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* Update copyright headers. (#2527)Larry Knox2023-03-101-1/+0
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* Backport H5Dchunk_iter to 1.10 branch (#1968)Mark Kittisopikul2023-02-211-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Backport H5Dchunk_iter to 1.10 branch * Add some accessory files, test still needs work * Apply proper formatting, and fix compile errors * Remove const from H5D__chunk_iter as per #1700 * Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info (#2074) * Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info * Modify chunk_info test to for unsigned / hsize_t types * Fix types in test * Add test_basic_query, helper functions to test/chunk_info.c 1_10 * H5Dchunk_iter now passes offsets in units of dataset elements, fix #1419 (#1969) * H5Dchunk_iter now passes chunk dimension scaled offsets, fix #1419 * Update docs for H5Dchunk_iter, H5Dget_chunk_info* Modified description for `H5Dchunk_iter`, `H5Dget_chunk_info`, and `H5Dget_chunk_info_by_coord` to the following * offset Logical position of the chunk’s first element in units of dataset elements * filter_mask Bitmask indicating the filters used when the chunk was written * size Chunk size in bytes, 0 if the chunk does not exist * Fix regression of #1419 * Add a note about return fail in 1.12 and older for invalid chunk index * Committing clang-format changes * Run clang-format on test/chunk_info.c --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1.10 clang 13 format #1933 (#1940)Allen Byrne2022-07-291-44/+44
| | | | | * clang 13 format #1933 * Correct workflow
* [1.10 Merge] Hdf5 1 10 warnings merge (#1754)jhendersonHDF2022-05-081-30/+29
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Warnings fixes (#1680) * Clean stack size warnings in sio_engine (#1687) * Fixes stack size warnings in tcoords.c (#1688) * Address some warnings from casting away of const (#1684) * Fixes stack size warnings in dtransform (#1696) * Fixes stack size warnings in set_extent test (#1698) * Be a bit safer with signed arithmetic, thus quieting some signed-overflow warnings from GCC (#1706) * Avoid a signed overflow: check the range of `entry_ptr->age` before increasing it instead of increasing it and then checking the range. This quiets a GCC warning. * Avoid the potential for signed overflow by rewriting expressions `MAX(0, fwidth - n)` as `MAX(n, fwidth) - n` for various `n`. This change quiets some GCC warnings. * Change some local variables that cannot take sensible negative values from signed to unsigned. This quiets GCC warnings about potential signed overflow. * In a handful of instances, check the range of a signed integer before increasing/decreasing it, just in case the increase/decrease overflows. This quiets a handful of GCC signed-overflow warnings. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix object size warnings in cache.c test (#1701) * Fix some const cast and stack/static object size warnings (#1700) * Fix various warnings * Move HDfree_const to H5private.h for wider use * Print output from all ranks in parallel tests on allocation failure * Move const pointer freeing macro to h5test.h for now * Fixes a bug where t_cache fails due to a string size being too small (#1720) * Fixes a bug where t_cache fails due to a string size being too small Recent warning reductions led to an incorrect string size being passed to h5_fileaccess, causing the test to silently fail. In addition to fixing the bug, the test will now fail noisily on setup failures. * Updates the t_cache test to fail noisily on setup errors * Fix a few Clang sanitizer warnings (#1727) * Stop lying about H5S_t const-ness (#1209) Hyperslabs can be reworked inside several H5S callbacks, making H5S_t non-const in some places where it is marked const. This change switches these incorrectly const H5S_t pointer parameters and variables to non-const where appropriate. * Fix a few warnings after recent H5S const-related changes (#1225) * Adjustments for HDF5 1.10 * Hdf5 1 12 Miscellaneous warnings fixes (#1718) * Fixes const issues in the version 2 B-trees (#1172) The operations that were changed are fundamentally not const since the shadow operation can modify the node structure when SWMR is in use. * Quiets const warning in H5RS code (#1181) * Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the (#1171) * Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the raw H5R_ref_t bytes to a heap buffer that's known to have the right alignment. * Committing clang-format changes * Use an automatic H5R_ref_t instead of malloc'ing one. Go ahead and initialize the H5R_ref_t to all-0s so that arbitrary stack content doesn't foul things up. Bail out with an error if `size` exceeds `sizeof(H5R_ref_t)`. