| Commit message (Collapse) | Author | Age | Files | Lines |
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* Fixes for a couple of trivial warnings (#676)
* Committing clang-format changes
* Trivial warning fixes:
* Removes an unused done target in H5Tbit.c
* Add (void) to quiet "ignored return value" warnings in the generators
(which generally ignore errors)
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes alternative function enter/leave macro scheme (#678)
* Committing clang-format changes
* Converted BEGIN_FUNC, etc. macros to FUNC_ENTER
* Rips out the BEGIN_FUNC, etc. macros
* Removes 'end if', etc. comments from H5HL package
* Committing clang-format changes
* Fixes an H5EA iterate issue
* Fixes an issue in the H5FA iterator code
* Further cleanup in bin/trace after macro removal
* Iterator changes in H5EA and H5FA
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Various CMake changes (#679)
* Committing clang-format changes
* Several CMake updates:
* Removes unused HDF5_ENABLE_HSIZET
* Switches TEST_SHELL_SCRIPTS to ON
* Sets SH_PROGRAM to bash instead of sh
* Set default build type back to RelWithDebInfo
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* err_compat test cleanup (#681)
* Committing clang-format changes
* Cleans up err_compat test and output
* Formatted source
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* CMake fix for sporadic flush2 failures (#692)
* Committing clang-format changes
* Runs the flush1/flush2 tests in their own directory
Avoids file deletions by other tests.
* Revert "Runs the flush1/flush2 tests in their own directory"
This reverts commit 746c04882434cb502e4231de8f7dd5acb4949f54.
Also pulls the flush files from the clean list, which is a simpler fix.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Ubsan fixes (#498)
* Fixed use of null pointer identified by UBSan
UBSan warned:
runtime error: member access within null pointer of type 'named_dt_t' (aka 'struct named_dt_t')
with these two tests:
H5REPACK-committed_dt_DFF
H5REPACK-committed_dt
Reformulated per @gnuoyd suggestion.
* Fixed undefined float -> unsigned char conversion in HL_test_image
* Removed dead skip_overflow_tests_g global
The global `skip_overflow_tests_g` was being set but never read.
* Don't treat 2d array as 1d array, fixing UBSan complaint in `CPP_testhdf5`
* Committing clang-format changes
* Remove extra ']' in line 730.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* BUG: DataSet assignment operator is missing (#503)
* BUG: DataSet assignment operator is missing
* Some compilers complain if the copy constructor is given explicitly
but the assignment operator is implicitly set to default.
* Explicitly defining the assignment operator allows us to properly
handle reference counters for shared resources.
* BUG: DataSet assignment operator is missing.
* Mimicking code of H5DataType::operator() as suggested by @bmribler.
* Added test
Description:
Added test for DataSet::operator= that Leengit added
Platform tested:
Linux/64 (jelly)
* Removed Author field.
* Commit clang format changes.
* Entry for Leengit's github PR #503
* Removed lines left by mistake
Co-authored-by: Binh-Minh Ribler <bmribler@hdfgroup.org>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Hdf5 merge pr7 (#516)
* Modify temporary rpath for testing in java example scripts.
* Update URL in source file Copyright headers for web copy of COPYING (license) file.
* Add release_docs/code-conventions.md file.
* Add script to test h5py.
* Fix script error.
* Add file h5pytest.yml.
* Test declaration of counter variables in for loops.
* Committing clang-format changes
* Committing clang-format changes
* Added [] to line 126 of H5LTanalyze.l.
Ran bin/genparser with flex v2.6.4 and Bison v3.0.4 on jelly.
* Revert "Added [] to line 126 of H5LTanalyze.l."
This reverts commit e4a9cee441efa75b16a8ee030c86189e186dd266.
* Revert extra commits to match canonical develop.
* Add cmake variable HDF5_LIB_INFIX (#7)
* Add cmake variable HDF5_LIB_INFIX
This infix is added to all library names after 'hdf5'.
e.g. the infix '_openmpi' results in the library name 'libhdf5_openmpi.so'
This name is used in packages on debian based systems.
