| Commit message (Collapse) | Author | Age | Files | Lines |
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* Update supported platforms
* Merge PR#3 changes from develop
* # WARNING: head commit changed in the meantime
Merge gcc 10 diagnostics option from develop
Merge CMake changes from develop
Merge warnings from develop
Merge #318 OSX changes from develop
Merge tools changes from develop
Merge test macros from develop
* Format updates
* Fix missing semicolon and format fix
* Format update
* Correct actions, remove java option
* Update autotools build files
* Add testfiles
* Fix configure issue with make flags
* Init fapls to default
* Update generated files and fix h5repack id closure
* update format
* Merges from develop
#358 patches from vtk
#361 fix header guard spelling
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* Update URL for COPYING file in copyright headers.
* Make fortran copyright headers uniformly spaced.
* Update url for Copyright file in c++/src/footer.html.
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Comments, whitespace
Simple init and if block brackets.
Minimal code changes limited to return value and spelling
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removed and replace it with new url for COPYING file.
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Bring r21561 from trunk back to 1.8 branch:
Correct error in loading local heap prefix & data block from the file.
Sometimes the local heap's prefix could be loaded before the data block (e.g.
using H5Oget_info), but then when the data block was loaded later, the free
list information would get lost, causing the heap's size to grow larger than
necessary. This is Jira bug #HDFFV-7767
Tested on:
Mac OS X/32 10.7.2 (amazon) w/debug
(h5committest coming up)
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Bring r18716 from trunk to 1.8 branch:
Bring r18715 from metadata journaling merging branch to trunk:
Changes to further align trunk with state of metadata journaling 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-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
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Bring r18171 from trunk to 1.8 branch (with appropriate tweaks):
Bring r18169 from 'merge_metadata_journaling' branch back to trunk:
Converge changes on metadata_journaling branch and trunk:
- Remove H5F_t* parameter from H5HL_unprotect()
- Remove H5F_t* parameter from H5HL_dirty()
- Remove H5F_t* parameter from H5O_unprotect()
- Bring changes to metadata caching routines back:
- H5AC_pin_protected_entry()
- H5AC_resize_pinned_entry()
- H5AC_unpin_entry()
- H5AC_mark_pinned_entry_dirty()
- H5AC_mark_pinned_or_protected_entry_dirty()
- Revise internal H5C routines to drop H5F_t* and/or H5C_t* as
parameter where possible
- Revise tests to follow internal routine changes
Also, other minor changes to speedup the 'cache' test.
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
Mac OS X/32 10.6.2 (amazon) in debug mode
Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
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Bring r18072 from trunk to 1.8 branch:
Bring r18071 from metadata journaling merge branch:
Refactor local heap routines with changes from metadata journaling
branch, along with other misc. changes as the changes on the metadata journaling
branch are being converged with the current state of the trunk.
Tested on:
Mac OS X/32 10.6.2 (amazon) debug & prod
Linux/64 2.6 (amani) prod
FreeBSD/64 (liberty) prod
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Bring r18045 from trunk to 1.8 branch:
Slush changes back & forth between trunk, the merging branch and the
metadata journaling branch to level them out to a reasonably common set of code
to work from for the next set of more significant changes.
Tested on:
FreeBSD/32 6.3 (duty) w/debug
(h5committested on trunk)
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Bring r15800 back from trunk:
- File free space branch changes through r15794
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
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Bring r15676 back from trunk:
Centralize all macros for declaring "magic numbers"/signatures for
objects in the file into src/H5Fprivate.h, so it's easier to know what
values have already been defined, etc.
Tested on:
Mac OS X/32 10.5.5 (amazon)
Too minor to require h5committest
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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.
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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.... :-)
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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:
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Purpose:
Bug Fix
Description:
If an HDF5 file grows larger than its address space, it dies and is unable to
write any data. This is more likely to happen since users are able to change
the number of bytes used to store addresses in the file.
Solution:
HDF5 now throws an error instead of dying. In addition, it "reserves" address
space for the local heap and for object headers (which do not allocate space
immediately). This ensures that after the error occurs, there is enough address
space left to flush the entire file to disk, so no data is lost.
A more complete explanation is at /doc/html/TechNotes/ReservedFileSpace.html
Platforms tested:
sleipnir, copper (parallel), verbena, arabica, Windows (Visual Studio 7)
Solution:
Platforms tested:
Misc. update:
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Update
Description:
A lot of modifications for the FPHDF5 stuff:
H5AC.c
H5ACprivate.h - Removed AC_find (it's replaced with AC_protect
and AC_unprotect). Added flushing if it's an FPHDF5 driver and
we're doing an AC_set or AC_unprotect with the dirty flag set.
H5B.c - Split up the B_flush function into different functions
since the one function was doing serialization which is better
left as a separate entity.
H5D.c - Removed some FPHDF5 code that was incorrect
H5F.c - Split up the F_flush function so that it no longer
allocates file space. Created new functions (F_init_superblock,
F_read_superblock, and F_write_superblock) for greater modularity
and so that the FPHDF5 non-captain processes can read the
superblock after the captain process writes it.
H5FD.c - Error message correction.
H5FDfphdf5.c - Removed MPI barrier call that wasn't needed.
H5FPclient.c
H5FPserver.c - Modified so that if a process requests data that
isn't exactly aligned, we can return it if we have the block that
contains the requested address.
H5G.c
H5Gent.c
H5Gnode.c
H5HL.c
H5HLpkg.h
H5HLprivate.h
H5Oefl.c - Removed the H5HL_peek function since it was doing a
(now unsafe) holding of the information in the cache. Replaced
with protect and unprotect calls.
H5TB.c - Error fix. The TB_dless function wasn't working
properly.
H5Gstab.c - Format change.
H5err.txt
H5Edefin.h
H5Einit.h
H5Epubgen.h
H5Eterm.h - Added new error code.
Platforms tested:
Modi4 (paralle, Fortran)
Sol (Fortran)
Linux (C++, Fortran)
Copper (Parallel, Fortran)
Misc. update:
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Code cleanup
Description:
Break some of the "debugging" routines into their own module, so they
aren't pulled into every executable, which certainly isn't going to use them.
Platforms tested:
h5committested
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