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[netCDF #DNR-108136]: Having problems when building NetCDF-Fortran with static libraries
- Subject: [netCDF #DNR-108136]: Having problems when building NetCDF-Fortran with static libraries
- Date: Fri, 21 Feb 2020 17:00:20 -0700
Hello,
Try modifying your configure command as follows:
./configure --prefix=/home/oriol/wrf-compiled/opt/netcdf-4.7.3/lib
--disable-shared $(nc-config --libs --static) $(nc-config --cflags)
This assumes that `nc-config` is on your path; if it is not, use the absolute
path to nc-config. Give this a try and let me know if it resolves the issue,
thanks!
-Ward
> Hello,
>
> I'm having problems when building NetCDF-Fortran 4.5.2 with static libraries.
> Required libraries (ZLIB, SZIP, HDF5, PNETCDF and NETCDF-C) are compiled
> statically without any problem. But for NetCDF-Fortran I'm getting this
> errors:
>
> ./configure --prefix=/home/oriol/wrf-compiled/opt/netcdf-4.7.3/lib
> --disable-shared
>
> [...]
> checking for MPI_File_open... yes
> checking netcdf.h usability... yes
> checking netcdf.h presence... yes
> checking for netcdf.h... yes
> checking for library containing nc_open... no
> configure: error: Could not link to netcdf C library. Please set LDFLAGS.
>
> The output of the config.log file is (find the full config.log file attached
> to this mail):
>
> [...]
> configure:22752: checking netcdf.h usability
> configure:22752: mpiicc -c -m64 -O3 -xHost -ip -no-prec-div -static-intel
> -fPIC -I/home/oriol/wrf-compiled/opt/zlib-1.2.11/include
> -I/home/oriol/wrf-compiled/opt/libpng-1.6.37/include
> -I/home/oriol/wrf-compiled/opt/szip-2.1.1/include
> -I/home/oriol/wrf-compiled/opt/hdf5-1.10.6/include
> -I/home/oriol/wrf-compiled/opt/pnetcdf-1.12.1/include
> -I/home/oriol/wrf-compiled/opt/netcdf-4.7.3/include conftest.c >&5
> configure:22752: $? = 0
> configure:22752: result: yes
> configure:22752: checking netcdf.h presence
> configure:22752: mpiicc -E
> -I/home/oriol/wrf-compiled/opt/zlib-1.2.11/include
> -I/home/oriol/wrf-compiled/opt/libpng-1.6.37/include
> -I/home/oriol/wrf-compiled/opt/szip-2.1.1/include
> -I/home/oriol/wrf-compiled/opt/hdf5-1.10.6/include
> -I/home/oriol/wrf-compiled/opt/pnetcdf-1.12.1/include
> -I/home/oriol/wrf-compiled/opt/netcdf-4.7.3/include conftest.c
> configure:22752: $? = 0
> configure:22752: result: yes
> configure:22752: checking for netcdf.h
> configure:22752: result: yes
> configure:22764: checking for library containing nc_open
> configure:22795: mpiicc -o conftest -m64 -O3 -xHost -ip -no-prec-div
> -static-intel -fPIC -I/home/oriol/wrf-compiled/opt/zlib-1.2.11/include
> -I/home/oriol/wrf-compiled/opt/libpng-1.6.37/include
> -I/home/oriol/wrf-compiled/opt/szip-2.1.1/include
> -I/home/oriol/wrf-compiled/opt/hdf5-1.10.6/include
> -I/home/oriol/wrf-compiled/opt/pnetcdf-1.12.1/include
> -I/home/oriol/wrf-compiled/opt/netcdf-4.7.3/include
> -L/home/oriol/wrf-compiled/opt/zlib-1.2.11/lib
> -L/home/oriol/wrf-compiled/opt/libpng-1.6.37/lib
> -L/home/oriol/wrf-compiled/opt/libpng-1.6.37/lib
> -L/home/oriol/wrf-compiled/opt/szip-2.1.1/lib
> -L/home/oriol/wrf-compiled/opt/hdf5-1.10.6/lib
> -L/home/oriol/wrf-compiled/opt/pnetcdf-1.12.1/lib
> -L/home/oriol/wrf-compiled/opt/netcdf-4.7.3/lib conftest.c -lm -lz -lpng
> -lsz -lhdf5_hl -lhdf5 -lpnetcdf -lnetcdf >&5
> icc: warning #10237: -lcilkrts linked in dynamically, static library not
> available
> /home/oriol/wrf-compiled/opt/netcdf-4.7.3/lib/libnetcdf.a(libnetcdfp_la-ncpdispatch.o):
> In function `NCP_create':
> ncpdispatch.c:(.text+0x5b): undefined reference to `ncmpi_create'
> [...]