(see https://packages.debian.org/jessie/amd64/libhdf5-openmpi-8/filelist)
This option is useful when testing projects on debian based systems with
custom builds of hdf5 while trying to minimize differences between the
custom setup and the environment created by installing system packages.
* Added RELEASE.txt entry for HDF5_LIB_INFIX.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Raphael Grimm <barcode@users.noreply.github.com>
* Fixes a segfault when H5Pset_mdc_log_options is called multiple times on a fapl (#601)
* Committing clang-format changes
* Fixes a segfault when H5Pset_mdc_log_options() is called multiple times
An internal string is incorrectly freed when the API call is invoked
multiple times on a property list, which will usually cause a segfault
to occur. On the first call the log location is NULL so the problem
doesn't occur.
Fixes HDFFV-11239
* Fixes typos
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix for a segfault when H5Pset_fapl_log is passed an invalid fapl ID (#607)
* Committing clang-format changes
* Fixes an issue where H5Pset_fapl_log sefaults when passed an invalid
fapl ID
This was due to a pointer-containing struct being memset after the first
internal API call. If the first call failed, the error condition would
check if the pointer was not NULL and then attempt to free it if not.
This would lead to the freeing of a wild pointer if an invalid fapl ID
were passed in.
This was fixed by reordering the memset and adding a test to ensure the
problem stays fixed.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes crashes when size_hint > UINT32_MAX is passed to H5Gcreate1 (#611)
* Committing clang-format changes
* Fixes incorrect size_hint handling in H5Gcreate1
* Updates the size hint type for group creation
* Updates the RELEASE.txt note
* Revert "Updates the RELEASE.txt note"
This reverts commit 3df386acca806d652bbe2209f7c4503b30f068ff.
* Reverts previous behavior to use a uint32_t struct field
* Updates RELEASE.txt
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Sean McBride <sean@rogue-research.com>
Co-authored-by: Lee Newberg <35611400+Leengit@users.noreply.github.com>
Co-authored-by: Binh-Minh Ribler <bmribler@hdfgroup.org>
Co-authored-by: Raphael Grimm <barcode@users.noreply.github.com>
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* Snapshot version 1.12 release 1-3. Update version to 1.12.1-4.
* First cut of the H5 public API documentation. (#80)
* First cut of the H5 public API documentation.
* Added H5Z "bonus track."
* Applied Quincey's patch.
* Added the missing patches from Quincey's original patch.
* H5PL (complete) and basic H5VL API documentation.
* Added H5I API docs.
* Added H5L API docs.
* First installment from Elena's H5T batch.
* Second installment of Elena's H5T batch.
* Final installment of Elena's H5T batch.
* Full set of current H5F documentation. (#105)
* First cut of the H5 public API documentation.
* Added H5Z "bonus track."
* Applied Quincey's patch.
* Added the missing patches from Quincey's original patch.
* H5PL (complete) and basic H5VL API documentation.
* Added H5I API docs.
* Added H5L API docs.
* First installment from Elena's H5T batch.
* Second installment of Elena's H5T batch.
* Final installment of Elena's H5T batch.
* Migrated documentation for SWMR functions.
* Catching up on MDC functions.
* Integrated the H5F MDC function documentation.
* Added MDC and parallel H5F functions.
* Slightly updated main page.
* Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST.
* Doxygen - added (mostly) beginner functions (#112)
* Doxygen - added (mostly) beginner functions
* Removed duplicate H5Pset_szip function
* Add src/H5module.h to MANIFEST.
* close #195. (#196)
* Update HDF5PluginMacros.cmake
* Update HDF5PluginMacros.cmake
* Avoid aligned access for references by decoding into temporary buffer and then copying the result into the actual buffer. Update test to be more thorough with using compound datatype fields everywhere. (#206)
* Modify temporary rpath for testing in java example scripts. (#230)
* Fix undefined left shifting of negative numbers (#338)
Undefined Bahavior Sanitizer errored here about left shifting negative numbers.
