./configure [REGENERATED]
./src/H5D.c
./src/H5O.c
Removed H5AC, H5B, and H5T from the default list of packages
to debug (because they're pretty expensive debugging), and
added H5O. Also fixed a bug for undefined variable in H5D when
H5S debugging is turned on but H5T debugging is turned off.
./config/conclude.in
Fixed installation of header files for building in a directory
other than the source directory. This fixes a bug where
H5config.h wasn't being installed.
./src/H5.c
./src/H5A.c
./src/H5D.c
./src/H5F.c
./src/H5G.c
./src/H5I.c
./src/H5Iprivate.h
./src/H5P.c
./src/H5R.c
./src/H5RA.c
./src/H5S.c
./src/H5T.c
./src/H5TB.c
./src/H5Tprivate.h
./src/H5Z.c
./src/H5detect.c
./src/H5private.h
Changed the way the library shuts down again. Now it handles
cycles between packages and isn't so sensitive to dependencies
between packages. A package might shut down only to be
restarted to process a request from some other package being
shut down. Loops are detected after 100 iteractions and the
shutdown is aborted with a message on standard error. This
also makes it a lot easier to debug.
./src/H5A.c
Fixed H5A_write() and H5A_read() so they pass a non-null
background buffer to the conversion functions. This is
necessary when an attribute has a compound data type.
./src/H5Flow.c
./src/H5Fprivate.h
./src/H5Fsec2.c
Reindented new Win32 stuff.
./src/H5Odtype.c
Fixed a bug when enumeration types are used in a compound data
type. The byte pointer wasn't incremented after the type
information was written.
./tools/h5ls.c
Compound data types display their total size because it's not
always obvious from looking at the members.
Scalar attributes show their space as `scalar' instead of
`{}'.
The index value is not printed for attributes that have only a
few values. Instead the word `Data:' is printed on the first
line of attribute data.
Named types display their data type only if verbose output was
requested.
in the H5F_low_access() and the H5F_sec2_open() functions I put code in here so
we can figure out the path of the file and store it in the search_t struct
added a new member to the H5F_search_t struct to store the path name
we needed this to be able to tell if a file is already open since NT does not
use the inode.
----------------------
./configure.in
./configure [REGENERATED]
./config/commence.in
A few tweaks to the makefile rules for rebuilding makefiles.
./src/H5detect.c
Fixed a really stupid mistake: resetting the signal handler
after a longjmp(). This should fix Bob's SIGBUS on Solaris.
----------------------
./Makefile.in
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./config/commence.in
./config/conclude.in
./config/dec-osf4.x
./config/depend.in
./config/freebsd
./config/linux-gnu
./config/linux-gnulibc1
./config/linux-gnulibc2
./config/solaris2.x
./examples/Makefile.in
./src/Makefile.in
./test/Makefile.in
./testpar/Makefile.in
./tools/Makefile.in
./tools/testh5dump.sh
Changes that allow hdf5 to be configured and compiled in a
directory other than the source directory. This is especially
useful if you want to concurrently compile with different
compilers and/or compile flags, or if the hdf5 source is on
read-only media like a CDROM. The changes were surprisingly
easy ;-) Here's what you can do now...
$ mkdir /tmp/build1 # or something
$ cd /tmp/build1
$ /cdrom/hdf5/configure # where ever the source is
$ make
Paul, you'll have to change the testh5toh4 script similar to
the way I changed testh5dump.sh. I started working on it but
then gave up because of a number of problems: (1) I had to
comment out all the tests that let h5toh4 choose the output
file name because it always tried to put the output file in
the same directory as the input file, (2) if path names are
used during the h4 dump then they interfere with the
diff. The test works fine when run in the source directory,
but try this instead:
$ gunzip <hdf5-1.1.67.tar.gz |tar xf -
$ chmod -R ugo-w hdf5-1.1.67
$ mkdir build
$ cd build
$ ../hdf5-1.1.67/configure
$ make check
Dan, I didn't modify the pablo/Makefile.in because I have no
way to test it. I think all you need to do is add a couple
lines before the @COMMENCE@ line and add a couple search
directories for header files. Anyway, it seems like almost an
exact duplicate of the src/Makefile.in, so it shouldn't be a
problem...
./Makefile.in
Removes a few more temporary files during make clean and
distclean.
./configure.in
I fixed the creation of the time-stamp files so that the
initial make doesn't have to regenerated all the makefiles
(only GNU make users will see any change).
