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Squashed 'src/externals/pio2/' changes from 602f71c..76c40a785
76c40a785 Merge pull request #1975 from jedwards4b/remove_protex a17a15327 remove unused protex markups f52ade075 Merge pull request #1974 from jedwards4b/fix_scalar_write_issue 3661a58bd derecho test script update 155be2fc9 update version 8b04e206f fix test for netcdf4 40bb45168 more github 1026fbd97 github tests again f01d36812 github tests again ab6c84b29 github tests again f1abc92cd github tests again d616e352a github tests again 3e6a435ad github tests again 20f1bcf94 github tests again 803298715 github tests again 24a9e1338 work on github tests e8d1be883 add derecho_testsuite.py 0ddbc2b8c fix scalar write issue, fix serial build issue 6d52a8c7d Merge pull request #1973 from jedwards4b/update/2.6.1 d9b6920e4 Merge branch 'main' into update/2.6.1 96a7d73d1 Merge pull request #1968 from jedwards4b/add_rpath 3d3a2f5dd Merge branch 'add_rpath' of github.com:jedwards4b/ParallelIO into add_rpath 3a4bfe06a resolve merge conflict ec1aef2c1 Merge branch 'main' into add_rpath 93b464bce update version 05e428451 Merge pull request #1972 from jedwards4b/bugfix/lustre 71b1fd248 try workflow again f377cab5c more workflow 10d4c3c67 fix for intel workflow 5b4717826 fix for intel workflow a42946660 add this back with a twist aa504dc8d add tmate for debugging workflows 513dbc8d0 fix ifort 1b68ba751 more cleanup 0bafcb4aa remove unused variables b4cb1ac34 update versions for github testing 3cf6ef570 clean up warnings 103a90991 more fixes for netcdf serial c45c4406a some fixes for netcdf serial bld 2cbf4bd0d potential fix for issue in branch bugtest/lustre 25b471d58 code changes to demo lustre performance bug ff7a19f21 add rpath variables to cmake build f45ba898b Merge pull request #1963 from jedwards4b/pio2.6.0rc1 a644bb61e update version d858d79d5 Merge pull request #1953 from jedwards4b/netcdf_integration_v5 4ac2b0e07 confusion about spack version 4fe8d187e confusion about spack version 020bfa712 skip test timeout pio_rearr_opts 2bd2c5d00 @develop should be @=develop (new change in spack)" ac3b0595b fix spack? 5e7a91e26 fix action b5244a576 spelling error 52e31e60a smarter about building parallelio 4003a79ea try this e0befe62b add tmate to debug eaffcf10f fix have_par_filters e437a94e7 fix some tests 95d9cf5c4 try this bc9534cb3 still trying bb08a8ff9 Merge branch 'main' into netcdf_integration_v5 cd8d7dbe9 remove unused arg 11c179e38 change test for par filters 11fc9d0a3 fix ifdef in fortran 38b8fef66 remove unused variable f240e34ef wrap filter_info 53462645c more cleanup 7390ec03d update autotools 77b579907 more cleanup f49d8ffbc reduce compiler warnings 3732b7c2b add test 3a0b1cd94 commit to move to gust 744bf5c3e Merge pull request #1962 from NCAR/jedwards4b-patch-1 c11ae47e9 Update README.md 44ab3d79b add pre-commit hook 30c3018a7 reorder to fix syntax error cdb55c733 prepare for pio 2.6.0 a5cbb28a6 add these and go to hackathon branch ad613dc55 add szip a16ca795f WIP 6af9cc985 cmake builds again 86101f2de add test for nc_inq_filter_avail 7119ddac7 more macro fixes 2247b3e65 more macro fixes fc8015f95 fix macros aede8723c fix testing again c0b49af55 add filter and quantize to fortran interface 02268a9fc add filter and quantize functionality 21cb6675d fix intel netcdf-c build f48a38b93 add back netcdf build 8c95ae17a try this 19e071bbe work on testing workflow 40ae6f019 update actions 152a0cf62 update actions cfc271e7c update actions 3b47163a6 update actions 6f88afa3b make it backward compatible 18eca188e fix the test 83176df55 add test, expected to fail 11a68cbd5 more fixes 6cf3810fe more fixes bd4517351 skip this test 6bb3a9b02 skip the check 93d82ad5e try again 3ffdd8124 more debugging 68b9a646b more debugging ab4ee59f5 try this 977ef90bf more fortran fixes dae38cdef more fortran fixes 3030489ea more fortran fixes cf92770d1 more fortran fixes dbc46c3f2 more fortran fixes ff513fbef fix fortran warnings 99fb47ac2 make it backward compatible abe19445a fix fortran warnings 6c8aad764 fix fortran warnings 54c3b8fab fix fortran warnings d0b8e5ebe fix fortran warnings 03079e75f fix fortran warnings 060fee736 make it backward compatible 09c5ded0a resolve merge conflicts d69dbe0ac passing all tests with NC_DISPATCH_VERSION=5 753464d2e fix declarations 77055f9e1 commit to try on cheyenne 7bce0e534 only run ncint tests for netcdf4 in netcdf4.9.0 and older 1747a4758 adding new filter functions 52649df69 determined test failure due to mpt/2.25 bug 781978d99 support versions 2-5 620f6741b Merge branch 'netcdf_integration_v5' of github.com:jedwards4b/ParallelIO into netcdf_integration_v5 3fd1b3e4e fix parens c404de8dd Merge branch 'main' into netcdf_integration_v5 2275ad951 stuck in testing 05173a655 Merge pull request #1952 from jedwards4b/master_to_main d3f134936 replace master with main 