Merge pull request ESMCI#1731 from NCAR/ejh_openmpi

Add C testing with openmpi-4.0.4, netcdf-c-4.7.4, pnetcdf-1.12.1

.github/workflows/a3.yml

@@ -0,0 +1,135 @@
+name: netcdf-4.7.4_pnetcdf-12.1_ncint
+
+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:$PATH"
+        export CC=/home/runner/openmpi/bin/mpicc
+        wget https://parallel-netcdf.github.io/Release/pnetcdf-1.12.1.tar.gz  &> /dev/null
+        tar -xzf pnetcdf-1.12.1.tar.gz
+        pushd pnetcdf-1.12.1
+        ./configure --prefix=/home/runner/pnetcdf --enable-shared --disable-cxx
+        make
+        sudo make install
+        popd
+    - name: autoreconf
+      run: autoreconf -i
+    - name: pio build
+      run: |
+        set -x
+        echo 'export PATH=/home/runner/openmpi/bin:$PATH' > .bashrc
+        echo $'alias mpiexec=\'mpiexec --oversubscribe\'' >> .bashrc
+        cat .bashrc
+        source .bashrc
+        export PATH="/home/runner/openmpi/bin:$PATH"
+        export CC=/home/runner/openmpi/bin/mpicc
+        ./configure --with-mpiexec='mpiexec --oversubscribe'
+        which mpiexec
+        make check
+        
+        

.github/workflows/autotools.yml

@@ -21,6 +21,12 @@ jobs:
     - 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

.github/workflows/cmake.yml

@@ -22,6 +22,12 @@ jobs:
     - 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

.github/workflows/cmake_ncint.yml

@@ -22,6 +22,12 @@ jobs:
     - 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

.github/workflows/strict_autotools.yml

@@ -21,6 +21,12 @@ jobs:
     - 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

CMakeLists.txt

@@ -442,3 +442,12 @@ configure_file (
   "${PROJECT_SOURCE_DIR}/cmake_config.h.in"
   "${PROJECT_BINARY_DIR}/config.h"
   )
+
+# Configure test scripts.
+set(MPIEXEC mpiexec)
+configure_file(
+  ${CMAKE_CURRENT_SOURCE_DIR}/tests/cunit/run_tests.sh.in
+  ${CMAKE_CURRENT_BINARY_DIR}/tests/cunit/run_tests.sh @ONLY)
+configure_file(
+  ${CMAKE_CURRENT_SOURCE_DIR}/examples/c/run_tests.sh.in
+  ${CMAKE_CURRENT_BINARY_DIR}/examples/c/run_tests.sh @ONLY)

configure.ac

@@ -202,6 +202,15 @@ if test "x$enable_developer_docs" = xyes; then
 fi
 AM_CONDITIONAL(BUILD_DOCS, [test "x$enable_docs" = xyes])
 
+# Did the user specify an MPI launcher other than mpiexec?
+AC_MSG_CHECKING([whether a user specified program to run mpi programs])
+AC_ARG_WITH([mpiexec],
+              [AS_HELP_STRING([--with-mpiexec=<command>],
+                              [Specify command to launch MPI parallel tests.])],
+            [MPIEXEC=$with_mpiexec], [MPIEXEC=mpiexec])
+AC_MSG_RESULT([$MPIEXEC])
+AC_SUBST([MPIEXEC], [$MPIEXEC])
+
 # Is doxygen installed?
 AC_CHECK_PROGS([DOXYGEN], [doxygen])
 if test -z "$DOXYGEN" -a "x$enable_docs" = xyes; then
@@ -390,6 +399,10 @@ AM_CONDITIONAL(NETCDF_INTEGRATION, [test "x$enable_netcdf_integration" = xyes])
 
 AC_CONFIG_FILES([tests/general/pio_tutil.F90:tests/general/util/pio_tutil.F90])
 
+# The user may have changed the MPIEXEC for these test scripts.
+AC_CONFIG_FILES([tests/cunit/run_tests.sh], [chmod ugo+x tests/cunit/run_tests.sh])
+AC_CONFIG_FILES([examples/c/run_tests.sh], [chmod ugo+x examples/c/run_tests.sh])
+
 # Args:
 # 1. netcdf_meta.h variable
 # 2. conditional variable that is yes or no.

examples/c/Makefile.am

@@ -16,7 +16,9 @@ TESTS = run_tests.sh
 endif # RUN_TESTS
 
 # Distribute the test script.
-EXTRA_DIST = run_tests.sh CMakeLists.txt example2.c
+EXTRA_DIST = run_tests.sh.in CMakeLists.txt example2.c
 
 # Clean up files produced during testing.
 CLEANFILES = *.nc *.log *.clog2 *.slog2
+
+DISTCLEANFILES = run_tests.sh

examples/c/run_tests.sh → examples/c/run_tests.sh.in

@@ -19,7 +19,7 @@ for EXAMPLE in $PIO_EXAMPLES
 do
     success1=false
     echo "running ${EXAMPLE}"
-    mpiexec -n 4 ./${EXAMPLE} && success1=true
+    @MPIEXEC@ -n 4 ./${EXAMPLE} && success1=true
     if test $success1 = false; then
         break
     fi
@@ -29,7 +29,7 @@ for EXAMPLE in $PIO_EXAMPLES_16
 do
     success2=false
     echo "running ${EXAMPLE}"
-    mpiexec -n 16 ./${EXAMPLE} && success2=true
+    @MPIEXEC@ -n 16 ./${EXAMPLE} && success2=true
     if test $success2 = false; then
         break
     fi

tests/cunit/Makefile.am

@@ -69,7 +69,9 @@ test_async_1d_SOURCES = test_async_1d.c pio_tests.h
 test_simple_SOURCES = test_simple.c test_common.c pio_tests.h
 
 # Distribute the test script.
-EXTRA_DIST = run_tests.sh CMakeLists.txt test_darray_frame.c
+EXTRA_DIST = run_tests.sh.in CMakeLists.txt test_darray_frame.c
 
 # Clean up files produced during testing.
 CLEANFILES = *.nc *.log decomp*.txt *.clog2 *.slog2
+
+DISTCLEANFILES = run_tests.sh

tests/cunit/run_tests.sh → tests/cunit/run_tests.sh.in

@@ -26,7 +26,7 @@ for TEST in $PIO_TESTS
 do
     success1=false
     echo "running ${TEST}"
-    mpiexec -n 4 ./${TEST} && success1=true
+    @MPIEXEC@ -n 4 ./${TEST} && success1=true
     if test $success1 = false; then
         break
     fi
@@ -38,7 +38,7 @@ for TEST in $PIO_TESTS_8
 do
     success2=false
     echo "running ${TEST}"
-    mpiexec -n 8 ./${TEST} && success2=true
+    @MPIEXEC@ -n 8 ./${TEST} && success2=true
     if test $success2 = false; then
         break
     fi