| Commit message (Collapse) | Author | Age | Files | Lines |
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Refactor generic property list initialization code to put property list
specific routines in property list modules, instead of scattered to the four
winds. Also, introduce property list class initialization objects, to make
adding new property list classes in the library easier.
Fix daily test failure by using H5Pget_elink_prefix() API routine instead
of looking at the "raw" generic property list information.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/C++ & FORTRAN
Linux/64 2.4 (mir) w/build-all & 1.6 compat
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Clean up compiler warnings...
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Bug fix.
Description:
H5FD_get_vfd_handle() would return okay even if an VFD did not have the
get_vfd_handle callback function defined.
Solution:
Return failure if get_vfd_handle function is not defined.
Tested:
in heping and copper.
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Altix (cobalt). There's a configure
option --enable-direct-vfd/--disable-direct-vfd to enable/disable Direct I/O support. The default
is enabled. There's a small test in test/vfd.c. Another way to test it is to set environment
variable HDF5_DRIVER to "direct" and run "make check" in the test/ directory. There'll be some
further improvement in the following checkin including allowing user to provide memory boundary
value, file block size, and copying buffer size.
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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
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File format is not stable, don't keep files produced!
Description:
First stage of checkins modifying the format of groups to support creation
order. Implement "dense" storage for links in groups.
Try to clarify some of the symbols for the H5L API.
Add the H5Pset_latest_format() flag for FAPLs, to choose to use the newest
file format options (including "dense" link storage in groups)
Add the H5Pset_track_creation_order() flag for GCPLs, to enable creation
order tracking in groups (although no index on creation order yet).
Remove --enable-group-revision configure flag, as file format issues are
now handled in a backwardly/forwardly compatible way.
Clean up lots of compiler warnings and other minor formatting issues.
Tested on:
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/FORTRAN & C++
Linux/64 2.4 (mir) w/enable-v1.6 compa
Mac OSX/32 10.4.8 (amazon)
AIX 5.3 (copper) w/parallel & FORTRAN
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since HDF5 no longer allocates file space lazily.
Tested on mir; should be only a cleanup, since the code isn't called from
anywhere.
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Refactor file memory allocation code slightly, to make it clearer, along
with adding/correcting some comments.
Tested on:
FreeBSD 4.11 (sleipnir)
Linux/64 2.4 (mir)
Solaris/64 2.9 (shanti)
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bug fix
calling h5tools_get_fapl running the mpio driver caused H5FD_pl_copy to
fail silently in some conditions. a MPI call was made before MPI_Init.
solution: corrected the MPI call to be made after MPI_Init and added error return
conditions to H5FD_pl_copy and h5tools_get_fapl
tested on copper parallel, mir, shanti
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Code maintenance
Description:
Remove flexible parallel code
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 (heping)
Solaris 2.9 (shanti)
Linux 2.4/64 (mir)
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Code optimization
Description:
Tweak file free space allocation routines to optimize them a bit.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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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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Bug fix
Description:
Check in fix that John found for bug in H5FD_extend() code - adjust
beginning as well as size of free block when "extending" another block of
space in the file.
Platforms tested:
FreeBsd 4.11 (sleipnir)
Too minor to require h5committest
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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
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Description: Data conversion function H5T_conv_i32le_f64le() was unused.
Because we have new conversion functions for integers and floating numbers,
this old function is taken out.
Platforms tested: fuss - simple change.
Misc. update:
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Code cleanup
Description:
Clean up various warnings reported by the Windows team.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Description: Removed support for SRB driver
Solution: Removed or modified appropriate files; ran reconfigure
to regenerate Makefile.in and configure files.
Platforms tested: heping and shanti
Misc. update: ran bin/chkmanifest on heping
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New feature
Description:
Search free list when checking for, or actually performing, extension of
an object in the file.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Solaris 2.9 (shanti)
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Retired GASS driver.
Platforms tested:
H5committested.
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Description: Removed PABLO from the source
Solution:
Platforms tested: arabica with 64-bit, copper with parallel,
heping with GNU C and C++ and PGI fortran (but
I disabled hl, there is some weird problem only
on heping: F9XMODFLAG is not
propagated to the Makefile files
Misc. update:
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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:
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Code cleanup
Description:
Various minor tweaks to clean code up and bring it into closer
syncronization with the release branch.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
h5committested
IRIX64 6.5 (modi4)
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Code cleanup, sorta
Description:
Added ifdef sections for "H5_USING_PURIFY" in various places in the code,
which are designed to reduce the spurious "uninitialized memory read" warnings
from purify which are actually OK. Note that this macro will have to be
turned on by adding it to the CFLAGS for the build - I didn't think it was
important enough to add a configure flag for.
