| Commit message (Collapse) | Author | Age | Files | Lines |
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Code cleanup, sorta
Description:
Added ifdef sections for "H5_USING_PURIFY" in various places in the code,
which are designed to reduce the spurious "uninitialized memory read" warnings
from purify which are actually OK. Note that this macro will have to be
turned on by adding it to the CFLAGS for the build - I didn't think it was
important enough to add a configure flag for.
Also, the changes in H5HG.c optimize the walks through the objects in a
heap to only look at the 'used' entries instead of all the 'allocated' entries.
Platforms tested:
Solaris 2.7 (arabica) w/purify
Not tested by h5committest
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Code optimization
Description:
Eliminate duplicated call to H5T_detect_class()
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
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Bug fix
Description:
Close memory leak I introduced in H5Sencode() routine.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
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Code optimization
Description:
Changed calloc() calls to malloc() calls allocating background buffers
during dataset writes, since the background buffer information will be read
from disk anyway, overwriting any existing values.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
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Purpose:
Bug fix
Description:
Modification time test (mtime) would die silently on some systems. This is
because the code is very system-dependant (it relies on getting the current
time and the timezone from the OS).
Solution:
mtime test now uses TEST_ERROR macro to print "FAILED" and to output where the
failure occurred. Configure script is a little smarter about whether
gettimeofday() function returns the timezone correctly.
Further bugs will need to be addressed on a system-by-system basis.
Platforms tested:
sleipnir, arabica, verbena, copper, windows (VC7)
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Purpose: Bug fix
Description: While working on the SZIP documentation with Frank, I realized
that when scanline was less than 4k and bigger than pixels_per_block,
it was not adjusted if number_of_blocks_per_scanline was bigger
than max_number_of_blocks_per_scanline.
Solution: Fixed the code. Unfortunately it didn't help with the problem
I had using h5repack with DOQGROD.he5 file.
Platforms tested: copper
Misc. update:
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Code cleanup
Description:
Clean up collective chunking code a bit.
Also, add '--enable-instrument' configure flag to have a mechanism for
determining that optimized operations happened correctly in the library (instead
of just the "normal" way) by allowing 'flag' properties to be set outside the
library and set when the "right" thing happens. This is mainly for debugging
and regression checks, so we make certain we don't break optimized I/O by
accident. It's enabled by default when --enable-debug is on (which is on by
default in the development branch and off by default in the release branch),
but can also be independently controlled with its own configure flag.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
IBM p690 (copper) w/parallel
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Code cleanup
Description:
Fixed reserved.c test to use h5_fileaccess/h5_fixname/h5_cleanup.
Updated RELEASE.txt for previous bug fix
Platforms tested:
sleipnir, verbena
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Code cleanup
Description:
Clean up various recent changes a little.
Platforms tested:
FreeBSD 4.10 (sleipnir)
Too minor to require h5committest
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Update.
Description:
Update all the hdf5 testing batch files.
Solution:
1. Updated dumptest.bat, difftest.bat, lstest.bat and repacktest.bat files
to match with correspondent testings in Unix.
2. Added one new batch file mask.bat to mask off time information displayed
in some h5ls tests. The time displayed with h5ls uses a system all that
accountants for the local timezone of the cumputer that run that tests. To solve
this issue, the time information has to be masked off. Otherwise, the expected
output may be different with the actual output.
3. Updated H5pubconf.h to enable szlib encoder.
Platforms tested:
Microsoft Visual C++ 6.0 on Windows XP and 2000.
(will test with .NET on Windows XP after this check-in.)
Misc. update:
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To test collective chunk IO properly.
Description:
See the previous message.
Solution:
See the previous message.
Platforms tested:
arabica(Sol 2.7), eirene(Linux), copper(AIX)
Misc. update:
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To add a special section of codes for collective-chunk IO tests.
Description:
The current patch of collective chunk IO support in HDF5 can only handle
some special("however, can cover many applications") cases,
Inside source code, we did a careful checking to make sure other cases would
not fall into this category and would not use collective IO.
We also would like to test whether those collective conditions were met in our
test programs.
The current parallel HDF5 handled those collective IO requests in a special way.
If the library finds it cannot do collective IO, it will silently change to independent IO.
So basically there is no better way to check whether the library is doing what it should do without "hacking" into HDF5 source codes for the purpose of testing. But the "hacking" should not affect library work and should be easily pulled out after we get more general collective IO algorithm to work.
With Quincey's suggestion, we used HDF5 property APIs to finish the job.
Solution:
The approach includes three parts:
1) In the test program, insert a property inside data transfer property list.
Set a default value for this property.
2) Inside H5Dio.c, when the library finds that it cannot do collective IO with chunking storage, it will change the default value.