2446bf96c Merge pull request #1951 from jedwards4b/external_actions_squash 4fc7cd3d4 with -> enable e3e3ca7b8 fix type in workflow 4bdd79ca8 fix cache 1288017de squash commit of external_actions fd1bdf842 Merge pull request #1949 from jedwards4b/pio2.5.10-candidate 21a0f7015 update version patch to 10 126beaeee Merge pull request #1944 from billsacks/fix_default_mode 64666d199 Merge branch 'master' into fix_default_mode 6fcb613a2 Merge pull request #1946 from jedwards4b/update_github_tests c73a4d63c remove redundant test 490565b4f once more 2f95d78aa fix ldflags d1138cb57 try ldflags 79df169fe try fflags instead 20a223277 add -static-libasan 830f226bf remove memory violating comment b7745d637 update address sanitizer runs 74203a41b oops wrong hdf5 version 53c6eec31 more github action tuning acc462641 more github mods 87e0e9432 netcdf integration currently only works with netcdf-c 4.7.4 6f5d6b340 need both FFLAGS and FCFLAGS? 647e68cdd try this 9a9db159b try this 877f691c7 try this 5a4d06c11 more github action fixes 0eac1ebb9 try run-name here 8abc70dc7 fix yaml formatting issues a2a7a1132 change FCFLAGS to FFLAGS ce5faf9cb try removing name and adding run_name 0e91b5e4d remove name use run_name dee848ba1 update checkout and cache actions 9a63af64f update run-name 2fafb1581 update software versions 95553d71f update github tests to use -fallow-argument-mismatch bbfe1b221 Fix default value of mode for PIO_openfile df1c069fa Merge pull request #1941 from ACCESS-NRI/pkg-config 48baa2b29 backup search of NetCDF using PkgConfig 157e559ff Merge pull request #1937 from jedwards4b/cmake_version_revert eef316fb2 make work with cmake 3.5.2 (esmf requirement) a61c76304 Merge pull request #1936 from jedwards4b/version_update a342a931d update version tags 6ab657ab5 Merge pull request #1935 from jedwards4b/update/spack_experiences df5ced6e8 shared lib as default leads to problems linking gptl 586fd2509 add CMAKE_POSITION_INDEPENDENT_CODE 9fd941936 Merge branch 'master' into update/spack_experiences f43b5a8d8 Merge pull request #1928 from kgerheiser/patch-1 e96aa094a change malloc to calloc for tmparray 66478b875 updates based on experiences with spack package f18736b64 Merge branch 'master' into patch-1 07d5d1658 Merge pull request #1932 from jedwards4b/updateto258 0767c56bf Merge branch 'master' into updateto258 741f01b06 Merge pull request #1929 from jedwards4b/readonly_init_decomp 42463401c update pio version to 2.5.8 fe8526389 turn off doxygen build in test 2e9e8d659 Merge branch 'readonly_init_decomp' of github.com:jedwards4b/ParallelIO into readonly_init_decomp 3e832ff92 turn off doxygen warnings 02fa28809 remove halo in test b033009c9 remove halo in test 8315a9583 revert netcdf version 992d5970d add debug flags 793c83be6 try again d292334f9 try again 98b30a053 looking for mem leak 5bd5cfb0e initialize exp_val 295b5da30 testing memleak issue a25ef8105 more doxygen 4f206ecac update docs a9dc65d65 try this 1dd48891d cleanup fortran interface 216faa114 fix format bf342d0bb Merge branch 'master' into readonly_init_decomp 72d31a229 add new file to autoconf build da18105e6 add the pioc_async.c file 11df9a2ff Merge branch 'readonly_init_decomp' of github.com:jedwards4b/ParallelIO into readonly_init_decomp adb084450 add a test for initdecomp_readonly 0eb7ad638 copy back from ESMF develop cd9dae11a Add BUILD_SHARED_LIBS option c3c042e32 Merge pull request #1926 from climbfuji/feature/update_license_to_apache2 23153d5ba Replace COPYRIGHT file with LICENSE file in Makefile.am db104184d Remove old COPYRIGHT file f09ce7d09 Create LICENSE c5d622612 Merge remote-tracking branch 'mydev/startlist_err_fix' into readonly_init_decomp 9215ad2f7 remove debug print statement 10c08240e better fix de3bc6ff5 debugging workflow eeaa57f4b debugging workflow 6ce4184cf debugging workflow 5de7f424c debugging workflow f97ef84d1 fix an error in computing startlist and countlist for pnetcdf e3d835e1e an attempt to reduce memory consumption and improve performance d13e39116 Merge pull request #1924 from jedwards4b/move_to_heap 233c141bd move this allocation to the heap 6954d2f6f Merge pull request #1923 from jedwards4b/version_257 8986c3174 update version to 2.5.7 ec0878108 Merge pull request #1922 from jedwards4b/change_cmake_minimum 959dcfc6a closer to requred cmake minimum a91d94c12 Merge pull request #1921 from jedwards4b/parallel_sort 8e1220f16 undo debug change a95b5b602 fix conflicting types c0e367b20 fix conflicting types ff14c8f26 cleanup and debug 6cb1b45ca remove check for size of MPI_Offset 5bc2d18bd debug github workflow 92ad82b5a debug github workflow aae9abfd0 remove debug print 41ee148f1 cleanup cd2e3ff37 add a comment 6f36ec155 fix run_unique_check dedf05a53 only check readonly on compute tasks 8ea3ec589 add parallel_sort to autoconf build 83f1d1482 Merge branch 'master' into parallel_sort ef4bebd9d consider this