Commit Graph

112 Commits

Author SHA1 Message Date
Quincey Koziol
43e3b45021 [svn-r6825] Purpose:
New feature/enhancement

Description:
    Chunked datasets are handled poorly in several circumstances involving
certain selections and chunks that are too large for the chunk cache and/or
chunks with filters, causing the chunk to be read from disk multiple times.

Solution:
    Rearrange raw data I/O infrastructure to handle chunked datasets in a much
more friendly way by creating a selection in memory and on disk for each chunk
in a chunked dataset and performing all of the I/O on that chunk at one time.

    There are still some scalability (the current code attempts to
create a selection for all the chunks in the dataset, instead of just the
chunks that are accessed, requiring portions of the istore.c and fillval.c
tests to be commented out) and performance issues, but checking this in will
allow the changes to be tested by a much wider audience while I address the
remaining issues.


Platforms tested:
    h5committested, FreeBSD 4.8 (sleipnir) serial & parallel, Linux 2.4 (eirene)
2003-05-07 16:52:24 -05:00
Albert Cheng
8eb1a6150f [svn-r6711] Purpose:
Bug fix

Description:
Sometimes when H5detect fails (incorrect code, incorrect mpi launch
command, insufficient resources,...), it generates an incomplete or
even empty H5Tinit.c file.  If the empty file is not removed but
the make is run again, make will just use the empty file to generate
the library which will have lots of missing routines.  Make won't
fail until much later and the missing routines would be puzzling
to inexperienced users.

Solution:
If H5detect fails, the generated H5Tinit.c will be removed unless
$HDF5_Make_Ignore is set.  This is similar to removing .o file if
the compile fails.

Platforms tested:
Copper (parallel) which has a condition causing H5detect to fail.
That verified the change works.
Eirene (parallel) in which H5detect runs well.  This verified the
change works in normal conditions too.
Did not do the h5committest because this is just a makefile change
and the above two tests covered it well.

Misc. update:
2003-04-17 23:30:26 -05:00
Quincey Koziol
92b6e81789 [svn-r6611] Purpose:
Code cleanup/new features

Description:
    Switch over to a new style for registering filters with the library -
instead passing in an ID, a string and a callback function to H5Zregister,
the client should pass in a single pointer to a H5Z_claass_t struct which
contains the ID, the description string and all the function callbacks as
fields.
    Added support for a new "can apply" callback for each filter, which is
called when a dataset is created to check whether the parameters for that
filter apply correctly to the combination of the datatype and the chunk size
(i.e. dataspace) for the dataset.
    Added support for a new "set local" callback for each filter, which
is called when a dataset is created (after the "can apply" filter callback)
and sets filter parameters that are specific to that particular dataset.
    Switched the filters we ship over to use the new H5Z_class_t struct for
their internal registrations and also added "set local" callbacks to the
szip and shuffle filters and a "can apply" callback to the szip filter.
    Lots of other code cleanups, etc. also


Solution:

Platforms tested:
    FreeBSD 4.8 (sleipnir) w/szip
    Linux 2.4 (sleipnir) w/szip
    Solaris 2.7 (arabica) w/FORTRAN
    IRIX64 6.5 (modi4) w/szip, FORTRAN & parallel

Misc. update:
2003-04-08 21:34:21 -05:00
Quincey Koziol
3c77efae1c [svn-r6578] Purpose:
Code cleanup

Description:
    Added lots of comments to existing filters, so they are easier to understand
and use as examples for future filters.  Cleaned up various bits of code, etc.

Solution:

Platforms tested:
    FreeBSD 4.8 (sleipnir)
    IRIX64 6.5 (modi4) w/parallel

Misc. update:
2003-04-03 08:52:30 -05:00
MuQun Yang
646ac38507 [svn-r6550] Purpose:
To support szip compression in HDF5

Description:
szip compression support is required by NASA ESDIS. The compression algorithm
is a good compression algorithm for scientific data. In HDF5, we add another filter
function to make szip as a default compression package as we did for gzip(or zlib).