3) Then the test program will recheck the value after H5Dwrite or H5Dread to evaluate whether
the current collective IO case is doing the right thing.
Note: The test won't stop after it finds that the library is not doing the right thing and probably it will finish normally. The current approach is that the test program just printed out an error message. It should be changed later.
Platforms tested:o
copper,arabica,eirene
Misc. update:
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Description: Line 38, "#define H5_NO_FREE_LISTS" were commented out during debugging
Solution: put back in.
Platforms tested: No test needed
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Description: This is the second step of checkin for encoding and decoding objects.
H5Tencode and H5Tdecode have been committed in the previous step. H5Sencode
and H5Sdecode are checked in this time.
Solution: Given object ID, these functions encode and decode object information
into and from binary buffer and return new object ID. They take advantage of the
existing codes of object header message and encode in the same format.
Platforms tested: fuss and h5committest.
Misc. update: RELEASE.txt
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Purpose: Maintenance
Description: Documented SZIP change.
Solution:
Platforms tested:
Misc. update:
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Purpose: Improvement
Description: HDF5 Library set pixels_per_scanline parameter to the size of the chunk's
fastest changing dimension. As a result, fastest changing dimension
of the chunk could not be bigger than 4K and smaller than pixels_per_block
value and szip compression couldn't be used for many real datasets.
Solution: Reworked algorithm how HDF5 sets pixels_per_scanline value; only chunks
with the total number of elements less than pixels_per_block value are rejected.
There is no restriction on the size of the chunk's fastest changing
dimension anymore.
Modified the test according to the new algorithm.
Platforms tested: verbena, copper, sol
Misc. update:
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Purpose: Improvement
Description: HDF5 Library set pixels_per_scanline parameter to the size of the chunk's
fastest changing dimension. As a result, fastest changing dimension
of the chunk could not be bigger than 4K and smaller than pixels_per_block
value and szip compression couldn't be used for many real datasets.
Solution: Reworked algorithm how HDF5 sets pixels_per_scanline value; only chunks
with the total number of elements less than pixels_per_block value are rejected.
There is no restriction on the size of the chunk's fastest changing
dimension anymore.
Platforms tested: verbena, copper, sol
Misc. update:
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Bug fix and feature.
Description:
The setenv was done in runtest but it has the effect will linger
onto the next test. So, if the first test sets $CXX to a certain
value, it lingers on the all following tests of the same host.
This is usually not desired.
Solution:
Move the actual setenv code to snapshot. Runtest now just parses them
and pass along the setenv request to snapshot.
Platforms tested:
no h5comittest which does not really test the change.
Hand tested in eirene with Tg-NCSA.
Misc. update:
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bug fixes
Description:
the return error code for a function was not initialized.
in HP-UX it happened that this variable was initialized to -1
causing the function to return with an error condtion
solution : initialized the variable to 0
the name of the dataset was printed after the differences in verbose mode
and report when differences were found
solution : check first if differences were found and then
print the name of dataset and differences
in verbose mode always print the name first
Solution:
Platforms tested:
linux
aix
solaris
Misc. update:
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Add t_coll_chunk.c at testpar for collective chunk IO test.
Description:
Solution:
Platforms tested:
Misc. update:
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update documentation and usage message
Description:
updated the html documentation for the new h5diff modes
added a section for h5repack
Solution:
Platforms tested:
linux
Misc. update:
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To add collective chunk IO tests.
Description:
three tests are added.
1. Only one hyperslab for each process, and this hyperslab is fit in exactly one chunk.
2. non-contiguous hyperslabs in each process, these hyperslabs are fit in one chunk.
3. Single hyperslab for each process, smaller chunk is assigned. Number of chunks for
every process is equal.
Solution:
the dataset size is set to be very small, will enlarge later.
Platforms tested:
AIX 5.1(copper)
Misc. update:
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Adding the first round of patches about supporting collective chunk IO in HDF5
Description:
The current HDF5 library doesn't support collective MPIO with chunk storage. When users set collective option in their data transfer with chunk storage, the library silently converted the option to INDEPENDENT and that caused trememdous performance penalty. Some application like
WRF-parallel HDF5 IO module has to use contiguous storage for this reason. However, chunking storage has its own advantage(supporting compression filters and extensible dataset), so to make collective MPIO possible inside HDF5 with chunking storage is a very important task.
This check-in make collective chunk IO possible for some special cases. The condition is as follows(either case is fine with using collective chunk IO)
1. for each process, the hyperslab selection of the file data space of each dataset is regular and it is fit in one chunk.
2. for each process, the hyperslab selection of the file data space of each dataset is single and the number of chunks for the hyperslab selection should be equal.