change, not yet working 5cd4f369a Merge pull request #1920 from jedwards4b/update_cmake_minimum f12a7c603 fix compmaster test 2ae945860 fix compmaster test 7edc061ba fix communicator 38f85db2d need to check readonly for subset c913401f8 only add fortran dependencie if fortran build enabled 9141ce508 clean up testing 628a60805 update minimum cmake version, based on the oldest I can access a95907685 Merge pull request #1916 from jedwards4b/remove_MPI_Offset_redef f6faded05 remove the redefinition of MPI_Offset and MPI_OFFSET 0dbdf3b43 Merge pull request #1915 from jedwards4b/update_version_2.5.6 949c4acde update version to 2.5.6 f49656d57 Merge pull request #1911 from jedwards4b/subset_rearr_fix fbd8a0a54 a little cleanup 2f106a310 fix in esmf mesh read 907954dea improvement 36d85f710 fix for subset rearranger bug in 2.5.5 fa73d277e Merge pull request #1906 from jedwards4b/fix_netcdf_src_path_for_workflow e136d362c fix it again ebc8c9009 revert configure, test github caches - all workflows passing 2ca91d809 add hdf5 version and dependancy 98bb52f88 more github action fb8172f29 fix cache 1f242695b fix libpath maybe 8cf23ae93 backout 4.8.1 use 4.7.4 ada3d061b more netcdf download 87a2a1105 get netcdf from github not unidata site a755d3a38 get netcdf from github not unidata site ffaeefe93 update NC_DISPATCH_VERSION c75831cea fix line return issue 63e54ed05 all netcdf downloads now updated 255657ced add oversubscribe 3bb48a798 cut and paste b67943796 cut and paste 758e18665 reformat with yamllint d0978d431 reformat with yamllint 924b80d3f reformat with yamllint 4f1fe5f62 reformat with yamllint 936bc928f reformat with yamllint e6837b890 reformat with yamllint 1c2236b8f reformat with yamllint a03b0bfba try again a9ad7893b try again 9a26ba14a try again 4a65c35c6 update netcdf download path e352fd214 Merge pull request #1902 from jedwards4b/64bitdata 5e6aa9037 #define PIO_64BIT_DATA NC_64BIT_DATA requires netcdf 4.4.0 or newer f50f03872 Merge pull request #1899 from jedwards4b/add_write_nc_decomp_support_fortran 776de3e5c move these to a seperate repo b70ffd283 add the decomps using lfs 9737b204d add decomp files using git lfs d3a8ec8da Merge branch 'master' into add_write_nc_decomp_support_fortran bb253aba2 add pio_finalize call a4ed64c14 Merge pull request #1896 from jedwards4b/pio_buffer_size_limit_rename d8da2d2b3 Merge branch 'master' into pio_buffer_size_limit_rename 97ea899d7 Merge pull request #1897 from jedwards4b/fortran_deletefile_returncode 9576b8533 fix documentation 79b24b3c7 make fortran_order logical 469cfcba6 add fortran interface to nc dof read and write routines, add a translate program 8b45af91d begin add fortran support for this 58c45f968 document new parameter 10b733273 fortran pio_deletefile return code, optional for backward compatiblity 51524e5d7 rename pio_buffer_size_limit to pio_pnetcdf_buffer_size_limit c1307bf21 Merge pull request #1887 from NCAR/ejh_version 1175c39c9 Merge branch 'master' into ejh_version 0fb64ab47 Merge pull request #1891 from jedwards4b/refactor_subset_method 765557a91 Merge branch 'master' into refactor_subset_method 856fb305e remove cperf from tests 226dbe93f debug cleanup badc1c033 changes for serial build dbb3e5440 document new routines acc35223b document new variable da1cb8ce5 Merge pull request #1886 from jedwards4b/address_sanitize_patch ad2819e59 undo whitespace changes 1e50df7e0 undo whitespace changes d304db9b7 undo whitespace changes f249286e4 undo whitespace changes f95d648b4 cleaning up b48c44e62 Merge branch 'master' into address_sanitize_patch e99ffcb1c working for SUBSET rearranger b8bfef8e9 continued development of piodecomptest 0f3214a35 an attempt to refactor the subset rearrange method a1526a296 Merge branch 'master' into ejh_version 877986194 Merge pull request #1883 from jedwards4b/pio_byte_to_mpi_signed_char c6d90dd8f changed version to 2.5.5 870649ba5 fix bug in pioc_read_nc_decomp_int 0e3762da5 remove tabs from file 1e21296cc fix an issue exposed by address sanitiser 699c65187 remove travis test documentation 35a5339a8 remove travis test ecf94f315 update tests adding pnetcdf for BYTE and CHAR 982e77468 pio_byte type should be mpi_signed_char and not mpi_byte 468c06a59 Merge pull request #1881 from jedwards4b/cmake_fortran_cleanup 6d518a071 Merge branch 'master' into cmake_fortran_cleanup e4087a375 only do cmake fortran if building fortran interface 6ffa5d1b1 Merge pull request #1879 from jedwards4b/cray_compiler_fix 297c5d096 fix inconsistancy in intent 4dafb796e Merge pull request #1876 from NCAR/ejh_ranlib 4586f2cf8 fixed overflow in test e85dc3785 Merge pull request #1875 from NCAR/ejh_fix_dist 2c67ab15a add exampleAsyncPio.F90 to the autotools build fc1a67924 Merge pull request #1871 from kgerheiser/bugfix/macos-common-symbols 7e2e00a6c Merge branch 'master' into bugfix/macos-common-symbols 77a1ea044 Pass -c to