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Commit Graph

1871 Commits

Author SHA1 Message Date
Jonathan Kim
6447935a19 [svn-r18958] Purpose:
Fixed Windows compile error. Renamed to use 'gid1' and 'gid2' instead of 'grp1' and 'grp2'. 
Description:
There is variable name confliction with 'grp1' ~ 'grp9' in Windows system. It occurs if H5private.h is included in the code.
2010-06-03 14:34:20 -05:00
Jonathan Kim
1a02e37f16 [svn-r18943] Purpose:
Support follow symbolic links.

Description:
    Add '--follow-symlinks' option to follow symbolic links (soft and external).
    Update help page according to RM.
    Remove some warning messages from compiler.

Tested:
    jam, amani and linew
2010-06-02 10:13:13 -05:00
Jonathan Kim
a5ca9e6ba9 [svn-r18873] Purpose:
Rename '--follow-links' to '--follow-symlinks' 

Description:
    The '--follow-links' option is to follow symbolic links (soft and external).
    Make the name more intuitive and specific to the feature.

Tested:
    jam, amani and linew
2010-05-21 15:12:22 -05:00
Allen Byrne
80e6dfe3ba [svn-r18856] Added CPack commands for installtion program
Tested: local linux and Windows
2010-05-19 15:11:00 -05:00
Jonathan Kim
6413372648 [svn-r18831] Purpose:
Resolve build issue on Windows due to the location of variable definition.

Tested:
    jam
2010-05-17 15:11:35 -05:00
Allen Byrne
a6698e571c [svn-r18816] Move progname and d_status functions from h5tools to h5tools_util
Tested:
    linux and windows
2010-05-14 16:54:59 -05:00
Allen Byrne
9564c48990 [svn-r18811] Removed references to packedbits files 2010-05-14 16:10:38 -05:00
Mike McGreevy
88de0e02f0 [svn-r18808] Purpose:
Fixed file cleanup during make distclean / make check.

Description:

    The h5jam Makefile and the h5importtestutil.sh script both included cleanup
    steps that removed "*.txt" from the directory. This resulted in the new
    CMake specific configuration file, CMakeLists.txt, getting blown away by 
    make distclean (for h5jam) and make check (for h5import).

    I've removed the *.txt from the h5jam Makefile as the directory looks to be
    getting cleaned appropriately without it, and I've modified the h5import
    script h5importtestutil.sh to point to the specific .txt files to clean.

Tested:

    jam
2010-05-14 15:29:57 -05:00
Allen Byrne
ae06433ab0 [svn-r18793] Add files to support building library with CMake
Tested: Local linux
2010-05-13 11:01:50 -05:00
Allen Byrne
df9d110fd4 [svn-r18788] Added h5tools.h include to h5diff_common.h to fix warnings about the new progname and status functions
Tested: local linux
2010-05-13 09:25:04 -05:00
Quincey Koziol
2b33e7ca2e [svn-r18785] Description:
Fix unterminated comment.

Tested on:
    None - just eyeballed.
2010-05-13 08:14:45 -05:00
Allen Byrne
68fa42f336 [svn-r18759] pull r18757 from 1.8 branch
Enable tools lib to be built as a dll on windows. Added two get/set functions for progname and d_status.
Also add windows import/export declarations to functions.
Updated error_mesg() and warn_mesg() to remove progname argument and use get functions

Tested:
   Windows, linux
2010-05-11 15:10:25 -05:00
Mike McGreevy
f0ecd71307 [svn-r18709] Purpose:
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.
2010-05-05 12:34:26 -05:00
Quincey Koziol
b9ca2f8f6f [svn-r18650] Description:
Bring back various minor tweaks & cleanups from the revise_chunks
branch.

Tested on:
        FreeBSD/32 6.3 (duty) in debug mode
        FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
        Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
                w/C++ & FORTRAN, w/threadsafe, in debug mode
        Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x,
                w/C++ & FORTRAN, in production mode
        Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
                w/szip filter, in production mode
        Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
                in production mode
        Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
        Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
2010-04-27 17:15:14 -05:00
Raymond Lu
6c5e42a967 [svn-r18648] In H5T_get_native_type of H5Tnative.c, I changed the way that the offset, alignment, and
size of nested compound type are calculated by using H5T_cmp_offset.  The old way had a bug 
in it (see bug ).