Solution:
Lift up the contiguous storage requirement for collective IO.
Use H5D_isstore_get_addr to get the corresponding chunk address. Then the original library routines will take care of getting the correct address to make sure that MPI FILE TYPE is built correctly for collective IO>
Platforms tested:
arabica(sol), copper(AIX), eirene(Linux)
parallel test is checked at copper.
Misc. update:
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bug fix for windows testing
Description:
A function called H5C_stats_reset doesn't have H5_DLL in front of it,
it cause windows DLL test failed.
Solution:
Add H5_DLL in front of it.
Platforms tested:
windows xp, sol 2.7, linux 2.4, aix 5.1
Misc. update:
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h5diff and h5repack changes
Description:
h5diff
introduced the following four modes of output:
Normal mode: print the number of differences found and where they occured
Report mode: print the above plus the differences
Verbose mode: print the above plus a list of objects and warnings
Quiet mode: do not print output (h5diff always returns an exit code of 1 when differences are found)
h5repack
added an extra parameter for SZIP filter (coding method)
the new syntax is
-f SZIP=<pixels per block,coding>
(pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN')
Example of use:
./h5repack -i file1 -o file2 -f SZIP=8,NN -v
updated usage messages, test scripts and files accordingly
Solution:
Platforms tested:
linux
AIX
solaris
Misc. update:
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Bug fix
Description:
Allow buffer parameter to H5Dread & H5Dwrite to be NULL if there are no
elements to transfer.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
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Purpose:
Bug Fix
Description:
Calling H5Sset_extent_simple to change a dataspace's maxdims from nonzero to
zero causes errors (infinite loops, seg faults, asserts) because the pointer
to the maximum size isn't cleaned up properly
Solution:
Clean up that pointer. Added a test for this case.
Platforms tested:
sleipnir (very minor change)
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Purpose:
Bug Fix
Description:
Trying to create the root group or the working group ("/" or ".") fakes out
HDF5 so that it neither creates a group nor returns an error.
Solution:
H5G_namei now throws an error if it was supposed to insert but didn't.
Platforms tested:
sleipnir, Visual Studio 7 (very minor change)
Misc. update:
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Feature
Description:
Showed the fortran compiler and FFLAGS and CXX compiler and CXXFLAGS
when the corresponding language API is enabled.
Platforms tested:
No h5committest since it is just a simple shell script change.
Tested in Eirene.
Misc. update:
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Code cleanup
Description:
Clean up a bunch of warnings and bring new code better inline with current
library coding practice.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
Misc. update:
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Update.
Description:
Due to source code change, added 2 new projects to the Windows tests and
removed some files from a Windows project. Updated h5repack testing batch file
in Windows. Did some minor updates for cache project.
Solution:
1. Added 2 new projects reserved and reserveddll to the Windows workspace. These two projects include
the new source code reserved.c.
2. testh5repack_filters.c and testh5repack_layout.c were removed from HDF5 1.7 branch by Pedro. Removed
these 2 files from h5repacktst project.
3. Pedro updated h5repack testings. Updated repacktest.bat batch file to match with new h5repack testings
in Unix.
4. cache project settings->Link->Ignore libraries: add libcd.lib for release version and libc.lib for
debug version.
Platforms tested:
Microsoft Visual C++ 6.0/.NET on Windows XP.
(Will test on Windows 2000 with Visual C++ 6.0 after this check-in).
Misc. update:
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Bump version # after making snapshot
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bug fix.
Description:
The previous patch of -D__GNUC__ was causing failure in the
newer compiler. The previous failure could not be repeated
any more. So, removed it.
Platforms tested:
Tested only in TG-NCSA since the change affects only the ia64 platform.
Misc. update:
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Bug fix
Description:
It uses the value of $ARCH as a gcc option but the linux clusters
at NCSA define $ARCH as environment variable with values that are
not a valid compiler option. That caused the configure to fail
because it was not able to compile at all.
Solution:
Change ARCH to lower case $arch (convention dictates environment
variables are upper cases.) Also preset $arch to null and do not
honor any pass it values.
Platforms tested:
Attempted to run h5committest but sol was failing due to /tmp
filled. Copper and verbena passed. Also passed in TG-NCSA.
Misc. update:
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bug fix, new feature
Description:
fixed bug in the parse function:
cases where we have an already inserted name but there is a new name also
example:
-f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20
dset1 is already inserted, but dset2 must also be (it was not)
added a CHECK_SZIP symbol to enable/disable checking of library related szip parameters
added the print of the filter name in verbose mode (confirms visually that the filter was applied )
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
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Purpose:
Bug fix
Description:
Replaced "unsigned long long" with hsize_t in H5MF
Added "return 0" at end of reserved.c test
Platforms tested:
arabica, sleipnir
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Purpose: New feature
Description: New API H5Tencode and H5Tdecode. Given object ID, H5Tencode encodes object information into a binary form. H5Tdecode decode an object information in a binary form, reconstructs the object and return a new object ID.