ranlib to include common symbols on macOS 6d4bb2879 Merge pull request #1870 from NCAR/ejh_fix_dox_version b05b483c1 fixed version 0dc7d8ff8 Merge pull request #1869 from NCAR/ejh_release a2bd6367a updating versions 357ca506c Merge pull request #1864 from jedwards4b/check_netcdf_errfix 9a4e836ca try this 59ad3368c cmake still failing add debug code 0638adedf set WITH_MPIEXEC --oversubscribe 35c04b6fa set WITH_MPIEXEC --oversubscribe a06dfa2de add oversubscribe option 73716f7e4 try --oversubscribe d44762937 revert change to strict autotools workflow c9a944862 Merge branch 'check_netcdf_errfix' of github.com:jedwards4b/ParallelIO into check_netcdf_errfix 4fe2cd24f merge master for workflow fixes 550160bca Merge branch 'master' into check_netcdf_errfix 813e7c159 Merge pull request #1860 from NCAR/ejh_2 264242b58 refreshing caches d86865dee refreshing caches faebeea33 refreshing caches 6ea34b9e4 refreshing caches 03ff8f545 remove enabled-shared pnetcdf option 8d44884f3 try fix for pnetcdf fac7ee7dd fix error in check_netcdf call and in detecting dap 612014640 Merge branch 'master' into ejh_2 0ec340c76 Merge pull request #1859 from NCAR/ejh_versions c67d8c279 resetting caches 1b901c0db triggering CI 2bab8b463 one more try 7accbbad3 updated version numbers for release of 2.5.3 53497cafb Merge pull request #1857 from jedwards4b/pnetcdf_support_cmake 6f0b9bf16 fix indicator for pnetcdf support in cmake c77a30d95 Merge pull request #1855 from jedwards4b/create_logfile_only_if_loglevel 983bd8e66 only create log files if log level > 0 989e026f5 Merge pull request #1854 from jedwards4b/redef_from_def_test 7df2e2afe remove this test, no longer valid 360a360ac Merge pull request #1852 from NCAR/ejh_readme af9b0733a commented out test_async_1d ca842d15a commented out test_async_1d 66132141f updating readme 5206ff4c5 updating readme c6fd1755c updating readme 47f466fd1 updating readme 8b2f798a4 Merge pull request #1851 from NCAR/ejh_cmake 4ea3f9362 turning on netcdf integration in cmake build 304b7296e Merge pull request #1850 from NCAR/ejh_next_1 2123df499 turned test code back on 40d9637c2 Merge pull request #1849 from NCAR/ejh_next 582d6f7b6 turned test code back off 0a41fbf89 turned test code back off d7eb8207b turned test code back on 41ac8bc7f turned test code back on 2f90688c7 turned test code back on 9f6b1b5c9 fixed type size in async code 16b469d00 turning test code back on 268c69929 Merge pull request #1848 from NCAR/ejh_preprocessor 558f24000 cleanup of automake and pre-processor symbols e8a87005b removed pre-processor symbol USE_NETCDF4 77a31b1bc Merge pull request #1844 from NCAR/ejh_no_pnetcdf_build 818eead20 commented out part of tst_async_multi 7b0b78b16 commented out part of tst_async_multi 41ea01e99 commented out part of tst_pio_async 388681f92 commented out part of test_async_1d 34f6b99db fixed no-pnetcdf workflow, renamed ubuntu latest workflow 463e37d4e adding new workflow dddf14773 Merge pull request #1843 from NCAR/ejh_warn c95152b6e fixed warnings and netcdf-integration build without pnetcdf 2d0c61c2e Merge pull request #1840 from NCAR/ejh_cmake_again_3 444c30dc4 fixing cmake workflow b43e67e44 fixing cmake workflow 42366fb63 Merge pull request #1836 from NCAR/ejh_cmake_again dcaba92f8 changed test timeout in cmake 19570c281 fixed code warning, removed print statements from test f632317cd make configure search for netcdf-fortran if --enable-fortran and --enable-netcdf-integration are used 57446873a debug test 9b5964267 add fortran build c6912419b fix paths 3705bbdf2 adding fortran f65e972e4 adding fortran d914a8353 adding cmake build 9accccb00 Merge pull request #1835 from NCAR/ejh_cmake_fortran_workflow 27d20a3be try a different cmake? ee9fe1b61 giving up on cmake build for now ebfb0e503 adding another cmake build 8fd204e80 adding another cmake build 219d72fb9 adding another cmake build ed0304884 turned off fortran in cmake build b56162ef1 fixed fortran test 5c34c279f turning on fortran build in cmake workflow ee329568b Merge pull request #1833 from NCAR/ejh_ncint_test_2 85f50f29d more testing da6015c2c Merge pull request #1831 from NCAR/ejh_ncint_test 11959c931 fixing ncint test for 4.7.4 by commenting out code 8dbde41a0 fixed comment ccbb2302f fix test_darray_multivar3.c 7172df901 turning on netcdf integration in workflow e53623410 Merge pull request #1826 from NCAR/ejh_test_more 1eb5a219d working on workflows 40ce8ea26 switching to pnetcdf-1.12.2 593e85371 adding testing 0f0558ffe adding testing 0f3502fa0 adding testing 862538461 Merge pull request #1823 from NCAR/ejh_more_tests 71a695cba working on asan build 70066f238 working on asan build b5801cd8b working on asan build 8fd651963 working on asan build a679c5bd5 adding testing with hdf5-1.10.7 3308d5e93 renamed workflow files to reduce confusion f34ef23a9 merged master 0887324d4 fixed warnings, trying to get asan workflow