Squashed 'src/externals/pio2/' changes from 602f71c..134c5209d

134c5209d Merge pull request ESMCI#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 ESMCI#1769 from jedwards4b/cdash_test_fixes 3eac73356 undo unessasary change 3d8956df3 fix pgi version and openmpi test error fed328b7c Merge pull request ESMCI#1767 from jedwards4b/update_cheyenne_tests e47b8f108 update cheyenne modules for ctest c90a7a287 Merge pull request ESMCI#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 ESMCI#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 ESMCI#1759 from jedwards4b/add_flib_set_fill 78d28a329 add set_fill to fortran interface 6f9fb5e Merge pull request ESMCI#1754 from NCAR/ejh_release 9efeee4 changed version numbers and so library numbers fd8b8c1 Merge pull request ESMCI#1753 from NCAR/ejh_no_compress 00104f8 no longer turn on deflate for vars automatically d0d4a98 Merge pull request ESMCI#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 ESMCI#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 ESMCI#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 ESMCI#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 ESMCI#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 ESMCI#1742 from NCAR/ejh_flags 666731d removed unused VARN pre-processor defines 3ce5db5 Merge pull request ESMCI#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 ESMCI#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 ESMCI#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 ESMCI#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 ESMCI#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 ESMCI#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 ESMCI#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 ESMCI#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 ESMCI#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 ESMCI#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 ESMCI#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 ESMCI#1720 from NCAR/ejh_next_6 0b2bebe removed unneeded pre-processor symbol from cmake_config.h.in 9b942c5 Merge pull request ESMCI#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 ESMCI#1718 from NCAR/ejh_next_3 4430bcd changed build summary 2676343 clean up travis file 7153ec9 removed constant 084f1c1 Merge pull request ESMCI#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 ESMCI#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 ESMCI#1710 from NCAR/ejh_cmake_fix 0300688 including HAVE_PAR_FILTERS in cmake config.h eed7d48 Merge pull request ESMCI#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 ESMCI#1705 from NCAR/ejh_fix_makefile 658b209 fixed makefile 9d4dbb7 Merge pull request ESMCI#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 ESMCI#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 ESMCI#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 ESMCI#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: 134c5209d8dd1b304dac16246ff794f255fbebb0
jedwards4b · Nov 4, 2020 · 25e5a1f · 25e5a1f
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diff --git a/.github/workflows/a3.yml b/.github/workflows/a3.yml
@@ -0,0 +1,147 @@
+name: netcdf-4.7.4_pnetcdf-12.1_ncint_openmpi_4.0.4
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    env:
+      CPPFLAGS: "-I/home/runner/openmpi/include -I/home/runner/hdf5/include -I/home/runner/netcdf-c/include -I/home/runner/netcdf-fortran/include -I/home/runner/pnetcdf/include"
+      LDFLAGS: "-L/home/runner/openmpi/lib -L/home/runner/hdf5/lib -L/home/runner/netcdf-c/lib -L/home/runner/netcdf-fortran/lib -L/home/runner/pnetcdf/lib"
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Installs
+      run: |
+        sudo apt-get install doxygen graphviz wget gfortran libjpeg-dev libz-dev
+    - name: cache-openmpi
+      id: cache-openmpi
+      uses: actions/cache@v2
+      with:
+        path: ~/openmpi
+        key: openmpi-${{ runner.os }}-4.0.4
+
+    - name: build-openmpi
