Bug fix (or more like feature)
Description:
MPI_File_open does not truncate the filesize if file already exists.
This created confusion during debugging as what the real file size
is. It also interfere the real write bandwidth since the times
required to allocate new disk-space vanishes for subsequent writes
that are for offset shorter than previous file sizes.
Added a MPI_File_set_size to reset the file size to 0 for every new
file.
Another bug is that the 'remove()' call may not work for MPIO/PHDF5
files. (e.g., filename may have some MPI prefix like "pfs:filename").
Replaced "remove" with MPI_File_delete for those cases.
Platforms tested:
modi4(pp) and eirene (pp)
Purpose:
parameter file
Description:
handle parameters in various special cases.
Users donot even have to use this file if they don't have those special needs.
1) memory optimization (should always be set to 0 without handling huge SDS array conversion)
2) unlimited dimension with zero current size, users can use this file to define
their chunk size.
Solution:
Platforms tested:
RedHat Zoot 6.2
Purpose:
a bug fix
a feature added
Description:
1.conversion of unlimited dimension data with the current dimensional size 0
2. Use a parameter file to control some special cases:
1) To subdivide the huge array into hyperslabs, a memory buffer size has i
to be set.
2) when current dimensional size is 0, a default chunk size can be set.
Solution:
bug fixed 1. Old approach: the current dimensional size is set to H5S_UNLIMITED, which is
a huge number. The default chunk size is set as a *FIXED* default value.
2. New approach: the current dimensional size is set to the current value 0.
Users can provide the chunk size through a parameter file.
Platforms tested:
eirene
[machines you have tested the changed version. This is absolute
important. Test it out on at least two or three different platforms
such as Big-endian-32bit (SUN/IRIX), little-endian-32(LINUX) and
64-bit (IRIX64/UNICOS/DEC-ALPHA) would be good.]
bug fix, new feature
Description:
Added HDF5 write in do_write.
Added a complete do_read.
Still need timing code for the read part.
Platforms tested:
eirene (pp), modi4(pp).
Did not test serial since all changes were done in parallel area.
Purpose:
Removing warnings
Description:
H5IdComponent::operator= shouldn't be virtual because the subclass'
operator= have different type for the rhs argument. Removed virtual.
Platforms tested:
SunOS 5.7 (arabica)
Linux 6.2 (eirene)
Purpose:
DOH!
Description:
Ugh! I forgot to add the -m flag to the list of "short" parameter
codes. It wasn't even looking for them. *sigh*
Solution:
Added it
Platforms tested:
Linux
Bug fixes, new features
Description:
There was a coding error in handling file open flags. Changed it
to use &.
Added do_cleanup to cleanup temporary test files but only if
$HDF5_NOCLEANUP is not set. This is consistent with other test programs.
Added logic so that each process is writing its own slabs of data only.
Moved the number of process, rank of process and the communicator used
for PIO run to be global variables. Makes the coding easier. (but this
is not thread-safe.)
Platforms tested:
modi4(pp) and eirene(pp).
Purpose:
Bug fixing
Description:
H5IdComponent::operator= shouldn't be virtual because the subclass'
operator= have different type for the rhs argument. Removed virtual
Platforms tested:
SunOS 5.7 (arabica)
IRIX64 (modi4) - only tested that the warnings went away, still working
on other configuration problems.
Code cleanup
Description:
Tweaked internal error handling macros to reduce the size of the library's
object code by about 10-20%.
Also cleaned up some compiler warnings...
Platforms tested:
FreeBSD 4.4 (sleipnir)
Purpose:
Feature Fix
Description:
Changed default size of file to 512MB. The "-m" flag is now in
megabytes as well. This makes running things a bit faster.
Platforms tested:
Linux
Purpose:
bug fixed
Description:
HDF4 Vdata is extensible, when converted, the new HDF4 data set should also be extensible.
Solution:
Make the HDF4 dataset converted from Vdata unlimited dimensions.
These three testing files should be updated accordingly.
Platforms tested:
Linux, RedHat 6.2
Purpose:
Bug Fix
Description:
Fixed so that it will display the correct timing data. It will also
write to the correct file (which it wasn't before).
Solution:
Put the code in for displaying the time. Had to change the way I was
passing an object to the pio_fopen() function from just being a
structure to being a pointer so that the changes could be propagated
back.
Platforms tested:
Linux
Purpose:
Bug Fix
Description:
I wasn't calculating the total time correctly.
