NOTICE: This version of the NSF Unidata web site (archive.unidata.ucar.edu) is no longer being updated.
Current content can be found at unidata.ucar.edu.
To learn about what's going on, see About the Archive Site.
NOTICE: This version of the NSF Unidata web site (archive.unidata.ucar.edu) is no longer being updated.
Current content can be found at unidata.ucar.edu.
To learn about what's going on, see About the Archive Site.
Dan, > The logs for "configure," "make" and "make check" are attached. In your configure output, the following lines means the header file for the netCDF C library is found, but not the library: > checking for netcdf.h... yes > checking for library containing nc_open... no > checking for nc_def_opaque... no > checking for nccreate... no The location of the netCDF library should have been specified with the LDFLAGS environment variable, which I see you've set as > LDFLAGS=-L/curc/tools/x_86_64/rh5/netcdf/4.2/hdf5/1.8.8/openmpi/1.4.5/intel/12.1.4/lib Is there actually a netCDF library in that directory, with a name like libnetcdf.a? If not, it looks like there's a problem with the PATH you used ... Also, I see you've explicitly turned off shared libraries with the "--disable-shared" configure option. Have you tried building with shared libraries? --Russ > -----Original Message----- > From: Unidata netCDF Support [mailto:address@hidden] > Sent: Wednesday, June 27, 2012 2:33 PM > To: Daniel Milroy > Cc: address@hidden > Subject: [netCDF #YWH-955421]: Error during "make check," NetCDF 4.2 Fortran > libs, Janus supercomputer > > Dan, > > > I forgot to mention before that I had set PATH to include > > /curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/bin, so in > > effect I've already tried that suggestion. I downloaded and built > > netcdf-fortran-4.4-beta1.tar.gz using options identical to my previous > > attempt with NetCDF 4.2. Unfortunately, "make check" fails with exactly > > the same error. > > OK, please send us the complete output of configure, make, and make check, > from the build with netcdf-fortran-4.2. > > We might be able to diagnose the problem from that. > > --Russ > > > -----Original Message----- > > From: Unidata netCDF Support [mailto:address@hidden] > > Sent: Wednesday, June 27, 2012 1:24 PM > > To: Daniel Milroy > > Cc: address@hidden > > Subject: [netCDF #YWH-955421]: Error during "make check," NetCDF 4.2 > > Fortran libs, Janus supercomputer > > > > Hi Dan, > > > > > Per request by NCAR, I've been attempting to build NetCDF 4.2 on the > > > Janus supercomputer (RHEL 5.6, kernel 2.6.18-238.12.1). I had no > > > problems building the NetCDF 4.2 C libraries, but I can't get the Fortran > > > libraries to install. Here are the options I've used to build > > > netcdf-fortran-4.2: > > > > > > CC=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/bin/m > > > pi > > > cc > > > FC=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/bin/m > > > pi > > > f90 > > > F90=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/bin/ > > > mp > > > if90 > > > F77=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/bin/ > > > mp > > > if90 > > > CXX=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/bin/ > > > mp > > > ic++ > > > MPICXX=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/b > > > in > > > /mpic++ > > > MPICC=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/bi > > > n/ > > > mpicc > > > MPIF77=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/b > > > in > > > /mpif77 > > > MPIF90=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/b > > > in > > > /mpif90 CPPFLAGS="-DgFortran > > > -I/curc/tools/x_86_64/rh5/netcdf/4.2/hdf5/1.8.8/openmpi/1.4.5/intel/12.1.4/include" > > > LDFLAGS=-L/curc/tools/x_86_64/rh5/netcdf/4.2/hdf5/1.8.8/openmpi/1.4. > > > 5/ > > > intel/12.1.4/lib > > > LD_LIBRARY_PATH=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel > > > -1 > > > 2.1.4/lib:/curc/tools/nonfree/redhat_5_x86_64/intel-12.1.4/composer_ > > > xe > > > _2011_sp1.10.319/debugger/lib/intel64:/curc/tools/nonfree/redhat_5_x > > > 86 > > > _64/intel-12.1.4/composer_xe_2011_sp1.10.319/mkl/lib/intel64:/curc/t > > > oo > > > ls/nonfree/redhat_5_x86_64/intel-12.1.4/composer_xe_2011_sp1.10.319/ > > > co > > > mpiler/lib/intel64:/curc/tools/free/redhat_5_x86_64/sun_jdk-1.6.0_23 > > > -x 86_64/lib:/curc/tools/free/redhat_5_x86_64/torque-2.5.8/lib > > > FFLAGS=-I/curc/tools/x_86_64/rh5/netcdf/4.2/hdf5/1.8.8/openmpi/1.4.5 > > > /i > > > ntel/12.1.4/include > > > > > > ./configure > > > --prefix=/curc/tools/x_86_64/rh5/netcdf/4.2/intel/netcdf-4.2_intel-12. > > > 1.4_hdf5-1.8.8_openmpi-1.4.5_fortran -disable-shared > > > > > > I can configure and make the Fortran libraries successfully, but the > > > following error is thrown during "make check:" > > > > > > [snip] > > > > > > /tmp/netcdf/netcdf-fortran-4.2/fortran/fort-varsio.c:115: undefined > > > reference to `nc_get_vars_int' > > > ../fortran/.libs/libnetcdff.a(fort-varsio.o): In function > > > `nf_put_vars_real_': > > > /tmp/netcdf/netcdf-fortran-4.2/fortran/fort-varsio.c:130: undefined > > > reference to `nc_put_vars_float' > > > ../fortran/.libs/libnetcdff.a(fort-varsio.o): In function > > > `nf_get_vars_real_': > > > /tmp/netcdf/netcdf-fortran-4.2/fortran/fort-varsio.c:142: undefined > > > reference to `nc_get_vars_float' > > > ../fortran/.libs/libnetcdff.a(fort-varsio.o): In function > > > `nf_put_vars_double_': > > > /tmp/netcdf/netcdf-fortran-4.2/fortran/fort-varsio.c:150: undefined > > > reference to `nc_put_vars_double' > > > ../fortran/.libs/libnetcdff.a(fort-varsio.o): In function > > > `nf_get_vars_double_': > > > /tmp/netcdf/netcdf-fortran-4.2/fortran/fort-varsio.c:157: undefined > > > reference to `nc_get_vars_double' > > > ../fortran/.libs/libnetcdff.a(fort-varsio.o): In function `nf_put_vars_': > > > /tmp/netcdf/netcdf-fortran-4.2/fortran/fort-varsio.c:160: undefined > > > reference to `nc_put_vars' > > > ../fortran/.libs/libnetcdff.a(fort-varsio.o): In function `nf_get_vars_': > > > /tmp/netcdf/netcdf-fortran-4.2/fortran/fort-varsio.c:163: undefined > > > reference to `nc_get_vars' > > > make[2]: *** [nf_test] Error 1 > > > make[2]: Leaving directory `/tmp/netcdf/netcdf-fortran-4.2/nf_test' > > > make[1]: *** [check-am] Error 2 > > > make[1]: Leaving directory `/tmp/netcdf/netcdf-fortran-4.2/nf_test' > > > make: *** [check-recursive] Error 1 > > > > > > What is causing this issue? > > > > I suspect it may be that the fortran/cfortran.h header file, used to handle > > differences in how C functions are called from Fortran for different > > compilers, is failing to provide the right macros for the mpif90 compiler > > you are using. > > > > One thing you could try is setting your PATH to include the directory in > > which the compilers are found, and just setting the environment variables > > that configure is using to the names of the executables, e.g. > > > > PATH=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/bin:$ > > PATH > > FC=mpif90 > > F90=mpif90 > > F77=mpif90 > > ... > > > > to see if that gets the right definitions of the cfortran.h macros. > > > > Alternatively, you could try the new beta release of the separate > > Fortran package, that makes use of the Fortran-2003 C-interoperability > > features, assuming your > > mpif90 compiler supports this. That completely avoids the old cfortran.h > > macros. > > > > Just get this version of the netCDF-Fortran package: > > > > ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-4.4-beta1.tar.gz > > > > also available as the beta release from the downloads page: > > > > http://www.unidata.ucar.edu/downloads/netcdf/netcdf-fortran/index.jsp > > > > In building it, just tell it where to find the installed netCDF-3 > > libraries, with CPPFLAGS and LDFLAGS, as you did for the netcdf-fortran-4.2 > > package. > > > > Please let us know if that works. > > > > --Russ > > > > > > Russ Rew UCAR Unidata Program > > address@hidden http://www.unidata.ucar.edu > > > > > > > > Ticket Details > > =================== > > Ticket ID: YWH-955421 > > Department: Support netCDF > > Priority: Normal > > Status: Closed > > > > > > Russ Rew UCAR Unidata Program > address@hidden http://www.unidata.ucar.edu > > > > Ticket Details > =================== > Ticket ID: YWH-955421 > Department: Support netCDF > Priority: Normal > Status: Closed > > Russ Rew UCAR Unidata Program address@hidden http://www.unidata.ucar.edu Ticket Details =================== Ticket ID: YWH-955421 Department: Support netCDF Priority: Normal Status: Closed