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* [svn-r18830] Updated CMake file with r18826Allen Byrne2010-05-171-0/+6
| | | | Tested: local linux
* [svn-r18826] Added packed bits tests on Compound and Array data types.Albert Cheng2010-05-173-0/+90
| | | | Tested: AlbertPax. Will do h5committest after check in.
* [svn-r18821] Packed bits codes tidy up. Removed codes that are not neededAlbert Cheng2010-05-155-30/+19
| | | | | | | | | any more. Changed algorithm of creating mask which now sits at the least significant bits. Display data by down shift first and then mask it for display. Changed the variable names to reflect the new purpose better. Tested: AlbertPax (linux)
* [svn-r18815] Move progname and d_status functions from h5tools to h5tools_utilAllen Byrne2010-05-144-34/+34
| | | | | Tested: linux and windows
* [svn-r18812] moved reference to noname-packedbits file to packed bits section Allen Byrne2010-05-141-1/+1
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* [svn-r18810] Bug fix:Albert Cheng2010-05-141-5/+5
| | | | | | | | Program failued in FreeBSD and Windows machines because uint is a local backward compatibility extension of Linux. Changed them to the proper "unsigned int". Tested: FreeBSD (liberty,duty), h5committested.
* [svn-r18809] Purpose:Mike McGreevy2010-05-143-3/+3
| | | | | | | | | | | | | | | | | | | 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
* [svn-r18798] Updated CMakeLists to match changes r18794-18796Allen Byrne2010-05-131-2/+69
| | | | | | Even figured out which are expected to fail! Tested: Local linux
* [svn-r18796] Enhancement 1853:Albert Cheng2010-05-135-92/+155
| | | | | | | | | | | | | | | | | | | | | | Install packed-bits feature for h5dump. tools/h5dump/h5dump.c: Added lots of error checking into parse_mask_list() to catch and flagged packed-bits argument errors. For now, the packed bits are limited to 1 byte (8 bits) range. tools/h5dump/testh5dump.sh.in Added 10 new packed-bits test to verify normal operation and argument error detection. tools/lib/h5tools.h: tools/lib/h5tools_str.c: tools/lib/h5tools.c: Only name changes of the packed-bit global variables to reflect the nature of the variable better, IMO. Tested: albertPax (linux) ------------------------------------------------------------------------
* [svn-r18795] Enhancement 1853:Albert Cheng2010-05-131-6/+169
| | | | | | | | | | Install packed-bits feature for h5dump. Added gent_packedbits() to generate the HDF5 test data file, packedbits.h5, for packed-bit feature test. Tested: albertPax (linux) ------------------------------------------------------------------------
* [svn-r18794] Enhancement 1853:Albert Cheng2010-05-1313-57/+752
| | | | | | | | | | | | | | | | | | | | | | | | | | Install packed-bits feature for h5dump. testfiles/packedbits.h5: New HDF5 test data file. Generated by h5dump/h5dumpgentest. testfiles/tpbitsLengthPositive.ddl: testfiles/tpbitsMaxExceeded.ddl: testfiles/tpbitsSigned.ddl: testfiles/tpbitsOffsetNegative.ddl: testfiles/tpbitsUnsigned.ddl: testfiles/tpbitsMax.ddl: testfiles/tpbitsIncomplete.ddl: testfiles/tpbitsOverlapped.ddl: testfiles/tpbitsLengthExceeded.ddl: testfiles/tpbitsOffsetExceeded.ddl: Expected output files created to test various components of the packed-bits feature. testfiles/tpackedbits2.ddl: testfiles/tpackedbits.ddl: Previous output files no longer used. Tested: albertPax (linux)
* [svn-r18787] Added h5tools.h include to h5diff_common.h to fix warnings ↵Allen Byrne2010-05-132-5/+20
| | | | | | about the new progname and status functions Tested: local linux
* [svn-r18786] Corrected typo which prevented non-windows diff tests to work ↵Allen Byrne2010-05-131-1/+1
| | | | | | correctly Tested: local linux
* [svn-r18784] Description:Quincey Koziol2010-05-131-1/+1
| | | | | | | Fix unterminated comment. Tested on: None - just eyeballed.