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Miscellaneous warnings fixes Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix several warnings (#747) Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Hdf5 1 10 parallel comp (#1644)jhendersonHDF2022-04-141-2/+15
| | | | | * Hdf5 1 10 parallel compression merge
* 1.10 Merge doxygen changes from develop (#1543)Allen Byrne2022-03-301-1/+1
| | | | | | | * Merge doxygen changes from develop * Remove 1.12 section * Minor comment cleanup
* Hdf5 merge issue 458 v110 (#465)Larry Knox2021-03-121-1/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * 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. * Update license url (#332) * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - src and test directories. * 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> * Fix clang-tidy suspicious string compare in H5A.c missed in merge. Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Sean McBride <sean@rogue-research.com>
* 1 10 merges from develop (#419)Allen Byrne2021-03-031-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev
* Hdf5 1 10 Update license url (#403)Larry Knox2021-03-011-1/+1
| | | | | | | | | | | | | | | | | | | | | | | * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * 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. * Update license url (#332) * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - src and test directories. Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Sean McBride <sean@rogue-research.com>
* Source formattedAllen Byrne2020-10-011-409/+390
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* Normalization with develop.Dana Robinson2020-07-201-1/+1
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* Merge of dataspace improvements from develop.Dana Robinson2020-07-161-10/+7
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* Add changes from PR #2049 to 1.10Chris Hogan2019-12-021-0/+1
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* Fix issue with direct chunk write not updating the "last chunk" indexNeil Fortner2019-03-191-2/+7
| | | | | cache. Fix issues involving datasets being "no allocated" when they contain cached raw data.
* Merge pull request #1380 in HDFFV/hdf5 from ↵Binh-Minh Ribler2019-01-021-1/+1
|\ | | | | | | | | | | | | | | | | | | ~BMRIBLER/hdf5_1_10_bmr:hdf5_1_10 to hdf5_1_10 This is merged now so it can be tested. * commit '74a3710a996fca5ed7fcb4dd8919a7a8521de1de': Revised per review. Description: Changed H5EA_iterate and H5FA_iterate as suggested. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test) Addressed HDFFV-10661 Description: - Fixed a bug triggered by tests in chunk_info.c. The returned value from a callback function was not checked in H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate(). This oversight caused a callback function to continue iterating even though it's supposed to stop. Vailin confirmed. - Addressed review comments and made various improvements on the tests. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
| * Addressed HDFFV-10661Binh-Minh Ribler2018-12-151-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | Description: - Fixed a bug triggered by tests in chunk_info.c. The returned value from a callback function was not checked in H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate(). This oversight caused a callback function to continue iterating even though it's supposed to stop. Vailin confirmed. - Addressed review comments and made various improvements on the tests. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
* | Removed 'VOL' versions of FUNC_ENTER macros as well as empty functionsDana Robinson2018-12-311-3/+0
|/ | | | orginally intended to support the full SWMR feature (from develop).