Also, the changes in H5HG.c optimize the walks through the objects in a
heap to only look at the 'used' entries instead of all the 'allocated' entries.
Platforms tested:
Solaris 2.7 (arabica) w/purify
Not tested by h5committest
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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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Code cleanup & minor optimization
Description:
Re-work the way interface initialization routines are specified in the
library to avoid the overhead of checking for them in routines where there is
no interface initialization routine. This cleans up warnings with gcc 3.4,
reduces the library binary size a bit (about 2-3%) and should speedup the
library's execution slightly.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/gcc34
h5committest
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allow users to register IDs and ID types at runtime.
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Code optimization
Description:
Allow global heap collections to grow in size (up to a 64K limit) if they
are able to. This allows them to grow to a more reasonable size than the 4K
minimum size.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
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Bug fix
Description:
Correct potential file corruption from mis-setting the metadata accumulator
address. (Bugfix contributed by Sean Monner <seanm@quadrus.com>)
Solution:
When the new metadata overlaps with the end of the metadata accumulator and
the accumulator grows in size, don't reset the address of the accumulator, since
it hasn't moved.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
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Checkpoint checkin of FP bug fixes. FP is still quite
buggy, but I must go deal with other matters.
Description:
Fixed two major bugs:
1) H5FPserver.c was clobbering meta data in its care.
2) H5FPserver.c was allocating the same space multiple
times, causing both data and meta data corruption.
Also made minor fixes, added debugging code, and familiarized
myself with the FP code.
All development work with FP enabled was done on Eirene.
On this platform, FP now passes its test reliably with
up to 9 processes. At 10 processes it seg faults every
time. I haven't looked into this issue.
There are also several known locking bugs which have to
be fixed. However, they are of sufficiently low probability
that I didn't bother with them on this pass.
FP has not been tested with deletions -- this should be
done.
Also, need to test FP chunked I/O.
Solution:
1) Modified cache in H5FPserver.c to merge changes correctly.
Found and fixed a bug in H5TB.c in passing.
2) Multiple space allocation was caused by a race condition
with set eoa requests.
Most of these eoa requests appeared to be superfluous, so
I deleted them.
Those issued during the superblock read seemed necessary,
so I inserted a barrier at the end of the superblock read,
to prevent races with allocations.
Platforms tested:
h5committested
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Fix build with C++ compiler
Description:
Add file driver header files for prototypes.
Platforms tested:
FreeBSD 4.9 (sleipnir) w/CC=g++
too obscure to require h5committest
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Code cleanup
Description:
Add destructor to match constructor fr VFLs when they are shut down by the
library.
Solution:
Added H5FD_*_term() routines to "undo" changes made in H5FD_*_init()
routines.
Platforms tested:
IBM p690 (copper)
too minor to require h5committest
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Bug fix/optimization
Description:
Address slowdown in MPI-I/O file metadata operations that was introduced
mid-stream. We now _require_ a POSIX compliant parallel file system for the
MPI-I/O file driver (as well as for the MPI-POSIX file driver).
Also optimized file open operation when the file is being created by
reducing the number of collective & syncronizing calls.
Additionally, refactor the MPI routines into a common place, eliminating
duplicated code.
Platforms tested:
FreeBSD 4.9 (sleipnir) w/parallel
h5committest
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Code cleanup
Description:
Clean up compiler warnings, especially the 'FUNC' variable not used which
comes out in production mode.
Solution:
Had to add a new FUNC_ENTER_NOAPI_NOINIT_NOFUNC macro for those non-API
functions which don't need the 'FUNC' variable defined. (This will be _so_
much easier when C99 is standard on all our supposed platforms, since it has a
__FUNC__ macro... )
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor for h5committest (although there were lots of files changed, the
change was minor in each one)
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Warning cleanup
Description:
Make a parameter 'const' to clean up a warning during compiles.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
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Code cleanup
Description:
Refactored handlier of VFL drivers in file access and data transfer property
lists in order to simplify and unify the code dealing with them.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
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Add feature
Description:
Add H5Fget_freespace() routine, to check the amount of free space in a
file. This information is only valid until the file is closed currently,
however (until we start recording the free space information in the file
itself).
Platforms tested:
FreeBSD 4.9 (sleipnir)
h5committest
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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 & bug fix
Description:
More de-linting...
Also correct a bug that lint exposed which was incrementing the incorrect
driver ID of a file driver and also no saving the correct driver ID for the
newly opened file.
