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[netCDF #YWH-955421]: Error during "make check," NetCDF 4.2 Fortran libs, Janus supercomputer

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