to build 6947e3114 Merge branch 'master' into ejh_more_tests d862880a7 added asan testing e341609e3 Merge pull request #1821 from NCAR/ejh_test_on 1464bf0a4 Merge branch 'master' into ejh_test_on ef34338ae fixed test_darray_multivar3.c 2d6de331b fixed test_darray_multivar3.c 1ef9493f0 Merge pull request #1820 from NCAR/ejh_default_blocksize 9e492a483 changed default blocksize 36eba03fa Merge pull request #1817 from NCAR/ejh_docs c7b3010cc documentation improvements 082fc0f32 documentation improvements cacb65e7b documentation improvements 9548daac5 fixed warnings in code 4200f55a1 Merge pull request #1809 from NCAR/ejh_perf_more ce23930d6 now setting chunksizes for netcdf4 performance runs f59373773 whitespace cleanup 6f7a1dcdf fixed mpe problem in test_simple.c 9a669de89 modification to perf program output 9abd0ca71 Merge pull request #1806 from NCAR/ejh_perf 329ef8f2d cleanup 9f912f859 merged master be3b13f22 fixes to test_perf2.c 84511247c Merge pull request #1805 from NCAR/ejh_fix_test 5df3c5dc6 whitespace cleanup 118e44a76 better async error handling in tests 57c03b9c3 whitespace cleanup 379983a92 more fixes for async test error handling 9bdf340a2 more work on async error handling 25d5bf4f0 more work on async error handling 3b550c794 more work on async error handling f83540176 more work on async error handling bb6adea7f fixed comment b44d3237c better handling for test failure in async tests 40da636a3 added AERR() macro for errors on async tests d8ec81a98 fixed comment 9cec790f1 fixed whitespace issues in pio_error.h d14471895 fix printing of some incorrect error codes in cunit tests 9dad4e97a Merge pull request #1802 from jedwards4b/avoid_msg_starving e6fc3e00b clean up test 90f497c14 change waitany to waitsome to avoid message starving 53bdadcbf Merge pull request #1800 from NCAR/ejh_docs_2 dd1b8d038 updated documentation and cleaned unneeded preprocessor symbols from test_perf2 and test_async_perf 5d0f8a5b0 Merge pull request #1799 from NCAR/ejh_t1 eec9e0b50 stop running test_async_perf with other CMakeList.txt tests c254d12f0 turned off logging in test e86c55cb6 try reducing the size of this test 358e71917 document new error code b51b8324c move large allocate from stack 4f01bc28b fix test 570abae1e add error for rearranger mismatch in async mode 564a15116 fix async_perf test 860f6f99f Merge branch 'more_async_tests' of github.com:jedwards4b/ParallelIO into more_async_tests a8493e337 add test_async_perf to cmake build 66564a550 Merge branch 'master' into more_async_tests 5852d9093 Merge pull request #1765 from t-brown/master 40da5e29c add SUBSET rearranger d741f3700 Merge branch 'master' into master 1a3fa8630 Merge pull request #1794 from NCAR/ejh_fix_perf 2184073b0 Merge branch 'master' into master 2a2a08dad turned off subset rearrarger in test_async_perf b51f6768c more improvements to performance programs 6a29e16eb merged master f0a9c0ad1 fixing test_async_perf 5ca0b5586 Merge pull request #1791 from jedwards4b/async_subset 6b08ffb66 now test both rearrangers in tst_perf2 d956b7904 added commas to output 7e385d133 fix test bbe58daf7 add tests c8f91fbca subset working in async 744b73163 Merge pull request #1790 from jedwards4b/add_nf_pio bbb9ed716 remove need for netcdf or pnetcdf fortran libs 53d652ed8 add netcdf fortran build 5d1ca6791 add nf_pio, netcdf now defines cdf5 format 8a0cb4f84 Merge pull request #1786 from jedwards4b/sort_only_on_compute 3d49f3008 array sort should only happen on compute tasks 7f28489f5 Merge pull request #1784 from jedwards4b/add_async_get_att_test 4b79b0203 add new function to include file 15921d6ff fix documentation biff d937cc331 add global_set_log_level, fix issue 5cd85396f add async test for get_att - test currently timesout 38d9acda5 Merge pull request #1782 from jedwards4b/async_fixes ffe4098c1 move malloc to correct location e05d8f2b0 remove unneeded change 7806081b4 changes for async interface 7e242f78b Merge pull request #1781 from jedwards4b/with_pnetcdf_cmake 6c4d85875 use WITH_PNETCDF in CMake build f960b3799 Merge branch 'master' into master 1d0dabdf3 Merge pull request #1778 from jedwards4b/add_pio_init_async_from_comms 1de5ded13 Merge branch 'add_pio_init_async_from_comms' of github.com:jedwards4b/ParallelIO into add_pio_init_async_from_comms 7a52d1d9d try this 875966b5b fix mem issue 60f9f17f3 fix documentation f63773317 remove .f90.in from gitignore file, add tests cf09cd22d remove unused var 7f28e28cf fix Makefile.am 8af4d74d9 try again 2d3cb219a fix test generation issue 4a012a898 add test to autoconf 155c11dee fix line length issue 01e9e31dd add async test from fortran bcc711331 remove set_log_level from test 8f10a32a2 remove debug print ea404f6b3 add PIOc_init_async_from_comms and test 53c5a2c23 Merge pull request #1776 from jedwards4b/update_f_examples 0f5da9dc3 Merge branch 'master' into update_f_examples a8acfd49d more doc