Porting error, CESM2.1.3

[11438023@zju_edu_cn]

Dear all,

I am trying to set up CESM2.1.3 on a new cluster.

Because I kept seeing the "NetCDF was not complied by the same version ..." error, I re-installed the NetCDF-c and Netcdf-fortran using the intel compiler.

However, I now see a new error that says: "/central/groups/carnegie_poc/leiduan_memex/CESM/my_cesm_sandbox/cime/src/externals/pio1/pio/pio_types.F90(13): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [NETCDF]"

Here is part of the error message:

[ 40%] Building Fortran object pio/CMakeFiles/pio.dir/pio_types.F90.o

cd /central/scratch/leiduan/test44/bld/intel/mpich/nodebug/nothreads/pio/pio1/pio && /central/software/Intel/2018.1/compilers_and_libraries_2018.1.163/linux/mpi/intel64/bin/mpiifort -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX -I/central/groups/carnegie_poc/leiduan_memex/CESM/my_cesm_sandbox/cime/src/externals/pio1/pio -I/central/scratch/leiduan/test44/bld/intel/mpich/nodebug/nothreads/pio/pio1/pio -I/usr/include -qno-opt-dynamic-align  -convert big_endian -assume byterecl -ftz -traceback -assume realloc_lhs -fp-model source    -O2 -debug minimal  -DTIMING -DLINUX -DNDEBUG -DHAVE_MPI -DPIO1  -DFORTRANUNDERSCORE -DCPRINTEL  -DFORTRANUNDERSCORE -DCPRINTEL -DHAVE_SLASHPROC -D_NO_MPI_RSEND -I. -I/central/scratch/leiduan/test44/bld/intel/mpich/nodebug/nothreads/include -I/central/scratch/leiduan/test44/bld/intel/mpich/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include -I/home/leiduan/lei_netcdf/netcdf4.6-intelf//include -I/central/scratch/leiduan/test44/bld/intel/mpich/nodebug/nothreads/include -c /central/groups/carnegie_poc/leiduan_memex/CESM/my_cesm_sandbox/cime/src/externals/pio1/pio/pio_types.F90 -o CMakeFiles/pio.dir/pio_types.F90.o

make[2]: Leaving directory `/central/scratch/leiduan/test44/bld/intel/mpich/nodebug/nothreads/pio/pio1'

make[1]: Leaving directory `/central/scratch/leiduan/test44/bld/intel/mpich/nodebug/nothreads/pio/pio1'

/central/groups/carnegie_poc/leiduan_memex/CESM/my_cesm_sandbox/cime/src/externals/pio1/pio/pio_types.F90(13): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [NETCDF]

     use netcdf                                  ! _EXTERNAL

---------^

/central/groups/carnegie_poc/leiduan_memex/CESM/my_cesm_sandbox/cime/src/externals/pio1/pio/pio_types.F90(383): error #6592: This symbol must be a defined parameter, an enumerator, or an argument of an inquiry function that evaluates to a compile-time constant.   [NF90_GLOBAL]

   integer, public, parameter :: PIO_global = nf90_global

----------------------------------------------^

/central/groups/carnegie_poc/leiduan_memex/CESM/my_cesm_sandbox/cime/src/externals/pio1/pio/pio_types.F90(384): error #6592: This symbol must be a defined parameter, an enumerator, or an argument of an inquiry function that evaluates to a compile-time constant.   [NF90_UNLIMITED]

   integer, public, parameter :: PIO_unlimited = nf90_unlimited[/ICODE]

It seems the model cannot find the netcdf (is this correct?) However, I think I have link it where in the .bash* I have:

export NETCDF_C=/home/leiduan/lei_netcdf/netcdf4.4-c
export NETCDF_C_LIB=$NETCDF_C/lib
export NETCDF_C_INC=$NETCDF_C/include
export PATH=$NETCDF_C/bin:$PATH
export LD_LIBRARY_PATH=$NETCDF_C/lib:$LD_LIBRARY_PATH

export NETCDF_F=/home/leiduan/lei_netcdf/netcdf4.6-intelf
export NETCDF_F_LIB=$NETCDF_F/lib
export NETCDF_F_INC=$NETCDF_F/include
export PATH=$NETCDF_F/bin:$PATH
export LD_LIBRARY_PATH=$NETCDF_F/lib:$LD_LIBRARY_PATH

In config_machine.xml I have:

<mpirun mpilib="mpich">
      <executable>mpirun</executable>
      <arguments>
        <arg name="num_tasks"> -n {{ total_tasks }} </arg>
        <arg name="lib">-genv LD_LIBRARY_PATH /home/leiduan/lei_netcdf/netcdf4.6-intelf/lib:$LD_LIBRARY_PATH</arg>
      </arguments>
    </mpirun>
    <module_system type="none">
    </module_system>
    <environment_variables>
      <env name="NETCDFROOT">/home/leiduan/lei_netcdf/netcdf4.6-intelf</env>
      <env name="OMP_STACKSIZE">64M</env>
    </environment_variables>

And in config_compiler.xml I have:

<NETCDF_PATH>/home/leiduan/lei_netcdf/netcdf4.6-intelf/</NETCDF_PATH>
  <SLIBS>
    <base> -L${NETCDF_PATH}/lib -I${NETCDF_PATH}/include -lnetcdf -lnetcdff -L$ENV{MKL_PATH} -lmkl_rt </base>
    <append MPILIB="mpich"> -mkl=cluster </append>
  </SLIBS>

Any idea how to solve this would be much appreciated.

Best regards,
Lei

 

[11438023@zju_edu_cn]

I solved it by re-installing an earlier version of NetCDF-c and NetCDF-f. It appear to me that the lastest one (4.9 for netcdf-c and 4.6 for netcdf-f) lacks some components that will be used during the building.

Now I can successfully build the case.