Purpose:
Change release note for new functions(H5Gget_comment, H5Arename,
H5Aget_storage_size).
Misc. update:
Update release_docs/RELEASE for bug fixes, new features, etc.
Purpose:
Added missing fortran functions h5set(get)_buffer_f.
Also added docs and tests for them.
Solution:
Currently functions do not accept conversion and background buffers.
This corresponds to H5set(get)_buffer call with buffer pointers
set to NULL. If there is a demand, I can overload the functions
to have new parameters and go through all trouble creating functions
for all supported datatypes.
Platforms tested:
Solaris 2.7, Linux 2.2., IRIX64-6.5
Purpose:
Added new F90 APIs
Description:
I added new F90 APIs, tests, and documentation for the following
functions:
h5fget_obj_count_f h5pequal_f h5tget_member_index_f
h5fget_obj_ids_f h5pget_fclose_degree_f
h5pset_fclose_degree_f
Documentation for exisiting functions was missing:
h5freopen_f, h5fflush_f, h5fmount_f, h5unmount_f, h5fget_create_plist_f,
h5fget_access_plist_f.
Platforms tested:
Solaris 2.7, Linux 2.2 and IRIX64-6.5
Purpose:
New API functions
Description:
Added API functions to return pointer to low-level file handle
(H5Fget_vfd_handle and H5FDget_vfd_handle) and related property list
setting functions(H5Pset_family_offset and H5Pset_multi_type).
Platforms tested:
Linux 2.2(eirene), Solaris 2.7(arabica), IRIX64 6.5(modi4)
Purpose:
Added new fortran functions
Description:
Source code, tests and documentation for h5glink2_f and h5gmove2_f
functions were added. I also added missing man page for h5glink_f
Platforms tested:
Solaris 2.7, IRIX64-6.5 and Liniux 2.2
Purpose:
Added missing fortran functions.
Description:
Four Library Fortran API functions have been added:
h5get_libversion_f, h5_check_version_f, h5garbage_collect_f and
h5dont_atexit_f. Only first two functions were tested.
Documentation file and RELEASE.txt were updated.
Platforms tested:
Solaris 2.7, IRIX64-6.5 and Linux 2.2
API name change
Description:
Change all "space time" references to "alloc time", including API functions
and macro definitions, etc.
Platforms tested:
FreeBSD 4.6 (sleipnir) w/C++
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/parallel & FORTRAN
Code cleanup/New Feature
Description:
Improve the space allocation in the file by re-using freed space more
effectively.
Platforms tested:
FreeBSD 4.6 (sleipnir) w/serial & parallel
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.
Purpose:
update windows support.
Description:
1. Since we don't support w98 anymore, delete the description about w98.
Actually DLL may work on w98.
2. Release dll work for new HDF5 release.
Solution:
Platforms tested:
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
Bug Fix
Description:
When parallel I/O is used, the MPI-I/O VFL driver uses a "lazy" model to
call MPI_File_set_view() in order to reduce the number of calls to this
function. However, this is unsafe, because if a collective I/O which uses
MPI derived types (and thus uses MPI_File_set_view()) is immediately
followed by an independent I/O, the code will attempt to call
MPI_File_set_view() in order to switch back to the default view of the
file. MPI_File_set_view() is a collective call however, and this causes
the application to hang.
Solution:
Removed "lazy" MPI_File_set_view() code, instead set the file view when it
is needed (with MPI derived types) and immediately set the file view back to
the default view before leaving the I/O routine.
Platforms tested:
IRIX64 6.5 (modi4) w/parallel. Also, tested with the latest development
and release code for the SAF library, which now works correctly with this
change. (Although the release branch of the SAF library seems to have a
bug, this 1.4.4 release candidate code gets as far as the version the SAF
library is released on top of (1.4.2-patch1, I believe)).
New feature.
Description:
There is some discussion among the SAF team as to whether it is better
to use MPI derived types for raw data transfers (thus needing a
MPI_File_set_view() call), or whether it is better to use a sequence of
low-level MPI types (i.e. MPI_BYTE) for the raw data transfer.
Solution:
Added an in internal flag to determine whether derived types are preferred
(the default), or whether they should be avoided. An environment variable
("HDF5_MPI_PREFER_DERIVED_TYPES") can be set by users to control whether MPI
types should be used or not. Set the environment variable to "0" (i.e.:
'setenv HDF5_MPI_PREFER_DERIVED_TYPES 0' to avoid using MPI derived types.
Platforms tested:
IRIX64 6.5 (modi4) w/parallel
Bug fix.
