Purpose:
turn on daylight feature on windows
Description:
currently we have to hard code daylight feature of windows to make it pass mtime test.
Solution:
Platforms tested:
linux 2.2.18
Bug Fix
Description:
Correct coordinates were not computed for iteration through irregular
hyperslab selection (although the points in the buffer that were selected
were correct).
Solution:
Add another array to track selection offset adjusted coordinates in the
selection.
Platforms tested:
FreeBSD 4.5 (sleipnir)
Bug Fix
Description:
Selection offsets were not being used correctly when iterating through
all hyperslabs selections and point selections.
Solution:
Use the selection offset appropriately.
Platforms tested:
FreeBSD 4.5 (sleipnir)
Migrate from configure macros of XYZ_ABC to H5_XYZ_ABC
Description:
configure generates many macros definitions on the fly and
were stored in src/H5config.h which is included by H5public.h.
But other software that uses hdf5 may also run their own configure.
There can be a clash in macro name space. We decided awhile ago
to prepend all generated macros with "H5_" to avoid conflicts.
The process has started and this commit completes it (at least attempt
to).
Solution:
Many macros symbols (e.g. SIZEOF_xxx and HAVE_xxx were changed to
H5_SIZEOF_xxx and H5_HAVE_xxx). Then H5private.h no longer includes
H5config.h. This cuts H5config.h away from HDF5 source code.
Pending issues:
The module of fortran and pablo are to be resolved in a different
commit.
Platforms tested:
eirene (parallel), arabica (solaris 7 --enable-fortran, --enable-cxx)
Purpose:
New feature
Description:
Allow H5Glink and H5Gmove to handle links across different locations.
Solution:
Added H5Glink2 and H5Gmove2 functions with new parameter of destination
location.
Platforms tested:
Linux 2.2(eirene)
Bug Fix.
Description:
When the fill value for a dataset is not set, the size is set to zero,
causing problems with filling unused areas in previously defined chunks
(i.e. when the dataset shrinks in size)
Solution:
Use the size of the elements in the dataset directly, instead of relying on
the size of the fill value (which must be the same size).
Platforms tested:
FreeBSD 4.5 (sleipnir)
Code cleanup
Description:
Previously, the I/O pipeline (pline), external file list (efl) and fill-
value (fill) structs were passed down the raw data function call chain,
even into and/or through functions which didn't use them. Since all three
of these pieces of information are available from the dataset creation
property list, just pass the dataset creation property list down the
function call chain and query for the information needed in a particular
function.
Platforms tested:
FreeBSD 4.5 (sleipnir)
Bug fix
Description:
$(LT_RUN) was used to execute ./H5detect in src/Makefile.in.
$RUNTEST was set to $(LT_RUN) which was used to execute sequential
executable. $(LT_RUN) is "../libtool --mode=execute". But libtool
invokes some commands that are not supported in the Tflops machine.
That caused failures during the build and check processes.
Solution:
Upon investigation, there does not seem to be need to use $(LT_RUN)
any more. The "libtool --mode=link" now generates a "fake" executable
that is actually a command-script file that can regenerate the real
executable with dynamic libraries hooks setup properly.
Undo all those $LT_RUN substitute and let $RUNSERIAL execute those
sequential executables.
Platforms tested:
Eirene(serial), modi4(parallel)
Code cleanup
Description:
Reduce gratuitous differences between H5D_write and H5D_read and also
remove distracting debugging printf's that were ifdef'd out.
Platforms tested:
FreeBSD 4.5 (sleipnir)
Code tweak.
Description:
Allow the 'fill' parameter of H5S_select_fill to be NULL and allocate a
temporary buffer for it, if so.
Platforms tested:
FreeBSD 4.5 (sleipnir)
Purpose:
update macro HDstat
Description:
The original defination of HDstat only defines HDstat as stat.
the file size defined at struct stat is int32,
However for files greater than 4G(or 2G)file, lookup of file size will
fail on windows when using stat. Add a macro for windows,define HDstat
as istat64.
This fix is the same as HDfstat macro.
Solution:
Platforms tested:
linux 2.2.18
Code cleanup
Description:
Clean up the H5B_iterate code to not have a single hard-wired iterator for
each interface which uses a B-tree, instead accept a function pointer which
determines the callback function. This allows additional iterator
callbacks to be defined without requiring additional H5B functions to be
created.
