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Add line to libhdf5settings file for status of Parallel writes to
filtered datasets status
Surround Parallel Compression code in MPI_VERSION >= 3 checks
Add disabled message for Parallel Compression built w/ MPI-2
Modify Parallel Compression tests to only run the parallel filtered read
tests when parallel filtered writes are disabled
Update big I/O code to handle being built with MPI-2
Add checks to CMakeLists.txt for MPI_Mprobe and MPI_Imrecv
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settings file.
Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1
autotools serial w/Java
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debug
symbols, asserts, profiling, and optimization.
Also much refactoring, improved help, and --enable-<foo> options will
now emit errors on nonsense (e.g.: --enable-foo="asdfasdf").
The libhdf5.settings.in file was also reformatted.
Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
serial and parallel autotools w/ various options
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library.
Buffers that will be written to disk will now always be cleared since
not doing this has huge security implications.
Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0, x86_64) gcc 5.2.1
serial autotools
parallel autotools (MPICH 3.1.4)
serial CMake
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Add --enable-memory-alloc-sanity-check option to configure, to track and
sanity check memory allocations within the library. This is orthogonal to the
--enable-using-memchecker option and can be used with/without it.
Tested on:
MacOSX/64 10.11.2 (amazon) w/serial & parallel
(h5committest forthcoming)
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Tested: h5committest --PASSED--
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--enable-fortran
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variable
from H5_CXX_SHARED (which no longer exists) to enable_static.
Tested on: jam (configure only - minor change)
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features/autotools_rework
branch.
Removed the configure option that allows selective disabling of individual
internal filters (fletcher32, shuffle, etc.).
This feature mucked up the code with a lot of #ifdefs, saved very little space,
and was not scalable to a general scheme for library size reduction. We've
decided to remove the feature while we investigate a more general scheme for
decreasing the library size.
Part of: HDFFV-9086
Tested on: h5committest
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autotools_rework branch:
- Remove Infering parallel compilers (C and Fortran) from configure.ac
- Remove restriction to build shared with parallel
- Cleanup parallel sections in configure.ac
- remove large file support checks
- MPE fixes.
tested with h5committest.
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Remove all traces of MPI-POSIX VFD and GPFS detection/code.
Remove remaining traces of stream VFD.
Remove testpar/t_posix_compliant test (it's not actually verifying anything).
Clean up H5D__mpio_opt_possible() further.
Moved environment variable that disables MPI collective operations into
MPI-IO VFD (instead of it being in src/H5S.c).
A few other small code cleanups.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/parallel & serial
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include test.
Tested: jam
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Items merged: fortran directory,
src/libhdf5.settings.in
configure.in configure
MANIFEST
Tested: (all platforms used by daily tests, both with --enable-fortran and --enable-fortran2003)
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General shared library improvements for CYGWIN / AIX
Description:
Shared libraries are disabled on both CYGWIN and AIX due
to inability to build them correctly. Part of the problem
in both of these situations is the lack of the libtool
flag -no-undefined, which tells libtool that all needed
symbols are defined at link time (a requirement on these
systems) and that it's okay to build shared libraries.
Another problem are lack of dependencies between wrapper
libraries and core C HDF5 library.
This patch addresses both of these by fixing configure to
add in -no-undefined flag for libtool during linking and
adds automake dependencies in the Makefile.am files.
After testing, both CYGWIN and AIX now generate shared
libraries, but there are still some test failures in each.
(cache_api, dt_arith, and testerror.sh on CYGWIN, and
fortran tests on AIX).
Even though the shared libraries are not quite perfect,
this is a general improvement to what we had before, so
I'm applying the patch anyways. Note that default behavior
of shared libraries on these systems being disabled has
NOT been changed and requires the use of the
--enable-unsupported to attempt to build them.
We will need to address the test failures in each
architecture prior to formally supporting shared
libraries on each.
