error building pnetcdf 1.9.0 by impi-2018

[Giuseppe_C_]

I am trying to build the pnetcdf 1.9.0 with shared enable by impi-2018:

source /users/home/opt/intel/parallel_studio_xe_2018.3.051/bin/psxevars.sh intel64

MPIF77=mpiifort MPIF90=mpiifort MPICC=mpiicc MPICXX=mpiicpc ./configure --prefix=/users/home/opt-intel_2018/parallel-netcdf/parallel-netcdf-1.9.0 --enable-shared

but I receive these errors:

make[3]: Entering directory `/users/home/SOFTWARE/netcdf/2018/parallel-netcdf-1.9.0/src/utils/ncmpigen'

  CC       main.o

  CC       load.o

  CC       escapes.o

  CC       getfill.o

  CC       init.o

  CC       genlib.o

  CC       ncmpigentab.o

  CCLD     ncmpigen

../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_cpystr'

../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_allocate'

../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_dealloc_allocatable'

../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_cpstr'

../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_alloc_allocatable'

../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_len_trim'

../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_array_copy_in'

../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_trim'

../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_contig_array'

../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_check_mult_overflow64'

../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_array_copy_out'

What i'an doing wrong?

Thanks

[Steve_Lionel]

What's happening is that, for the command that creates the executable, it isn't referencing the Intel Fortran run-time libraries. I gather that CCLD invokes the C compiler to run ld, and it doesn't know how to find the Fortran libraries.I think that if you had CCLD run ifort instead for this step it would work. There are probably other ways to solve it, and I assume others will suggest them (Linux not being my strong point.)

[Juergen_R_R]

We also use the C compiler as linker for our main library which is Fortran code to make it besser accessible from external programs. For gcc/gfortran this works as gcc automatically links in all run-time libraries necessary. For ifort this doesn't work. We get access to the runtime libraries using the AC_FC_LIBRARY_LDFLAGS command from autotools  during our configure process, store these  in the FCLIBS variable and use them during linking. 

[Giuseppe_C_]

Sorry but I do not know how to use your advice, this is my configure:

module load INTEL/intel_xe_2018 

module load IMPI/intel_mpi_2018

export MPICC=mpiicc

export MPIF77=mpiifort

export MPIFC=mpiifort

export MPIF90=mpiifort

export MPIF90=mpif90

export MPICXX=mpiicpc

./configure --enable-shared --prefix=/users/home/opt-intel_2018/parallel-netcdf/parallel-netcdf-1.9.0 

Can you help me?

Thanks

[Juergen_R_R]

E.g., on  MAC OS X we get the flags from our configure script, and those flags are then stored in the environment variable

FCLIBS = '-L/opt/intel/compilers_and_libraries_2019.0.070/mac/compiler/lib -L/usr/lib -lifportmt -lifcoremt -limf -lsvml -lipgo -lintlc -lpthread'

When we build our library, we add $(FCLIBS) in the link command according to 

lib<your_project_name>_la_LIBADD +=  $(FCLIBS)

Note that this is autotools-specific, for cmake you need to add this to the linker flags, which would be something like

-DCMAKE_EXE_LINKER_FLAGS = '-L/ .... '  or something similar, I am not really familiar with cmake. 

[Giuseppe_C_]

Thanks Juergen, thanks at all.

I have solved getting FCLIBS from the Makefile and doing, after configure:

make LDFLAGS="fclibs contents"

Regards