>
> The environment variables are (set by: export ENV_VAR="value"):
>
> LD_LIBRARY_PATH =
> /opt/intel/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin:/opt/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/libfabric/lib:/opt/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/lib/release:/opt/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/lib:/opt/intel/compilers_and_libraries_2019.5.281/linux/tbb/lib/intel64/gcc4.7:/opt/intel/compilers_and_libraries_2019.5.281/linux/tbb/lib/intel64/gcc4.7:/home/oriol/wrf-compiled/opt/zlib-1.2.11/lib:/home/oriol/wrf-compiled/opt/szip-2.1.1/lib:/home/oriol/wrf-compiled/opt/hdf5-1.10.6/lib:/home/oriol/wrf-compiled/opt/pnetcdf-1.12.1/lib:/home/oriol/wrf-compiled/opt/netcdf-4.7.3/lib
>
> CPPFLAGS = -I/home/oriol/wrf-compiled/opt/zlib-1.2.11/include
> -I/home/oriol/wrf-compiled/opt/libpng-1.6.37/include
> -I/home/oriol/wrf-compiled/opt/szip-2.1.1/include
> -I/home/oriol/wrf-compiled/opt/hdf5-1.10.6/include
> -I/home/oriol/wrf-compiled/opt/pnetcdf-1.12.1/include
> -I/home/oriol/wrf-compiled/opt/netcdf-4.7.3/include
>
> LDFLAGS = -L/home/oriol/wrf-compiled/opt/zlib-1.2.11/lib
> -L/home/oriol/wrf-compiled/opt/libpng-1.6.37/lib
> -L/home/oriol/wrf-compiled/opt/libpng-1.6.37/lib
> -L/home/oriol/wrf-compiled/opt/szip-2.1.1/lib
> -L/home/oriol/wrf-compiled/opt/hdf5-1.10.6/lib
> -L/home/oriol/wrf-compiled/opt/pnetcdf-1.12.1/lib
> -L/home/oriol/wrf-compiled/opt/netcdf-4.7.3/lib
>
> The compilers used for all the libraries are:
>
> CC=mpiicc
> CXX=mpiicpc
> FC=mpiifort
> F77=mpiifort
> F90=mpiifort
> F9X=mpiifort
> CFLAGS='-m64 -O3 -xHost -ip -no-prec-div -static-intel -fPIC'
> CXXFLAGS='-m64 -O3 -xHost -ip -no-prec-div -static-intel -fPIC'
> FFLAGS='-m64 -O3 -xHost -ip -no-prec-div -static-intel -fPIC'
>
> It seems that NetCDF-Fortran cannot find the NetCDF-C static library, but the
> static library is still there:
>
> ls -l /home/oriol/wrf-compiled/opt/netcdf-4.7.3/lib
> total 1836
> -rw-r--r--. 1 root root 1868740 Feb 19 13:59 libnetcdf.a
> -rwxr-xr-x. 1 root root 1441 Feb 19 13:59 libnetcdf.la
> -rw-r--r--. 1 root root 1581 Feb 19 13:59 libnetcdf.settings
> drwxr-xr-x. 2 root root 23 Feb 19 13:59 pkgconfig
>
> The content of libnetcdf.settings is:
>
> # NetCDF C Configuration Summary
> ==============================
>
> # General
> -------
> NetCDF Version: 4.7.3
> Dispatch Version: 1
> Configured On: Wed Feb 19 13:58:56 UTC 2020
> Host System: x86_64-pc-linux-gnu
> Build Directory: /tmp/netcdf-c-4.7.3
> Install Prefix: /home/oriol/wrf-compiled/opt/netcdf-4.7.3
>
> # Compiling Options
> -----------------
> C Compiler:
> /opt/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/bin/mpiicc
> CFLAGS: -m64 -O3 -xHost -ip -no-prec-div -static-intel -fPIC
> CPPFLAGS: -I/home/oriol/wrf-compiled/opt/zlib-1.2.11/include
> -I/home/oriol/wrf-compiled/opt/libpng-1.6.37/include
> -I/home/oriol/wrf-compiled/opt/szip-2.1.1/include
> -I/home/oriol/wrf-compiled/opt/hdf5-1.10.6/include
> -I/home/oriol/wrf-compiled/opt/pnetcdf-1.12.1/include
> LDFLAGS: -L/home/oriol/wrf-compiled/opt/zlib-1.2.11/lib
> -L/home/oriol/wrf-compiled/opt/libpng-1.6.37/lib
> -L/home/oriol/wrf-compiled/opt/libpng-1.6.37/lib
> -L/home/oriol/wrf-compiled/opt/szip-2.1.1/lib
> -L/home/oriol/wrf-compiled/opt/hdf5-1.10.6/lib
> -L/home/oriol/wrf-compiled/opt/pnetcdf-1.12.1/lib
> AM_CFLAGS:
> AM_CPPFLAGS:
> AM_LDFLAGS:
> Shared Library: no
> Static Library: yes
> Extra libraries: -lpnetcdf -lhdf5_hl -lhdf5 -lm -lz -lpng -lsz
> -lhdf5_hl -lhdf5 -lpnetcdf
>
> # Features
> --------
> NetCDF-2 API: yes
> HDF4 Support: no
> HDF5 Support: yes
> NetCDF-4 API: yes
> NC-4 Parallel Support: yes
> PnetCDF Support: yes
> DAP2 Support: no
> DAP4 Support: no
> Byte-Range Support: no
> Diskless Support: yes
> MMap Support: no
> JNA Support: no
> CDF5 Support: yes
> ERANGE Fill Support: yes
> Relaxed Boundary Check: yes
>
>
> Please, could you help me solving the issue?
>
> Thanks in advance,
>
> Oriol
>
>
>
Ticket Details
===================
Ticket ID: DNR-108136
Department: Support netCDF
Priority: Normal
Status: Closed
===================
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