In that spirit, remove the H5B_prune_by_extent call and convert the
H5F_istore callback routine for it into a callback routine for H5B_iterate.
Platforms tested:
FreeBSD 4.5 (sleipnir)
Code cleanup
Description:
Platform dependent code related to the struct stat and fstat
calls polluted source codes. Hard to maintain.
Solution:
Platform dependent code are moved to H5private.h and then internal
code can #include H5private.h. Repeat those macro definition for
the stdio and multi drivers since they area examples for writing
a virtual file driver. They must not use any internal code.
Platforms tested:
eirene (parallel), modi4 (serial including gass driver.)
Code cleanup
Description:
Update 'indent' flags for library to include some flags in later versions
of GNU indent.
Platforms tested:
FreeBSD 4.5 (sleipnir)
Code Cleanup
Description:
Remove "knowledge" about external file storage from H5D_init_storage and
call H5F_seq_write instead, which handles things correctly.
Platforms tested:
FreeBSD 4.5 (sleipnir)
Code cleanup
Description:
Got rid of the "H5T_BKG_TEMP" setting that was used internally to the
library, since temporary background buffers are now handled by the
individual conversion routines instead of in a global background buffer.
No APIs were changed or affected by this.
Platforms tested:
FreeBSD 4.5 (sleipnir)
Bug fix
Description:
When several level deep nested compound & VL datatypes are used, the data
in the nested compound datatypes is incorrectly sharing the same "background
buffer", causing data corruption when the data is written to the file.
Solution:
Allocate a separate background buffer for each level of the nested types
to convert. (Also allocate temporary background buffers for array
datatypes, where this sort of problem could occur also)
Added more regression tests to check for these errors.
Platforms tested:
FreeBSD 4.5 (sleipnir) & Solaris 2.6 (baldric)
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.
Purpose:
H5Dset_extent API function
Description:
1 new public function: H5Dset_extent, that allows shrinking a dataset
several private functions that free the previously allocated chunks
H5F_istore_prune_by_extent, H5B_prune_by_extent : removes the chunks
H5F_istore_initialize_by_extent : initializes them with the fill value
H5S_select_fill is used to fill the selection in the memory buffer
Platforms tested:
Windows 2000
SUN( arabica)
LINUX (eirene)
IRIX64 (modi4)
Feature
Description:
Added comments that this is intended as an example of file driver.
Added a macro detection at the end to flag if non-public definitions
are used. (only check for H5private.h which is mostly likely used.
Not bullet proof at all.)
Platforms tested:
eirene.
New Feature
Description:
Added new H5Dfill() routine to fill the elements in a selection for a
memory buffer with a fill value. This is a user API wrapper around some
internal routines which were needed for the fill-value modifications
from Raymond as well as Pedro's code for reducing the size of a chunked
dataset.
Platforms tested:
FreeBSD 4.5 (sleipnir) [and IRIX64 6.5 (modi4) in parallel, in a few
minutes]
Purpose:
New feature
Description:
Added a query function H5Tget_member_index for compound and enumeration
data types, to retrieve member's index by its name.
Platforms tested:
Linux 2.2
Minor h5ls bugfix for compound types with array members.
(Similar changes shortly for 1.4 branch).
2002-04-02 10:22:55 Robb Matzke <matzke@arborea.spizella.com>
* H5F_istore_read: Realigned a couple of comments.
Bug Fix & Code Cleanup
Description:
The MPI-IO optimized transfer routines
(H5S_mpio_spaces_read/H5S_mpio_space_write) are not being invoked in all
the cases where they could be used.
Additionally, the code for determining if an optimized transfer is wrapped
into the actual I/O transfer routine in a very confusing way.
Solution:
Re-enabled MPI-IO optimized transfer routines in all the cases where they
should work.
Extracted all the pre-conditions for optimized transfers into separate
routines from the transfer routines.
Platforms tested:
FreeBSD 4.5 (sleipnir) & IRIX64 6.5 (modi4)
Features.
Description:
Error stack used to report only hdf5 predefined error messages
because it takes only static strings. Runtime defined messages
were not pushed to the stack.