cleanup cad018af7 more documentation and refinment 4fd48cfce add some documentation 9e999911c correct ranks in async 0f65ecc0d cleanup a27009b57 working example from fortran 81c778517 Merge pull request #1774 from jedwards4b/unique_name_err_buffer e079cb408 make example resultlen distinct names from that in pio_error.h c30ff49c5 make example err_buffers distinct names from that in pio_error.h e26c200c2 work on async interface 092a618ee begin work on fortran async interface 66449308c Merge branch 'master' into master 7309b9b60 Merge pull request #1772 from jedwards4b/more_fortran_interface c59a6d644 remove bad assumption 0a565e497 more fortran interface changes 2d4202846 remove debug print c9e5d01aa fix nfget 74afc2a9a cleanup c7813144d fix test var io from fortran 1caa8c15c add pio_fill 134c5209d Merge pull request #1771 from jedwards4b/fortran_interface_updates c91eb59c0 back out setting of fillvalue in pio_darray f3b63c9cc untabify 01830e4eb fix whitespace 5ae954910 try again 94ff81b6a undo last change and see if travisci will pass 91520c20c read_darray sets fillvalue 736c0745c add target attribute 7bd521922 more minor changes 0ba4b787d implement pio_inq_var_fill in fortran, add tests e7d621b0b Merge pull request #1769 from jedwards4b/cdash_test_fixes 3eac73356 undo unessasary change 3d8956df3 fix pgi version and openmpi test error fed328b7c Merge pull request #1767 from jedwards4b/update_cheyenne_tests e47b8f108 update cheyenne modules for ctest 364a445bf Adding an autoconf check for C99. c90a7a287 Merge pull request #1761 from jedwards4b/remove_pio_use_malloc 3e432479a untabify c files b7b9b52e1 untabify pio_darray.c 9fc01568a Merge branch 'master' into remove_pio_use_malloc b241756e7 Merge pull request #1763 from jedwards4b/fix_int_overflow 1c9dd2823 fix integer overflow issue noted in nag compiler 9d3470f5e fix doc generation error 34809b99a fully remove pio_use_malloc macro b9855cdb5 Merge pull request #1759 from jedwards4b/add_flib_set_fill 78d28a329 add set_fill to fortran interface 6f9fb5e Merge pull request #1754 from NCAR/ejh_release 9efeee4 changed version numbers and so library numbers fd8b8c1 Merge pull request #1753 from NCAR/ejh_no_compress 00104f8 no longer turn on deflate for vars automatically d0d4a98 Merge pull request #1752 from NCAR/ejh_bget d048ed5 working on cmake test build cbf9b17 working on cmake test build 4c54550 merged 14672d4 working on cmake test build a98bf4a Merge branch 'master' into ejh_bget 14ba346 Merge pull request #1751 from NCAR/ejh_docs 668bdd3 more bget fixes c992327 added cmake to test build bad9cee removed bget 2f3ed11 removed bget d23ae96 more fortran doc work d751d49 improving fortran docs e97f239 improving fortran docs 3a77973 Merge pull request #1747 from NCAR/ejh_ncint_deflate 73eaa0c added endianness f97e666 now testind def_var_endian 9c88c0e now properly getting chunksizes thru ncint c298e79 developing test 09dc756 added deflate to the test 5853389 modifying tst_var_compress f11724c added tst_var_compress.c 39b0940 merged master 64cdf4b Merge pull request #1746 from NCAR/ejh_mpi_check 286f529 removed cmake build from github testing c2492f1 dealing with der_var_endian and def_var_chunking in netcdf integration layer 245a212 adding PIO_NCINT_def_var_deflate b25c930 added check for MPI c569627 Merge pull request #1743 from NCAR/ejh_more_tests_2 261d8b6 increased time-out c6c6138 added cmake build to a4.yml adbb0d8 removed flags from fortran cmake build 63662f5 Merge pull request #1742 from NCAR/ejh_flags 666731d removed unused VARN pre-processor defines 3ce5db5 Merge pull request #1741 from NCAR/ejh_more_testing_2 81de16e adding Fortran to build summary 6ec562a MPIEXEC in examples/f03 directory, also set FC in fortran build e835926 turning on fortran build in github CI, also fixing mpiexec in tests/performance a5fb922 handle mpiexec for fncint and general dirs 9e4a39e trying to get gcc version 3c02032 Merge pull request #1738 from NCAR/ejh_more_testing eb23c9f fixing order of chunksizes 15a191b fixing order of chunksizes e37d19a fixed chunksizes type size error in F90 api 13cb7c7 fixed shell script with new test name f1e58bd renamed test 5ff9844 fixed docs 5c2ae65 adding pio_inq_var_chunking 6675467 more test development f114fbc further test development a54de42 further test development cbed988 further test development cdc01a1 turn of netcdf integration in github workflow 05ce8e3 added ftst_vars.F90 to CMake build 9d3ff03 added ftst_vars.F90 to CMake build e9f4f75 starting to add ftst_vars.F90 2987785 turning on ncint f6feb76 Merge pull request #1737 from NCAR/ejh_flags_next 5f8e9fa more testing in new workflow 71eace1 more testing in new workflow c2919cb more testing in new workflow 87e38c5 more testing in new workflow dd0400c more testing in new workflow 1733a7a adding mpich workflow a31c6f8 adding mpich workflow 138f4f1 adding mpich