| Commit message (Collapse) | Author | Age | Files | Lines |
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Bug fixes and code cleanup
Description:
Lots of changes here:
- Fixed bug #691 - when shared datatypes are used in attributes they
are incorrectly copied into the attribute instead of referring
the the named datatype in the file. This required bumping the
version of the attribute message. The new version of the attribute
message is only written out when a shared datatype is used in
the attribute. [Also, this format change made the size of the
attribute smaller.]
- Added information to attribute debugging routine so that shared
datatypes are displayed correctly with the h5debug tool.
- Refactored the H5O* routines to extract code that was common to
several routines into subroutines to call.
- Added 'link' method for H5O message sub-classes, which increments
the link count on shared objects when a message is created which
shares them.
- Corrected [unreported] bug where the link count was not being
decremented on the shared object when a object header message
with a reference to that object was deleted from the file.
- Reduced size of shared message from 49 bytes (which was incorrect
anyway and should have been 48 bytes) to 10 bytes, which required
bumping the version of "shared" messages.
- Refactored some of the shared datatype routines to allow for easier
queries of "committedness" internally to the library and also
added routine to easily increment/decrement the reference count of
a shared datatype.
Platforms tested:
FreeBSD 4.9 (sleipnir)
h5committest
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Bug Fix
Description:
The FPHDF5 code couldn't create a dataset then access it. Turns out
that the "O_find_in_ohdr" code was protecting the object header which
pulls it into the cache then unprotecting it. However, this caused
the cache entry to be blown away and THEN we'd try to reread the
entry (via AC_protect) but it didn't have all of the data that the
find_in_ohdr function decodes for us decoded. It was also kind of
unnecessary since we can just protect then call O_find_in_ohdr.
Solution:
Removed the AC_protect and AC_unprotect from O_find_in_ohdr. Called
AC_protect before calling the O_find_in_ohdr function.
Platforms tested:
Linux (Fortran, C++)
IRIX (parallel, Fortran)
Sun (Fortran)
Misc. update:
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Removed Dead Code
Description:
Some of the FPHDF5 code was dead (I thought it'd be useful at one
point, but was wrong).
Solution:
Removed
Platforms tested:
Linux (FPHDF5 specific. No need for h5committest)
Misc. update:
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Code cleanup
Description:
Patch up a few places where the metadata cache could ask for a read lock
instead of a write lock and other minor code cleanups.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to need h5committest
Misc. update:
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Update
Description:
Added extra parameter to the H5AC_protect() function that indicates
if the cache being asked for is going to be written to or just read
from. Those AC_protect calls that were H5AC_find calls are now
read-only. The rest are writes.
Platforms tested:
Linux (h5committest not needed due to size and small impact)
Misc. update:
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Removal of H5AC_find()
Description:
The H5AC_find() function is mostly redundant and with the new
Flexible Parallel HDF5 stuff, we need to do locking on metadata
returned from the H5AC_find() anyway. So, all of the locking stuff
will be placed in the H5AC_{un}protect() functions. The H5AC_find()
is no longer needed.
Solution:
Replaced all H5AC_finds with H5AC_protects and H5AC_unprotects.
Platforms tested:
Linux (Fortran & C++)
Solaris (Fortran)
Irix (Parallel & Fortran)
Misc. update:
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Code cleanup/bug fix
Description:
Move metadata cache calls around a bit so they protect the usage of the
metadata better.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too small to need h5committest
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Fix, of a sort
Description:
Some of the code would get an object from the cache via the
H5AC_find() function and then modify the returned object. This
behavior is incorrect as the pointer returned via the H5AC_find()
function is supposed to be read only.
Solution:
Changed the H5AC_finds to H5AC_protect() instead and added the
appropriate H5AC_unprotect() function.