H5config.in needs to be regenerated by autoheader for SZIP flags.
Solution:
A new file called H5Zszip.c will be added in the Makefile.in
Flags like: HAVE_FILTER_SZIP    should be auto-generated by autoheader.

Platforms tested:
Since there are changes of configure.in and configure,I didn't use h5committest.                                    I tested with four platforms.
1) Linux 2.4 (eirene)
2) Solaris 2.7(arabica)
3) windows 2000(VS 6.0)
4) SGI IRIX6.5-64(modi4)
For test 1)-3), only basic C tests were done
For modi4 test, I tested 64-bit C,parallel and fortran.                                                         All tests passed, except a warning message from szip library when checksum is used in some order, which doesn't
cause any real problems.

Misc. update:
2003-04-01 10:27:45 -05:00
Quincey Koziol
474a1434bd [svn-r6436] Purpose:
New internal feature

Description:
    Add internal API for building and working with heaps (H5HP).  This will be
    used for the LRU algorithm in the new metadata cache code.

Platforms tested:
    Tested h5committest {arabica (fortran), eirene (fortran, C++)
	modi4 (parallel, fortran)}
    FreeBSD 4.7 (sleipnir)
2003-02-24 15:25:13 -05:00
Quincey Koziol
946c606452 [svn-r6411] Purpose:
Code cleanup

Description:
    Clean up miscellaneous warnings which have crept into the code.

    Fix "_POSIX_C_SOURCE not defined" warning on FreeBSD.

    Adjust gcc compiler flags to be more concise for production mode.

    Refactor the H5O code so that there is a stronger boundary between code
    in the H5O package and code in the library which just calls H5O routines.

Platforms tested:
    Tested h5committest {arabica (fortran), eirene (fortran, C++)
	modi4 (parallel, fortran)}
    FreeBSD 4.7 (sleipnir) serial & parallel and gcc 2.95.4 & gcc 3.2.2

Misc. update:
    Update MANIFEST if you add or remove any file.
2003-02-17 10:54:15 -05:00
Raymond Lu
d2bfd727ca [svn-r6400]
Purpose:
    Change feature
Description:
    Switch to Fletcher32 from Adler32 checksum
Platforms tested:
    arabica, eirene, modi4
Misc. update:
    MANIFEST and RELEASE.txt updated.
2003-02-12 15:07:21 -05:00
Quincey Koziol
7d63d5e3ff [svn-r6395] Purpose:
Code cleanup.

Description:
    Break up the ~9350 line H5T.c module into smaller pieces, which contain
    code for a particular feature or support for a datatype class.

    This should make the "main" H5T code (still in H5T.c) easier to support,
    as well as removing some of the "minor" routines from the user applications
    which don't use them (my rough estimates show about 4% reduction (~30K on
    a FreeBSD machine) in optimized, staticly-linked binaries for very simple
    programs)

Platforms tested:
    Tested h5committest {arabica (fortran), eirene (fortran, C++)
	modi4 (parallel, fortran)}

    FreeBSD 4.7 (sleipnir)

Misc. update:
    Update MANIFEST
2003-02-12 08:44:31 -05:00
Bill Wendling
273479f8f8 [svn-r6392] Purpose:
Update

Description:
    Folded in Quincey's changes to the caching stuff. (Stole the code
    from the H5FDmpio driver).

    Roughed in some code for doing a read from the SAP. Also roughed in
    code for doing a write. However, the write requires an OID, which I'm
    not sure how to pass down into the driver (maybe via the
    dxpl_id?...but then it has always to be set before calling one of
    these routines...).

    Removed some of the global variables which were there because of the
    FPHDF5 stuff...

    Removed the H5Ofphdf5.* stuff from the Makefile.in, since I'm pretty
    sure it's going away and I don't want to waste time updating that
    module if that's the case...so just don't compile it.