Tested:
h5committested & CYGWIN tested (on bangan)
(AIX tested by Albert on bp-login2)
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- Revise shared Fortran library disabling scenarios in configure
- Improve configure output summary
Description:
Shared Fortran libraries are not supported on Mac, but were being
disabled by configure in a way that also forced the C libraries
to be static-only. This has been fixed, so now only shared Fortran
is disabled while shared C can remain.
This prompted two additional changes:
1. While working on the check that addresses whether or not
shared Fortran libraries are allowed, removed old and no
longer needed check(s) that disable shared Fortran
libraries with HP, Intel 8, PGI, and Absoft compilers.
(Essentially, Mac is the only situation in which Fortran
shared are disabled by configure.)
2. Having two different states of libraries (i.e. shared C
library with static-only Fortran library) was not apparent
in the configure summary, which labeled all libraries as
either shared and/or static. I've added lines to both the
C++ and Fortran output sections to list shared/static-ness
of these libraries specifically.
Additionally, I've made sure that the new --enable-unsupported
configure option correctly overrides configure if it tries to
disable a shared library.
Tested:
jam, fred, & h5committest
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fortran and c++ compilers in libhdf5.settings file and configure output (r18836), to install examples as part of make install (r18680), and to provide scripts to compile and run the examples after they are installed (r18817).
Tested with new/h5committest on amani, heiwa, and jam.
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Improve configure's large-file support control.
Description:
Modified configure to now attempt to add defines necessary for
supporting largefiles on all systems, instead of solely on linux. This
is in response to user requests to enable largefile support on Solaris
by default, as well as to give extra control on AIX (instead of just
jamming the necessary flag into the config files).
The old --enable-linux-lfs flag has been removed in favor of the
--enable-largefile flag (enabled by default), which can be used on all
platforms.
On systems where large files cannot be supported in this manner,
configure will report as such.
Tested:
h5committest
AIX (NCSA's blue_print machine)
duty, liberty, and linew.
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Configure / Config File Fixes
Description:
1. Made AM_CPPFLAGS assignments in configure a bit safer. (i.e., check to
ensure include paths exist before adding them to AM_CPPFLAGS).
2. Change AIX config file to add -D_LARGE_FILES into AM_CXXFLAGS instead
of H5_CXXFLAGS (same with *_CFLAGS). This will propagate it into
h5c++, where it is needed to compile correctly.
3. Added missing line containing AM_CFLAGS to configure output summary.
Tested:
h5committest, and uP (AIX machine, via Albert).
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CFLAGS overhaul
Description:
Modified the way configure handles CFLAGS.
(note: all changes also apply to FCFLAGS, CXXFLAGS, CPPFLAGS, and LDFLAGS).
1. The configure process will now always preserve a user's CFLAGS
environment variable setup. Any additional flags necessary for compilation
added at configure time will be passed into the Makefiles as AM_CFLAGS,
which is an automake construct to be used in addition to CFLAGS.
This will allow a user to have the final say, as CFLAGS will always appear
later in the compile line than AM_CFLAGS. Additionally, setting CFLAGS
during make will no longer completely erase all flags set by configure,
since they're maintained in AM_CFLAGS.
2. Additionally, where possible, flags previously being assigned directly
into CFLAGS (and thus propagating into h5cc) have now been redirected into
H5_CFLAGS, so they're used ONLY for compiling hdf5, and not embedded into
the h5cc wrapper script as well.
*Note that H5_CFLAGS ultimately is assigned into AM_CFLAGS for use in the
Makefiles. Complete description of changes and build process will be
included in a Configure Document that Elena and I are working on.
3. Removed unsupported config files. This includes:
config/dec-osf*
config/hpux11.00
config/irix5.x
config/powerpc-ibm-aix4.x
config/rs6000-ibm-aix5.x
config/unicos*
4. Modified configure summary to display additional values. Specifically,
appropriate AM_* variables are being shown, as well as H5_FCFLAGS and
H5_CXXFLAGS, which were for some reason not already present.
Tested:
- H5committest
- Tested on all THG / NCSA machines, using several combinations of the more
prominent configure options (c++, fortran, szip, threadsafe, parallel,
et cetera). (Thanks to Quincey for rysnc testing setup!)
