merging changes from main

.github/workflows/ecosim-ci.yml

@@ -0,0 +1,77 @@
+name: EcoSIM CI
+
+on: [workflow_dispatch, push, pull_request]
+
+#env:
+  # Customizing build type
+  # BUILD_TYPE: DEBUG
+
+jobs:
+  build-ubuntu:
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - name: package-install
+      run: |
+        sudo apt-get -qq update
+        sudo apt -qq -y install gfortran cmake
+        sudo apt -qq -y install libcurl4 libcurl4-gnutls-dev curl 
+        sudo apt -qq -y install autoconf automake
+#        if/when system hdf5 is needed	
+#	 sudo apt -qq -y libhdf5-openmpi-dev
+
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+
+    - name: ecosim-build
+      shell: bash
+      run: |
+        echo "Building EcoSIM"
+        bash build_EcoSIM.sh CC=`which gcc` CXX=`which g++` FC=`which gfortran`
+#
+#       continue-on-error: true
+#
+#    - name: did-build-ubuntu-fail
+#      run: |
+#        cat build/Linux-x86_64-double-Debug/3rd-partylibs/netcdf_c_config*.log
+
+  build-rocky:
+    runs-on: ubuntu-latest
+
+    container:
+      image: rockylinux/rockylinux:8.10
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: package-install-rocky
+      run: |
+        cat /etc/os-release
+        dnf -qq -y update
+        dnf -qq -y install gcc-gfortran gcc-c++
+        dnf -qq -y install cmake
+        dnf -qq -y install which
+        dnf -qq -y install git
+        dnf -qq -y install curl curl-devel
+        dnf -qq -y install autoconf automake libtool libxml2-devel
+#        if/when system hdf5 is needed
+#        dnf install -y dnf-plugins-core
+#        dnf install -y epel-release
+#        dnf config-manager -y --set-enabled powertools
+#        dnf install -y hdf5 hdf5-devel hdf5-static
+
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+
+    - name: ecosim-build-rocky
+      shell: bash
+      run: |
+        echo "Building EcoSIM"
+        bash build_EcoSIM.sh CC=`which gcc` CXX=`which g++` FC=`which gfortran`
+
+#      continue-on-error: true
+#    - name: did-build-rocky-fail
+#      run: |
+#        cat build/Linux-x86_64-double-Debug/3rd-partylibs/netcdf_c_config*.log

CMakeLists.txt

@@ -212,12 +212,9 @@ if (ATS_ECOSIM)
     endif()
 
     set(ECOSIM_TPLS "${NETCDF_FLIBS} ${NETCDF_CLIBS} ${Z_LIBRARY} ${HDF5_LIBRARY} -lhdf5_hl -ldl -lz -lcurl -lhdf5 -lnetcdf -lnetcdff")
-
+    
 else()
     add_subdirectory(3rd-partylibs)
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ffpe-trap=invalid,zero,overflow,underflow")
-    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${NETCDF_CFLAGS} -ffpe-trap=invalid,zero,overflow,underflow")
-    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${NETCDF_FFLAGS} -ffpe-trap=invalid,zero,overflow,underflow")
 
     #string(REPLACE "-ffpe-trap=invalid" "" CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS}")
 endif()

README.md

@@ -8,23 +8,23 @@ git clone --recursive git@github.com:jinyun1tang/EcoSIM.git
 
 ## Building
 
-use the script to build the code:
+Use the script in the root directory to build the code:
 
 sh build_EcoSIM.sh
 
-you can also run as a bash script:
+or run it as a bash script:
 
 ./build_EcoSIM.sh
 
-This should build and link all the required tpls
+This should do everything including building and linking all the required tpls, and configuring, building and linking EcoSIM itself.
 
 The executable will be found in ./build/bin/ecosim.f90.x
 
-This has been tested with gcc on multiple systems, but not intel compilers
+This has been tested with gcc on multiple systems, but not intel compilers. See the .github/workflow/ecosim-ci.yml file for examples. You will need cmake to use the build_EcoSIM.sh script.  
 
-## additional options
+## Additional options
 
-Opening the build_EcoSIM.sh script there are some opttional parameters you can set:
+The build_EcoSIM.sh script lets you set some opttional parameters:
 
 debug=0
 mpi=0
@@ -46,7 +46,7 @@ You can also set options via the command line, for example:
 
 ./build_EcoSIM.sh CC=/path/to/cc CXX=/path/to/cxx FC=/path/to/fortran --debug --regression_test
 
-run
+Run
 
 ./build_EcoSIM.sh --help 
 

build_EcoSIM.sh

@@ -21,7 +21,7 @@ function status_message()
 
 ############# EDIT THESE! ##################
 
-debug=1
+debug=0
 mpi=0
 shared=0
 verbose=1
@@ -35,9 +35,9 @@ systype=""
 print_help() {
     echo "Usage: $0 [OPTIONS]"
     echo "Options:"
-    echo "  --CC=<compiler>        Set C compiler"
-    echo "  --CXX=<compiler>       Set C++ compiler"
-    echo "  --FC=<compiler>        Set Fortran compiler"
+    echo "  CC=<compiler>          Set C compiler"
+    echo "  CXX=<compiler>         Set C++ compiler"
+    echo "  FC=<compiler>          Set Fortran compiler"
     echo "  --regression_test      Enable regression test"
     echo "  --debug                Enable debug mode"
     echo "  --mpi                  Enable MPI"

cmake/Modules/set_up_compilers.cmake

@@ -14,12 +14,14 @@ macro(set_up_compilers)
     set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-int-to-pointer-cast -Wno-pointer-to-int-cast")
     set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-discarded-qualifiers")
     set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-sign-conversion -Wno-maybe-uninitialized")
+    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${NETCDF_CFLAGS} -ffpe-trap=invalid,zero,overflow,underflow")
 
     if (BUILD_SHARED_LIBS)
       set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
       set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC")
       set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -fPIC")
     endif()
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ffpe-trap=invalid,zero,overflow,underflow")
 
     if (LINUX EQUAL 1)
       # Counter some of GCC's more recent stinginess on Linux.
@@ -57,7 +59,7 @@ macro(set_up_compilers)
 
     endif()
     set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fdefault-real-8 -fdefault-double-8")
-    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -Wno-unused-variable -ffpe-trap=invalid")
+    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -Wno-unused-variable -ffpe-trap=invalid,zero,overflow,underflow")
     set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -Wno-unused-parameter -Wno-unused-function")
     set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -Wuninitialized -Wno-unused-dummy-argument")
     set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -ffree-line-length-none")