32 10.5.4 (amazon)
More tests forthcoming
|
|
|
|
|
|
|
|
|
|
| |
Rename new error handling API routines from H5E<foo>_stack() to
H5E<foo>2().
Tested on:
Mac OS X/32 10.4.9 (amazon)
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
|
|
|
|
|
|
|
|
|
| |
copyright notice.
Tested platform:
Kagiso only since it is only a comment block change. If it works in one
machine, it should work in all, I hope. Still need to check the parallel
build on copper.
|
|
|
|
|
|
|
|
|
| |
More progress on creation order for attribbutes - they are now basically
working for "compact" attribute storage.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
|
|
|
|
|
|
|
| |
The problem
came from the EOA for the whole MULTI file. It's taken out because it's
meaningless for MULTI file. Instead, each individual file has its EOA.
|
| |
|
|
|
|
|
|
|
|
| |
Take out separate memory type in the file for SOHM objects and create
aliases for existing memory types for SOHM use.
Tested on:
FreeBSD/32 4.11 (sleipnir)
|
|
|
|
|
|
|
|
|
|
|
|
| |
This feature is still in progress; Shared Object Header Messages are not
complete as a feature and are not thoroughly tested. There are still
"TODO" comments in the code (comments with the word "JAMES" in them,
so as not to be confused with other TODO comments).
Hopefully this checkin will reduce the liklihood of conflicts as I finish
implementing this feature.
All current tests pass on juniper, copper (parallel), heping, kagiso, and mir.
|
|
|
|
|
|
|
|
|
| |
Clean up some of the warnings on 64-bit Linux...
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
Too minor to require h5committest
|
|
|
|
|
|
|
|
|
|
|
| |
Code cleanup
Description:
Trim trailing whitespace in Makefile.am and C/C++ source files to make
diffing changes easier.
Platforms tested:
None necessary, whitespace only change
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
New feature
Description:
Check in baseline for compact group revisions, which radically revises the
source code for managing groups and object headers.
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
This initiates the "unstable" phase of the 1.7.x branch, leading up
to the 1.8.0 release. Please test this code, but do _NOT_ keep files created
with it - the format will change again before the release and you will not
be able to read your old files!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
Solution:
There's too many changes to really describe them all, but some of them
include:
- Stop abusing the H5G_entry_t structure and split it into two separate
structures for non-symbol table node use within the library: H5O_loc_t
for object locations in a file and H5G_name_t to store the path to
an opened object. H5G_entry_t is now only used for storing symbol
table entries on disk.
- Retire H5G_namei() in favor of a more general mechanism for traversing
group paths and issuing callbacks on objects located. This gets us out
of the business of hacking H5G_namei() for new features, generally.
- Revised H5O* routines to take a H5O_loc_t instead of H5G_entry_t
- Lots more...
Platforms tested:
h5committested and maybe another dozen configurations.... :-)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Repair synchronization bug in the metadata cache in PHDF5
Also repair numerous other bugs that surfaced in testing the
bug fix.
Description:
While operations modifying metadata must be collective, we allow
independant reads. This allows metadata caches on different processes
to adjust to different sizes, and to place the entries on their dirty
lists in different orders. Since only process 0 actually writes
metadata to disk (all other processes thought they did, but the writes
were discarded on the theory that they had to be collective), this made
it possible for another process to modify metadata, flush it, and then
read it back in in its original form (pre-modification) form. The
possibilities for file corruption should be obvious.
Solution:
Make the policy that only process 0 can write to file explicit, and
visible to the metadata caches. Thus only process 0 may flush dirty
entries -- all other caches must retain dirty entries until they are
informed by process 0 that the entries are clean.
Synchronization is handled by counting the bytes of dirty cache entries
created, and then synching up between the caches whenever the sum
exceeds an (eventually user specified) limit. Dirty metadata creation
is consistent across all processes because all operations modifying
metadata must be collective.
This change uncovered may bugs which are repaired in this checkin.
It also required modification of H5HL and H5O to allocate file space
on insertion rather than on flush from cache.
Platforms tested:
H5committest, heping(parallel & serial)
Misc. update:
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Code cleanup
Description:
Trim trailing whitespace, which is making 'diff'ing the two branches
difficult.
Solution:
Ran this script in each directory:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
|
|
|
|
|
|
|
|
|
|
|
| |
Description: pgcc version 6.0x have optimization (-O, -O2, or -O3) problem.
It caused multi driver test to fail. The problem happened in a macro
definition.
Solution: Detect these versions and add option "-Mx,28,0x8" to the compiler
to avoid the problem if optimization is enable.
Platforms tested: mir and fuss - simple change.
|
|
|
|
|
|
|
|
|
|
|
| |
Description: PGCC compiler on mir(AMD Opeteron) has a bug for optimization,
causing the multi driver test to fail. The compiler handles a macro in this
file incorrectly.
Solution: Slightly change the definition of this macro to avoid the problem
temporarily.
Platforms tested: h5committest, optimization and debug on mir.
|
|
|
|
|
|
|
|
|
|
|
| |
Code cleanup
Description:
Clean up various warnings reported by the Windows team.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
|
|
|
|
|
|
|
|
|
|
|
| |
Code cleanup
Description:
Make more of the loops over the types of memory use the existing macros.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Solaris 2.9 (shanti)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bug fix
Description:
The GASS VFL driver header file was bringing in the <string.h> header file,
which several other source code modules needed also, but weren't including
explicitly themselves.
Solution:
Add includes for <string.h> to files which actually need them.
Platforms tested:
FreeBSD 4.11 (sleipnir) w/C++ as CC
Configuration not tested by h5committest...
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-)
Description:
Generally speaking, this is the "signed->unsigned" change to selections.
However, in the process of merging code back, things got stickier and stickier
until I ended up doing a big "sync the two branches up" operation. So... I
brought back all the "infrastructure" fixes from the development branch to the
release branch (which I think were actually making some improvement in
performance) as well as fixed several bugs which had been fixed in one branch,
but not the other.
I've also tagged the repository before making this checkin with the label
"before_signed_unsigned_changes".
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel & fphdf5
FreeBSD 4.10 (sleipnir) w/threadsafe
FreeBSD 4.10 (sleipnir) w/backward compatibility
Solaris 2.7 (arabica) w/"purify options"
Solaris 2.8 (sol) w/FORTRAN & C++
AIX 5.x (copper) w/parallel & FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN
Linux 2.4 (heping) w/FORTRAN & C++
Misc. update:
|
|
|
|
|
|
|
|
|
|
|
|
| |
Description: Restore 6 old error API functions back to the library to be backward
compatible with v1.6. They are H5Epush, H5Eprint, H5Ewalk, H5Eclear, H5Eset_auto,
H5Eget_auto. These functions do not have error stack as parameter.
Solution: Internally, these functions use default error stack.
Platforms tested: h5committest and fuss.
Misc. update: RELEASE.txt
|