- With regards to new automated testing, anything *necessary* for
compilation will be caught by the daily tests as it stands now. (i.e.,
if LDFLAGS is not properly set when szip is used, linking will fail).
Additionally, with regards to which flags get into h5cc, if any
*necessary* flags have been improperly removed, then daily tests should
fail during make installcheck. Additional machine-specific desired
behaviors and/or checks may have to be set up separately within the
daily tests, so this is something to work on.
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Removed duplicated information due to previous incompleted changes.
Also rearranged the entries to a more logical combinations.
Tested: h5committest.
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Changed blank spacing in Fortran output so the output aligns correctly
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Fixed spacing issue for fortran summary line.
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Description: cleaning up configure related to removal of --disable-hsizet
flag, which we no longer support.
Tested: kagiso
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Improvement.
Description:
src/libhdf5.settings was the initial configure summary and is installed.
Then configure is changed to dump a summary of the configure settings to
the output and also append it to src/libhdf5.settings. That created
two different output formats and duplicated information. This is the
initial attempt to clean up this confusion and unify the output format.
It is decided to use the src/libhdf5.settings template as the unified means.
This requires more macros symbols be defined. The following symbols are
all related to generating the src/libhdf5.settings file.
AC_SUBST(EXTERNAL_FILTERS)
AC_SUBST(MPE) MPE=no
AC_SUBST(STATIC_EXEC) STATIC_EXEC=no
AC_SUBST(HDF_FORTRAN) HDF_FORTRAN=no
AC_SUBST(FC) HDF_FORTRAN=no
AC_SUBST(HDF_CXX) HDF_CXX=no
AC_SUBST(CXX) HDF_CXX=no
AC_SUBST(HDF5_HL) HDF5_HL=yes
AC_SUBST(GPFS) GPFS=no
AC_SUBST(LINUX_LFS) LINUX_LFS=no
AC_SUBST(INSTRUMENT) INSTRUMENT=no
AC_SUBST(CODESTACK) CODESTACK=no
AC_SUBST(HAVE_DMALLOC) HAVE_DMALLOC=no
AC_SUBST(DIRECT_VFD) DIRECT_VFD=no
AC_SUBST(THREADSAFE) THREADSAFE=no
AC_SUBST(STATIC_SHARED)
AC_SUBST(enable_shared)
AC_SUBST(enable_static)
AC_SUBST(UNAME_INFO) UNAME_INFO=`uname -a`
The src/libhdf5.settings.in has CONDITIONAL's added to it too. The
untrue conditions turned into a "#" and these lines are cleaned by the
post processing script.
Platform tested:
h5committest on kagiso, smirom and linew.
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Added C proprocessor flags and non-library linker flags to the
description.
./src/H5T.c [1.2, 1.3]
Changed return type in tracing macros to H5Tenum_nameof() and
H5Tenum_valueof().
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----------------------
./configure.in
./configure [REGENERATED]
./src/libhdf5.settings.in [NEW]
./config/conclude.in
./INSTALL
./MANIFEST
A file called `libhdf5.settings' is installed along with the
libraries and it contains a list of various things that might
be of interest to someone using the library (such as what
compiler/options were used and what other libraries might need
to be linked to satisfy external references). We can add more
things as it becomes necessary. Here's a sample...
SUMMARY OF THE HDF5 CONFIGURATION
=================================
HDF5 Version: hdf5-1.1.106
Configured on: Tue Jun 8 11:38:52 EDT 1999
Configured by: matzke@llnl.gov at Spizella Software
Configure mode: development
Host system: i686-pc-linux-gnulibc1
Byte sex: little-endian
Libraries: static, shared
Parallel support: mpicc
Installation point: /usr/local
Compiler: mpicc (egcs-2.91.66)
Compiler switches: -Wall -g
Extra libraries: -lmfhdf -ldf -lz -ljpeg -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages: d,e,f,g,hg,i,mm,o,p,s,v,z
API Tracing: yes
File addresses: large
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