Added the means and macros to push MPI error strings onto the
hdf5 error stack. Added a new minor error class as H5E_MPIERR
for this class of messages.
H5Epulbic.h, H5E.c:
Added H5E_MPIERR and its minor class description.
H5Eprivate.h:
Added HMPI_XXX macros to push MPI error strings to the stack.
H5FDmpio.c:
Changed couple places to use the new macros to test the new
macros. A more through changes to make use of these new
macros will be done later.
Platforms tested:
eirene (serial, parallel)
modi4(parallel)
Autotools Update
Description:
I've updated autoconf, automake, and libtool to the latest/greatest
versions; 2.53, 1.6, and 1.4.2 resp.
Many changes come with the new versions:
- ltconfig is no longer used
- acconfig.h is no longer used (#define values are declared with
the macro)
- regeneration of all of the aclocal.m4, configure, and
H5config.h.in files.
- new config.{guess,sub} files
- new ltmain.sh file
Platforms tested:
AIX (blue), and Linux
Code cleanup
Description:
The function pointer for doing parallel I/O was being set in the H5D_read
and H5D_write routines instead of in H5S_conv, where it belongs.
Solution:
Added an extra 'flags' parameter to H5S_find to allow the function to
determine when to set the MPIO functions instead of the regular optimized
I/O routines and get rid of code messing with the function pointer in the
H5D routines.
Platforms tested:
IRIX64 6.5 (modi4)
Bug Fix & Feature
Description:
The selection offset was being ignored for optimized hyperslab selection
I/O operations.
Additionally, I've found that the restrictions on optimized selection
I/O operations were too strict and found a way to allow more hyperslabs
to use the optimized I/O routines.
Solution:
Incorporate the selection offset into the selection location when performing
optimized I/O operations.
Allow optimized I/O on any single hyperslab selection and also allow
hyperslab operations on chunked datasets.
Platforms tested:
FreeBSD 4.5 (sleipnir)
Bug Fix (sorta)
Description:
"small" contiguous hyperslabs were not being detected correctly by
H5S_hyper_select_contigous() leading to poorer performance than possible.
Solution:
Corrected check for small hyperslabs. Also cleaned up the H5S_find() code.
Platforms tested:
FreeBSD 4.5 (sleipnir)
Purpose:
Bug fix(#697)
Description:
Variable-length string wasn't treated as string.
Solution:
Added character set and padding into VL string type.
Platforms tested:
FreeBSD
Merge of name component length limit bugfix from 1.4 branch.
A couple of very minor typos fixed.
2002-03-18 14:30:58 Robb Matzke <matzke@arborea.spizella.com>
* H5B_assert: Fixed typos in comments.
Purpose:
fix a windows bug
Description:
1. To create a >4GB file, fstati64 has to be used instead of fstat.
change fstat to fstati64 for WIN32 macroes. Some discussions are going on
the general issue on how to better handle with WIN32 or other similar platform.
This check-in is just a reminder not to forget the windows bug.
2. erase a WIN32 macro(include winsock2.h) at h5detect.c. It is not a problem now.
Solution:
use fstati64 instead of fstat for win32.
Platforms tested:
windows2000(confirmed at linux machine eirene)
Bug Fix
Description:
The H5Gget_objinfo() function was not setting the 'fileno' field in the
H5G_stat_t struct passed in.
Solution:
Added a "file serial number" to each file currently open in the library
and put that in the 'fileno' field. If a file is opened twice (with
H5Fopen) and the VFL driver detects that it is the same file (i.e. the
two file structures have the same "shared file info" in the library's
memory structures), they will have the same serial number.
This serial number has two drawbacks:
- If a VFL driver doesn't/can't detect that two calls to H5Fopen with
the same file actually _are_ the same file, each will get a
different serial number
- If the same file is closed and re-opened, the serial number will be
different.
It is be possible to fix the second drawback for many VFL drivers, but it
would be a lot of effort and probably isn't worth it until we've got a
good reason to do it. Dunno if we'll ever be able to fix the first
drawback...
Platforms tested:
FreeBSD 4.5 (sleipnir)
VS: ----------------------------------------------------------------------