+      if: steps.cache-openmpi.outputs.cache-hit != 'true'
+      run: |
+        wget https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.4.tar.gz &> /dev/null
+        tar -xzf openmpi-4.0.4.tar.gz
+        pushd openmpi-4.0.4
+        ./configure --prefix=/home/runner/openmpi
+        make
+        sudo make install
+        popd
+    - name: cache-hdf5
+      id: cache-hdf5
+      uses: actions/cache@v2
+      with:
+        path: ~/hdf5
+        key: hdf5-${{ runner.os }}-1.10.6-openmpi-4.0.4
+
+    - name: build-hdf5
+      if: steps.cache-hdf5.outputs.cache-hit != 'true'
+      run: |
+        set -x
+        export PATH="/home/runner/openmpi/bin:$PATH"
+        export CC=/home/runner/openmpi/bin/mpicc
+        wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.6/src/hdf5-1.10.6.tar.gz &> /dev/null
+        tar -xzf hdf5-1.10.6.tar.gz
+        pushd hdf5-1.10.6
+        ./configure --prefix=/home/runner/hdf5 --enable-parallel --disable-tools --disable-fortran --disable-cxx --enable-parallel-tests
+        make
+        sudo make install
+        popd
+    - name: cache-netcdf-c
+      id: cache-netcdf-c
+      uses: actions/cache@v2
+      with:
+        path: ~/netcdf-c
+        key: netcdf-c-${{ runner.os }}-4.7.4-openmpi-4.0.4
+
+    - name: build-netcdf-c
+      if: steps.cache-netcdf-c.outputs.cache-hit != 'true'
+      run: |
+        set -x
+        export PATH="/home/runner/openmpi/bin:$PATH"
+        export CC=/home/runner/openmpi/bin/mpicc
+        wget https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-c-4.7.4.tar.gz &> /dev/null
+        tar -xzf netcdf-c-4.7.4.tar.gz
+        pushd netcdf-c-4.7.4
+        ./configure --prefix=/home/runner/netcdf-c --disable-dap --disable-utilities
+        make -j
+        sudo make install
+        popd
+    - name: cache-netcdf-fortran
+      id: cache-netcdf-fortran
+      uses: actions/cache@v2
+      with:
+        path: ~/netcdf-fortran
+        key: netcdf-fortran-${{ runner.os }}-4.5.3-openmpi-4.0.4
+
+    - name: build-netcdf-fortran
+      if: steps.cache-netcdf-fortran.outputs.cache-hit != 'true'
+      run: |
+        set -x
+        export PATH="/home/runner/openmpi/bin:$PATH"
+        export CC=/home/runner/openmpi/bin/mpicc
+        wget https://github.com/Unidata/netcdf-fortran/archive/v4.5.3.tar.gz &> /dev/null
+        tar -xzf v4.5.3.tar.gz
+        pushd netcdf-fortran-4.5.3
+        ./configure --prefix=/home/runner/netcdf-fortran
+        make -j
+        sudo make install
+        popd
+    - name: cache-pnetcdf
+      id: cache-pnetcdf
+      uses: actions/cache@v2
+      with:
+        path: ~/pnetcdf
+        key: pnetcdf-${{ runner.os }}-1.12.1-openmpi-4.0.4
+
+    - name: build-pnetcdf
+      if: steps.cache-pnetcdf.outputs.cache-hit != 'true'
+      run: |
+        set -x
+        export PATH="/home/runner/openmpi/bin:$PATH"
+        export CC=/home/runner/openmpi/bin/mpicc
+        wget https://parallel-netcdf.github.io/Release/pnetcdf-1.12.1.tar.gz  &> /dev/null
+        tar -xzf pnetcdf-1.12.1.tar.gz
+        pushd pnetcdf-1.12.1
+        ./configure --prefix=/home/runner/pnetcdf --enable-shared --disable-cxx
+        make
+        sudo make install
+        popd
+    - name: autotools build
+      run: |
+        set -x
+        echo 'export PATH=/home/runner/openmpi/bin:$PATH' > .bashrc
+        source .bashrc
+        export PATH="/home/runner/openmpi/bin:$PATH"
+        export CC=/home/runner/openmpi/bin/mpicc
+        autoreconf -i
+        ./configure --with-mpiexec='mpiexec --oversubscribe'
+        cat config.h
+        make check
+    - name: cmake build
+      run: |
+        set -x
+        echo 'export PATH=/home/runner/openmpi/bin:$PATH' > .bashrc
+        source .bashrc
+        export CC=mpicc
+        mkdir build
+        cd build
+        export LD_LIBRARY_PATH="/home/runner/netcdf-c/lib:/home/runner/pnetcdf/lib:/home/runner/hdf5/lib:/home/runner/openmpi/lib:$LD_LIBRARY_PATH"
