| Commit message (Collapse) | Author | Age | Files | Lines |
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Add call to reset cached chunk info after initialization of chunk data
storage.
Tested on:
Linux/64 2.4(smirom) w/parallel
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H5D_istore_writevv and H5D_istore_readvv to
H5D_chunk_write and H5D_chunk_read to avoid frequent lock and unlock and to improve some
performance.
Tested with h5committest on THG machines.
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Minor code & comment cleanups
Tested on:
Mac OS X/32 10.4.10 (amazon)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Refactor fill value buffer code into one location, for better long-term
maintenance.
Tested on:
Mac OS X/32 10.4.10 (amazon)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Improve efficiency of writing VL-datatype fill values.
Tested on:
Mac OS X/32 10.4.9 (amazon)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Fix writing variable-length datatype fill values for contiguous dataset
storage
Tested on:
Mac OS X/32 10.4.9 (amazon)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Change back to clearing memory buffers by default, but give users option
to disable this, for performance reasons (--disable-clear-file-buffers).
Also, add configure option (--enable-using-memchecker) to conveniently
control making the library "play nice" with memory checking tools like valgrind
and purify.
Tested on:
Mac OS X/32 10.4.9 (amazon)
FreeBSD/32 6.2 (duty)
Linux/32 2.6 (kagiso)
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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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Get rid of two different types of fill value struct (merge H5O_fill_t
and H5O_fill_new_t) and clean up & simplify dataset initialization code.
(In preparation for shared object header message method call
refactoring).
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
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checking in
code to copy shared messages. Should be fewer memory leaks and fewer
"uninitialized memory reads."
Tested on kagiso, smirom, and Windows.
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Fix problem with copying objects when the dataset to copy has an "older"
version of the layout message and needs to compute the size of the dataset's
storage after the dataspace information is available.
Minor random cleanups also...
Tested on:
FreeBSD/32 4.11 (sleipnir)
Too minor/weird to test w/h5committest...
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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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Finish new version of the I/O pipeline message, which is much smaller than
the previous version. This version is used with the "use the latest version
of the format" flag.
Closed several memory leaks/overruns (found with valgrind).
Also, lots of compiler & formatting cleanups.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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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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Review, revise & checkin in Peter's latest round of object copy changes,
which add basic support for datasets & attributes with reference datatypes.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Clean up some compiler warnings.
Tested on:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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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
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New feature
Description:
Check in Peter's code to add support for "shallow copy", "create
intermediate groups", "no attributes" and "expand soft links" support.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 (chicago) w/ & w/o group-revision enabled
h5committest
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New/expanded features
Description:
Check in Peter's changed for the object copy code:
- Allow/fix copying datasets using named variable-length datatypes
- Start adding framework for property list to control how object
copying occurs.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Bug fix & new feature
Description:
Support variable-length datatypes in compact data storage and chunked
data storage, along with attributes.
Bug fix on the H5T_vlen_set_loc to allow for changing the file on a
variable-length datatype on disk.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4
Can't h5committest right now, due to missing cache files.
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Code cleanup
Description:
Fix a bunch of warnings flagged by Windows compilers.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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New feature
Description:
Add in a combination of Peter's & my code to support copying
variable-length data from one file to another, although currently only
supported with contiguous data storage.
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committest
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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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Code cleanup
Description:
Clean up & standardize a bit in preparation for coding standards
discussion.
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: 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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Bug fix/code cleanup
Description:
Clean up raw data I/O code to bundle the I/O parameters (dataset, DXPL ID,
etc) into a single struct to pass around through the dataset I/O routines,
since they are always passed together, until very near the bottom of the I/O
stack.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Solaris 2.7 (arabica)
IRIX64 6.5 (modi4)
h5committest
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Purpose:
Feature
Description:
Datatypes and groups now use H5FO "file object" code that was previously
only used by datasets. These objects will hold a file open if the file
is closed but they have not yet been closed. If these objects are unlinked
then relinked, they will not be destroyed. If they are opened twice (even
by two different names), both IDs will "see" changes made to the object
using the other ID.
When an object is opened using two different names (e.g., if a dataset was
opened under one name, then mounted and opened under its new name), calling
H5Iget_name() on a given hid_t will return the name used to open that hid_t,
not the current name of the object (this is a feature, and a change from the
previous behavior of datasets).
Solution:
Used H5FO code that was already in place for datasets. Broke H5D_t's, H5T_t's,
and H5G_t's into a "shared" struct and a private struct. The shared structs
(H5D_shared_t, etc.) hold the object's information and are used by all IDs
that point to a given object in the file. The private structs are pointed
to by the hid_t and contain the object's group entry information (including its
name) and a pointer to the shared struct for that object.
This changed the naming of structs throughout the library (e.g., datatype->size
is now datatype->shared->size). I added an updated H5Tinit.c to windows.zip.
Platforms tested:
Visual Studio 7, sleipnir, arabica, verbena
Misc. update:
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Bug fix
Description:
1 - Dataset contiguous storage cache information had a bug where it was
possible to try to access invalid cache information if the cache wasn't filled
the first time it attempted to loop through the list of offset/length vectors.
2 - Additionally, the contiguous storage cache information was being used
in certain circumstances from the chunked dataset I/O code path, which was
generally fatal since the chunk storage and contiguous storage information
were stored together in a union.
Solution:
1 - Avoid special case of first trip through loop over offset/length
I/O vectors and always check for the contiguous storage sieve buffer buffer
being NULL.
2 - Change the union containing the chunk and contiguous storage cache
information into a struct, allowing both to be used at the same time.