workflow d677d07 adding mpich workflow 28429a5 fixing MPIEXEC in library summary for CMake builds 22d1160 Merge pull request #1735 from NCAR/ejh_cmake f130a86 adding fields to build summary f835a8d removing unneeded logging pre-processor macro from CMake build 9d8c81a clean up 1b788c9 more fixing for flib and clib, now fixing _PNETCDF e6960d9 more fixing for flib and clib 1bb4b57 now fixing for flib 510e955 fixing CMake determination of _NETCDF4 843f6d9 commented out more unneeded flag setting in cmake adf6308 commented out more unneeded flag setting in cmake 6d767b2 commented out more unneeded flag setting in cmake d37b976 taking away flag from CMake build 54ee841 Merge pull request #1734 from NCAR/ejh_doc_fix 35742c6 now ncint tests repect WITH_MPIEXEC 151affd now ncint tests repect WITH_MPIEXEC 181373a fixing docs, cleanup of test workflow e715d07 Merge pull request #1733 from NCAR/ejh_openmpi_2 7b874db clean up 7ddbfe7 trying to deal with MPIEXEC in CMake 41b1588 trying to deal with MPIEXEC in CMake 280c4b9 trying to deal with MPIEXEC in CMake b501e62 trying to deal with MPIEXEC in CMake 7bcf9f3 trying to deal with MPIEXEC in CMake f5906b1 trying to deal with MPIEXEC in CMake 672259c trying to deal with MPIEXEC in CMake 4815763 trying to deal with MPIEXEC in CMake ba379cc trying to deal with MPIEXEC in CMake 2138bd3 trying to deal with MPIEXEC in CMake b2820c2 trying to deal with MPIEXEC in CMake e802925 trying to deal with MPIEXEC in CMake b1fabee trying to deal with MPIEXEC in CMake 4174cf9 trying to deal with MPIEXEC in CMake 7422324 trying to deal with MPIEXEC in CMake deed510 trying to deal with MPIEXEC in CMake d561d64 trying to deal with MPIEXEC in CMake c0466f9 more work on cmake build 6eb1b7a more cmake build 1ac66e0 more cmake build 51791cb more cmake build fc04c72 more cmake build afb423b more cmake build ddb380f more cmake build 9e654d8 more cmake build 4c1ca9e more cmake build feada9c more cmake build f2bbbbf more cmake build e23ce03 more cmake build 1013818 more cmake build 081b863 more cmake build 36b7c7b more cmake build f38d8ae more cmake build c16d88a more cmake build 7f547ee starting to add cmake build of C library 00e667f Merge pull request #1731 from NCAR/ejh_openmpi 0f2db9d converting more tests to use new --with-mpiexec option c7fc47a converting more tests to use new --with-mpiexec option dc8275d converting more tests to use new --with-mpiexec option 2af2aeb adding tests/cunit/run_tests.sh.in db613c3 adding tests/cunit/run_tests.sh.in e4fb33c adding --with-mpiexec option to configure 2d908a1 adding --with-mpiexec option to configure d76dd49 trying to get openmpi mpiexec working 3822956 trying to get openmpi mpiexec working 558a3b9 trying to get openmpi mpiexec working ba2b719 trying to get openmpi mpiexec working 493353a trying to get openmpi mpiexec working dcb5e08 trying to get openmpi mpiexec working a96671f trying to get openmpi mpiexec working f283a80 trying to get openmpi mpiexec working 0903e62 trying to get openmpi mpiexec working 5a96af8 trying to get openmpi mpiexec working 2d9bf6b adding PIO b35ee21 adding PIO 2bf634f adding PIO cc1dc81 adding PIO 8b243ca adding PIO 3681f56 adding PIO 0c5dbbd adding PIO 1120342 adding PIO 8984b26 adding PIO 7a5c3f3 adding PIO 8f86595 adding PIO 4d1a709 adding PIO 61ef8de adding netcdf-fortran and pnetcdf 6d2b2a9 adding netcdf-fortran and pnetcdf 35dda9d adding netcdf-fortran and pnetcdf 49ab2d7 adding netcdf-c 1199dd3 adding HDF5 1c5ab76 adding HDF5 ae45f2b adding HDF5 ab77827 adding HDF5 dc6eb09 adding HDF5 2b766e2 fixing apt-get for curl 5d9b54b building openmpi 0697d04 building openmpi 0043527 Merge pull request #1725 from NCAR/ejh_next_9 41b62fb fixed warning, turned of -Werror for fortran to try and get github workflow building c76f148 fixed warning, turned of -Werror for fortran to try and get github workflow building 32640e6 fixed warning, turned of -Werror for fortran to try and get github workflow building 3b63878 fixed warning, turned of -Werror for fortran to try and get github workflow building fb4052a turning on -Wall for strict autotools build aa9f62c turning on -Wall for strict autotools build 1085b95 Merge branch 'master' into ejh_next_9 23c5c50 Merge pull request #1726 from jedwards4b/reduce_search_netcdf 43f1315 remove more redundant find_package calls 6526724 add space cc11af9 no netcdf fortran in this test 8b97bd5 remove debug print statements 57f939f only search for netcdf at top level fe2fb7a removed extra workflow for now 5acda4b error out of cmake if netcdf-c dispatch table wont work for netcdf integration 52367bd trying to add another workflow a043a91 trying to add another workflow 9be18ae took comments out of workflow file b26239d adding netCDF interation to build summary and pio_meta.h f1a83f3 Merge pull request #1715 from NCAR/ejh_ncint e57c5aa properly dealing with ncint_mod.F90 in cmake build 78dd092 clean up 15527bf cleaned up cmake_config.h.in a604f76 added new github workflow for netCDF integration with cmake 08c7999 now all ncint tests work 444f023 more work on ncint in cmake build 6bd5fa4 moved cmake build of ncint into src/clib dir, now test works! 