Tested on jam.  I tested the same change for 1.8 on amani, linew, and jam.
2010-04-27 16:35:53 -05:00
Jonathan Kim
5edb7aabe4 [svn-r18642] Purpose:
Fix for Bug 1793 - h5ls on a non-existent file gives 0 return code

Description:
    After the fix, h5ls returns 1 (EXIT_FAILURE) if non-existent file is given.

Tested:
    jam, amani, linew
2010-04-27 15:22:48 -05:00
Jonathan Kim
249acc0355 [svn-r18614] Purpose:
Fix for bug 1817 : h5copy fail to copy dangling link by specifying 
    link path directly

Tested:
    jam, amani, linew
2010-04-22 13:17:35 -05:00
Mike McGreevy
0cf2a97cfb [svn-r18579] Purpose:
Autotool Upgrade / Libtool Bug Fix

Description:

    Updated autotools referenced in bin/reconfigure as follows:

    Autoconf 2.64 --> Autoconf 2.65
    Automake 1.11 --> Automake 1.11.1
    Libtool 2.2.6a --> Libtool 2.2.6b-mcg

    The referenced libtool version is a custom version of 2.2.6b. It 
    has been tweaked to fix a bug in libtool that occurs
    when using PGI 10.0 compilers. A check incorrectly categorizes
    the C++ compiler as version 1.0 instead of 10.0, and the link
    line is subsequently set up incorrectly and fails to compile.

    A patch has been made available and will be included in the next
    release of libtool, but in the meantime I've applied the patch to a custom
    installation as indicated above. This bin/reconfigure now references
    the custom installation, and the resulting configure script will correctly
    categorize the PGI 10.0 C++ compiler.

    Ran bin/reconfigure to regenerate configure and makefiles.

Tested:

    jam and amani with PGI 10.0 compilers.
    h5committest
2010-04-15 16:17:22 -05:00
Quincey Koziol
3dd92875b2 [svn-r18548] Description:
Minor cleanups to compile with PGI C compiler 10.x.

Tested on:
    Linux 2.4/32 (jam) w/PGI 10.x C and F90 compilers
2010-04-12 21:09:48 -05:00
Jonathan Kim
9a359c8224 [svn-r18457] Purpose:
Add test cases for bug1797 - h5repack doesn't handle references in 
    compound and vlen datatypes for attributes 

Description:
    Add test cases ahead as waiting for H5Acopy to complete the fix.
    1. obj references in attr of compound type
    2. region references in attr of compound type
    3. obj references in attr of vlen type
    4. region references in attr of vlen type

NOTE:
    This test is skipped now and will be included when code part is completed.
    ( H5Acopy() replaces copy_attr() )
    The file&code can be used for lib portion test.

Tested:
    jam, amani, linew
2010-03-25 16:40:59 -05:00
Jonathan Kim
20fd1f47b7 [svn-r18454] Purpose:
Fix for the bug1726 - NPOESS: h5repack loses attributes for datasets of 
    type H5T_REFERENCE.

Description:
    include test cases.
    also test cases for attribute with object and region reference.

Tested:
    jam, amani, linew
2010-03-25 12:29:51 -05:00
Jonathan Kim
1267cda989 [svn-r18449] Purpose:
Resolve build issue on Sloaris due to white space from the previous
   checkin r18447

Tested:
    jam, amani , linew
2010-03-24 19:20:44 -05:00
Jonathan Kim
16c2440108 [svn-r18447] Purpose:
Bug1727 - NPOESS: h5copy should copy region references

Description:
   Tested and added test cases from previous checkin r18319
   Reference Manual and tool's usage section for '-f ref' option is updated
   for more comprehensibility.

Tested:
    jam
2010-03-24 15:58:41 -05:00
Jonathan Kim
2ee0071176 [svn-r18442] Purpose:
Resolve windows build issue from previous checkin r18425

Description:
    The previous checkin was for bug1814 - NPOESS: h5repack doesn't handle 
    references to the groups as an element of a dataset 

Tested:
    jam
2010-03-23 14:12:47 -05:00
Jonathan Kim
8c9b42fcf3 [svn-r18425] Purpose:
Fix for bug1814 - NPOESS: h5repack doesn't handle references to the groups 
    as an element of a dataset 

Description:
    handles object reference to named-datatype as well.
    Add test cases.