Platforms tested:
FreeBSD 4.10 (sleipnir)
h5committested
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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 & 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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Code optimization
Description:
Revised dataspace selections to use a more "object oriented" mechanism
to set the function pointers for each selection and selection iterator. This
reduces the amount and number of times that dataspace selection info has to
be copied.
Additionally, change hyperslab selection information to be dynamically
allocated instead of an inline struct.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
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Refactor code
Description:
Move chunk and contiguous cached raw data from file information to dataset
information. This simplifies a number of internal interfaces, aligns the
code with it's purpose better and should allow more optimizations to the
chunked data I/O performance.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir)
h5committest
Misc. update:
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Code optimization & bug fix
Description:
When dimension information is being stored in the storage layout message
on disk, it is stored as 32-bit quantities, possibly truncating the dimension
information, if a dimension is greater than 32-bits in size.
Solution:
Fix the storage layout message problem by revising file format to not store
dimension information, since it is already available in the dataspace.
Also revise the storage layout data structures to be more compartmentalized
for the information for contiguous, chunked and compact storage.
Platforms tested:
FreeBSD 4.9 (sleipnir) w/parallel
Solaris 2.7 (arabica)
h5committest
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Bug fix/code cleanup
Description:
Copy Robb's feature in SSlib that checks that the name of the function
used in the FUNC_ENTER macro is actually the name of function.
Fixed a bunch of typos & copy-n-pasto's for functions with incorrect names.
Platforms tested:
FreeBSD 4.9 (sleipnir) w/parallel
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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Bug fix
Description:
Code was using an internal DXPL with collective I/O turned on during
independent I/O operations to fill dataset on disk.
Solution:
Switched to internal DXPL with independent I/O
Platforms tested:
FreeBSD 4.9 (sleipnir)
FreeBSD 4.9 (sleipnir) w/parallel
Linux 2.4 (verbena) w/fortran & C++
Solaris 2.7 (arabica) w/64-bit extensions enabled
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Bug fix
Description:
When datasets are deleted from a file, they are removed from the sieve
buffer, but instead of invalidating only the part of the sieve buffer affected,
the sieve buffer code would throw away the entire sieve buffer, potentially
including other raw data in the buffer that hadn't been written to disk yet.
Solution:
Improve the sieve buffer clearing code to handle partial invalidations.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Refactoring code
Description:
Refactored "IS_H5FD_MPIO || IS_H5FD_MPIPOSIX || IS_H5FD_FPHDF5" combination
of macros in many places into single IS_H5FD_MPI macro, which has the same
definition, but should be easier to maintain.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Code cleanup
Description:
Clean up various minor warnings in the library.
Platforms tested:
FreeBSD 4.8 (sleipnir)
too small to need h5committest
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Code cleanup/Feature removal
Description:
Remove "round robin" writing of metadata in MPI VFDs (and a couple of other
places). This never really worked the way I hoped it would and it causes
problems on certain machines.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/parallel
Too small for triple check.
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Update code
Description:
Move "PABLO_MASK" definition above header file inclusion to avoid problems
with inline functions in header files.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Bug fix
Description:
An earlier checkin changed some of the assumptions about single block
hyperslabs, causing them to fail in odd ways.
Solution:
Fix errors with single block hyperslabs by keying off of count==1 instead
of stride==1.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/parallel
h5committested
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Code cleanup
Description:
Clean up warnings exposed by compiling on O2K. Also, revert some of Bill
and my changes to the H5S_mpi_opt_types_g, etc. and settle them back into their
original location.
Platforms tested:
h5committested.
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New feature/enhancement
Description:
Chunked datasets are handled poorly in several circumstances involving
certain selections and chunks that are too large for the chunk cache and/or
chunks with filters, causing the chunk to be read from disk multiple times.
Solution:
Rearrange raw data I/O infrastructure to handle chunked datasets in a much
more friendly way by creating a selection in memory and on disk for each chunk
in a chunked dataset and performing all of the I/O on that chunk at one time.
There are still some scalability (the current code attempts to
create a selection for all the chunks in the dataset, instead of just the
chunks that are accessed, requiring portions of the istore.c and fillval.c
tests to be commented out) and performance issues, but checking this in will
allow the changes to be tested by a much wider audience while I address the
remaining issues.
Platforms tested:
h5committested, FreeBSD 4.8 (sleipnir) serial & parallel, Linux 2.4 (eirene)
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Code Improvements/Bug Fixes
Description:
Comparison of equality of a double/float variable to 0.0 is not
guaranteed to work and is bad practice.
In H5Fcontig.c, a warning was given by a statement like:
x = (++x) % y;
This could be confusing to a compiler I suppose.
In H5RS.c, a typedef of a structure was being tagged by the compiler
as "useless" because it had the form:
typedef struct foo {
int var1;
/* ... */
}; /* <--- note no name for this typedef */
The statement "typedef struct foo foo" is already in the header file.
Solution:
Test that the absolute value of the variable is < a very small
positive number.
Changed "x = (++x) % y" to "++x; x %= y;" instead.
Removed the "typedef" from the structure in the H5RS.c file.
Platforms tested:
Modi4 (Parallel & Fortran)
Verbena (C++ & Fortran)
Arabica (Fortran)
Misc. update:
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New feature.
Description:
Added ability to free space used for storing raw data for both contiguous
and chunked datasets.
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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Update
Description:
Final support addition for FPHDF5. Wherever there was an equivalent
MPIO or MPIO/POSIX call/check, I placed an FPHDF5 call/check there as
well, with the appropriate #ifdefs in place.
The hdf5.h is updated with the H5FDfphdf5.h driver #include.
Platforms tested:
Linux & Modi4
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