Platforms tested:
(simulated h5committest by hand since it doesn't work for me)
Linux (Fortran, C++)
Solaris (Fortran)
AIX (Fortran, C++)
SGI (Parallel, Fortran)
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Revert erroneous comment
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Bug fix
Description:
The metadata cache 'destroy' callback routines need the file handle in
order for certain callback routines (currently just the H5HG one) to perform
extra cleanups. The recent change to call the 'destroy' callback from the
'clear' callback omitted this parameter.
Solution:
Add the file handle to the metadata cache 'clear' callbacks.
Platforms tested:
FreeBSD 4.8 (sleipnir)
too small to need 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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Code cleanup
Description:
Changed lines like:
H5E_clear(H5E_get_my_stack());
to:
H5E_clear(NULL);
which performs the same operation.
Platforms tested:
h5committested
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Code cleanup
Description:
Change some variables that are keywords in C++ to non-keywords.
Platforms tested:
FreeBSD 4.8 (sleipnir)
too minor to require full h5committest
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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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Code cleanup
Description:
Improve file format debugging output.
Platforms tested:
FreeBSD 4.8 (sleipnir)
Triple check not needed
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New feature
Description:
Track changes in the internal metadata API with clearing the metadata
dirty flag without flushing object.
Added ability to delete an object header in the file and restore all the
space referenced by various header messages.
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/code cleanup/new feature
Description:
Fix h5debug to work correctly again, with all the changes over the past
few months.
Improved and cleaned up debugging output available in h5debug.
Platforms tested:
FreeBSD 4.7 (sleipnir)
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Code cleanup
Description:
Clean up miscellaneous warnings which have crept into the code.
Fix "_POSIX_C_SOURCE not defined" warning on FreeBSD.
Adjust gcc compiler flags to be more concise for production mode.
Refactor the H5O code so that there is a stronger boundary between code
in the H5O package and code in the library which just calls H5O routines.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir) serial & parallel and gcc 2.95.4 & gcc 3.2.2
Misc. update:
Update MANIFEST if you add or remove any file.
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Bug Fix
Description:
Metadata cache in parallel I/O can cause hangs in applications which
perform independent I/O on chunked datasets, because the metadata cache
can attempt to flush out dirty metadata from only a single process, instead
of collectively from all processes.
Solution:
Pass a dataset transfer property list down from every API function which
could possibly trigger metadata I/O.
Then, split the metadata cache into two sets of entries to allow dirty
metadata to be set aside when a hash table collision occurs during
independent I/O.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir) serial & parallel
Misc. update:
Updated release_docs/RELEASE
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Bug fix
Description:
Currently, when the library encounters an object header message that isn't
know, it fails to open that object in the file.
Solution:
Allow the library to skip over the unknown object header message and
continue to process the remaining messages, in the hope that the skipped
message isn't important later. If it is important, it will be caught at
a higher level of the library.
Platforms tested:
FreeBSD 4.7 (sleipnir)
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Code cleanup/new feature.
Description:
Split FUNC_LEAVE into API and non-API specific versions. This allows a
solution to compiling this branch with C++, as well as reducing the size
of the binaries produced.
Platforms tested:
FreeBSD 4.7 (sleipnir) w/serial, parallel (including MPE) & thread-safe
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Lots of performance improvements & a couple new internal API interfaces.
Description:
Performance Improvements:
- Cached file offset & length sizes in shared file struct, to avoid
constantly looking them up in the FCPL.
- Generic property improvements:
- Added "revision" number to generic property classes to speed
up comparisons.
- Changed method of storing properties from using a hash-table
to the TBBT routines in the library.
- Share the propery names between classes and the lists derived
from them.
- Removed redundant 'def_value' buffer from each property.
- Switching code to use a "copy on write" strategy for
properties in each list, where the properties in each list
are shared with the properties in the class, until a
property's value is changed in a list.
- Fixed error in layout code which was allocating too many buffers.
- Redefined public macros of the form (H5open()/H5check, <variable>)
internally to only be (<variable>), avoiding innumerable useless
calls to H5open() and H5check_version().