Description:
The chunking code was using internal allocation routines to put blocks on
a free list for reuse, instead of using the system allocation routines (ie.
malloc, free, etc.). This causes problems when user filters attempt to
allocate/free chunks for their algorithm's use.
Solution:
Switched the chunking code back to using the system allocation routines,
we can address performance issues with them if it becomes a real problem.
Platforms tested:
Linux 2.2.x (eirene) && IRIX64 6.5 (modi4)
Code optimization
Description:
Avoid creating MPI types (and thus requiring a MPI_File_set_view() call)
when contiguous selections are used for dataset I/O. This should be a
performance improvement for those sorts of selections.
Platforms tested:
Linux 2.2.x (eirene) w/parallel && IRIX64 6.5 (modi4) w/parallel & FORTRAN
Bug fix
Description:
I/O on "Regular" hyperslab selections could fail to transfer correctly
if the number of elements in the selection's row did now fit "evenly"
into the buffer being used for the transfer.
Solution:
Correct the calculation of the block & count offsets within the optimized
"regular" hyperslab routines.
Platforms tested:
FreeBSD 4.5 (sleipnir)
Update
Description:
Explained that, if the user uses the "make install prefix=NEW_DIR"
option, they'll need to modify the installed h5cc file to reflect the
change.
Bug Fix
Description:
H5Dcreate and H5Tcommit allow "empty" compound and enumerated types (i.e.
ones with no members) to be stored in the file, but this causes an assertion
failure and is somewhat vapid.
Solution:
Check the datatype "makes sense" before using it for H5Dcreate and
H5Tcommit.
Platforms tested:
FreeBSD 4.5 (sleipnir)
Bug Fix (#709)/Code improvement.
Description:
Allow chunks for chunked datasets to be cached when file is open for
read-only access.
Platforms tested:
IRIX64 6.5 (modi4) w/parallel
Bug fix (bug #777)
Description:
Current code allows a compound datatype to be inserted into itself.
Solution:
Check if the ID for the member is the same as the ID for the compound
datatype and reject it if so.
Platforms tested:
FreeBSD 4.5 (sleipnir)
Bug Fix for bug #789
Description:
Creating a 1-D dataset region reference caused the library to hang (go into
an infinite loop).
Solution:
Corrected algorithm for serializing hyperslab regions.
Platforms tested:
FreeBSD 4.5 (sleipnir)
New feature.
Description:
Added a "small data" block allocation mechanism to the library, similar to
the mechanism used for allocating metadata currently.
See the RFC for more details:
http://hdf.ncsa.uiuc.edu/RFC/SmallData/SmallData.html
This reduces the number of I/O operations which hit the disk for my test
program from 19 to 15 (i.e. from 393 to 15, overall).
Platforms tested:
Solaris 2.7 (arabica) w/FORTRAN and FreeBSD 4.5 (sleipnir) w/C++
Purpose:
Bug fix (#699), fix provided by a user, approved by Quincey
Description:
When a scalar dataspace was written to the file and then
subsequently queried with the H5Sget_simple_extent_type function,
type was reported H5S_SIMPLE instead of H5S_SCALAR.
Solution:
Applied a fix (see bug report 699)
Platforms tested:
Solaris 2.7 and Linux 2.2.18
Code improvement
Description:
The metadata aggregation code in the library was not terribly smart about
extending contiguous regions of metadata in the file and would not extend
them as far as possible. This causes space in the file to be wasted, also.
Solution:
Be smarter about extending the space used in the file for metadata by
checking whether new metadata blocks allocated in the file are at the end
of the current metadata aggregation region and append them to the metadata
region if so. This has the nice side benefit of reducing the number of
bytes we waste in the file and reducing the size of the file by a small
amount in some cases.
This reduces the number of I/O operations which hit the disk for my test
program from 53 to 19 (i.e. from 393 to 19, overall).
Platforms tested:
Solaris 2.7 (arabica) w/FORTRAN and FreeBSD 4.5 (sleipnir) w/C++
Bug Fix
Description:
The "dirty" flag for symbol table entries and symbol table nodes was not
being cleared when they were flushed to the file, causing lots of extra
metadata I/O.
Solution:
Reset the symbol table entry & nodes' flags when thy are flushed to disk.
This reduces the number of I/O operations which hit the disk for my test
program from 83 to 53 (i.e. from 393 to 53, overall).
Platforms tested:
Solaris 2.7 (arabica) w/FORTRAN & FreeBSD 4.5 (sleipnir) w/C++