Platforms tested:
    Linux
2003-02-10 16:53:08 -05:00
Quincey Koziol
168d67dbd2 [svn-r6383] Purpose:
New feature for developers.

Description:
    Added "function stack" tracing to library.  This allows developers (there
    is no public API) to call H5FS_print within the library and get a listing
    of the functions traversed to reach that point in the library.  Eventually,
    I may add support for reporting the parameters to each function also...

    Mainly for debugging parallel I/O programs, but I think it will come in
    handy in other cases also.

    The function stack tracking is controlled with a configure switch:
    --enable-funcstack, which defaults to enabled currently.  When we branch
    for 1.6, we should change the default setting on the branch to be disabled.

    Also, added a destructor to the thread-specific keys when thread-safety is
    turned on in the library.  Otherwise, they were leaking memory and causing
    difficult to debug errors in threaded programs (like the test/ttsafe test).

Platforms tested:
    Tested h5committest {arabica (fortran), eirene (fortran, C++)
	modi4 (parallel, fortran)}

    FreeBSD 4.7 (sleipnir) w/thread-safety enabled.

Misc. update:
    Updated MANIFEST with new files added (src/H5FS.c & src/H5FDprivate.h)

    Update release_docs/RELEASE with thread-safety bug fix.
2003-02-07 16:14:19 -05:00
Bill Wendling
4507d01c42 [svn-r6380] Purpose:
Update
Description:
    Added support for the H5FDfphdf5.[ch] file driver.
Platforms tested:
    Linux
2003-02-06 17:08:31 -05:00
Raymond Lu
3879dcce1b [svn-r6375]
Purpose:
    New feature
Description:
    Added Adler32 checksum as a filter in pipeline
Platforms tested:
    arabica (fortran), eirene (, C++), modi4 (parallel, fortran)
Misc. update:
    Update release_docs/RELEASE.
2003-02-04 13:50:56 -05:00
Quincey Koziol
127dc2f80d [svn-r6308] Purpose:
Bug fix

Description:
    Currently, when the library encounters an object header message that isn't
    know, it fails to open that object in the file.

Solution:
    Allow the library to skip over the unknown object header message and
    continue to process the remaining messages, in the hope that the skipped
    message isn't important later.  If it is important, it will be caught at
    a higher level of the library.

Platforms tested:
    FreeBSD 4.7 (sleipnir)
2003-01-21 15:20:13 -05:00
Quincey Koziol
f8da76cb9f [svn-r6266] Purpose:
Code cleanup/new feature.

Description:
    Split FUNC_LEAVE into API and non-API specific versions.  This allows a
    solution to compiling this branch with C++, as well as reducing the size
    of the binaries produced.

Platforms tested:
    FreeBSD 4.7 (sleipnir) w/serial, parallel (including MPE) & thread-safe
2003-01-10 15:26:02 -05:00
Quincey Koziol
9a433b99a5 [svn-r6252] Purpose:
Lots of performance improvements & a couple new internal API interfaces.