./src/H5R.c
Changed a return type from `intn' to `int' for an API
function.
./src/H5detect.c
Added the volatile qualifier to a couple more variables.
./tools/h5tools.c
Fixed a compiler warning about an unused local.
./tools/h5toh4.c
Initialized `optind' to 1 because it's zero on my system. It
should always be one on a unix system.
./tools/testh5toh4
Redirected "broken pipe" messages to /dev/null so outut is
formatted correctly.
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./src/H5private.h
Temporarily commented out the code that tries to link a simple
MPI-IO application because I'm not sure how to pass $LDFLAGS
and $LIBS to the compiler.
Removed the `--enable-parallel=ibm' switch because the library
we link with is either -lmpcc or -lmpcc_r but not both. The
only way to tell is to see what compiler was specified (mpcc
or mpcc_r) but if that compiler is specified then we don't
need any libraries (the compiler script supplies them). That
leaves just two choices: the user must use a compiler script:
CC=mpcc ./configure
or the user must state which library is desired:
LDFLAGS='-lmpcc' ./configure --enable-parallel
Checks for <setjmp.h>, longjmp(), and signal(). We don't check
for setjmp() because it could be a macro (in fact, Posix
requires it to be a macro) and if longjmp() is present then
setjmp() is probably present too ;-)
./src/H5detect.c
The alignment detection loop uses SIGBUS and setjmp/longjmp
instead of fork/wait in order to get around bugs with forking
in conjunction with mpich. This hasn't been tested on the
SP-2 yet but it does work on the DEC Alpha.
./test/Makefile.in
./testpar/Makefile.in
./tools/Makefile.in
Changed the order that libraries are linked so -lhdf5 is
always before $LDFLAGS.
----------------------
./config/*-aix4.* [REMOVED]
./config/*-aix4.x [NEW]
./config/solaris2.5 [REMOVED]
./config/solaris2.x [NEW]
./configure.in
./configure [REGENERATED]
./MANIFEST
Changed the names of the IBM-SP2 config files by replacing the
minor version numbers with an `x'. The solaris config warns
about old versions of gcc.
The RUNSERIAL value is set to the empty string by default. The
config/* file (or user) can override it by setting it to some
other value.
The `--enable-parallel' with no flags turns on the
HAVE_PARALLEL constant in the source code but doesn't add any
MPI or MPI-IO libraries to the link line.
If we are compiling for parallel then configure checks that we
can actually link a very simple program. This has the benefit
of detecting config errors before we waste time compiling the
entire library.
Configure recognizes `mpcc_r' as a parallel compiler.
./src/H5A.c
./src/H5Apublic.c
Fixed some compiler warnings. Changed the return type of
H5Aget_name() from hssize_t to ssize_t because the name can
never be larger then memory.
are five new API functions for querying selections:
H5Sget_select_hyper_nblocks - retrieves the number of hyperslab blocks
in current hyperslab selection for a
dataspace
H5Sget_select_elem_npoints - retrieves the number of element points
in current element selection for a
dataspace
H5Sget_select_hyper_blocklist - retrieves a list of the hyperslab blocks
in current hyperslab selection for a
dataspace
H5Sget_select_elem_pointlist - retrieves a list of the element points
in current element selection for a
dataspace
H5Sget_select_bounds - retrieves a n-dimensional bounding box
containing current selection.
H5Flow.c:
Document previous changes (same changes committed by Robb first.)
H5Fprivate.h:
Change DECODE macros to do sign extension.
(Sign extension can be skipped if machines use the exact sizes.)
H5Sall.c:
Fixed a typo in return value.
H5private.h:
Fixed a typo and also changed the strategy of the int16_t and
uint16_t typedef. Now will use short as long as it is at least
2 bytes big.
Bug fix
Problem:
On Solaris2.5, once the library has been compilied with any type of
optimization, a bus error comes up in the "dtypes" test.
Solution:
The problem appears to be in the compilers' version of memcpy() that
is used when optimized. Instead of substituting HDmemmove(), on
Solaris, the problem is also taken care of by preparing the second
argument to HDmemcpy(). The datatype pointer is copied to a separate
char pointer which is then used as the second argument to HDmemcpy().
For some reason, it isn't enough to simply cast the datatype pointer.
Platform tested:
Solaris2.5
----------------------
./configure.in
./configure [REGENERATED]
The path for a command is calculated explicitly the hard way
because `type -path' isn't portable.