+        cmake -Wno-dev -DWITH_MPIEXEC='/home/runner/openmpi/bin/mpiexec;--oversubscribe' -DNetCDF_C_LIBRARY=/home/runner/netcdf-c/lib/libnetcdf.so -DNetCDF_C_INCLUDE_DIR=/home/runner/netcdf-c/include -DPnetCDF_PATH='/home/runner/pnetcdf' -DPIO_ENABLE_FORTRAN=Off -DPIO_HDF5_LOGGING=On -DPIO_USE_MALLOC=On -DPIO_ENABLE_LOGGING=On -DPIO_ENABLE_TIMING=Off .. || (cat CMakeFiles/CMakeOutput.log && cat CMakeFiles/CMakeError.log)
+        cat config.h
+        make VERBOSE=1
+        make tests VERBOSE=1
+        ctest -VV
+
+        
+        
diff --git a/.github/workflows/a4.yml b/.github/workflows/a4.yml
@@ -0,0 +1,147 @@
+name: netcdf-4.7.4_pnetcdf-12.1_ncint_mpich-3.3
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    env:
+      CPPFLAGS: "-I/home/runner/mpich/include -I/home/runner/hdf5/include -I/home/runner/netcdf-c/include -I/home/runner/netcdf-fortran/include -I/home/runner/pnetcdf/include"
+      LDFLAGS: "-L/home/runner/mpich/lib -L/home/runner/hdf5/lib -L/home/runner/netcdf-c/lib -L/home/runner/netcdf-fortran/lib -L/home/runner/pnetcdf/lib"
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Installs
+      run: |
+        sudo apt-get install doxygen graphviz wget gfortran libjpeg-dev libz-dev
+    - name: cache-mpich
+      id: cache-mpich
+      uses: actions/cache@v2
+      with:
+        path: ~/mpich
+        key: mpich-${{ runner.os }}-3.3.2
+
+    - name: build-mpich
+      if: steps.cache-mpich.outputs.cache-hit != 'true'
+      run: |
+        wget http://www.mpich.org/static/downloads/3.3.2/mpich-3.3.2.tar.gz &> /dev/null
+        tar -xzf mpich-3.3.2.tar.gz
+        pushd mpich-3.3.2
+        ./configure --prefix=/home/runner/mpich
+        make
+        sudo make install
+        popd
+    - name: cache-hdf5
+      id: cache-hdf5
+      uses: actions/cache@v2
+      with:
+        path: ~/hdf5
+        key: hdf5-${{ runner.os }}-1.10.6-mpich-3.3.2
+
+    - name: build-hdf5
+      if: steps.cache-hdf5.outputs.cache-hit != 'true'
+      run: |
+        set -x
+        export PATH="/home/runner/mpich/bin:$PATH"
+        export CC=/home/runner/mpich/bin/mpicc
+        wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.6/src/hdf5-1.10.6.tar.gz &> /dev/null
+        tar -xzf hdf5-1.10.6.tar.gz
+        pushd hdf5-1.10.6
+        ./configure --prefix=/home/runner/hdf5 --enable-parallel --disable-tools --disable-fortran --disable-cxx --enable-parallel-tests
+        make
+        sudo make install
+        popd
+    - name: cache-netcdf-c
+      id: cache-netcdf-c
+      uses: actions/cache@v2
+      with:
+        path: ~/netcdf-c
+        key: netcdf-c-${{ runner.os }}-4.7.4-mpich-3.3.2
+
+    - name: build-netcdf-c
+      if: steps.cache-netcdf-c.outputs.cache-hit != 'true'
+      run: |
+        set -x
+        export PATH="/home/runner/mpich/bin:$PATH"
+        export CC=/home/runner/mpich/bin/mpicc
+        wget https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-c-4.7.4.tar.gz &> /dev/null
+        tar -xzf netcdf-c-4.7.4.tar.gz
+        pushd netcdf-c-4.7.4
+        ./configure --prefix=/home/runner/netcdf-c --disable-dap --disable-utilities
+        make -j
+        sudo make install
+        popd
+    - name: cache-netcdf-fortran
+      id: cache-netcdf-fortran
+      uses: actions/cache@v2
+      with:
+        path: ~/netcdf-fortran
+        key: netcdf-fortran-${{ runner.os }}-4.5.3-mpich-3.3.2
+
+    - name: build-netcdf-fortran
+      if: steps.cache-netcdf-fortran.outputs.cache-hit != 'true'
+      run: |
+        set -x
+        export PATH="/home/runner/mpich/bin:$PATH"
+        export CC=/home/runner/mpich/bin/mpicc
+        wget https://github.com/Unidata/netcdf-fortran/archive/v4.5.3.tar.gz &> /dev/null
+        tar -xzf v4.5.3.tar.gz
+        pushd netcdf-fortran-4.5.3
+        ./configure --prefix=/home/runner/netcdf-fortran
+        make -j
+        sudo make install
+        popd
+    - name: cache-pnetcdf
+      id: cache-pnetcdf