- Reuse already zeroed buffers in H5F_contig_fill instead of
constantly re-zeroing them.
- Don't write fill values if writing entire dataset.
- Use gettimeofday() system call instead of time() system when
checking the modification time of a dataset.
- Added reference counted string API and use it for tracking the
names of objects opening in a file (for the ID->name code).
- Removed redundant H5P_get() calls in B-tree routines.
- Redefine H5T datatype macros internally to the library, to avoid
calling H5check redundantly.
- Keep dataspace information for dataset locally instead of reading
from disk each time. Added new module to track open objects
in a file, to allow this (which will be useful eventually for
some FPH5 metadata caching issues).
- Remove H5AC_find macro which was inlining metadata cache lookups,
and call function instead.
- Remove redundant memset() calls from H5G_namei() routine.
- Remove redundant checking of object type when locating objects
in metadata cache and rely on the address only.
- Create default dataset object to use when default dataset creation
property list is used to create datasets, bypassing querying
for all the property list values.
- Use default I/O vector size when performing raw data with the
default dataset transfer property list, instead of querying for
I/O vector size.
- Remove H5P_DEFAULT internally to the library, replacing it with
more specific default property list based on the type of
property list needed.
- Remove redundant memset() calls in object header message (H5O*)
routines.
- Remove redunant memset() calls in data I/O routines.
- Split free-list allocation routines into malloc() and calloc()-
like routines, instead of one combined routine.
- Remove lots of indirection in H5O*() routines.
- Simplify metadata cache entry comparison routine (used when
flushing entire cache out).
- Only enable metadata cache statistics when H5AC_DEBUG is turned
on, instead of always tracking them.
- Simplify address comparison macro (H5F_addr_eq).
- Remove redundant metadata cache entry protections during dataset
creation by protecting the object header once and making all
the modifications necessary for the dataset creation before
unprotecting it.
- Reduce # of "number of element in extent" computations performed
by computing and storing the value during dataspace creation.
- Simplify checking for group location's file information, when file
has not been involving in file-mounting operations.
- Use binary encoding for modification time, instead of ASCII.
- Hoist H5HL_peek calls (to get information in a local heap)
out of loops in many group routine.
- Use static variable for iterators of selections, instead of
dynamically allocation them each time.
- Lookup & insert new entries in one step, avoiding traversing
group's B-tree twice.
- Fixed memory leak in H5Gget_objname_idx() routine (tangential to
performance improvements, but fixed along the way).
- Use free-list for reference counted strings.
- Don't bother copying object names into cached group entries,
since they are re-created when an object is opened.
The benchmark I used to measure these results created several thousand
small (2K) datasets in a file and wrote out the data for them. This is
Elena's "regular.c" benchmark.
These changes resulted in approximately ~4.3x speedup of the
development branch when compared to the previous code in the
development branch and ~1.4x speedup compared to the release
branch.
Additionally, these changes reduce the total memory used (code and
data) by the development branch by ~800KB, bringing the development
branch back into the same ballpark as the release branch.
I'll send out a more detailed description of the benchmark results
as a followup note.
New internal API routines:
Added "reference counted strings" API for tracking strings that get
used by multiple owners without duplicating the strings.
Added "ternary search tree" API for text->object mappings.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
Other platforms/configurations tested?
FreeBSD 4.7 (sleipnir) serial & parallel
Solaris 2.6 (baldric) serial
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New Feature. Support for new FPHDF5 Feature
Description:
More support for the FPHDF5 feature. This splits the H5D_create
function into separate parts which update the metadata cache. It was
necessary to split apart the H5O_create function to do a similar
thing since it would allocate real space on the hard disk.
I'm checking this up now so that I don't get too far away from what
the CVS repository has and so that others may look at the code and
retch^H^H^H^H^Hmarvel at it. If there are any comments, send them my
way.