* Updated new API functionsBinh-Minh Ribler2018-11-051-1/+1
| | | | | | | | | | | | | | Description: - Per Vailin's review, revised H5Dget_chunk_info_by_coord to handle non-existing chunk and H5Dget_num_chunks and H5Dget_chunk_info to handle dataset with no data. - Addressed other review comments - Note that additional tests will be added as we need to send users these functions asap for feedback. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1011test)
* New API functionsBinh-Minh Ribler2018-10-291-0/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | Description: Added functions to query chunk information: H5Dget_num_chunks(dset_id, fspace_id, *nchunks) Gets the number of written chunks that intersect with the given dataspace. However, in this version, the intersection is not yet completed. Thus, the number of all written chunks will be returned. H5Dget_chunk_info_by_coord(dset_id, *coord, *filter_mask, *addr, *size) Given a chunk's coordinates, returns the chunk's filter, address, and size. H5Dget_chunk_info(dset_id, fspace_id, index, *coord, *filter_mask, *addr, *size) Given a chunk's index, returns the chunk's coordinates, filter, address, and size. The chunk belongs to a set of chunks that have nonempty intersection with the specified dataspace. However, in this version, the intersection is not yet completed, and the index is of all the written chunks. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1011test)
* Finished move of H5DOread/write_chunk calls to H5D.Dana Robinson2018-04-301-2/+0
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* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-03-181-4/+7
|\ | | | | | | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
| * Fix for daily test failuresVailin Choi2018-02-141-0/+3
| | | | | | | | | | | | | | | | Move the declarations for the three arrays of versions from H5Opkg.h: (1) H5O_layout_vers_bounds to H5Dpkg.h (2) H5O_dtype_ver_bounds to H5Tpkg.h (3) H5O_sdspace_ver_bounds to H5Spkg.h This is to fix Windows' complaint for unresolved symbols.
| * HDFFV-9724 Corrected files and verified testsAllen Byrne2017-12-281-1/+2
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| * Revert "Merge pull request #826 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to ↵lrknox2017-12-221-2/+1
| | | | | | | | | | | | | | develop" This reverts commit b1223dd653e65e076af92b2dfe236f3704da81c8, reversing changes made to b25f123f5f5e25c1447a6a02861cb7c7265c12f2.
| * HDFFV-9724 Initial changes and testAllen Byrne2017-12-111-1/+2
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* | Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-103/+73
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* Normalization with VOL integration branch.Dana Robinson2017-11-301-0/+2
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* Remove tabsAllen Byrne2017-11-081-68/+68
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* Suggested changes from code reviewJordan Henderson2017-07-071-2/+1
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* Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Jordan Henderson2017-07-051-6/+8
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '6428a637752753cc8a9007c0c3c38b9ea9cc97fd': (165 commits) Skip HDFFV-10160 filenotclosed test for split/multi driver Temporary skip this test for split/multi driver. Further investigation to resolve the failure is needed. Please enter the commit message for your changes. Lines starting More minor whitespace cleanup Fixed a minor comment typo in H5R.c * Reverted removal of H5I_REFERENCE to avoid breaking binary compatibility. * Added a quick H5I_REFERENCE smoke check to test_misc19() in tmisc.c. Added missing free() call to test_misc19(). Purged the unused H5I_REFERENCE from the library. Added a test for VFD IDs to testhdf5. Revert "Partial removal of NDEBUG ifdefs from the library." Partial removal of NDEBUG ifdefs from the library. Removed compiler flag cleanup since Solaris chokes on it. Fix for HDFFV-10160 Modifications to fix the assertion/abort failure when the application does not close the file. Fixed a bug in autotools Fortran processing where a test for the presence of a C long double type always returned true. Updated the --enable-debug/production handling in configure.ac so that it more reliably indicates that the configure option can no longer be used. Previously, using --enable-debug="", etc. would not trigger an error (even though such usage is unlikely). Added awk processing to remove extraneous whitespace from H5_ flags in configure. Fixed a comment in configure.ac HDFFV-10219 another mode change HDFFV-10219 change subset to use BINARY mode for h5dump HDFFV-10219 default input binary to NATIVE Set default of var to NATIVE HDFFV-10219 - disable h5dump tests until h5import NATIVE is fixed ...
| * Fix for HDFFV-10051Vailin Choi2017-05-091-0/+1
| | | | | | | | | | Fix missing declaration for H5D__layout_compact_dirty_test(). Tested on mayll and osx1010test.
| * Incorporate patch from GE Healthcare (HDFFV-9934)Vailin Choi2017-04-251-0/+3
| | | | | | | | | | This is the same patch that had already been integrated to 1.8 branch (pull request #387). Tested on moohan, ostrich, platypus, emu, osx1010test, quail, kituo, mayll.
| * Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| | | | | | | | | | | | | | | | | | | | 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.