Tested:
    jam, amani, linew
2010-03-18 16:38:09 -05:00
Quincey Koziol
bcd6c3f7cc [svn-r18420] Description:
Re-run bin/reconfigure to catch up with recent rearrangements, remove some
unused srcdir headers and duplicated code in main test header.

Tested on:
    Mac OS X/32 10.6.2 (amazon) w/debug & prod
    Linux/32 2.6 (jam)
2010-03-18 07:45:29 -05:00
Quincey Koziol
1809f040c9 [svn-r18419] Description:
Clean up srcdir querying code more, extracting it into single header file,
to avoid compiler warnings.

Tested on:
    Mac OS X/32 10.6.2 (amazon) w/debug & prod
    Linux/32 2.6 (jam)
2010-03-18 07:23:04 -05:00
Quincey Koziol
cd2534d9ba [svn-r18418] Description:
Centralize common code for srcdir lookups.

Tested on:
    Mac OS X/32 10.6.2 (amazon) w/debug & prod
    Linux/32 2.6 (jam)
2010-03-18 07:04:39 -05:00
Quincey Koziol
0ac03c7890 [svn-r18414] Description:
Add copyright to new files
2010-03-17 16:48:09 -05:00
Quincey Koziol
fd547cd11f [svn-r18413] Description:
Unify srcdir handling for test executables and allow them to use the srcdir
setting from configure time without requiring the 'srcdir' environment variable
be set (although you still can, to override the built in setting).  Attempted
to get this right for Windows builds also.

    Also add dependency between src/H5Tinit.c and src/libhdf5.settings, so
that the test/testcheck_version.sh script works correctly.

Tested on:
    Linux/32 2.6 (jam)
    Mac OS X/32 10.6.2 (amazon)
2010-03-17 16:38:20 -05:00
Jonathan Kim
73957db459 [svn-r18399] Note:
missed to add extra files from previous check-in (r18398)

Description:
    add test cases for h5copy - copy external links with/without ‘–f ext’ 
    option (relate to bug 1733)

Tested:
    jam, amani and linew
2010-03-09 16:03:25 -05:00
Jonathan Kim
a1a509083b [svn-r18398] Description:
add test cases for h5copy - copy external links with/without ‘–f ext’ 
    option (relate to bug 1733)

Tested:
    jam, amani and linew
2010-03-09 15:51:30 -05:00
Jonathan Kim
9f514c2b7d [svn-r18331] Description:
Update to use H5Gcreate2 instead of H5Gcreate.
    Remove mis-used type related code.

Tested:
    jam, amani and linew
2010-02-24 16:08:02 -05:00
Jonathan Kim
a3e8a52f17 [svn-r18329] Description:
Fix to handle $srcdir for nightly test as well as local testing

Tested:
    jam, amani and linew
2010-02-24 12:42:59 -05:00
Jonathan Kim
47f98f2618 [svn-r18320] Forgot to remove comments for cleaning up test.out file from previous checkin r18319. 2010-02-23 14:38:10 -05:00
Jonathan Kim
07be86a8ea [svn-r18319] Purpose:
Bug1727 - h5copy: add test cases for object and region references

File added:
    tools/h5copy/testfiles/h5copy_ref.out.ls
    tools/h5copy/testfiles/h5copy_ref.h5

Tested:
    jam, linew
2010-02-23 14:23:29 -05:00
Allen Byrne
28a9bf5f47 [svn-r18317] Updated test script to match *nix shell script. Also corrected 629 file exit code 2010-02-23 14:02:27 -05:00
Jonathan Kim
387b6bf5f5 [svn-r18312] Description:
move data1,data2 array declarations on top of each functions for 
    Windows build

Tested on Jam
2010-02-23 10:22:16 -05:00
Quincey Koziol
2bcb812832 [svn-r18302] Description:
Tweak allocation of attribute tables created from densely stored attributes
to allow for better cleanup on errors (like when the type of corruption from
Bz#1755 is encountered).

