The compiler was not found during case.build even it was set in config_machines.xml

[Aaron-Hsieh-0129]

Hello,

I'm trying to run default E3SM case (same configuration as run_e3sm.template.sh) using an unsupported machine.
When I was running the building program, it showed the errors like this.

cat /work/aaron900129/E3SMv3/E3SM_test/build/mct.bldlog.251031-172335
/work/aaron900129/E3SM/externals/mct/configure CC= FC= MPICC= MPIFC= FCFLAGS='  -I/work/aaron900129/E3SMv3/E3SM_test/build/nvhpc/openmpi/nodebug/threads/include' CPPDEFS='' CFLAGS=' -I/work/aaron900129/E3SMv3/E3SM_test/build/nvhpc/openmpi/nodebug/threads/include' LDFLAGS=''  NETCDF_PATH=/work/aaron900129/netcdf-c_install  --srcdir /work/aaron900129/E3SM/externals/mct
checking for cc... cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether cc accepts -g... yes
checking for cc option to enable C11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking whether byte ordering is bigendian... no
checking for nagfor... no
checking for xlf95... no
checking for pgf95... pgf95
checking whether the compiler supports GNU Fortran... no
checking whether pgf95 accepts -g... yes
checking for Fortran flag to compile .F90 files... none
checking for mpif90... mpif90
checking for MPI_Init... yes
checking for mpif.h... yes
Checking Compiler Version
checking how to get the version output from pgf95... -V
checking for Fortran flag to compile preprocessed .F files... none
checking how to define symbols for preprocessed Fortran... -D
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking how to get verbose linking output from pgf95... -v
checking for Fortran libraries of pgf95...  -L/work/aaron900129/netcdf-cxx_install/lib -L/work/aaron900129/pnetcdf_install/lib -L/work/aaron900129/netcdf-c_install/lib -L/work/aaron900129/hdf5_install/lib -L/work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/comm_libs/openmpi/openmpi-3.1.5/lib -L/work/aaron900129/cuda/lib64 -L/work/aaron900129/zstd_install/lib64 -L/work/aaron900129/zfp_install//lib64 -L/work/aaron900129/sz_install/lib64 -L/work/aaron900129/amgx_install/lib -L/work/aaron900129/adios2_install/lib64 -L/work/aaron900129/kokkos_install/lib64 -L/work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/math_libs/lib64 -L/work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/compilers/lib -L/work/aaron900129/nvhpc_24_9/Linux_x86_64/24.9/cuda/12.6/lib64 -L/work/aaron900129/local/lib -L/work/aaron900129/gcc9/lib -L/work/aaron900129/gcc9/lib64 -L/usr/lib64 -L/usr/lib/gcc/x86_64-redhat-linux/8/ -L/usr/lib/gcc/x86_64-redhat-linux/8//../../../../lib64 -lnvf -lnvomp -ldl -lnvhpcatm -latomic -lpthread -lnvcpumath -lnsnvc -lnvc -lrt -lm
checking for dummy main to link with Fortran libraries... unknown
configure: error: in `/work/aaron900129/E3SMv3/E3SM_test/build/nvhpc/openmpi/nodebug/threads/mct':
configure: error: linking to Fortran libraries from C fails
See `config.log' for more details
ERROR: configure: error: in `/work/aaron900129/E3SMv3/E3SM_test/build/nvhpc/openmpi/nodebug/threads/mct':
configure: error: linking to Fortran libraries from C fails
See `config.log' for more details%

It seems that the program didn't find my compilers (mpicc, mpic++, mpif90) even I set it inside the <E3SM>/cime_config/config_machines.xml.

If I run the command by specifying the compiler, it works successfully.
(/work/aaron900129/E3SM/externals/mct/configure CC=mpicc FC=mpif90 MPICC=mpicc MPIFC=mpif90 FCFLAGS=' -I/work/aaron900129/E3SMv3/E3SM_test/build/nvhpc/openmpi/nodebug/threads/include' CPPDEFS='' CFLAGS=' -I/work/aaron900129/E3SMv3/E3SM_test/build/nvhpc/openmpi/nodebug/threads/include' LDFLAGS='' NETCDF_PATH=/work/aaron900129/netcdf-c_install --srcdir /work/aaron900129/E3SM/externals/mct)

---

Here shows how I set the machines.