There is one outstanding issue, though. I need to use non-API
functions in the FPHDF5 stuff. I'm using some APIs right now and
should migrate to using others. At the moment, I'm putting that on
the back burner until I'm more along in the implementation.
Platforms tested:
Arabica (C++)
Eirene (Parallel)
Modi4 (Parallel)
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Code cleanup
Description:
Clean up ID->name code:
- Reformat to better match library coding standard
- Changed several algorithms to be more efficient
- Integrated into library more smoothly
Platforms tested:
eirene w/FORTRAN & C++
arabica w/FORTRAN
modi4 w/FORTRAN & parallel
sleipnir
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Purpose:
Added 'ID to name' support
Description:
There is a new API function H5Iget_name
Most of the changes are on H5G.c , regarding the symbol table entry struct H5G_entry_t
which has 2 new fields 'name' and 'old_name'
A new private function was introduced H5G_ent_copy, that does a deep copy
between 2 symbol table entries
The test file is getname.c
Platforms tested:
windows 2000, Linux, Solaris
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Purpose:
Design for compact dataset
Description:
Compact dataset is stored in the header message for dataset layout.
Platforms tested:
arabica, eirene.
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Code cleanup
Description:
Changed the last HRETURN* statements in the FUNC_ENTER macros into HGOTO*
macros, which reduces the size of the library binary in certain
configurations by another 10%
Platforms tested:
FreeBSD 4.6 (sleipnir) serial & parallel, IRIX64 6.5 (modi4) serial &
parallel
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Purpose:
Merged from 1.4 branch
Description:
API tracing improvements
Platforms tested:
Linux (--disable-hsizet didn't work before my changes and still doesn't
work, but --enable-hsizet is fine).
Note: This checkin includes temporary code in H5FDmpiposix.c to turn
off GPFS byte range token prefetches on ASCI/Blue. Once the HDF5 API
supports the necessary prerequisite functionality this temporary code
can be migraged up above HDF5.
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Code cleanup
Description:
Clean up a few warnings which were showing up with --enable-production
turned on.
Platforms tested:
FreeBSD 4.6 (sleipnir) serial & parallel
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Code cleanup
Description:
Change most (all?) HRETURN_ERROR macros to HGOTO_ERROR macros, along with
HRETURN macros to HGOTO_DONE macros. This unifies the error return path
from functions and reduces the size of the library by up to 10% on some
platforms.
Additionally, I improved a lot of the error cleanup code in many routines.
Platforms tested:
FreeBSD 4.6 (sleipnir) serial & parallel and IRIX64 6.5 (modi4) serial &
parallel.
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Bug Fix
Description:
It was possible to create corrupted metadata information (either in memory
or in the file or both) with a parallel I/O program because of the way
metadata writes were being handled for writes out of the metadata cache.
Solution:
Added a dataset transfer property called "block before metadata write"
which is used by the MPI-I/O and MPI-posix drivers to sync up all the
processes before attempting a metadata write. This property is currently
only for metadata writes from the metadata cache.
Platforms tested:
IRIX64 6.5 (modi4) w/parallel
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Code Bug Fix
Description:
Under certain [obscure] circumstances, an object header would get paged out
of the metadata cache, and when it was accessed again and brought back into
the cache, and immediately had additional metadata added to it (an
attribute, usually, or perhaps adding an object to a group), and needed to
be extended with a continuation message, but there was no room in any
existing object header chunks for the continuation message and an existing
object header message needed to be moved to the new object header chunk (I
told you it was obscure :-), the object header message moved to the new
chunk (not the new metadata being added) would get corrupted. *whew* :-)
Solution:
Actually copy the "raw" object header message information of the object
header message being moved to the new chunk, instead of relying on the
"native" object header message information being re-encoded when the object
header is flushed. This is because when an object header is paged out of
the metadata cache and subsequently brought back in, the "native"
information pointer in memory is reset to NULL and only the "raw"
information exists.