./config/freebsd
./config/linux-gnu
./config/linux-gnulibc2
Changed the way files reference each other.
./config/gnu-flags [NEW]
./config/dec-flags [NEW]
These files figure out what flags to pass to certain compilers
so we can reuse code in more than one config/* file. They
also have better warning messages when old compilers are used.
./config/linux-gnulibc1
./config/dec-osf4.x
These files use the new *-flags files.
./src/H5D.c
./src/H5Onull.c
./src/H5Tconv.c
./tools/h5ls.c
Fixed a compiler warning.
./src/H5detect.c
Added a better comment to the top of the generated file.
----------------------
./INSTALL
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
Improvements for parallel library. If you have a properly
working mpicc you should be able to just say:
$ CC=mpicc ./configure
and you will see
checking for mpirun... /usr/local/mpi/bin/mpirun
checking for parallel support files... skipped
checking how to run on one processor...
/usr/local/mpi/bin/mpirun -np 1
checking how to run in parallel...
/usr/local/mpi/bin/mpirun -np $$NPROCS
To quote from the INSTALL file....
*** Parallel vs. serial library
The HDF5 library can be configured to use MPI and MPI-IO for
parallelizm on a distributed multi-processor system. The easy
way to do this is to have a properly installed parallel
compiler (e.g., MPICH's mpicc or IBM's mpcc) and supply that
executable as the value of the CC environment variable:
[NOTE: mpcc is not tested yet]
$ CC=mpcc ./configure
$ CC=/usr/local/mpi/bin/mpicc ./configure
If no such wrapper script is available then you must specify
your normal C compiler along with the distribution of
MPI/MPI-IO which is to be used (values other than `mpich' will
be added at a later date):
$ ./configure --enable-parallel=mpich
If the MPI/MPI-IO include files and/or libraries cannot be
found by the compiler then their directories must be given as
arguments to CPPFLAGS and/or LDFLAGS:
$ CPPFLAGS=-I/usr/local/mpi/include \
LDFLAGS=-L/usr/local/mpi/lib/LINUX/ch_p4 \
./configure --enable-parallel=mpich
If a parallel library is being built then configure attempts
to determine how to run a parallel application on one
processor and on many processors. If the compiler is mpicc
and the user hasn't specified values for RUNSERIAL and
RUNPARALLEL then configure chooses `mpirun' from the same
directory as `mpicc':
RUNSERIAL: /usr/local/mpi/bin/mpirun -np 1
RUNPARALLEL: /usr/local/mpi/bin/mpirun -np $${NPROCS:=2}
The `$${NPROCS:=2}' will be substituted with the value of the
NPROCS environment variable at the time `make check' is run
(or the value 2).
./testpar/Makefile.in
Saying `make check' (or `make test') will run the tests on two
processors by default. If you define NPROCS then that many
processors are used instead:
$ NPROCS=4 make check
./configure.in
Fixed (hopefully) bugs with detecting whether __attribute__
and __FUNCTION__ are special keywords for the compiler.
./Makefile.in
Saying `make install' from the top level directory shows
instructions for using shared libraries.
./config/commence.in
./src/Makefile.in
./test/Makefile.in
./testpar/Makefile.in
./tools/Makefile.in
Moved the @top_srcdir@ into the makefiles because it was
expanded too early and had the wrong value.
./INSTALL
Added a warning that if the wrong version of hdf4 tools are
installed then `make check' will fail in the tools directory.
Bug fix
Problem:
On Solaris2.5, once the library has been compilied with any type of
optimization, a bus error comes up in the "dtypes" test.
Solution:
The problem appears to be in the compilers' version of memcpy() that
is used when optimized. Apparently, the same optimization problem
is not associated with the similar function memmove(). So, as a
solution to this problem, memmove() is substituted in for memcpy().
Platform tested:
Solaris2.5
----------------------
./INSTALL
Reorganized and added some additional examples.
./MANIFEST
./aclocal.m4 [NEW]
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./bin/ltconfig [NEW]
./bin/ltmain.sh [NEW]
Added tests to determine how to compile shared libraries and
how to link programs with them before the libraries are
installed. Also how to install and uninstall shared
libraries. The configure step also prints the names of the
config files it's trying to load for easier debugging.