Solution: Use object header functions H5O_dtype_decode and H5O_dtype_encode to
facilitate them. The encoded binary is exactly like object header information.
This is the first step checkin. Will check in H5Sencode and H5Sdecode later.
Platforms tested: h5committed and fuss.
Misc. update: will update release.txt after 2nd step checkin.
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Purpose:
Description:
Missed adding a test file in previous commit.
Solution:
Platforms tested:
Misc. update:
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Purpose:
Bug Fix
Description:
If an HDF5 file grows larger than its address space, it dies and is unable to
write any data. This is more likely to happen since users are able to change
the number of bytes used to store addresses in the file.
Solution:
HDF5 now throws an error instead of dying. In addition, it "reserves" address
space for the local heap and for object headers (which do not allocate space
immediately). This ensures that after the error occurs, there is enough address
space left to flush the entire file to disk, so no data is lost.
A more complete explanation is at /doc/html/TechNotes/ReservedFileSpace.html
Platforms tested:
sleipnir, copper (parallel), verbena, arabica, Windows (Visual Studio 7)
Solution:
Platforms tested:
Misc. update:
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Bug fix
Description:
Correct problems with "resurrecting" a dataset in a file. (This occurs
when a dataset which is open gets unlinked from the group hierarchy (making it
"dead" and marked for deletion in the file) and then is re-linked to the group
hierarchy). Note that the current solution applies only to datasets, further
work will fix this for groups and named datatypes also.
Also, fix the "debug" routines to be a little more helpful in certain
situations.
Additionally, fix a locking bug in the symbol table node splitting routine
which could be [one of] the cause[s] of the file corruption in flexible
parallel operation.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
h5committested
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h5repack changes
Description:
there were some requests to change some minor h5repack features
h5repack only made a warning about a non available filter in verbose mode ( -v )
without -v it kept silent, and users sometimes missed this warning
the request was that it should print this warning always. so, the new format, is e.g
./h5repack -i test_szip.h5 -o out.h5
Warning: dataset </dset_szip> cannot be read, SZIP filter is not available
due to this, and to avoid a lot of these messages in the shell test script, I modified
the script h5repack.sh so that it detects the presence of all filters in the environment
(previously it only detected SZIP)
the test files were also divided in more files , to make the script code easier to
follow
Solution:
Platforms tested:
linux
AIX (no szip)
solaris (no szip, no gzip )
Misc. update:
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Bug fix
Description:
Fix error in chunked dataset I/O where data written out wasn't read
correctly from a chunked, extendible dataset after the dataset was extended.
Also, fix parallel I/O tests to gather error results from all processes,
in order to detect errors that only occur on one process.
Solution:
Bypass chunk cache for reads as well as writes, if parallel I/O driver is
used and file is opened for writing.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
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Code optimization
Description:
Re-work the insertion of a new child into an existing node, to exploit
some speedups for adding the rightmost child, since this is a very common case
when appending records to an unlimited size dataset.
Also, hoist the checks for the tree's 'K' value into a field in the shared
information about the tree, instead of re-calculating them all the time.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
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Code optimization
Description:
Avoid calling vector comparison routine when operating on 1-D chunks.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
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Correct typo in file format for compact layout information
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Update.
Description:
Update new files into Windows workspace.
Solution:
Add H5RC.c and H5RCprivate.h to hdf5 and hdf5dll projects in Windows workspace.
Platforms tested:
MS Visual C++ 6.0 on Windows 2000.
(will test on Windows XP with Visual C++ 6.0 and .NET after this check-in)
Misc. update:
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Code optimization
Description:
Refactor B-tree code to extract all common information for a B-tree into a
shared structure that is pointed to by all the nodes in tree (instead of being
included in each node).
Also re-order B-tree node comparison checks for chunked datasets to
check for >= the upper node first, since the comparison is a bit "heavy" and
this check is more likely to succeed when you are adding records to the
dataset.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
(also, recent h5dump commits have broken testing...)
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h5dump new tests
Description:
added new tests for the print of array indices (nested objects, several ranks)
Solution:
Platforms tested:
linux
AIX
solaris
Misc. update:
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Description:
Changed call to H5File::getFileSize according to C library and
removed CHECK for this call because failure will be handled by
exception.
Platforms tested:
FreeBSD 4.10 (sleipnir)
Linux 2.4 (eirene)
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