Description:
    Performance Improvements:
        - Cached file offset & length sizes in shared file struct, to avoid
            constantly looking them up in the FCPL.
        - Generic property improvements:
            - Added "revision" number to generic property classes to speed
                up comparisons.
            - Changed method of storing properties from using a hash-table
                to the TBBT routines in the library.
            - Share the propery names between classes and the lists derived
                from them.
            - Removed redundant 'def_value' buffer from each property.
            - Switching code to use a "copy on write" strategy for
                properties in each list, where the properties in each list
                are shared with the properties in the class, until a
                property's value is changed in a list.
        - Fixed error in layout code which was allocating too many buffers.
        - Redefined public macros of the form (H5open()/H5check, <variable>)
            internally to only be (<variable>), avoiding innumerable useless
            calls to H5open() and H5check_version().
        - Reuse already zeroed buffers in H5F_contig_fill instead of
            constantly re-zeroing them.
        - Don't write fill values if writing entire dataset.
        - Use gettimeofday() system call instead of time() system when
            checking the modification time of a dataset.
        - Added reference counted string API and use it for tracking the
            names of objects opening in a file (for the ID->name code).
        - Removed redundant H5P_get() calls in B-tree routines.
        - Redefine H5T datatype macros internally to the library, to avoid
            calling H5check redundantly.
        - Keep dataspace information for dataset locally instead of reading
            from disk each time.  Added new module to track open objects
            in a file, to allow this (which will be useful eventually for
            some FPH5 metadata caching issues).
        - Remove H5AC_find macro which was inlining metadata cache lookups,
            and call function instead.
        - Remove redundant memset() calls from H5G_namei() routine.
        - Remove redundant checking of object type when locating objects
            in metadata cache and rely on the address only.
        - Create default dataset object to use when default dataset creation
            property list is used to create datasets, bypassing querying
            for all the property list values.
        - Use default I/O vector size when performing raw data with the
            default dataset transfer property list, instead of querying for
            I/O vector size.
        - Remove H5P_DEFAULT internally to the library, replacing it with
            more specific default property list based on the type of
            property list needed.
        - Remove redundant memset() calls in object header message (H5O*)
            routines.
        - Remove redunant memset() calls in data I/O routines.
        - Split free-list allocation routines into malloc() and calloc()-
            like routines, instead of one combined routine.
        - Remove lots of indirection in H5O*() routines.
        - Simplify metadata cache entry comparison routine (used when
            flushing entire cache out).
        - Only enable metadata cache statistics when H5AC_DEBUG is turned
            on, instead of always tracking them.
        - Simplify address comparison macro (H5F_addr_eq).
        - Remove redundant metadata cache entry protections during dataset
            creation by protecting the object header once and making all
            the modifications necessary for the dataset creation before
            unprotecting it.
        - Reduce # of "number of element in extent" computations performed
            by computing and storing the value during dataspace creation.
        - Simplify checking for group location's file information, when file
            has not been involving in file-mounting operations.
        - Use binary encoding for modification time, instead of ASCII.
        - Hoist H5HL_peek calls (to get information in a local heap)
            out of loops in many group routine.
        - Use static variable for iterators of selections, instead of
            dynamically allocation them each time.
        - Lookup & insert new entries in one step, avoiding traversing
            group's B-tree twice.
        - Fixed memory leak in H5Gget_objname_idx() routine (tangential to
            performance improvements, but fixed along the way).
        - Use free-list for reference counted strings.
        - Don't bother copying object names into cached group entries,
            since they are re-created when an object is opened.

        The benchmark I used to measure these results created several thousand
        small (2K) datasets in a file and wrote out the data for them.  This is
        Elena's "regular.c" benchmark.

        These changes resulted in approximately ~4.3x speedup of the
        development branch when compared to the previous code in the
        development branch and ~1.4x speedup compared to the release
        branch.

        Additionally, these changes reduce the total memory used (code and
        data) by the development branch by ~800KB, bringing the development
        branch back into the same ballpark as the release branch.

        I'll send out a more detailed description of the benchmark results
        as a followup note.

    New internal API routines:
        Added "reference counted strings" API for tracking strings that get
            used by multiple owners without duplicating the strings.
        Added "ternary search tree" API for text->object mappings.

Platforms tested:
    Tested h5committest {arabica (fortran), eirene (fortran, C++)
	modi4 (parallel, fortran)}
    Other platforms/configurations tested?
        FreeBSD 4.7 (sleipnir) serial & parallel
        Solaris 2.6 (baldric) serial
2003-01-09 12:20:03 -05:00
MuQun Yang
93d91678f5 [svn-r6088]
Purpose:
   add H5Zshuffle.c at Makefile.in
Description:
Solution:
Platforms tested:
eirene,modi4,arabica
Misc. update:
2002-11-13 11:36:08 -05:00
Bill Wendling
42e07130b8 [svn-r6026] Purpose:
Feature Add
Description:
    New Makefiles and H5config.h.in file for the Flexible Parallel HDF5
    stuff.
Platforms tested:
    Eirene, Arabica, Modi4
2002-10-23 14:31:45 -05:00
Raymond Lu
29da4951f8 [svn-r5879]
Purpose:
    Design for compact dataset
Description:
    Compact dataset is stored in the header message for dataset layout.
Platforms tested:
    arabica, eirene.
2002-08-20 11:18:02 -05:00
Quincey Koziol
c85063bfad [svn-r5872] Purpose:
Code cleanup