* [svn-r18779] Add ${DESTDIR} to scripts and Makefiles so that make ↵Larry Knox2010-05-1211-55/+55
| | | | | | DESTDIR=<install directory> install, installcheck and uninstall is supported for installing examples, since they are now installed as part of make install. This was necessary for rpmbuilds, but should also be supported otherwise. Tested: amani, jam, linew with committest, rpmbuild on jam and amani.
* [svn-r18777] Moved declaration to top of function, windows compiler issue.Allen Byrne2010-05-121-5/+5
| | | | Tested: Windows
* [svn-r18773] Add files to support building library with CMakeAllen Byrne2010-05-1213-0/+2642
| | | | Tested: Local linux
* [svn-r18758] Corrected missed progname to function instanceAllen Byrne2010-05-111-1/+1
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* [svn-r18757] Enable tools lib to be built as a dll on windows. Added two ↵Allen Byrne2010-05-1133-489/+577
| | | | | | | | | | get/set functions for progname and d_status. Also add windows import/export declarations to functions. Updated windows - H5pubconf.h for packed bits function Tested: Windows, linux
* [svn-r18743] enhancement 1853:Albert Cheng2010-05-079-4/+381
| | | | | | | | | | | | | | | | | | | | | | | | | Install packed-bits feature for h5dump. Allen has installed the feature in the NPOESS feature branch. I ported it back to the v1.8 branch for v1.8.5 release. tools/h5dump/testh5dump.sh.in: Added tests for the packed-bits feature. tools/h5dump/h5dump.c tools/h5dump/h5dump.h Added code to parse and handled the packed-bits request. tools/lib/h5tools.h tools/lib/h5tools_str.c tools/lib/h5tools.c Added code to print packed-bits. tools/testfiles/tpackedbits2.ddl tools/testfiles/tnofilename-with-packed-bits.ddl tools/testfiles/tpackedbits.ddl Expected output files for packed-bits feature. Tested: h5committested the NPOESS branch. Tested in the linux VM machine in my Dove.
* [svn-r18710] Purpose:Mike McGreevy2010-05-0511-11/+11
| | | | | | | | | | | | | | | | | | | | | | | | | | 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 is being deprecated in favor of the --enable-largefile flag (enabled by default), which can be used on all platforms. --disable-linux-lfs can still be used to disable largefile support (on linux) when the --enable-largefile flag is not specified. 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.
* [svn-r18701] ID 1853:Albert Cheng2010-05-0411-0/+11
| | | | | | | | Added the configure option --enable-h5dump-packed-bits for the h5dump optional feature. Tested: Jam (default and --disable-h5dump-packed-bits).
* [svn-r18652] Description:Quincey Koziol2010-04-278-13/+18
| | | | | | | | | | | | Bring r18650 from trunk to 1.8 branch: Bring back various minor tweaks & cleanups from the revise_chunks branch. Tested on: FreeBSD/32 6.3 (duty) in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode (h5committested on trunk)
* [svn-r18646] In H5T_get_native_type of H5Tnative.c, I changed the way that ↵Raymond Lu2010-04-271-0/+1
| | | | | | | | | 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 #1850). Tested on amani, linew, and jam.