I added the machine information in <E3SM>/cime_config/config_machines.xml like this

<machine MACH="twnia2">
    <DESC>Taiwan2</DESC>
    <NODENAME_REGEX>gp2d</NODENAME_REGEX>
    <OS>LINUX</OS>
    <COMPILERS>nvhpc</COMPILERS>
    <MPILIBS>openmpi</MPILIBS>
    <PROJECT>MST114049</PROJECT>
    <SAVE_TIMING_DIR>/work/aaron900129/E3SM_output/</SAVE_TIMING_DIR>
    <SAVE_TIMING_DIR_PROJECTS>.*</SAVE_TIMING_DIR_PROJECTS>
    <CIME_OUTPUT_ROOT>/work/aaron900129/E3SM_output/scratch</CIME_OUTPUT_ROOT>
    <DIN_LOC_ROOT>/work/aaron900129/E3SM_input/inputdata</DIN_LOC_ROOT>
    <DIN_LOC_ROOT_CLMFORC>/work/aaron900129/E3SM_input/inputdata/atm/datm7</DIN_LOC_ROOT_CLMFORC>
    <DOUT_S_ROOT>/work/aaron900129/E3SM_output/scratch/archive/$CASE</DOUT_S_ROOT>
    <BASELINE_ROOT>/work/aaron900129/baselines/$COMPILER</BASELINE_ROOT>
    <CCSM_CPRNC>/work/aaron900129/tools/cprnc/cprnc</CCSM_CPRNC>
    <GMAKE_J>8</GMAKE_J>
    <TESTS>e3sm_integration</TESTS>
    <NTEST_PARALLEL_JOBS>4</NTEST_PARALLEL_JOBS>
    <BATCH_SYSTEM>slurm</BATCH_SYSTEM>
    <SUPPORTED_BY>E3SM</SUPPORTED_BY>
    <MAX_TASKS_PER_NODE>48</MAX_TASKS_PER_NODE>
    <MAX_MPITASKS_PER_NODE>48</MAX_MPITASKS_PER_NODE>
    <PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED>
    
    <mpirun mpilib="default">
      <executable>mpirun</executable>
      <arguments>
        <arg name="num_tasks">-n {{ total_tasks }} -std e3sm.log.$LID </arg>
      </arguments>
    </mpirun>

    <module_system type="none" />

    <RUNDIR>$CIME_OUTPUT_ROOT/$CASE/run</RUNDIR>
    <EXEROOT>$CIME_OUTPUT_ROOT/$CASE/bld</EXEROOT>
    <TEST_TPUT_TOLERANCE>0.1</TEST_TPUT_TOLERANCE>
    <MAX_GB_OLD_TEST_DATA>1000</MAX_GB_OLD_TEST_DATA>

    <environment_variables>
      <env name="PERL5LIB">/work/aaron900129/miniconda3/lib/perl5</env>
      <env name="CC">mpicc</env>
      <env name="CXX">mpic++</env>
      <env name="FC">mpif90</env>
    </environment_variables>
    <environment_variables compiler="nvhpc">
      <env name="NETCDF_C_PATH">/work/aaron900129/netcdf-c_install</env>
      <env name="NETCDF_FORTRAN_PATH">/work/aaron900129/netcdf-fortran_install</env>
      <env name="PNETCDF_PATH">/work/aaron900129/pnetcdf_install</env>
      <env name="PNETCDF_PATH">/work/aaron900129/pnetcdf_install</env>
      <env name="CC">mpicc</env>
      <env name="CXX">mpic++</env>
      <env name="FC">mpif90</env>

      <env name="PATH">$ENV{PATH}</env>
      <env name="LD_LIBRARY_PATH">$ENV{LD_LIBRARY_PATH}</env>
      <env name="LIBRARY_PATH">$ENV{LIBRARY_PATH}</env>
      <env name="C_INCLUDE_PATH">$ENV{C_INCLUDE_PATH}</env>
      <env name="ADD_SLIBS">$ENV{LIBRARY_PATH}</env>
      <env name="FFLAGS">$ENV{C_INCLUDE_PATH}</env>
      <env name="CMAKE_POLICY_VERSION_MINIMUM">3.5</env>

      <env name="OMP_STACKSIZE">128M</env>
      <env name="OMP_PROC_BIND">spread</env>
      <env name="OMP_PLACES">threads</env>
    </environment_variables>
  </machine>

I also added a cmake file (<E3SM>/cime_config/Depends.twnia2.nvhpc.cmake) to ensure the compilers were set successfully.

set(CC "mpicc")
set(CXX "mpic++")
set(FC "mpif90")
set(MPICC "mpicc")
set(MPICXX "mpic++")
set(MPIFC "mpif90")

Could anyone teach me how to set the environment correctly? Any suggestion is much appreciated, thanks a lot!