    Also, add some code to h5dump to display an error message when the
attribute iteration for an object fails.

Tested on:
        FreeBSD/32 6.3 (duty) in debug mode
        FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
        Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
                w/C++ & FORTRAN, w/threadsafe, in debug mode
        Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x,
                w/C++ & FORTRAN, in production mode
        Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
                w/szip filter, in production mode
        Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
                in production mode
        Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
        Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
        Mac OS X/32 10.6.2 (amazon) in debug mode
        Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
                in production mode
2010-02-19 23:29:08 -05:00
Jonathan Kim
ee757e449b [svn-r18273] Purpose:
bugzilla 1754: h5diff: support comparing through links.

Description:
    Fix incorrect (or hanging) behavior in parallel mode when specifying 
    invalid combination of command options. 
    (ex: -v and -q , --no-dangling-links without --follow-links)
    Add relate test case
    Update h5diffgentest.c due to add test files this and previous time

Note:
    svn  (prior to this)
    svn  (original check-in)

Tested:
    h5committest (jam, amani and linew)
2010-02-18 11:51:12 -05:00
Jonathan Kim
ad9e876b0c [svn-r18266] Purpose:
bugzilla 1754: h5diff: support comparing through links.
    (original check-in svn revision )
Description:
    fix the hang issue in parallel mode when compare external-link.
    add --no-dangling-links option. 
    add test cases (#450-#459) relate to the new option.
    improve test script to check exit code.
    update --help relate to the new options.
    correct some indentations.

Tested:
    h5committest (jam, amani and linew)
2010-02-16 14:43:05 -05:00
Vailin Choi
29837fe71f [svn-r18258] Rename the following files:
h5stat_newgrat-A.ddl --> h5stat_newgrat-UA.ddl
h5stat_newgrat-G.ddl --> h5stat_newgrat-UG.ddl
h5stat_filters-D.ddl --> h5stat_filters-UD.ddl
h5stat_filters-T.ddl --> h5stat_filters-UT.ddl

h5committested.
2010-02-15 13:29:52 -05:00
Vailin Choi
1bc5ffb965 [svn-r18240] Changes to h5stat in response to bug 1778:
1. Gather attribute information for named datatype
2. Revert names of long options back to original
3. Add new tests & *ddl for testing -G, -D, -T, -A options

h5committested.
2010-02-12 14:34:30 -05:00
Quincey Koziol
c462a2ec1f [svn-r18212] Description:
Bring revisions from Coverity fixing branch to trunk:

r18184:
Fixed Coverity issue 373.  Allocated memory freed in line 762 in case of error.

r18185:
Fixed Coverity issues 357 & 358.  Added check for NULL pointer before use.

r18186:
Fix coverity item 65.   Added code to h5unjam to correctly handle failures in
read() and write, and also to correctly handle writes that write less than
requested.

r18187:
Fix coverity items 115 and 116.   Added code to H5Tenum.c to correctly close
opened datatypes in case of failure.

r18188:
Fixed Coverity issue 46.  Check that dataset->shared is not null when freeing
memory after error.

r18190:
Fix coverity item 95.   Added code to H5T_create_vlen to correctly close
allocated datatype in case of failure.

r18191:
Fixed Coverity error 59.  Checked sfirst for -1 value before use in line 10533.

r18192:
Fix Coverity items 121 and 28

Added Asserts:
121: assert that all dimensions of count have values greater than zero.
28: assert curr_span pointer is not null before dereference.

Note: still need too add checks in hyperslab APIs that fail
     when count values are zero, and appropriate tests.

r18194:
Fixed Coverity issues 61 & 62. Checked variable snpoints for value < 0 in line
218.

Tested on:
    Mac OS X/32 10.6.2 (amazon) w/debug & production
    (already daily tested on coverity branch)
2010-02-04 21:56:25 -05:00
Quincey Koziol
fd70b2afa8 [svn-r18197] Description:
Trim trailing whitespace from source code files with this command:

find . \( -name "*.[ch]" -or -name "*.cpp" -or -name "*.f90" \) -print |xargs -n 1 sed -i "" 's/[[:blank:]]*$//'

Tested on:
    None - eyeballed only
2010-01-29 23:29:13 -05:00
Jonathan Kim
0b761d78c7 [svn-r18170] Skipped 3 test cases for parallel mode which caused hang.
They are external-link test cases with following link option.
The related code was checked in as svn  and  to support follwing
links for h5diff.
The test cases will be added back when find solution for parallel mode.