./bin/config.guess
./bin/config.sub
Replaced with a newer version from GNU. The changes we made
to that file to report `irix6.x' and `FreeBSD' without version
numbers have been incorporated into configure.in instead. In
the future, do not change these two files (see the top of
configure.in instead). By the way, this update was required to
get shared libraries working.
./config/linux [REMOVED]
./config/linux-gnulibc1 [NEW]
./config/linux-gnu [NEW]
./config/alpha-dec [REMOVED]
./config/alpha-dec-osf4.0 [REMOVED]
./config/dec-osf4.x [NEW]
./config/irix5.3 [REMOVED]
./config/irix5.x [NEW]
./config/irix64 [REMOVED]
./config/freebsd
Moved config files around to agree with output from the new
config.guess. The linux file was split into gnu (RedHat),
gnulibc1, and gnulibc2 versions. The alpha-dec file was
removed (I think it was unused) and the alpha-dec-osf4.0 was
changed to dec-osf4.x. The irix5.3 file renamed to irix5.x and
the irix64 file was renamed to irix6.x. The freebsd file was
changed to point to linux-gnulibc1. These changes were tested
on:
Linux 2.0
Linux 2.1
FreeBSD 3.2
Irix 5.3
Irix64 6.2
Irix64 6.4
HP/UX 10.20
OSF1 4.0
./config/alphaev56-dec-osf4.x
./config/irix64
Added warnings similar to linux/freebsd about using compilers
with known bugs.
./config/commence.in
./config/conclude.in
./src/Makefile.in
./test/Makefile.in
./testpar/Makefile.in
./tools/Makefile.in
Added definitions for shared libraries. This has been tested
on the following systems:
Linux 2.0
Linux 2.1
FreeBSD 3.2
Irix 5.3
Irix64 6.2
Irix64 6.4
HP/UX 10.20 static only
OSF1 4.0
If you want to disable use of shared libraries (you probably
do for development purposes since it takes a lot longer to
compile and because you have to run dynamically linked
programs in a special way if the library hasn't been
installed) then add `--disable-shared' to the configure
command line. This is all documented in the INSTALL file.
./bin/release
Temprarily commented out the MANIFEST checking when running
under svf since svf is about to be replaced by a newer
version. This change only affects error checking during the
release process.
./Makefile.dist
./Makefile.in
Added `make check' which does the same thing as `make _test'
since the former is endorsed by the GNU coding style and
people are used to it. The old `make _test' still works too
(and so does `make test' if you use GNU make).
----------------------
./INSTALL
Added instructions for using other compilers on Irix platforms.
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./src/H5private.h
The presence of <sys/sysinfo.h> and <sys/proc.h> is only
checked on DEC/Alpha because there are too many problems
including these headers on other systems.
./config/irix6.x
./config/irix64
Removed `-ansi' and added a comment. Converting an ASCII UTC date
and time to a time_t value is not defined by ANSI or Posix but
is available if we don't use `-ansi'. This allows the dataset
modification time messages to be read properly by
H5Gget_objinfo().
./src/H5Tconv.c
Fixed a compiler warning.
./test/dtypes.c
./test/hyperslab.c
./test/istore.c
Fixed compiler warnings in printf() statements.
----------------------
./INSTALL
Added warnings and a disclaimer about GNU, DEC, Irix64, and NT
compilers that generate incorrect machine code.
./configure.in
./src/H5private.h
Detects and includes <sys/param.h> which is needed on FreeBSD
before <sys/proc.h> even though we only really using anything
from <sys/proc.h> on the DEC Alpha.
./config/irix64
Turned off warnings for duplicate definitions from the linker
because -lnsl on irix has the same stuff in it as -lc.
./config/irix6.x
Split up the CC and CFLAGS settings like with irix64 so that
compilers besides `-n32' can be used.
./bin/snapshot
The snapshots are tagged with names like hdf5-1_1_52 which is
similar to the way the releases are tagged (cvs doesn't allow
dots in tags).
./test/dtypes.c
./src/H5private.h
./src/H5Tconv.c
Fixed some alignment violations on the DEC when using high
optimization levels. The DEC incorrectly optimizes certain
memcpy() and memmove() calls when the source argument is not
word aligned if the call looks like it's copying an atomic
data type.
./test/hyperslab
Worked around code generation bugs in the Irix64 Mongoose 7.00
compiler by casting some `unsigned long' values to `unsigned'
in an expression.
./src/H5Ocomp.c
Fixed a place where %d was used to print a size_t.