Description:
    Move get/set routines for each type of property list (file creation,
    dataset creation, file access and dataset transfer) into their own source
    code module.

Platforms tested:
    FreeBSD 4.6 (sleipnir)
2002-08-12 13:13:27 -05:00
Quincey Koziol
363ec52b7c [svn-r5799] Purpose:
New feature.

Description:
    Added MPI-posix VFL driver.  This driver uses MPI to coordinate actions, but
    performs I/O directly with posix sec(2) I/O functions.  This driver should
    _NOT_ be used if the file accessed is not on a parallel filesystem.

Platforms tested:
    FreeBSD 4.6 (sleipnir) w/parallel & IRIX64 6.5 (modi4) w/parallel
2002-07-15 10:21:32 -05:00
Albert Cheng
112fb8d45c [svn-r5257] Purpose:
Bug fix
Description:
    $(LT_RUN) was used to execute ./H5detect in src/Makefile.in.
    $RUNTEST was set to $(LT_RUN) which was used to execute sequential
    executable.  $(LT_RUN) is "../libtool --mode=execute".  But libtool
    invokes some commands that are not supported in the Tflops machine.
    That caused failures during the build and check processes.
Solution:
    Upon investigation, there does not seem to be need to use $(LT_RUN)
    any more.  The "libtool --mode=link" now generates a "fake" executable
    that is actually a command-script file that can regenerate the real
    executable with dynamic libraries hooks setup properly.
    Undo all those $LT_RUN substitute and let $RUNSERIAL execute those
    sequential executables.
Platforms tested:
    Eirene(serial), modi4(parallel)
2002-04-25 09:48:52 -05:00
Albert Cheng
e22c095636 [svn-r4757] Purpose:
Removing the DPSS (gridstorage) driver source code.
Description:
    The DPSS (using Grid-Storage) driver is retired.
    Removed the configure option with-gridstorage from configure.in.
    Cvs remove the following files
    ./src/H5FDdpss.c
    ./src/H5FDdpss.h
    ./test/dpss_read.c
    ./test/dpss_write.c

    Regenerated Dependencies files (some had to be hand-edited since
    'make depend' did not cover them.)
    Removed reference to DPSS Virtual file driver from H5F.c.
Platforms tested:
    modi4 (Parallel; -with-gass=...), eirene, arabica (fortran, cxx).
2001-12-30 00:23:38 -05:00
Quincey Koziol
6ab0e9f092 [svn-r4620] Purpose:
Code cleanup
Description:
    Get rid of IDs from internal function calls and some small cleanups from
    the old-stype => generic property list conversion.
Platforms tested:
    FreeBSD 4.4 (hawkwind)
2001-11-20 14:07:22 -05:00
Bill Wendling
aa99c5d5a5 [svn-r3640] Purpose:
Bug Fix
Description:
    For some reason, the H5FDstream.h file was defined not once, not
    twice, but three whole times in the install part...
Solution:
    Removed all but one of those.
2001-03-15 12:17:30 -05:00
Quincey Koziol
7921315a33 [svn-r3304] Purpose:
Code update
Description:
    Remove ragged array code & tests from library before release.
Platforms tested:
    FreeBSD 4.2 (hawkwind)
2001-01-18 18:30:23 -05:00
Quincey Koziol
ba28c64ba7 [svn-r2652] Purpose:
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)
2000-10-10 02:43:38 -05:00
Quincey Koziol
b53bfca418 [svn-r2611] Purpose:
Rearrange code
Description:
    The data sieve buffering code for contiguously stored datasets was
    wedged in the H5F_arr_read/H5F_arr_write routines.
Solution:
    Created a new H5Fcontig.c to hold I/O routines for contiguously stored
    datasets (like H5Fistore.c for chunked dataset I/O routines) and moved
    data sieving code into those routines.
Platforms tested:
    Solaris 2.6 (i.e. baldric)
2000-09-28 14:12:43 -05:00
Bill Wendling
8272da0b67 [svn-r2574] Purpose:
H5FDstream.h needs to be installed.
Description:
	H5FDstream.h is included in the hdf5.h file and needs to be
	installed with the other public headers.
Solution:
	Added it to the rest of the install headers.
2000-09-19 12:42:50 -05:00
Thomas Radke
c275f5e9c7 [svn-r2559] Purpose:
Add the Stream VFD sources to the appropriate makefile variables.