Tested on Jam
2010-01-26 18:39:42 -05:00
Jonathan Kim
98639557ac [svn-r18166] Purpose:
Take care of test case fail for h5repack from checkin (r18164)

Description:
    Previous checkin didn't allow h5diff to return succeed when a link's 
    target object doesn't exist. Changed it to succeed with warning.
    (Need to discuss related feature)

Tested on Jam
2010-01-25 19:20:16 -05:00
Jonathan Kim
985a261886 [svn-r18165] Purpose:
Add test cases for h5diff check-in (svn revision ).

Description:
    This test cases are for testing comparing through various link combinations
    relate to bugzilla report 1754.
    Also improved the test script to handle external link cases and
    simplified to use single line instead of double for each test cases. 

Tested on Jam
2010-01-25 17:02:35 -05:00
Jonathan Kim
79cd5838d1 [svn-r18164] Purpose:
Add a feature to compare through links. Relate to bugzilla report 1754.

Description:
    Currently, h5diff command only compares the name(path) of target object 
    not the actual data. With this feature, h5diff will go through the link(s) 
    and figure out the actual object at the end of the link and compare data 
    if exist. Internally we have hard-link, soft-link, external-link (as part 
    of user_defined-link). This feature will provide a user transparent 
    experience when comparing link objects as the user can specify any of 
    those 3 type of links to be compared in any combination.

Tested on Jam.
2010-01-25 16:43:48 -05:00
Quincey Koziol
bb25c85e79 [svn-r18159] Description:
Bring Coverity fixes from 1/22/10 session to trunk:

r18137:
219: Initialized hid_t to -1 and added close to error block.
189-191: Initialized line to NULL and added free line, and close fp to error block.

r18138:
19: Moved code block for printing that the number of enums is empty to the error block. (Would never have been executed otherwise)

r18139:
Fix coverity item 58.  Moved code related to displaying the parent of a repeated
group to the else(isRoot) section, as the root group has no parent.

r18140:
218: Initialized ret_value variable to -1. Because of throw Exception in default case of switch, the coverity problem would not have executed anyway. Good pratice is to initialize variables.

r18141:
Fix coverity item 92.  Added code to H5E_register_class to free cls in case of
an error.

r18142:
Fix coverity item 91.  Added code to H5E_create_msg to free msg in case of an
error.

r18143:
fixed issue 14,
took away "if" and used #ifndef_xxx.

r18144:
Fix coverity item 110.   Added code to H5Eget_minor to free msg_str in case of
an error.

r18145:
fixed coverity  removed "aligned", it is always NULL.

r18146:
Fix coverity item 109.   Added code to H5Eget_major to free msg_str in case of
an error.

r18147:
Fixed coverity  and , Check for bad pointer(s), but can't issue error, just leave

r18148:
Fix coverity item 97.   Added code to H5FD_fapl_open to free copied_driver_info
in case of an error.

r18149:
Fix coverity item 96.   Added code to H5FD_dxpl_open to free copied_driver_info
in case of an error.

r18150:
Fix Coverity issue : Protected cache_ptr dereferences with "if(pass)"
block

r18151:
Fix coverity item 93.   Added code to H5FL_fac_init to free factory and new_node
in case of an error.

r18152:
Fix coverity items 98 and 99.   Added code free allocated space in case of
error.

r18155:
124: Freed head pointer before jumping to done. There was no error handling block and normal exit used same path out.
120-123: Freed list of lists in error handling block.

r18156:
Fix coverity issues 179, 180, 181, 182, 183, 184, 186, 320, 407.  These were resource leak issues where allocated memory was not freed, generally in the case of tests that failed.

Tested on:
    Mac OS X/32 10.6.2 (amazon) debug & production
2010-01-23 02:00:00 -05:00