* [svn-r18643] Purpose:Jonathan Kim2010-04-272-2/+7
| | | | | | | | | | | Fix for Bug 1793 - h5ls on a non-existent file gives 0 return code Description: Merged from hdf5 trunk r18642. After the fix, h5ls returns 1 (EXIT_FAILURE) if non-existent file is given. Tested: jam
* [svn-r18615] Purpose:Jonathan Kim2010-04-226-160/+205
| | | | | | | | | | | Fix for bug 1817 : h5copy fail to copy dangling link by specifying link path directly Description: Merged from hdf5 trunk r18614. Tested: jam, amani
* [svn-r18580] Purpose:Mike McGreevy2010-04-1511-13/+13
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* [svn-r18550] Description:Quincey Koziol2010-04-131-1/+1
| | | | | | | | | | Bring r18548 from trunk to 1.8 branch: Minor cleanups to compile with PGI C compiler 10.x. Tested on: Mac OS X/32 10.6.3 (amazon) (tested on trunk)
* [svn-r18455] Purpose:Jonathan Kim2010-03-257-403/+701
| | | | | | | | | | | Fix for the bug1726 - NPOESS: h5repack loses attributes for datasets of type H5T_REFERENCE. Description: Merged from hdf5 trunk rXXX Tested: jam
* [svn-r18450] Purpose:Jonathan Kim2010-03-251-3/+3
| | | | | | | | Resolve build issue on Sloaris due to white space from the previous checkin r18448 Tested: jam
* [svn-r18448] Purpose:Jonathan Kim2010-03-241-5/+15
| | | | | | | | | | | | | Bug1727 - NPOESS: h5copy should copy region references Description: Merged from hdf5 trunk r18447. Tested and added test cases from previous checkin r18321 Reference Manual and tool's usage section for '-f ref' option is updated for more comprehensibility. Tested: jam
* [svn-r18443] Purpose:Jonathan Kim2010-03-231-1/+2
| | | | | | | | | | | Resolve windows build issue from previous checkin r18427 Description: The previous checkin was for bug1814 - NPOESS: h5repack doesn't handle references to the groups as an element of a dataset Tested: jam
* [svn-r18427] Purpose:Jonathan Kim2010-03-185-5/+341
| | | | | | | | | | | | | Fix for bug1814 - NPOESS: h5repack doesn't handle references to the groups as an element of a dataset Description: Merged from hdf5 trunk r18425 handles object reference to named-datatype as well. Add test cases. Tested: jam
* [svn-r18400] Purpose:Jonathan Kim2010-03-095-1/+281
| | | | | | | | | | | add test cases for h5copy - copy external links with/without ‘–f ext’ option (relate to bug 1733) Description: merged from hdf5 trunk (r18398 and r18399) Tested: jam
* [svn-r18332] Description:Jonathan Kim2010-02-241-16/+5
| | | | | | | | Update to use H5Gcreate2 instead of H5Gcreate. Remove mis-used type related code. Tested: jam, amani and linew
* [svn-r18330] Description:Jonathan Kim2010-02-241-1/+1
| | | | | | | | Fix to handle $srcdir for nightly test as well as local testing Merged from hdf5 18329. Tested: jam, amani and linew
* [svn-r18321] Purpose:Jonathan Kim2010-02-235-21/+407
| | | | | | | | | | | | | | Bug1727 - h5copy: add test cases for object and region references Note: merged from hdf5 trunk 18319 and 18320 File added: tools/h5copy/testfiles/h5copy_ref.out.ls tools/h5copy/testfiles/h5copy_ref.h5 Tested: jam
* [svn-r18318] Updated test script to match *nix shell script. Also corrected ↵Allen Byrne2010-02-231-1/+1
| | | | | | 629 file exit code Tested: windows
* [svn-r18313] Description:Jonathan Kim2010-02-231-15/+10
| | | | | | | move data1,data2 array declaration on top of each functions for Windows build Tested on Jam
* [svn-r18303] Description:Quincey Koziol2010-02-201-28/+84
| | | | | | | | | | | | | | | Bring r18302 from trunk to 1.8 branch: 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: Mac OS X/32 10.6.2 (amazon) w/debug & production (h5committested on trunk)
* [svn-r18279] Purpose:Jonathan Kim2010-02-19123-616/+3161
| | | | | | | | | | Work for bugzilla 1754: h5diff: support comparing through links. Description: merged from hdf5 trunk (18164, 18165, 18166, 18167, 18170, 18266, 18273) Tested: h5committest (jam, amani and linew)
* [svn-r18270] Changes to h5stat in response to bug 1778:Vailin Choi2010-02-1714-171/+392
| | | | | | | | 1. Gather attribute info for named datatype, 2. Fixed -T, -G, -A, -D options 3. Brought over some changes from trunk h5stat h5committested.