+      uses: actions/cache@v2
+      with:
+        path: ~/pnetcdf
+        key: pnetcdf-${{ runner.os }}-1.12.1-mpich-3.3.2
+
+    - name: build-pnetcdf
+      if: steps.cache-pnetcdf.outputs.cache-hit != 'true'
+      run: |
+        set -x
+        export PATH="/home/runner/mpich/bin:$PATH"
+        export CC=/home/runner/mpich/bin/mpicc
+        wget https://parallel-netcdf.github.io/Release/pnetcdf-1.12.1.tar.gz  &> /dev/null
+        tar -xzf pnetcdf-1.12.1.tar.gz
+        pushd pnetcdf-1.12.1
+        ./configure --prefix=/home/runner/pnetcdf --enable-shared --disable-cxx
+        make
+        sudo make install
+        popd
+    - name: cmake build
+      run: |
+        set -x
+        gcc --version
+        echo 'export PATH=/home/runner/mpich/bin:$PATH' > .bashrc
+        source .bashrc
+        export CC=/home/runner/mpich/bin/mpicc
+        export FC=/home/runner/mpich/bin/mpifort
+        export LD_LIBRARY_PATH="/home/runner/netcdf-c/lib:/home/runner/mpich/lib:/home/runner/hdf5/lib:/home/runner/netcdf-fortran/lib:/home/runner/pnetcdf/lib:$LD_LIBRARY_PATH"
+        mkdir build
+        cd build
+        cmake -Wno-dev -DNetCDF_C_LIBRARY=/home/runner/netcdf-c/lib/libnetcdf.so -DNetCDF_C_INCLUDE_DIR=/home/runner/netcdf-c/include -DPnetCDF_PATH='/home/runner/pnetcdf' -DPIO_ENABLE_FORTRAN=Off -DPIO_ENABLE_LOGGING=On -DPIO_ENABLE_TIMING=Off .. || (cat CMakeFiles/CMakeOutput.log && cat CMakeFiles/CMakeError.log)
+        make VERBOSE=1
+        make tests VERBOSE=1
+#        ctest -VV
+    - name: autotools build
+      run: |
+        set -x
+        gcc --version
+        echo 'export PATH=/home/runner/mpich/bin:$PATH' > .bashrc
+        source .bashrc
+        export CC=/home/runner/mpich/bin/mpicc
+        export FC=/home/runner/mpich/bin/mpifort
+        autoreconf -i
+        ./configure --enable-fortran
+        make -j check
+        
+        
diff --git a/.github/workflows/autotools.yml b/.github/workflows/autotools.yml
@@ -1,4 +1,4 @@
-name: autotools
+name: autotools_ubuntu_latest
 
 on:
   push:
@@ -14,31 +14,42 @@ jobs:
     env:
       CC: mpicc
       FC: mpifort
-      CPPFLAGS: "-I/usr/include -I/usr/local/include"
-#      CFLAGS: "-std=c99  -fsanitize=address -fno-omit-frame-pointer -Werror"
-#      FFLAGS: "-fsanitize=address -fno-omit-frame-pointer"
-#      FCFLAGS: "-fsanitize=address -fno-omit-frame-pointer -Werror"
+      CPPFLAGS: "-I/usr/include -I/usr/local/include -I/home/runner/pnetcdf/include"
+      LDFLAGS: "-L/home/runner/pnetcdf/lib"
 
     steps:
     - uses: actions/checkout@v2
     - name: Installs
       run: |
+        set -x
+        sudo gem install apt-spy2
+        sudo apt-spy2 check
+        sudo apt-spy2 fix --commit
+        # after selecting a specific mirror, we need to run 'apt-get update'
+        sudo apt-get update
         sudo apt-get install netcdf-bin libnetcdf-dev doxygen graphviz wget gfortran libjpeg-dev libz-dev openmpi-bin libopenmpi-dev 
+    - name: cache-pnetcdf
+      id: cache-pnetcdf
+      uses: actions/cache@v2
+      with:
+        path: ~/pnetcdf
+        key: pnetcdf-${{ runner.os }}-1.11.0
 
-    - name: pnetcdf build
+    - name: build-pnetcdf
+      if: steps.cache-pnetcdf.outputs.cache-hit != 'true'
       run: |
-        wget https://parallel-netcdf.github.io/Release/pnetcdf-1.11.0.tar.gz 
+        set -x
+        wget https://parallel-netcdf.github.io/Release/pnetcdf-1.11.0.tar.gz &> /dev/null
         tar -xzvf pnetcdf-1.11.0.tar.gz
-        ls -l
         pushd pnetcdf-1.11.0
-        ./configure --prefix=/usr --enable-shared
+        ./configure --prefix=/home/runner/pnetcdf --enable-shared --disable-cxx
         make
         sudo make install
         popd
 
     - name: autoreconf
       run: autoreconf -i
     - name: configure
-      run: ./configure
-    - name: make distcheck
-      run: make distcheck
+      run: ./configure --enable-fortran --enable-docs
+    - name: make check
+      run: make -j check