Platforms tested:
Solaris 2.7 (arabica) & FreeBSD 4.5 (sleipnir)
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Code cleanup
Description:
Broke the FUNC_ENTER macro into several macros, with more specialized
uses (which followup mail will describe). This was designed to move
most/all of the checks which could be done at compile time to that point,
instead of needlessly performing them (over & over :-) at run-time.
This reduces the library's size (and thus staticly linked binaries) and
has a minor speedup effect also.
Platforms tested:
IRIX64 6.5 (modi4) with parallel & FORTRAN enabled, and additional testing
on FreeBSD and Solaris immediately after the checkin.
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Code cleanup.
Description:
Took Robb's recent ideas for improving the FUNC_ENTER/FUNC_LEAVE macros
equivalents in the SAF library and adapted them to our library. I added
an additional macro which is equivalent to FUNC_ENTER:
FUNC_ENTER_NOINIT - Has the API tracing code, etc. from FUNC_ENTER but
none of the library or interface initialization code. This is to
be used _only_ for static functions and those which explicitly
cannot have the library or interface initialization code enabled
(like the API termination routines, etc.).
This allowed many more of the functions in the library [but not all yet :-(]
to be wrapped with FUNC_ENTER[_NOINIT]/FUNC_LEAVE pairs.
It also reduced the size of the library and executables (by cutting out a
bunch of code which was never executed), I'll e-mail the exact results when
I've finished editing it.
Platforms tested:
IRIX64 6.5 (modi4)
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Code cleanup
Description:
The parallel I/O file driver is optimized to only write metadata with one
process (and broadcast the results to the other processes). This is
currently enabled by a separate call to H5FD_mpio_tas_allsame() before
each metadata write to the file. This can easily lead to problems where
the prelude function call is omitted before the actual write code or, in
a threaded environment, lead to race condititions where the value set is
reset before being used.
Solution:
Since we only want to write metadata from one process, key off of the 'type'
parameter (which has information about whether the data being written it
metadata or raw data) to H5FD_mpio_write() as the method for determining
whether to only write from one process or not.
Platforms tested:
IRIX64 6.5 (modi4)
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Purpose:
New feature
Description:
Fill-value's behaviors for contiguous dataset have been redefined.
Basicly, dataset won't allocate space until it's necessary. Full details
are available at http://hdf.ncsa.uiuc.edu/RFC/Fill_Value, at this moment.
Platforms tested:
Linux 2.2.
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Code cleanup
Description:
Windows is generating hundreds of warnings from some of the practices in
the library. Mostly, they are because size_t is 32-bit and hsize_t is
64-bit on Windows and we were carelessly casting the larger values down to
the smaller ones without checking for overflow.
Also, some other small code cleanups,etc.
Solution:
Re-worked some algorithms to eliminate the casts and also added more
overflow checking for assignments and function parameters which needed
casts.
Kent did most of the work, I just went over his changes and fit them into
the the library code a bit better.
Platforms tested:
FreeBSD 4.4 (hawkwind)
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Code cleanup for better compatibility with C++ compilers
Description:
C++ compilers are choking on our C code, for various reasons:
we used our UNUSED macro incorrectly when referring to pointer types
we used various C++ keywords as variables, etc.
we incremented enum's with the ++ operator.
Solution:
Changed variables, etc.to avoid C++ keywords (new, class, typename, typeid,
template)
Fixed usage of UNUSED macro from this:
char UNUSED *c
to this:
char * UNUSED c
Switched the enums from x++ to x=x+1
Platforms tested:
FreeBSD 4.4 (hawkwind)
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Code cleanup (sorta)
Description:
When the first versions of the HDF5 library were designed, I remembered
vividly the difficulties of porting code from a 32-bit platform to a 16-bit
platform and asked that people use intn & uintn instead of int & unsigned
int, respectively. However, in hindsight, this was overkill and
unnecessary since we weren't going to be porting the HDF5 library to
16-bit architectures.