* [svn-r18213] Description:Quincey Koziol2010-02-051-14/+45
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r18212 from trunk to 1.8 branch: 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)
* [svn-r18198] Description:Quincey Koziol2010-01-3028-662/+662
| | | | | | | | | Trim trailing whitespace from source code files, with following command: find . \( -name "*.[ch]" -or -name "*.cpp" -or -name "*.f90" \) -print |xargs -n 1 sed -i "" 's/[[:blank:]]*$//' Tested on: None - eyeballed only
* [svn-r18160] Description:Quincey Koziol2010-01-232-102/+42
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r18159 from trunk to 1.8 branch: 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 #18 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 #81 and #82, 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 #29: 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
* [svn-r18135] Purpose:Jonathan Kim2010-01-2112-16/+8
| | | | | | | | | | | | Additional fix relted to the fix of bug1672. Description: The fix of bug1672 caused some changes of output which required modifying some test cases. After some discussion, restoring the changes of the test cases was decided. After many experiments for the solution, this fix was made so the code which improved performance can stay. Tested on Jam.
* [svn-r18130] Purpose:Jonathan Kim2010-01-213-2/+13
| | | | | | | Add test case relate to bug1749. Also corrected command echo line which is not match with actual test. Tested on Jam.
* [svn-r18127] Purpose:Jonathan Kim2010-01-201-12/+2
| | | | | | | | | | | | | Fix for bug1749: Incorrect code in diff() function for links compare Also removed duplicated redundant code, which improves performance. Description: When comparing file1 to file2 and both files contain same soft-links and/or external-links, if file2's target object path name is longer than file1's target object path name, the current code allocates memory buffer incorrectly, so it could end up buffer overflow or wrong result. Tested on Jam.
* [svn-r18110] Description:Quincey Koziol2010-01-154-21/+15
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r18109 from trunk to 1.8 branch: Bring r18076-18096 from hdf5_1_8_coverity branch to trunk: r18076: Correct Coverity issue #1 by removing dead code r18077: Fix coverity item 142. When an error occurred while copying a linked list in H5S_point_copy, the library would not free the partially allocated list. Added code to free the list in this case. r18078: Correct Coverity issue #2 by removing impossible to reach code. r18079: Correct #3 by removing impossible to reach code. r18080: Correct Coverity issue #4 by removing impossible to reach code. r18081: fix coverity 26 , check (dblik->parent) before calls H5HF_man_iblock_detach(). r18082: Fixed coverity issues 321 and 316. 321: freed sm_buf in error handling to remove resource leak. Also set sm_buf to NULL after other instances in which it is freed to prevent double free. 316: initialized nmembs to 0. r18083: Correct Coverity issue #6 by removing debugging knob from error reporting code. r18084: Fix coverity item 269 + others. When a error occurred in a function using the h5tools error framework, the "past_catch" variable would not be set to true because that statement was before the label that goto jumped to. This could cause a failure in the cleanup section to go back to the start of the section, freeing variables twice, etc. Moved the label infront of past_catch=TRUE. r18085: fixed coverity #27, check if (heap) before use heap->obj.... r18086: fixed coverity #28, check curr_span not null before use it at if(curr_span && (io_bytes_left==0 || curr_seq>=maxseq)) r18087: Correct Coverity issue #7 by cleaning up correctly on error r18088: Correct Coverity #8 by removing unchanged variable checking code. r18089: Correct Coverity issue #9 - remove impossible to reach code. r18090: Correct Coverity issue #11 by removing impossible to reach code. Also clean up some minor style issues. r18091: Fix coverity items 314 and 318. Changed the improper assertion of the return value of a library function to a check, and a return(void) on failure. r18092: Fix coverity item 70. Changed the improper assertion of the return value of a library function to a check, and a return(void) on failure. r18093: Correct Coverity issue #12 by removing dead code. r18094: Correct Coverity issue #16 by removing debugging code. r18095: Fixed coverity issue # 271. Removed redundant checking and freeing of sm_buf1 and sm_buf2. r18096: Correct Coverity issue #17 by refactoring test to remove dead code. Also, removed previous "coverity" statements in comments, we'll review those issues again and see if we can figure them out, now that we have more experience with Coverity. Tested on: Mac OS X/32 10.6.2 (amazon) debug & prod
| * [svn-r18095] Fixed coverity issue # 271.Mike McGreevy2010-01-081-5/+0
| | | | | | | | Removed redundant checking and freeing of sm_buf1 and sm_buf2.
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