Merge pull request #4462 from ESMCI/update_docker

- Adds missing conda compiler packages
- Cleans up docker.cmake, removes redundant cmake variables found in gnu.cmake
- Fixes compiling/running cases with active components

Test suite: pytest
Test baseline: n/a
Test namelist changes: n/a
Test status: n/a

Fixes n/a
User interface changes?: N
Update gh-pages html (Y/N)?: N

docker/Dockerfile

@@ -44,14 +44,19 @@ RUN mamba install --yes -c conda-forge \
             rm -rf /opt/conda/pkgs/*
 
 # Install version locked packages
+# gcc, gxx, gfortran provide symlinks for x86_64-conda-linux-gnu-*
+# ar and ranlib are not symlinked
 RUN mamba install --yes -c conda-forge \
             libnetcdf=${LIBNETCDF_VERSION}=*openmpi* \
             netcdf-fortran=${NETCDF_FORTRAN_VERSION}=*openmpi* \
             esmf=${ESMF_VERSION}=*openmpi* \
             gcc_linux-64=${GCC_VERSION} \
             gxx_linux-64=${GCC_VERSION} \
             openmpi-mpifort \
-            gfortran_linux-64=${GCC_VERSION} && \
+            gfortran_linux-64=${GCC_VERSION} \
+            gcc \
+            gxx \
+            gfortran && \
             rm -rf /opt/conda/pkgs/* && \
             ln -sf /opt/conda/bin/x86_64-conda-linux-gnu-ar /opt/conda/bin/ar && \
             ln -sf /opt/conda/bin/x86_64-conda-linux-gnu-ranlib /opt/conda/bin/ranlib

docker/docker.cmake

@@ -1,71 +1,11 @@
-set(AR "/opt/conda/bin/x86_64-conda-linux-gnu-ar")
-string(APPEND CFLAGS " -mcmodel=medium")
-if (compile_threaded)
-  string(APPEND CFLAGS " -fopenmp")
-endif()
-if (DEBUG)
-  string(APPEND CFLAGS " -g -Wall -fbacktrace -fcheck=bounds -ffpe-trap=invalid,zero,overflow")
-endif()
-if (NOT DEBUG)
-  string(APPEND CFLAGS " -O")
-endif()
-if (COMP_NAME STREQUAL csm_share)
-  string(APPEND CFLAGS " -std=c99")
-endif()
 string(APPEND CXXFLAGS " -std=c++14")
-if (compile_threaded)
-  string(APPEND CXXFLAGS " -fopenmp")
-endif()
-if (DEBUG)
-  string(APPEND CXXFLAGS " -g -Wall -fbacktrace")
-endif()
-if (NOT DEBUG)
-  string(APPEND CXXFLAGS " -O")
-endif()
-if (COMP_NAME STREQUAL cism)
-  string(APPEND CMAKE_OPTS " -D CISM_GNU=ON")
-endif()
-string(APPEND CMAKE_OPTS " -D CMAKE_AR=/opt/conda/bin/x86_64-conda-linux-gnu-ar")
-string(APPEND CMAKE_OPTS " -DCMAKE_Fortran_COMPILER_RANLIB=/opt/conda/bin/x86_64-conda-linux-gnu-ranlib")
-string(APPEND CMAKE_OPTS " -DCMAKE_C_COMPILER_RANLIB=/opt/conda/bin/x86_64-conda-linux-gnu-ranlib")
-string(APPEND CMAKE_OPTS " -DCMAKE_CXX_COMPILER_RANLIB=/opt/conda/bin/x86_64-conda-linux-gnu-ranlib")
-string(APPEND CPPDEFS " -DFORTRANUNDERSCORE -DNO_R16 -DCPRGNU")
-if (DEBUG)
-  string(APPEND CPPDEFS " -DYAKL_DEBUG")
-endif()
-set(SLIBS "-L/opt/conda/lib -lnetcdf -lnetcdff")
-set(CXX_LIBS "-lstdc++")
-set(CXX_LINKER "FORTRAN")
-string(APPEND FC_AUTO_R8 " -fdefault-real-8")
-string(APPEND FFLAGS " -I/opt/conda/include -mcmodel=medium -fconvert=big-endian -ffree-line-length-none -ffixed-line-length-none")
-if (compile_threaded)
-  string(APPEND FFLAGS " -fopenmp")
-endif()
-if (DEBUG)
-  string(APPEND FFLAGS " -g -Wall -fbacktrace -fcheck=bounds -ffpe-trap=zero,overflow")
-endif()
-if (NOT DEBUG)
-  string(APPEND FFLAGS " -O")
-endif()
-string(APPEND FFLAGS_NOOPT " -O0")
-string(APPEND FIXEDFLAGS " -ffixed-form")
-string(APPEND FREEFLAGS " -ffree-form")
-set(HAS_F2008_CONTIGUOUS "FALSE")
-if (compile_threaded)
-  string(APPEND LDFLAGS " -fopenmp")
-endif()
-set(SLIBS " -L/opt/conda/lib -lnetcdff -lnetcdf")
+string(APPEND CXX_LIBS " -lstdc++")
+string(APPEND SLIBS " -L/opt/conda/lib -lnetcdf -lnetcdff")
+string(APPEND FFLAGS " -I/opt/conda/include")
 set(MPI_PATH "/opt/conda")
-set(MPICC "/opt/conda/bin/mpicc")
-set(MPICXX "/opt/conda/bin/mpicxx")
-set(MPIFC "/opt/conda/bin/mpif90")
 set(NETCDF_C_PATH "/opt/conda")
 set(NETCDF_FORTRAN_PATH "/opt/conda")
 set(PNETCDF_PATH "/opt/conda")
-set(SCC "/opt/conda/bin/x86_64-conda-linux-gnu-gcc")
-set(SCXX "/opt/conda/bin/x86_64-conda-linux-gnu-g++")
-set(SFC "/opt/conda/bin/x86_64-conda-linux-gnu-gfortran")
-set(SUPPORTS_CXX "TRUE")
 if (CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER_EQUAL 10)
   string(APPEND FFLAGS " -fallow-argument-mismatch  -fallow-invalid-boz ")
 endif()