Solution:
I had to subtract the previous time from the current time. This
wasn't being done...DOH
Platforms tested:
Linux
Purpose:
Modify H5Fclose behavior
Description:
The HDF5 actual file close behaves in several ways in terms of if there
are still objects(dataset, group, datatype) opened in file.
Solution:
Added a new file access property, file close degree. It has four values,
H5F_CLOSE_DEFAULT
H5F_CLOSE_WEAK
H5F_CLOSE_SEMI
H5F_CLOSE_STRONG
The way a file is closed is decided by these values.
Platforms tested:
IRIX64 6.5, SunOS 5.6, FreeBSD 4.4
Bug Fix
Description:
The file metadata macros generate unaligned access warnings on the IA64
architecture.
Solution:
Got rid of bogus big-endian vs. little-endian differentiation when encoding
and decoding file metadata and use proper set of macros to prevent unaligned
access problems.
This fixes bug #672.
Platforms tested:
FreeBSD 4.4 (sleipnir)
Bug Fix
Description:
The code in H5Sselect_hyperslab_valid contained an fencepost error and is
allowing selections which overlap the extent by exactly one element in any
dimension to pass as valid instead of flagging the selection as invalid.
This bug only affects hyperslabs which have been OR'ed together, not the
selection from a single H5Sselect_hyperslab.
This fixes bug #550.
Solution:
Changed an '>' to an '>=' and added new regression test to check for error.
Platforms tested:
FreeBSD 4.4 (sleipnir)
Purpose:
Small Fixes
Description:
After conversation with Albert, here are some small fixes for the
performance stuff. Not too significant. Though, we did add the
"buffer size" as a parameter I pass to the engine.
Purpose:
Feature Fix
Description:
Added code so that it measures the time it takes to do I/O and return
that to the calling function.
This code doesn't quite work yet. There is something wrong with the
MPI code in the "pio_engine.c" file...I don't know what's up with
it...
Platforms tested:
Linux
Purpose:
Bug Fix
Description & Solution:
In the test for "namespace", we needed to include the "iostream"
header file to remove errors for strict compilers who need iostream
for namespaces. I moved the test for namespace to after the test for
"old header filenames" to make sure that I'm #including the correct
iostream ("iostream" or "iostream.h").
Platforms tested:
Linux
Bug fix
Description:
Cleaned up obvious syntax errors to make it to compile.
Changed unnecessarily unsigned variables to signed to avoid
messy compiler warnings.
Platforms tested:
eirene (parallel)
Bug fix.
Description:
Fix fortran stub for H5P[gs]et_hyper_cache.
Solution:
Made the fortran subs not execute any function calls into the library,
unless v1.4 compatibility is turned on.
Elena will be following this up with a real fix.
Platforms tested:
FreeBSD 4.4 (hawkwind)
Bug fix
Description:
A a build had occurred in the source tree ($CURRENT) and did not
do a distclean, the left over files would interfere with srcdir
build.
Solution:
Added a "make distclean" in the "checkout" option to clean up
the $CURRENT just in case. Not necessarily the most optimal
spot to do the cleaning but convenient.
Platforms tested:
Eirene.
Code cleanup
Description:
Property that H5P(g|s)et_hyper_cache uses is no longer in use inside the
library.
Solution:
Removed H5P(g|s)et_hyper_cache API functions, except when backward
compatibility is turned on. When backward compatibility is turned on,
the property is defined by the library, but unused internally.
Platforms tested:
FreeBSD 4.4 (sleipnir)
Purpose:
Expanded descriptions and minor copy edits.
Description:
H5Fcreate, H5Fopen, H5Fclose
Changes stemming from Albert's H5Fxxx proposal
Added IN/OUT designations to parameters.
Minor formatting and copy edits
[Sorry, but "no space left on device" error prevents deletion
of extra blank lines!]
Platforms tested:
IE 5
Backward Compatibility Fix
Description:
One of H5P[gs]et_buffer's parameters changed between v1.4 and the
development branch.
Solution:
Added v1.4 compat stuff around H5P[gs]et_buffer implementation and testing
to allow v1.4.x users to continue to use their source code without
modification.
These changes are for everything except the FORTRAN wrappers - I spoke with
Elena and she will make the FORTRAN wrapper changes.
Platforms tested:
FreeBSD 4.4 (hawkwind)
Backward Compatibility Fix
Description:
One of H5P[gs]et_sieve_buf_size's parameters changed between v1.4 and the
development branch.
