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Bug fix
Description:
Relax restrictions on parallel I/O to allow compressed, chunked datasets
to be read in parallel (collective access will be degraded to independent
access, but will retrieve the information still).
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Solaris 2.7 (arabica)
IRIX64 6.5 (modi4)
h5committest
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Bug fix & code cleanup
Description:
More dataset cleanups to get to a point where we can fix the chunked I/O
bug.
Also fix a couple of errors in the recent file object resurrection changes
which should hopefully address the recent daily test failres (H5T.c)
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Solaris 2.7 (arabica)
h5committest
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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:
(Same change to release branch)
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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Backport feature
Description:
Backport Kent's collective chunk I/O work to date into the release branch.
Also, minor code cleanups, etc.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
IRIX64 6.5 (modi4)
h5committested
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Code optimization
Description:
Set up datatype ID for dataset's datatype on disk. This allows us to avoid
repeatedly copying the datatype when an ID is needed.
Also, clean up a few warnings in various other places.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
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Purpose:
Handled SZIP without the encoder present.
Description:
It is now an error for a user to try to create, extend, or write to a
dataset without the encoder present in their SZIP library.
Added H5Zget_filter_info to provide users with a way to query HDF5
about the presence (or lack thereof) of the SZIP encoder.
Platforms tested:
Windows
Verbena
Arabica
Copper
Misc. update:
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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
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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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Code optimization
Description:
Query the dataset creation and transfer properties less often.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.9 (sleipnir) w/parallel
h5committested
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Code cleanup
Description:
Limit the scope on more function prototypes/macros/typedefs.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest not necessary.
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Code cleanup.
Description:
Move many package or internal function prototypes and macro definitions
into tighter scope according to their current use.
Added more comments where appropriate.
Eliminate ancient, unused functions.
Added a couple "accessor" functions to get parts of data structures which
were moved out of scope.
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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./src/H5D.c
./src/H5Dprivate.h
./src/H5Dpkg.h [REMOVED]
./src/H5Tpkg.h
./src/H5Tprivate.h
Rearranged some header stuff so H5A doesn't have to include
the package-private header files that don't belong to it.
./src/H5E.c
Added the H5E_ATTR message to the major error struct.
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