Description:
     Added H5FDstream.c to the LIB_SRC variable and H5FDstream.h
     to the PUB_HDR variable for building the Stream VFD.
2000-09-15 06:49:28 -05:00
Bill Wendling
fb75b8a89c [svn-r2285] A \ was needed at the end of one of the definitions to make gmake work. 2000-05-19 16:35:40 -05:00
Quincey Koziol
d894ed6d0d [svn-r2276] Modifed thread-safety code to more closely align with rest of HDF5 coding
standards.
2000-05-19 09:51:50 -05:00
Chee-Wai Lee
e26f4e5eed [svn-r2264] Added Thread-safe feature. This is the phase 1 implementation
that all HDF5 API functions are protected by a mutex lock. Basically,
serialized all API calls.  To use it, use
configure --enable-threadsafe --with-pthread
2000-05-18 14:13:33 -05:00
Quincey Koziol
5c354908b9 [svn-r2223] Added logging version of sec2 file driver. This is _reallly_ useful for
tracking the actual I/O locations and space used in a file during an
application.
2000-05-08 18:09:59 -05:00
Quincey Koziol
37f774f5a9 [svn-r2164] Remove debugging information... 2000-04-19 18:13:23 -05:00
Quincey Koziol
7438609ee2 [svn-r2162] Various small fixes to address SGI compiler warnings. 2000-04-19 18:11:06 -05:00
Raymond Lu
9b825f6f63 [svn-r2141] Fixed some mix up from the last cvs commit. 2000-04-13 11:58:07 -05:00
Raymond Lu
0461ad7f43 [svn-r2137] Add SRB as a new VFL, add related info into these source codes. 2000-04-13 10:16:20 -05:00
Quincey Koziol
02e4ee5edf [svn-r2073] Added free-list code to the library and took out the older "temporary buffer"
code, since the functionality was superceded.  See the followup document for
details on the free-list code.
2000-04-04 16:00:31 -05:00
Albert Cheng
096e2b6754 [svn-r1976] Added the .lo of H5detect and H5Tinit to the cleanup list. 2000-02-18 19:59:57 -05:00
Albert Cheng
9ca6cfa0aa [svn-r1975] Purpose:
Configuration improvement

Problem:
Arabica has a zlib library that is a dynamic lib in /usr/ncsa/lib.
Binary generated would fail to run with a missig libz.so complain
if /usr/ncsa/lib is not in $LD_LIBRARY_PATH.  This exposed the
problem that if the binary is linked with -L$mylibpath -lxyz
where libxyz is a dynamic type, the binary can't run if $mylibpath
is not in $LD_LIBRARY_PATH (or equivalent) or as part of the
system default library paths (e.g., /usr/lib, /usr/local/lib).
This problem also caused failures during configure (when trying
to see what format to print long long) and during H5detect.
The base cause is because libtool does not "transfer" the
knowledge of -L$mylibpath to the wrapper file its mode=link
generates.