Solution:
Added v1.4 compat stuff around H5P[gs]et_sieve_buf_size implementation and
testing to allow v1.4.x users to continue to use their source code without
modification.
There are no C++ or FORTRAN wrappers for these functions.
There are also no regression tests for these functions... :-(
Platforms tested:
FreeBSD 4.4 (hawkwind)
Backward Compatibility Fix
Description:
One of H5P[gs]et_meta_block_size's parameters changed between v1.4 and the
development branch.
Solution:
Added v1.4 compat stuff around H5P[gs]et_meta_block_size implementation and
testing to allow v1.4.x users to continue to use their source code without
modification.
There are no C++ or FORTRAN wrappers for these functions.
There are also no tests for these API functions currently... :-(
Platforms tested:
FreeBSD 4.4 (hawkwind)
Backward Compatibility Fix
Description:
H5Pset_fapl_log's parameters have changed from a simple "verbosity" level
to bit-masked flags to enable various behaviors.
Solution:
Added in v1.4 compat stuff, on the unlikely chance that others are actually
using this code in some production way.
There are no C++ or FORTRAN wrappers for this call.
Platforms tested:
FreeBSD 4.4 (hawkwind)
Bug fix
Description:
Snapshot does "make check" directly, instead of building all
binary first. This means it does not cover code that are not
tested (e.g., example, perform). (That explained why the errors
in the PIO performance code were not reported in daily test but
blew up when people built the library the "normal" way.)
It is done this way so that the snaptest aborts as soon as
the first test failed rather than after all code are compiled.
Solution:
Add "make" (to build all binary) before "make check".
The allows snaptest to fail as soon as the first compiling failure.
If we wish the snaptest to abort on the first test failure, the two
can be swapped as "make check && make ...". (It would appear strange
to run tests then make binary.)
Platforms tested:
Would be tested in the daily test tonight. (I should have tested
it first but I started this commit process already. Sorry.)
Backward Compatibility Fix
Description:
One of H5P[gs]et_sym_k's parameters changed between v1.4 and the development
branch.
Solution:
Added v1.4 compat stuff around H5P[gs]et_sym_k implementation and testing
to allow v1.4.x users to continue to use their source code without
modification.
These changes are for everything except the FORTRAN wrappers - I spoke with
Elena and she will make the FORTRAN wrapper changes.
Platforms tested:
FreeBSD 4.4 (hawkwind)
Backward Compatibility Fix
Description:
One of H5P[gs]et_cache's parameters changed between v1.4 and the development
branch.
Solution:
Added v1.4 compat stuff around H5P[gs]et_cache implementation and testing
to allow v1.4.x users to continue to use their source code without
modification.
These changes are for everything except the FORTRAN wrappers - I spoke with
Elena and she will make the FORTRAN wrapper changes.
Platforms tested:
FreeBSD 4.4 (hawkwind)
Purpose:
Eliminated warnings
Description:
On IRIX and Windows 98, if a function, that returns a value, throws
an exception in "else" statement, the compiler still complains that
the function doesn't return a value.
Solution:
Replaced:
if (something valid)
return a value
else
throw an exception
with:
if (something invalid)
throw an exception
return a value
Platforms tested:
Windows 98
SunOS 5.7 (arabica)
Linux 6.2 (eirene)
IRIX64 (modi4) - only tested that the warnings went away, still working
on other configuration problems.
Purpose:
Code Cleanup and Feature Add
Description:
Finally checking in the changes I made to the performance code. It
just modularizes it a bit more and performs some more checks, etc. I
also renamed the timer functions to be more inline with how other
things are named here...
Platforms tested:
Linux
Bug fix
Description:
Missing a statement for an else branch when HAVE_GETTIMEOFDAY was defined,
which caused most machines to fail compiling.
Solution:
Re-arranged if/else statement to eliminate problem.
Platforms tested:
FreeBSD 4.4 (sleipnir)
Code cleanup
Description:
Changed the logging file driver to use bitmasked flags for features to
enable, instead of using a verbosity level.
Platforms tested:
Solaris 2.6 (baldric)
Purpose:
Bug Fix
Description:
We needed to support C++ on SP3. Libtool was putting a "-bnso" flag
on the compile line. This was causing the C++ compiler to barf..
Solution:
Removed the line.
Platforms tested:
OSF5.1
