| Commit message (Collapse) | Author | Age | Files | Lines |
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Code cleanup
Description:
Removed more compiler warnings, etc.
Platforms tested:
Linux 2.2.x (eirene) w/parallel
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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)
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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
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Code Cleanup
Description:
Removed some compiler warnings.
Solution:
In a few cases, NULL was being returned when a FAIL was supposed to
be returned instead. There were some header files which needed to be
included in a few of the sources. A couple of if-then statements had
assignments in the conditional part. The compiler warned that they
should have extra "()"s around them. Made the code check the values
instead.
Platforms tested:
Linux (parallel) Modi4 (parallel)
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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 improvement.
Description:
Propagated the "fill time" property into the parallel chunk allocation
routine, allowing it to avoid writing fill values to each new chunk
allocated. This improves the performance of chunked datasets in parallel
I/O to be on par with contiguous datasets again (on modi4).
Platforms tested:
IRIX64 6.5 (modi4)
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Bug fix/Code improvement.
Description:
Currently, the chunk data allocation routine invoked to allocate space for
the entire dataset is inefficient. It writes out each chunk in the dataset,
whether it is already allocated or not. Additionally, this happens not
only when it is created, but also anytime it is opened for writing, or the
dataset is extended. Worse, there's too much parallel I/O syncronization,
which slows things down even more.
Solution:
Only attempt to write out chunks that don't already exist. Additionally,
share the I/O writing between all the nodes, instead of writing everything
with process 0. Then, only block with MPI_Barrier if chunks were actually
created.
Platforms tested:
IRIX64 6.5 (modi4)
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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)
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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)
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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)
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Code cleanup
Description:
Clean up warnings from gcc 3.1
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Code cleanup
Description:
Re-indented new code to match coding style of rest of library.
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Code Cleanup
Description:
Clean up compiler warnings from the last bunch of checkins
Platforms tested:
FreeBSD 4.5 (sleipnir)
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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)
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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.
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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)
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Merge of name component length limit bugfix from 1.4 branch.
A couple of very minor typos fixed.
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Bug fix
Description:
When a block was preempted from the chunk cache, it is possible that one
of the pointers in the algorithm is invalidated and would generate a core
dump.
Solution:
Re-calculate the internal pointer and move the the preemption after the
re-calc.
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Code speedup
Description:
Chunking I/O routines are reading in an entire chunk when performing I/O
on the chunk, even if the chunk will be too large to cache.
Solution:
If the chunk is too large to cache, uncompressed and has been allocated
space in the file, or if we are using the MPI-I/O VFD, perform the I/O
directly to the chunk, instead of reading the chunk into memory, updating
it and immediately writing the entire chunk back out.
Platforms tested:
FreeBSD 4.5 (sleipnir) (using serial access) and IRIX64 6.5 (modi4) (using
parallel access with MPI-I/O)
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Bug fix
Description:
Moved some executable code out of an assert() and check the results of the
code with an assert().
Platforms tested:
Solaris 2.6 (baldric)
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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
Description:
Get rid of IDs from internal function calls.
Platforms tested:
FreeBSD 4.4 (hawkwind)
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Kludge
Description:
Since we're only about halfway through converting the internal use of
property lists from the "old way" to the generic property lists, we turned
off snapshots to avoid exposing lots of API changes to users, until the
APIs settled down.
Getting the snapshots rolling again seems to have become a priority, so
some changes are going to have to be made now that were going to be
postponed until we were completely finished with the conversion. This
requires that the old API functions be able to deal with both the old
and new property lists smoothly.
Solution:
Kludge together the property list code so that they can transparently handle
dealing with both the old and new property lists
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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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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Code Cleanup
Description:
Changed POSIX function calls to the HD* way of doing things. Checked
with checkposix and tested on Linux.
Platforms tested:
Linux
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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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* 2000-11-07 Robb Matzke <matzke@llnl.gov> (H5F_istore_preempt)
Returns error if call to
H5F_istore_flush() failed.
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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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reduce malloc
abuse.
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machines. They
should (hopefully) work on all platforms again now.
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assert() macros
to double-check things. I've turned them back on again now. I also changed
the internal representation of a few struct fields to be float instead of
double, since the HP/UX 10.20 compiler was having problems with the alignment
of the doubles.
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"temporary buffer"
code, since the functionality was superceded. See the followup document for
details on the free-list code.
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Bug fix for parallel mode.
Description:
H5FD_mpio_tas_allsame was called for all cases, even when
MPIO is not used for access. That corrupted the internal
file handle structure.
Solution:
Define a macro, IS_H5FD_MPIO(f), for testing if f is opened with
MPIO access. Will call H5FD_mpio_tas_allsame only if this
condition is true.
Platform tested:
O2K, both -64 and -n32 modes.
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form of H5_HAVE_PARALLEL and H5_HAVE_GASS.
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only currently),
but I fixed lots of misc. compiler warnings in other code and also tracked down
the memory overwrite bug that was causing the development branch to core dump
on most machines.
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----------------------
./src/H5D.c
Added additional elements to a variable initializer in
H5Dvlen_get_buf_size() to shut up a warning message. Also
added the API tracing call.
./src/H5F.c
Added file opening optimizations. If the driver doesn't
support the ability to determine when two file handles refer
to the same file (like MPIO and GASS) then H5F_open() makes
fewer calls to the driver's open callback. Also, if the
tentative file access flags are the same as the original flags
then H5F_open() makes fewer calls to the file device.
./src/H5FD.c
./src/H5FDprivate.h
./src/H5FDpublic.h
Added H5FD_get_class() so the library can get information
about what file driver callbacks are defined. This will be
useful when more optimization functions are added to the VFL,
such as for MPIO derived datatype I/O.