Solution:
bin/ltmain.sh:
    Changed it so that it transfers the libpaths from -Llibpaths
    to the wrapper generated.  I used the already defined variable
    finalize_shlibpath.  Not sure it is correct to use it this way.
    Need to check on this.
configure.in:
    Put in a patch to transfer information from LDFLAGS to LD_LIBRARY_PATH
    right before the AC_TRY_RUN.  The above fix for ltmain.sh does not
    work here because libtool is generated later than this point.
    There should be a cleaner way to do this.
    Removed the hardcode of NCSA_LT_LINK_EXE because it is no longer
    needed.
commence.in:
    Removed the hardcode of NCSA_LT_LINK_EXE because it is no longer
    needed.
Makefile.in:
    Another patch of LDFLAGS to LD_LIBRARY_PATH because I could not
    make it to generate H5detect in the wrapper form of libtool.
    Need to make it to use the libtool correctly. Later.

Platform tested:
arabica (solaris 2.7)
baldric (solaris 2.6)
2000-02-18 07:53:32 -05:00
Quincey Koziol
0fd1ac6740 [svn-r1951] Tweaks to detect the shared libraries on NCSA's systems, so that Albert's
automated tests will work correctly on arabica.
2000-01-29 19:37:28 -05:00
Raymond Lu
173c0b6fe5 [svn-r1925] DPSS is checked in. 1999-12-21 17:17:55 -05:00
Robb Matzke
4b2dbd5651 [svn-r1832] * 1999-11-16
** configure.in
** configure				[REGENERATED]
** src/H5private.h
** src/H5public.h
** src/Makefile.in
	Generates an H5pubconf.h file which is just like H5config.h except all
	the preprocessor symbols have `H5_' prepended. This was done so that
	the configuration results can be used in public header files without
	polluting the namespace.

** src/H5.c
	Added H5I_REFERENCE and H5I_VFL to the API tracing code so their names
	are printed instead of just numbers.

** src/H5FDstdio.c
** tools/h5import.c
** tools/h5repart.c
** tools/pdb2hdf.c
	Changed to use the `H5_' versions of configure results since these
	files include only the public API.

** test/big.c
	Removed a compiler warning.

** test/h5test.c
	Removed unused code.
1999-11-16 14:08:14 -05:00
Robb Matzke
eb8747499d [svn-r1802] Changes since 19991019
----------------------

./MANIFEST
./configure.in
./configure			[REGENERATED]
	Added more checking for `make' features.

./Makefile.in
./doc/Makefile.in
./doc/html/Makefile.in
./doc/html/Tutor/Makefile.in
./examples/Makefile.in
./pablo/Makefile.in
./src/Makefile.in
./test/Makefile.in
./testpar/Makefile.in
./tools/Makefile.in
./config/commence.in
./config/conclude.in
./config/depend.in		[REMOVED]
./config/depend1.in		[NEW]
./config/depend2.in		[NEW]
./config/depend3.in		[NEW]
./config/depend4.in		[NEW]
./config/dependN.in		[NEW]
	The directory search stuff was moved into commence.in, thereby
	shortening the Makefile.in prologues.

./doc/html/Dependencies		[NEW]
./doc/html/Tutor/Dependencies	[NEW]
./examples/Dependencies		[NEW]
./src/Dependencies		[NEW]
./test/Dependencies		[NEW]
./testpar/Dependencies		[NEW]
./tools/Dependencies		[NEW]
	The `.distdep' files were all renamed to `Dependencies' to make them
	more obvious. They are required (but may be empty) in every directory
	that has a Makefile.in that ends with @CONCLUDE@ (you'll get an
	obvious error from make if you forgot to create one).

./bin/trace
./src/H5.c
	Added H5E_major_t and H5E_minor_t although tracing only prints the
	integer value.

./src/H5E.c
./src/H5Epublic.h
	Added tracing information.

./src/H5FDcore.c
./src/H5FDfamily.c
./src/H5FDgass.c
./src/H5FDmpio.c
./src/H5FDsec2.c
./src/H5FDstdio.c
	Fixed places where FUNC_LEAVE() evaluated it's argument more than
	once.

