It appears that it is linking against a libnetcdf that was built as a shared
library. Can you confirm that there are no other netcdf installs on your
system beyond the one you have created in /hpctmp2/tmsyx/latest/netcdf? This
behavior would be explained if it was linking against a shared library that was
not on the LD_LIBRARY_PATH, causing the C runtime to fail to find the library
containing the symbols that it is complaining about.
Try this; go into /hpctmp2/tmsyx/latest/netcdf/lib and run:
$ nm libnetcdf.a | grep nc_inq_varndims
Does nc_inq_varndims appear defined in the library? If so, then your netcdf
fortran install is not linking against this library, and must be linking
against a different one. If nc_inq_varndims is not present, then I am at a
loss as there is no reason it would not be.
I hope this information is helpful; ideally we can identify an alternative
netcdf version (it would be older, but not necessarily very old, if it lacks
nc_inq_varndims) and perhaps remove it.
Have a good day,
-Ward
>
> Hi,
>
> I am compiling NETCDF Fortran 4.4.4 and from my understanding the program
> could not link to the NETCDF-C library.
>
> I have compiled NETCDF-C with HDF, szip, zlib as below:
>
> ---------------------------------------------------------
> HDF5 (hdf5-1.8.18)
>
> export CC=mpiicc
> export CFLAGS='-O1'
> export CXX=mpiicpc
> export CXXFLAGS='-O1'
> export CPP='icc -E'
> export CXXCPP='icpc -E'
> export F9X=mpiifort
> export FC=mpiifort
> export FCFLAGS='-O1'
> export LDFLAGS="-L/hpctmp2/tmsyx/latest/zlib/lib
> -Wl,-rpath=/hpctmp2/tmsyx/latest/zlib/lib"
>
> ./configure --prefix=/hpctmp2/tmsyx/latest/hdf5 --enable-shared=no
> --enable-static --enable-fortran --disable-silent-rules --enable-debug=all
> --with-zlib=/hpctmp2/tmsyx/latest/zlib --with-szlib=/hpctmp2/tmsyx/latest/szip
>
> ---------------------------------------------------------
> NETCDF-C (netcdf-4.3.3.1)
>
> export CPPFLAGS=-I/hpctmp2/tmsyx/latest/hdf5/include
> export LDFLAGS="-L/hpctmp2/tmsyx/latest/hdf5/lib -lhdf5_hl -lhdf5
> -L/hpctmp2/tmsyx/latest/zlib/lib -lz -L/hpctmp2/tmsyx/latest/szip/lib -lsz"
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/hpctmp2/tmsyx/latest/hdf5/lib
>
> export CC=icc
> export CXX=icpc
> export CFLAGS='-O1 -xHost -ip -no-prec-div -static-intel'
> export CXXFLAGS='-O1 -xHost -ip -no-prec-div -static-intel'
> export F77=ifort
> export FC=ifort
> export F90=ifort
> export FFLAGS='-O1 -xHost -ip -no-prec-div -static-intel'
> export CPP='icc -E'
> export CXXCPP='icpc -E'
>
> ./configure --prefix=/hpctmp2/tmsyx/latest/netcdf --enable-shared=no
> --enable-static --enable-netcdf-4 --disable-dap
> ---------------------------------------------------------
> NETCDF-F (netcdf-fortran-4.4.4)
>
> sh /app1/centos6.3/Intel/xe_2015/bin/compilervars.sh intel64
>
> export CC=icc
> export CXX=icpc
> export CFLAGS='-O1 -xHost -ip -no-prec-div -static-intel'
> export CXXFLAGS='-O1 -xHost -ip -no-prec-div -static-intel'
> export F77=ifort
> export FC=ifort
> export F90=ifort
> export FFLAGS='-O1 -xHost -ip -no-prec-div -static-intel'
> export CPP='icc -E'
> export CXXCPP='icpc -E'
>
> export
> INCLUDE=/hpctmp2/tmsyx/latest/netcdf/include:/hpctmp2/tmsyx/latest/hdf5/include:$INCLUDE
> export CPPFLAGS="-I/hpctmp2/tmsyx/latest/netcdf/include
> -I/hpctmp2/tmsyx/latest/hdf5/include -I/hpctmp2/tmsyx/latest/zlib/include"
> export LDFLAGS="-L/hpctmp2/tmsyx/latest/netcdf/lib
> -L/hpctmp2/tmsyx/latest/hdf5/lib -L/hpctmp2/tmsyx/latest/zlib/lib
> -L/hpctmp2/tmsyx/latest/szip/lib"
> export LIBS="-lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz -lsz"
>
> ./configure --prefix=/hpctmp2/tmsyx/latest/netcdf --enable-static
> --disable-shared
>
> ---------------------------------------------------------
> If I set the LIBS var as above, the ./configure will stop with this error:
> âchecking whether the C compiler works... noâ
>
> If I unset LIBS var, the ./configure went fine, along with make command.