Currently, the extra uintn & intn typedefs are causing problems for users
who'd like to include both the HDF5 and HDF4 header files in one source
module (like Kent's h4toh5 library).
Solution:
Changed the uintn & intn's to unsigned and int's respectively.
Platforms tested:
FreeBSD 4.4 (hawkwind)
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Code cleanups, mostly..
Description:
Work on pacifying the SGI compiler to get the generic properties working
correctly with --enable-parallel and --enable-fortran. It's not quite
fixed yet, but I need to head home and these patches help... :-/
Platforms tested:
IRIX64 6.5 (modi4)
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New Features!
Description:
Start migrating the internal use of property lists in the library from the
older implementation to the new generic property lists.
Currently, only the dataset transfer property lists are migrated to the
new architecture, all the rest of the property list types are still using
the older architecture.
Also, the backward compatibility features are not implemented yet, so
applications which use dataset transfer properties may need to make the
following changes:
H5Pcreate(H5P_DATASET_XFER) -> H5Pcreate_list(H5P_DATASET_XFER_NEW)
and
H5Pclose(<a dataset transfer property list>) -> H5Pclose_list(id)
This still may have some bugs in it, especially with Fortran, but I should
be wrapping up those later today.
Platforms tested:
FreeBSD 4.4 (hawkwind)
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Bug Fix, Code Cleanup, Code Optimization, etc.
Description:
Fold in the hyperslab speedups, clean up compile warnings and change a
few things from using 'unsigned' or 'hsize_t' to use 'size_t' instead.
Platforms tested:
FreeBSD 4.3 (hawkwind), Solaris 2.7 (arabica), Irix64 6.5 (modi4)
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Code clean/bug fix
Description:
H5FL (free-list manager) code currently is taking an hsize_t as the size
of a memory block to allocate. On many machines, the size of an hsize_t
is greater than the size of a size_t, potentially leading to incorrect
memory allocations in rare circumstances.
Solution:
Changed hsize_t parameters and variables to size_t.
Platforms tested:
FreeBSD 4.3 (hawkwind)
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Update
Description:
Changed
#include <hdf_file.h>
construct to
#include "hdf_file.h"
so that the GNU compiler can more easily pick up the dependencies
which it places in the .depend and Dependencies files. Also
regenerated the Dependencies to go along with this.
Platforms tested:
Linux
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Code cleanup.
Description:
Fixed _lots_ (I mean _tons_) of warnings spit out by the gcc with the
extra warnings. Including a few show-stoppers for compression on IRIX
machines.
Solution:
Changed lots of variables' types to more sensible and consistent types,
more range-checking, more variable typecasts, etc.
Platforms tested:
FreeBSD 4.2 (hawkwind), IRIX64-64 (modi4)
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Updating debugging information for new features, etc.
Description:
Lots of the new features added to the library during the last year or so
have been added without updating the debugging routines used by h5debug.
Solution:
Added more of the new features (although not all of them) to the debugging
routines for h5debug. Also included some more information to expand on
the information printed from h5debug.
Platforms tested:
FreeBSD 4.2 (hawkwind)
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Feature symmetry
Description:
A while ago I needed to get the 'type' of data being accessed during writes
to the VFL driver, so I put in code to get the information down there.
Albert asked for the same information during reads, so I've added that in.
Tested:
FreeBSD 4.1.1 (hawkwind)
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Maintainance & performance enhancements
Description:
Re-arranged header files to protect private symbols better.
Changed optimized regular hyperslab I/O to compute the offsets more
efficiently from previous method of using matrix operations.
Added sequential I/O operations at a more abstract level (at the same level
as H5F_arr_read/write), to support the optimized hyperslab I/O.
Platforms tested:
Solaris 2.6 (baldric) & FreeBSD 4.1.1 (hawkwind)
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