./src/H5FDcore.c
./src/H5FDfamily.c
./src/H5FDmpio.c
./src/H5FDmulti.c
./src/H5FDsec2.c
The driver symbols (like H5FD_CORE, etc) are actually function
calls. The functions were fixed to return correct values even
after calling H5close().
./src/H5FDmulti.c
./src/H5FDmulti.h
Added support for opening a file when parts are missing (only
if the caller explicitly allows that in the file access
property list).
Moved some common code sequences into macros or functions.
Added better support for reopening files. All the application
has to know is that the file is a multi file and the base name
from which all the member names are created.
More debugging output when the file is opened with the
H5F_ACC_DEBUG flag.
Fixed various bugs.
./src/H5Fistore.c
Chunked raw data was accidently allocated as meta data instead
of raw data.
./src/H5I.c
The H5Iget_type() function fails when invoked with an old
object ID (an ID which has been closed down).
./test/h5test.c
Added an extra argument when setting the multi file access
property lists so the test fails if it can't open one of the
sub-files.
./tools/h5ls.c
Improved the algorithm for deciding what file driver to
use. It basically tries all of the predefined drivers and is
now able to open family, split, and multi files without
looking for special characters in the file name.
Added `-e' and `--errors' switches which cause errors from
libhdf5 to be reported on stderr in addition to the simple
error message displayed by h5ls.
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----------------------
./src/H5D.c
./src/H5F.c
./src/H5FDmpio.c
./src/H5Fistore.c
./src/H5Fprivate.h
./src/H5Smpio.c
The `driver_id' for a file was accidently put in two
structs. I removed it from the H5F_file_t struct since it's
really an attribute of the VFL stuff.
More careful incrementing/decrementing the driver ID to fix a
memory leak.
./src/H5P.c
Rewrote H5Pcreate() in terms of H5P_copy() of a default
property list. This fixes some referencing counting bugs.
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----------------------
./src/H5D.c
./src/H5F.c
./src/H5Fistore.c
./src/H5Smpio.c
Incorporated previous changes into MPIO special cases. These
are mostly due to the fact that most of the members of the
file->shared->fapl struct have been moved into the
file->shared->file->shared struct (`file' is an H5F_t*).
./src/H5I.c
Fixed a bug with closing the library w.r.t. the VFL stuff. The
VFL layer introduced reference counts on object ID's and the
library termination functions freed these objects in the wrong
order. Now H5I_clear_group() does not normally remove objects
with a reference count larger than one because it assumes that
those objects are currently in use by the library.
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----------------------
./MANIFEST
./src/H5FDmulti.c [NEW]
./src/H5FDmulti.h [NEW]
./src/Makefile.in
./src/hdf5.h
The split driver was reimplemented as a more general "multi"
driver which is capable of splitting data into multiple files
like the family driver except the partioning is done by memory
usage type instead of address. The H5Pset_fapl_split()
function just calls H5Pset_fapl_multi() with arguments which
prepare to split the address space into two files: meta and
raw data.
This is the first version. I plan to allow the open() call to
relax a bit which would allow one to open an hdf5 file when
only the meta-data file is present. This would allow a very
large file to be split and stored on tape and the relatively
small meta file to be mirrored on disk to allow limited
browsing of the file (any request for raw data would fail).
./src/H5private.h
./src/H5F.c
./src/H5FD.c
./src/H5FDprivate.h
./src/H5FDpublic.h
./src/H5FDcore.c
./src/H5FDfamily.c
./src/H5FDmpio.c
./src/H5FDsec2.c
Added the ability for a file driver to store information in
the superblock which would be needed if the file were opened
again later for reading. The format is driver-defined which
allows users to extend it however they like.
./doc/html/H5.format.html
Added information about the new driver information block of
the superblock. This is where file drivers store information
they need in order to reopen the file later.
./src/H5F.c
./src/H5Fprivate.h
./src/H5FD.c
./src/H5FDprivate.h
./src/H5FDpublic.h
./src/H5FDcore.c
./src/H5FDfamily.c
./src/H5FDmpio.c
./src/H5FDsec2.c
./src/H5Fistore.c
./src/H5R.c
The file access properties and the file access property list
were decoupled, which allows the property list to more cleanly
contain properties for various levels of the file and which
allows the property list to be modified more cleanly when
opening files.
./src/H5.c
./src/H5FDpublic.h
Removed H5FD_MEM_META and H5FD_MEM_GROUP since they're never
used.
./src/H5D.c
Changed the way we detect the MPIO driver in all these special
cases.
./src/H5F.c
./src/H5Rpublic.h
./test/tfile.c
The default file sizeof(offset) was changed to be a function
of haddr_t instead of hsize_t.
THE H5RPUBLIC.H DEFINITIONS WILL HAVE PROBLEMS IF THE USER
CREATES A FILE WITH NON-DEFAULT OFFSET AND SIZE SIZES!
./src/H5F.c
Fixed an uninitialized memory access bug in file closing
related to the VFL.
./src/H5T.c
./src/H5Tpublic.h
Added an H5T_NATIVE_HADDR predefined datatype which
corresponds to the `haddr_t' type.
./test/Makefile.in
Reformatted long lines.
./test/big.c
./test/cmpd_dset.c
./test/dsets.c
./test/dtypes.c
./test/extend.c
./test/external.c
Removed the H5F_ACC_DEBUG flag from file creation/open calls.
./test/big.c
Plugged a memory leak.
./test/h5test.c
Added support for the `multi' driver.
Removed #warning about not having the stdio driver. Plans are
to not implement it since the sec2 driver serves the same
purpose and testing didn't show any difference in execution
times between the two.
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