> However, I hit another wall when running make check with a lot of undefined
> reference errors.
>
> My apologies for this long email but I had this issue for almost 2 weeks now
> and I am desperately trying to solve this issue. Attached are the config.log
> file with 2 other log files which are output of âmakeâ and âmake
> checkâ commands.
>
> Thank you in advance for your support!
>
> Cheers,
> Ethan
>
>
> Hi,
>
> I am compiling NETCDF Fortran 4.4.4 and from my understanding the program
> could not link to the NETCDF-C library.
>
> I have compiled NETCDF-C with HDF, szip, zlib as below:
>
> ---------------------------------------------------------
> HDF5 (hdf5-1.8.18)
>
> export CC=mpiicc
> export CFLAGS='-O1'
> export CXX=mpiicpc
> export CXXFLAGS='-O1'
> export CPP='icc -E'
> export CXXCPP='icpc -E'
> export F9X=mpiifort
> export FC=mpiifort
> export FCFLAGS='-O1'
> export LDFLAGS="-L/hpctmp2/tmsyx/latest/zlib/lib
> -Wl,-rpath=/hpctmp2/tmsyx/latest/zlib/lib"
>
> ./configure --prefix=/hpctmp2/tmsyx/latest/hdf5 --enable-shared=no
> --enable-static --enable-fortran --disable-silent-rules --enable-debug=all
> --with-zlib=/hpctmp2/tmsyx/latest/zlib --with-szlib=/hpctmp2/tmsyx/latest/szip
>
> ---------------------------------------------------------
> NETCDF-C (netcdf-4.3.3.1)
>
> export CPPFLAGS=-I/hpctmp2/tmsyx/latest/hdf5/include
> export LDFLAGS="-L/hpctmp2/tmsyx/latest/hdf5/lib -lhdf5_hl -lhdf5
> -L/hpctmp2/tmsyx/latest/zlib/lib -lz -L/hpctmp2/tmsyx/latest/szip/lib -lsz"
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/hpctmp2/tmsyx/latest/hdf5/lib
>
> export CC=icc
> export CXX=icpc
> export CFLAGS='-O1 -xHost -ip -no-prec-div -static-intel'
> export CXXFLAGS='-O1 -xHost -ip -no-prec-div -static-intel'
> export F77=ifort
> export FC=ifort
> export F90=ifort
> export FFLAGS='-O1 -xHost -ip -no-prec-div -static-intel'
> export CPP='icc -E'
> export CXXCPP='icpc -E'
>
> ./configure --prefix=/hpctmp2/tmsyx/latest/netcdf --enable-shared=no
> --enable-static --enable-netcdf-4 --disable-dap
> ---------------------------------------------------------
> NETCDF-F (netcdf-fortran-4.4.4)
>
> sh /app1/centos6.3/Intel/xe_2015/bin/compilervars.sh intel64
>
> export CC=icc
> export CXX=icpc
> export CFLAGS='-O1 -xHost -ip -no-prec-div -static-intel'
> export CXXFLAGS='-O1 -xHost -ip -no-prec-div -static-intel'
> export F77=ifort
> export FC=ifort
> export F90=ifort
> export FFLAGS='-O1 -xHost -ip -no-prec-div -static-intel'
> export CPP='icc -E'
> export CXXCPP='icpc -E'
>
> export
> INCLUDE=/hpctmp2/tmsyx/latest/netcdf/include:/hpctmp2/tmsyx/latest/hdf5/include:$INCLUDE
> export CPPFLAGS="-I/hpctmp2/tmsyx/latest/netcdf/include
> -I/hpctmp2/tmsyx/latest/hdf5/include -I/hpctmp2/tmsyx/latest/zlib/include"
> export LDFLAGS="-L/hpctmp2/tmsyx/latest/netcdf/lib
> -L/hpctmp2/tmsyx/latest/hdf5/lib -L/hpctmp2/tmsyx/latest/zlib/lib
> -L/hpctmp2/tmsyx/latest/szip/lib"
> export LIBS="-lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz -lsz"
>
> ./configure --prefix=/hpctmp2/tmsyx/latest/netcdf --enable-static
> --disable-shared
>
> ---------------------------------------------------------
> If I set the LIBS var as above, the ./configure will stop with this error:
> âchecking whether the C compiler works... noâ
>
> If I unset LIBS var, the ./configure went fine, along with make command.
> However, I hit another wall when running make check with a lot of undefined
> reference errors.
>
> My apologies for this long email but I had this issue for almost 2 weeks now
> and I am desperately trying to solve this issue. Attached are the config.log
> file with 2 other log files which are output of âmakeâ and âmake
> checkâ commands.
>
> Thank you in advance for your support!
>
> Cheers,
> Ethan
>
Ticket Details
===================
Ticket ID: EPW-963095
Department: Support netCDF
Priority: Normal
Status: Closed
===================
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