9f57a5c ncint build working! eaa0656 now building ncint directory with cmake cab47c3 merged changes from master a59a55b Merge pull request #1722 from NCAR/ejh_next_7 a1a04ef moved .f90 to .F90 089a7ec turning off logging in a test 5b7f801 more fortran flag cleanup 5f190e8 more fortran flag cleanup 7067c63 cleanup of flags in test/unit autotools build 4d6e4f8 more flag cleanup a91eed9 more flag cleanup db93ea5 more changes so that all fortran files use config.h 0a10f86 adding some cmakedefines 6213867 cleanup of flag use in src/flib 4f80a53 Merge pull request #1720 from NCAR/ejh_next_6 0b2bebe removed unneeded pre-processor symbol from cmake_config.h.in 9b942c5 Merge pull request #1719 from NCAR/ejh_next_5 b258478 removed troublesome strnlen() function 85edfb8 removed more unneeded pre-processor stuff 1ac844f removed more unneeded pre-processor stuff 8a82dea removed more unneeded pre-processor stuff 8a8ba30 more removal of unneeded pre-processor symbols 4754ab5 removed unneeded check of _NETCDF ad4eddb removed NETCDF flag c99eb28 Merge pull request #1718 from NCAR/ejh_next_3 4430bcd changed build summary 2676343 clean up travis file 7153ec9 removed constant 084f1c1 Merge pull request #1716 from NCAR/ejh_next 90d9af6 removed config constant that is unused anywhere... f269769 fixed setting of configure define in cmake b38aaef starting to add ncint code to cmake build a28ec8c fixing cmake use of defines c5794a8 trying to fix cmake build 768c0c4 merged master a9ed7f1 Merge pull request #1714 from NCAR/ejh_fix_cmake_2 b985532 fixed creation of config.h on read-only filesystem 52ac327 adding support for NETCDF_INTEGRATION option to cmake, also fixing cmake build issue in read-only directories 116cd6e Merge pull request #1710 from NCAR/ejh_cmake_fix 0300688 including HAVE_PAR_FILTERS in cmake config.h eed7d48 Merge pull request #1707 from NCAR/ejh_cache_2 c0aa71a now trying caching for cmake build fc96bb3 now trying caching for cmake build 6d93e73 now trying caching for cmake build 359bc44 now trying caching for cmake build 9b46b90 now trying caching for cmake build e307f96 now trying caching for strict pnetcdf build ab5f234 now trying caching for pnetcdf build 7e40029 now trying caching for pnetcdf build e11337c now install pnetcdf in subdirectory 2376632 Merge pull request #1705 from NCAR/ejh_fix_makefile 658b209 fixed makefile 9d4dbb7 Merge pull request #1700 from NCAR/ejh_4_7_2 ce1828a took out caching attempt 09a7b2c added comment bb3fc14 cmake determination of par filters presence 5e51323 attempting to cache pnetcdf build in workflow 3482946 changed fortran test to ignore deflate tests on NETCDF4P iotype f591b8c now use HAVE_PAR_FILTERS in test_pioc.c 8a298dc now check for netcdf-c disptach version in autoconf and cmake f66d558 fixed detection of 4.7.2 in autoconf to work for old netcdf releases that don't have netcdf_meta.h 042ea81 added nc-config output to travis 3f45048 added nc-config output to travis e049af4 added nc-config output to travis 8ac93fe added nc-config output to travis 783ff4d added nc-config output to travis 4ed861e added nc-config output to travis e0eb090 disallow netcdf-c-4.7.2 for both cmake and autotools builds a14b65b Merge pull request #1698 from NCAR/ejh_test_simple ee339d0 fixed cmake running on 4 procs 62d09ee called MPI_Finalize() in test_simple.c 8f40a3a cleaned up simple test 39d4c79 merged master eedc46c Merge pull request #1696 from NCAR/ejh_fix_test_leak 4438bf5 turns out we need fortran for pnetcdf 28fcb48 turn off cxx and fortran for pnetcdf build 56243cf turn off netcdf-integration in travis testing 88cf3d1 turn on netcdf-integration in travis testing abef381 fixed memory leaks in tests 64a117c Merge pull request #1690 from NCAR/ejh_docs_2 e663bf3 removing redundant build 05ad86b turning on fortran build for autotools 90a1a20 turning on fortran build for autotools 0876585 turning on fortran build for autotools dd9d7dd trying doc build a different way 0cdc421 trying doc build a different way 0e6e349 trying doc build a different way 282e338 now can turn on deflate with netcdf-4 parallel e7cdd55 got working for current state of play 3d4b09e now reading and checking data aee02f3 getting test_simple working a430197 getting test_simple working 09965b8 added unlimited dim, also creating decomp 137db07 now creating dim and var in test_simple 0c15892 starting to fill in test_simple 56ea154 developing simple test 958d9b9 added test_simple.c git-subtree-dir: src/externals/pio2 git-subtree-split: 76c40a7855c99403bfd9e3dee9062c7fe58b4391
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