* | Switch working branch from master to developJordan Henderson2017-01-131-0/+5
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* Bring SWMR support in to the main development branch. (Finally!) More testsQuincey Koziol2016-12-021-0/+1
| | | | and the tool and API wrappers will be coming in over the weekend.
* Code style and warning cleanups, from revise_chunks branch.Quincey Koziol2016-11-061-0/+6
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* Added code to create the test file for all chunk index and layout types.Dana Robinson2016-09-301-0/+1
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* [svn-r30075] Description:Quincey Koziol2016-06-141-0/+10
| | | | | | | | | | Bring object/dataset/group/named datatype features from revise_chunks branch to trunk. Also CMake support for h5format_convert and a bunch of misc. cleanups. Tested on: MacOSX/64 10.11.5 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29924] Description:Quincey Koziol2016-05-121-0/+4
| | | | | | | | Bring h5format_convert tool from revise_chunks branch to trunk. Tested on: MacoSX/64 10.11.4 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29850] Description:Quincey Koziol2016-05-011-0/+1
| | | | | | | | | | Bring H5DOappend(), H5P[s|g]et_object_flush_cb, and H5P[s|g]et_append_flush from revise_chunks branch to trunk. Brings along updated metadata cache entry tagging, and the internal object flush routine. Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29770] Description:Quincey Koziol2016-04-231-0/+1
| | | | | | | | Bring 'none' chunk index from revise_chunks branch to trunk. Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (w/check-vfd) (h5committest forthcoming)
* [svn-r29738] Description:Quincey Koziol2016-04-191-0/+1
| | | | | | | | Bring "single" chunk index from revise_chunks branch to trunk. Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (w/check-vfd) (h5committest forthcoming)
* [svn-r29659] Added fixed array chunk indexing from revise_chunks.Dana Robinson2016-04-071-0/+5
| | | | | Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1 Autotools serial w/ Java, Fortran, & C++
* [svn-r29635] Description:Quincey Koziol2016-04-051-0/+27
| | | | | | | | | Bring support for earray and v2 B-trees from revise_chunks branch to trunk. Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29614] Description:Quincey Koziol2016-04-031-0/+1
| | | | | | | | | Bring updated code for setting chunk size information from revise_chunks branch. Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29612] Description:Quincey Koziol2016-04-031-0/+2
| | | | | | | | | Bring updated layout and EFL property comparisons and new "latest format" flags from revise_chunks branch. Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29607] Description:Quincey Koziol2016-04-021-0/+3
| | | | | | | | | Bring "don't filter partial edge chunks" capability from revise_chunks to trunk. Tested on: MacOSX/64 10.11.4 (amazon) w/debug, production & parallel (h5committest forthcoming)
* [svn-r29549] Minor normalization w/ revise_chunks in preparation for big merge.Dana Robinson2016-03-241-6/+6
| | | | | | Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1 autotools serial autotools parallel (MPICH 3.1.4)
* [svn-r29548] Minor normalization w/ trunk in preparation for big merge.Dana Robinson2016-03-241-1/+1
| | | | | | Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1 autotools serial autotools parallel (MPICH 3.1.4)
* [svn-r29182] Re-commit of HDFFV-8740 fix, which adds the ability to configureDana Robinson2016-02-221-0/+2
| | | | | | | | | | | | external dataset storage path behavior. This check-in fixes a bug in the original check-in where the external path stored in the file struct was not copied on reopen causing subsequent dataset operations to fail. Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 autotools serial w/ fortran and C++ autotools parallel (MPICH 3.1.4) w/ fortran
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