Platforms tested:
FreeBSD 4.8 (sleipnir)
too minor for h5committest
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Code cleanup
Description:
More linting...
Platforms tested:
FreeBSD 4.8 (sleipnir)
too minor to need h5committest
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Added some comments, etc.
Platforms tested:
FreeBSD 4.8 (sleipnir)
too trivial for h5committest
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Update
Description:
Added an extra flag to the clear functions that triggers a "destroy"
of the object being cleared if necessary. This is a fix for the
FPHDF5 stuff which had an object sticking around after it was
cleared. (In FPHDF5, some processes are in charge of destroying the
object, but all processes might actually allocate the object.)
Platforms tested:
AIX (Copper: Fortran & C++)
Linux (Verbena: Fortran & C++)
IRIX (Modi4: Parallel & Fortran)
(Sol is down)
Misc. update:
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Feature change & code cleanup
Description:
Changed fileno field in H5FD_t struct from 'unsigned long[2]' to just
'unsigned long'.
Changed over code to handle the fileno change.
Chased error API changes
Platforms tested:
h5committested
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Code cleanup
Description:
Correct name of H5FD_term_interface function in FUNC_ENTER macro.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Bug fix.
Description:
Corrected fencepost error which was incorrectly checking for merging
metadata at the front of the metadata accumulator. This now allows the
metadata cache to cache I/O operations more efficiently.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
Linux 2.4 (burrwhite) w/FORTRAN
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/parallel & FORTRAN
(h5committest not run due to my ongoing difficulties with C++ on burrwhite).
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Bug fix
Description:
This fixes a bug in the low-level metadata caching code in the library
which could possibly lose metadata during file I/O when a lot of objects are
inserted into a group.
This also fixes a couple of (similar) fencepost bugs in the B-tree
deletion code.
Solution:
For the metadata bug - call the low-level driver's 'write' routine instead
of H5FD_write.
For the B-tree bug - include the correct number of keys.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
Linux 2.4 (burrwhite) w/FORTRAN
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN & parallel
(h5committest is still not working for me on burrwhite)
Misc. update:
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Update & Bug Fix
Description:
The "free" protocol was missing. Added that to the server side.
When doing a "create" of a file (with no other data structures
created), the freespace in the file wasn't being reclaimed.
Solution:
After adding the free protocol, we put the burden of running through
the FD_free function on the SAP instead of each client.
Platforms tested:
Linux
Misc. update:
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Bug Fix & Update
Description:
FPHDF5 was creating files which didn't have the EOA field in the
superblock set correctly. It turns out that the SAP was keeping this
information to itself instead of giving it to the client processes.
Naughty SAP!
Solution:
Have the SAP send this information back to the clients so that they
can update the superblock as necessary. This now creates a file (with
just the root group) that looks correct! Only problem is that there's
extra file space being allocated. Also, at program termination,
there's an infinite loop...
Platforms tested:
H5committests (run by hand on burrwhite, arabica, and modi4)
Misc. update:
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Bug fix and Update
Description:
From Quincey's comments on the code I checked in last night:
- In H5F_close call, the "private" processes should call the
H5F_flush with the "CLEAR_ONLY" flag.
- There's no need for a special case for FPHDF5 in the
FD_real_alloc function since FPHDF5 doesn't define an alloc
function.
- The return type of H5Pset_fapl_fphdf5 should be herr_t instead
of hid_t. I don't know how it got that way in the first place.
- The variable names for MPI types and the structure typedefs
should be switched: H5FP_request/H5FP_request_t to
H5FP_request_t/H5FP_request and so on.
- In the H5FP.c module, I was commiting the H5FP_request MPI
datatype but using the wrong offset field...
Platforms tested:
Linux...will test on others, but these are mostly FPHDF5 changes.
Misc. update:
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Update
Description:
When doing an allocation, check to see, if it's an FPHDF5
driver, if only the captain should be performing the allocation
Platforms tested:
Linux, Modi4, Sol
Misc. update:
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Finish code cleanup
Description:
Wrap up the conversion of H5F_flush's multiple boolean flags into a single
bitfield of flags by pushing the flags down into the H5AC_flush and
H5F_istore_flush routines.
Also, changed the flags from H5_FLUSH_<foo> to H5F_FLUSH_<foo> to be more
consistent with rest of library.
And reverted the changes to H5FDflush and H5FD_flush routines.
Platforms tested:
FreeBSD 4.7 (sleipnir)
Solaris 5.8 (sol)
IRIX64 6.5 (modi4) w/parallel
Misc. update:
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