* Fixes various warnings noticed on Windows (#425)
* Fixes various warnings noticed on Windows
- Adds a prototype for our implementation of vasprintf
- Return type of H5_get_utf16_str() is now non-const
- Fixes possible uninitialized return type in Wremove_utf8
- Better isolation of fork() code in accum.c:test_swmr_write_big()
- Better isolation of non-zlib code in dsets.c:test_filter_delete()
- Removed unused variable in trefer.c:test_reference_cmpnd_obj()
* Fixes clang-format issues
* Applied clang-tidy readability-non-const-parameter warning fixes auto… (#429)
* Automatically applied clang-tidy readability-avoid-const-params-in-decls fixes
Removes useless const declarations.
* Fixed most readability-non-const-parameter warnings
These changes were made automatically by clang-tidy, but I manually reverted the changes related to the H5Z_func_t signature.
* Reformat source with clang v10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Added C++11 override keyword where appropriate (#433)
Added H5_OVERRIDE macro for compatibility with both C++11 and older.
* Various clang tidy warning fixes (#448)
* Fixed clang-tidy bugprone-reserved-identifier warnings
* Fixed clang-tidy bugprone-assert-side-effect warnings
* Fixed clang-tidy bugprone-copy-constructor-init warning
* Fixed clang-tidy readability-redundant-preprocessor warning
For error_test.c the removed code was already dead, because it was in the else of an `#if H5_USE_16_API` block.
Based on H5Location.h, I think p_get_ref_obj_type was meant to be in `#ifndef DOXYGEN_SHOULD_SKIP_THIS` and an `#endif` was missing. Similarly, in the header, getObjTypeByIdx is only in H5_NO_DEPRECATED_SYMBOLS, not DOXYGEN_SHOULD_SKIP_THIS.
* Fixed clang-tidy readability-redundant-string-init warnings
* Fixed some clang-tidy performance-type-promotion-in-math-fn warnings
* Fixed clang-tidy performance-unnecessary-value-param warnings
* Reformat source with clang v10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Removed checks/workarounds for pre-C++89 compatibility (#449)
After 30+ years, just assume that the following exist:
- extension-less includes
- namespaces
- std::
- static_cast
- bool
* Fixed all clang-tidy bugprone-suspicious-string-compare warnings (#451)
* Fixed all clang-tidy bugprone-suspicious-string-compare warnings
This change was generated entirely by clang-tidy itself.
* Reformat code with clang v10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Remove 2 functions incorrectly merged from develop in a cherry-pick merge of PR #451.
Co-authored-by: Gerd Heber <gheber@hdfgroup.org>
Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Quincey Koziol <quincey@koziol.cc>
Co-authored-by: Sean McBride <sean@rogue-research.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
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file - src and test directories.
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* OESS-98 fix tools test for plugins
* sync fork
* Merge of changes from dev
* Move problem option to bottom of the list until fixed
* HDFFV-11106 - fix parsing optional args
* HDFFV-11106 add note
* grammer fix
* Whitespace after clang formatting
* Undo format version 11 changes
* Update check to working version
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* Basic alignment with async branch - trivial changes to reduce clutter in overall diff.
* Update minor error code to reflect change within library
* Update the error output to match library
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Comments and whitespace
Skip file-locking and cache changes
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header file, FUNC_ENTER / LEAVE, etc). Removed remaining personal email
addresses from library source code (still needs cleaned from other directories).
Misc. warning, style, and whitespace cleanup.
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* commit '145ef3ceee20c28a443bd11507c58858bea3f889':
more cleanup
change it back
pick up missing piece
fix unused related warnings
removed unused parameter
more fix and address comments
remove unsed var,function,macro, etc
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to develop
* commit '0a2bb11b248df6841daabca3970df5d8504adfc7':
address problems from comments
fix and address comments
change according to previous comments
add missing piece
remove unnecessary check macro
fix intel compile warnings
Revert "fix warnings from Intel compiler"
Revert "fix warnings and some text alignment"
Revert "let hdf5 pick up the right compiler in Intel environment"
Revert "fix issues from previous PR comments"
Revert "using a different MACRO"
using a different MACRO
fix issues from previous PR comments
let hdf5 pick up the right compiler in Intel environment
fix warnings and some text alignment
fix warnings from Intel compiler
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- Added casts to quiet H5MM_memcpy warnings
- Removed char * casts from HDmemcpy
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hdf5_1_10
* commit '54957d37f5aa73912763dbb6e308555e863c43f4':
Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes.
Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh.
Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1
Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
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"child serialized / unserialized" messages and support from the cache image
branch.
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and the tool and API wrappers will be coming in over the weekend.
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supporting metadata cache callback changes, etc.
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new 'entry cleaned' notify action innstead.
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entries, they are now completely handled in the clients.
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Cleanup whitespace to align w/revise_chunks branch
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
(h5committest forthcoming)
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Tested on:
Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
serial only
(these changes have been in revise_chunks for a long time)
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Complete revamp of package initialization/shutdown mechanism in the library.
Each package now has a single init/term routine.
This new way should avoid packages being re-initialized during library
shutdown and is also be _much_ more proactive about giving feedback for
resource leaks internal to the library.
Introduces a new "module" header file for packages in the library
(e.g src/H5Fmodule.h) which sets up some necessary package configuration macros
for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly
modified version of this header, src/H5FDdrvr_module.h)
Also cleaned up a bunch of resources leaks all across the library and tests,
along with addressing many warnings, as I encountered them.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
Linux/64 3.10.x (kituo) w/serial & parallel
Linux/64 2.6.x (ostrich) w/serial
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this by modifying
metadata cache clients to clear unused memory in the buffer after serializing.
Tested: ummon; jam, koala, ostrich (h5committest)
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Merge v3 metadata cache changes to trunk. Yay! :-)
Tested on:
MacOSX/64 10.10.3 (amazon) w/serial & parallel
Linux/32 2.6.x (jam) w/serial & parallel
(daily tested on branch)
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Normalize trunk against the metadata_cache_merge branch, in preparation
for merging the branch into the trunk.
Tested on:
MacOSX/64 10.10.3 (amazon) w/serial & parallel
Linux/64 2.6.x (koala) w/serial
Linux/32 2.6.x (jam) w/serial & parallel
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* H5_ATTR_FORMAT(X,Y,Z) __attribute__((format(X, Y, Z)))
- Rename UNUSED attribute characterstic to H5_ATTR_UNUSED.
- Rename NORETURN attribute characterstic to H5_ATTR_NORETURN
tested with h5committest.
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Clean up H5FA interface, to align w/v3 metadata cache changes
Tested on:
MacOSX/64 10.10.3 (amazon) w/serial & parallel
Linux/32 2.6.* (jam) w/serial & parallel
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project for
view objects. The addition of view objects in the fastforward project
is expected to be brough into the trunk sometimes in the future, which
is why we need to make this change.
Tested Manually on Jam and Ostrich.
Tested with h5commitest - Koala with intel compilers failed, but nothing had to do with those changes.
error on Koala: error while loading shared libraries: libirng.so
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Bring recent tweaks to extensible and fixed array file formats from
revise_chunks branch back to trunk.
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, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
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Bring r18672 from metadata journaling "merging" branch to trunk:
Mostly changes to move to only using one 'user data' parameter for
calls to H5AC_protect(), along with some minor reformatting code cleanups.
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-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.3 (amazon) in debug mode
Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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Clean up compiler warnings.
Tested on:
Mac OS X/32 10.6.3 (amazon) w/debug
(too minor to require h5committest)
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Streamline & cleanup data structure 'destroy' calls from metadata
client destroy callbacks.
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 10.6.3 (amazon) in debug mode
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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
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Correct & simplify client callback context for extensible and fixed
array data structures.
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 (smirom) 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
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Bring most of Vailin's changes to the fixed array data structure back
to the trunk, including new regression test for data structure.
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/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) 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 10.5.8 (amazon) in debug mode
Mac OS X/32 10.5.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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Bring r17154 from 'revise_chunks' branch to trunk:
Add fixed array data structure. (For initial use as a chunk index)
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/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) 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 10.5.7 (amazon) in debug mode
Mac OS X/32 10.5.7 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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