[netCDF #EPW-963095]: Compilation of NETCDF Fortran 4.4.4

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:
> “checking whether the C compiler works... no”
> 
> 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 “make” and “make check” 
> 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:
> “checking whether the C compiler works... no”
> 
> 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 “make” and “make check” 
> 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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