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

Dan,

> > 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 ...
> 
> The contents of the directory are:
> libnetcdf.a  libnetcdf.la  pkgconfig
> 
> > Also, I see you've explicitly turned off shared libraries with the 
> > "--disable-shared" configure option.  Have you tried building with shared 
> > libraries?
> 
> I've tried that, but "make" fails with a "no such file or directory" error.  
> I can't remember the file or directory in question, but it is the same error 
> that NetCDF 4.1.3 throws when I try to build it with shared libraries.

Well, evidently the mpif90 Fortran compiler can't link with the libnetcdf.a 
library.
Some other things to try are 

  - Make sure the libnetcdf.a library is 64-bit, assuming that's what your 
Fortran compiler
    expects to link with.  You can do that with the "file" command to see what 
kind of
    object libnetcdf.a is.

  - Look at how pkgconfig in that directory wants you to link use that library. 
 For example,
    if that directory is <DIR>, try invoking

      export PKG_CONFIG_PATH=<DIR>
      pkg-config --libs --cflags netcdf

    to see if you need some flag you're not using.

  - Look at config.log to see the actual source for the program with a call to
    nc_open, to see how mpif90 is being called to compile and lik with it.  
There
    may be an error message in config.log providing more information than that 
nc_open
    can't be found.  If you can play with mpif90 flags to get that example 
program
    linking, it will be easier to see what's needed to get the 
netcdf-fortran-4.2
    build to work.

Sorry, that's all I can think of at this point.  If you want to extract the 
config.log
output relevant to not finding nc_open, I can see if there's anything obvious 
that jumps
out at me.  Here's what is in config.log for finding a library containing 
nc_open:

configure:19683: checking for library containing nc_open
configure:19714: gcc -o conftest -g -O2 -I/usr/local/include  conftest.c  >&5
/tmp/ccivm8m4.o: In function `main':
/home/russ/nf/trunk/conftest.c:46: undefined reference to `nc_open'
collect2: ld returned 1 exit status
configure:19714: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "netCDF-Fortran"
| #define PACKAGE_TARNAME "netcdf-fortran"
| #define PACKAGE_VERSION "4.2"
| #define PACKAGE_STRING "netCDF-Fortran 4.2"
| #define PACKAGE_BUGREPORT "address@hidden"
| #define PACKAGE_URL ""
| #define PACKAGE "netcdf-fortran"
| #define VERSION "4.2"
| #define TEMP_LARGE "."
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define pgiFortran 1
| #define NF_INT1_T byte
| #define NF_INT2_T integer*2
| #define NF_INT1_IS_C_SIGNED_CHAR 1
| #define NF_INT2_IS_C_SHORT 1
| #define NF_INT_IS_C_INT 1
| #define NF_REAL_IS_C_FLOAT 1
| #define NF_DOUBLEPRECISION_IS_C_DOUBLE 1
| #define NCBYTE_T byte
| #define NCSHORT_T integer*2
| #define HAVE_NETCDF_H 1
| /* end confdefs.h.  */
| 
| /* Override any GCC internal prototype to avoid an error.
|    Use char because int might match the return type of a GCC
|    builtin and then its argument prototype would still apply.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| char nc_open ();
| int
| main ()
| {
| return nc_open ();
|   ;
|   return 0;
| }
configure:19714: gcc -o conftest -g -O2 -I/usr/local/include  conftest.c 
-lnetcdf   >&5
configure:19714: $? = 0
configure:19731: result: -lnetcdf

Note that it first reports it's not found, but then succeeds at linking, using 
"-lnetcdf".

--Russ

> -----Original Message-----
> From: Unidata netCDF Support [mailto:address@hidden]
> Sent: Friday, June 29, 2012 11:31 AM
> To: Daniel Milroy
> Cc: address@hidden
> Subject: [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/bi
> > > > n/
> > > > mp
> > > > if90
> > > > F77=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/bi
> > > > n/
> > > > mp
> > > > if90
> > > > CXX=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/bi
> > > > n/
> > > > 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_int
> > > > el
> > > > -1
> > > > 2.1.4/lib:/curc/tools/nonfree/redhat_5_x86_64/intel-12.1.4/compose
> > > > r_
> > > > 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_sp1.10.31
> > > > 9/
> > > > 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.g
> > > z
> > >
> > > also available as the beta release from the downloads page:
> > >
> > > http://www.unidata.ucar.edu/downloads/netcdf/netcdf-fortran/index.js
> > > p
> > >
> > > 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
> 
> 
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