	Added tracing information.

	Wrapped long lines.

./config/gnu-flags
	Fixed a syntax error when we don't have a gnu compiler.
1999-11-01 10:21:16 -05:00
Quincey Koziol
e0cbe0c5c8 [svn-r1785] Added stdio VFL driver, which uses the new public H5E calls. 1999-10-20 12:51:03 -05:00
Robb Matzke
20e748496e [svn-r1732] Changes since 19991007
----------------------

./src/H5FDcore.c
	Includes private headers instead of public in order to use the
	`UNUSED' macro.

./src/H5FDpublic.h
	Includes H5public.h just in case.

./src/H5P.c
	Removed two unused variables in H5P_copy()

./src/H5FDgass.h
	Fixed a C++ comment after a `#endif'

./src/Makefile.in
	The H5FDgass.h file is public and must be installed in order for
	applications to be able to use HDF5.

./tools/h5tools.c
	Removed an unused variable.
1999-10-07 11:51:49 -05:00
Albert Cheng
06c8da20b1 [svn-r1621] Added GASS driver. Coded by Saurabh Bagchi, bagchi@uiuc.edu.
Minor changes done to test/gass_xxx.c so that they print the
test skip message when GASS driver is not available.

This change is the implementation of GASS within HDF5-1.3 (HDF5 with Virtual
File Layer). The GASS driver gives the facility of accessing HDF files on
remote ftp servers. To use the GASS driver, the option --with-gass=<GASS path>
shoud be specified with configure. An example of the command line used to
test the distribution was:
./configure --disable-shared --without-hdf4
--with-gass=/afs/ncsa/projects/hdf/v5/bagchi/globus/GLB/development/sparc-sun-solaris2.6_nothreads_standard_debug/include,/afs/ncsa/projects/hdf/v5/bagchi/globus/GLB/development/sparc-sun-solaris2.6_nothreads_standard_debug/lib
--disable-parallel

The user should change the path to point to his local GASS installation.

Documentation about the features of GASS and the HDF-GASS design is available
separately and till it is put up on the official web site, anyone interested
may contact me.

Test programs to read, write or append remote files have been provided in the
test directory as "gass_read.c", "gass_write.c", "gass_append.c". The test
programs have the ftp site to access #define-d at the top of the file which
the user can change accordingly.

./src/H5Epublic.
	Added new error type for file close.
./src/H5F.c
	Added hooks for the GASS driver.
./src/H5public.h
	Added header files for GASS & Globus.
./src/Makefile.in
	Added dependancy on GASS driver in LIB_SRC.
./src/hdf5.h
	Included header file for GASS driver.
./src/H5FDgass.c	[NEW]
	Routines for the GASS driver.
./src/H5FDgass.h	[NEW]
	Header file for the GASS driver.

./test/Makefile.in
	Added dependancy on the gass test routines.
./test/gass_read.c
	File to test remote file reading using GASS.
./test/gass_write.c
	File to test remote file writing using GASS.
./test/gass_append.c
	File to test remote file appending using GASS.
1999-08-30 23:55:00 -05:00
Robb Matzke
99d84a8f4c [svn-r1619] ./src/H5O.c [1.2, 1.3]
Fixed a read-uninitialized-memory error that resulted in the
	file containing small amounts (<8 bytes each) of uninitialized
	data. These padding areas (which are never read by hdf5) are
	initialized to zero now.

./MANIFEST
./src/H5Z.c
./src/H5Zdeflate.c			[NEW]
./src/H5Zprivate.h
./src/H5Zpublic.h
./src/Makefile.in
	The zlib filter was moved to a separate file but is still
	automatically defined.
1999-08-30 14:59:37 -05:00
Robb Matzke
cc89b8a605 [svn-r1572] Changes since 19990810
----------------------

./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.
1999-08-17 14:12:59 -05:00