AMBER Archive (2008)

Subject: AMBER: netcdf configure returned 1

From: Jens Lattig (Jens.Lattig_at_toulouse.inserm.fr)
Date: Thu Jun 05 2008 - 08:46:45 CDT

Dear valued colleagues,

I would like to ask for some help solving my problems in installation
of AmberTools under Ubuntu 8.04.

I run the configure_at several times and optimized the environment.

Still one error message occurred:

jensl_at_jensl-desktop:/opt/amber10/src$ sudo ./configure_at -mpi gcc
   Setting AMBERHOME to /opt/amber10

   Mopac and resp will be compiled with g77

   Testing the C compiler:
         mpicc -m32 -o testp testp.c
   OK

   Testing the g77 compiler:
        g77 -O0 -fno-second-underscore -o testp testp.f
   OK

   Testing flex:
   OK

   Configuring netcdf; (may be time-consuming)

   netcdf configure returned 1
   NETCDF configure failed! Check the netcdf_config.log file

Of course, I had a look in the netcdf_config.log but - to be honest -
I do not see a solution of the problem. Especially because

   checking how to run the C++ preprocessor... /lib/cpp
   configure: error: C++ preprocessor "/lib/cpp" fails sanity check

while /lib/cpp exists, and

   See `config.log' for more details.

is not possible, due to non existing config.log file.

Every suggestion would be a great help to me.

Thank you in advance.

Jens

PS: For the trouble shooting - the complete netcdf_config.log:

   configure: netCDF 3.6.2
   checking build system type... i686-pc-linux-gnu
   checking host system type... i686-pc-linux-gnu
   checking for a BSD-compatible install... /usr/bin/install -c
   checking whether build environment is sane... yes
   checking for gawk... no
   checking for mawk... mawk
   checking whether make sets $(MAKE)... yes
   checking whether to enable maintainer-specific portions of Makefiles... no
   configure: checking user options
   checking whether CXX is set to ''... no
   checking whether FC is set to ''... no
   checking whether F90 is set to ''... no
   checking whether documentation is to be installed... no
   checking whether Fortran compiler(s) should be tested during
configure... yes
   checking whether configure should try to set compiler flags... yes
   checking whether FFIO will be used... no
   checking whether to skip C++, F77, or F90 APIs if compiler is broken... yes
   checking whether only the C library is desired... no
   checking whether examples should be built... yes
   checking whether F77 API is desired... no
   checking whether F90 API is desired... no
   checking whether fortran type sizes should be checked... yes
   checking whether C API is desired... yes
   checking where to get netCDF C-only library for separate fortran
libraries...
   checking whether CXX API is desired... no
   checking whether v2 netCDF API should be built... yes
   checking whether the ncgen/ncdump should be built... yes
   checking whether large file (> 2GB) tests should be run... no
   checking whether extreme numbers should be used in tests... yes
   checking where to put large temp files if large file tests are run... .
   checking whether a win32 DLL is desired... no
   checking whether separate fortran libs are desired... no
   configure: finding C compiler
   checking for C compiler default output file name... a.out
   checking whether the C compiler works... yes
   checking whether we are cross compiling... no
   checking for suffix of executables...
   checking for suffix of object files... o
   checking whether we are using the GNU C compiler... yes
   checking whether mpicc accepts -g... yes
   checking for mpicc option to accept ISO C89... none needed
   checking for style of include used by make... GNU
   checking dependency style of mpicc... gcc3
   checking whether mpicc and cc understand -c and -o together... yes
   checking for an ANSI C-conforming const... yes
   configure: finding Fortran compiler (will not be used if Fortran API is
   not desired)
   checking for xlf90... no
   checking for fort... no
   checking for xlf95... no
   checking for ifort... no
   checking for ifc... no
   checking for efc... no
   checking for pgf95... no
   checking for lf95... no
   checking for gfortran... gfortran
   checking whether we are using the GNU Fortran compiler... yes
   checking whether gfortran accepts -g... yes
   checking for xlf... no
   checking for fort... no
   checking for xlf95... no
   checking for ifort... no
   checking for ifc... no
   checking for efc... no
   checking for pgf77... no
   checking for lf95... no
   checking for gfortran... gfortran
   checking whether we are using the GNU Fortran 77 compiler... yes
   checking whether gfortran accepts -g... yes
   configure: finding C++ compiler (will not be used if C++ API is not desired)
   checking for cl... no
   checking for KCC... no
   checking for CC... no
   checking for cxx... no
   checking for cc++... no
   checking for xlC... no
   checking for aCC... no
   checking for c++... no
   checking for g++... no
   checking for egcs... no
   checking for gcc... gcc
   checking whether we are using the GNU C++ compiler... no
   checking whether gcc accepts -g... no
   checking dependency style of gcc... gcc3
   checking for a sed that does not truncate output... /bin/sed
   checking for grep that handles long lines and -e... /bin/grep
   checking for egrep... /bin/grep -E
   checking for ld used by mpicc... /usr/bin/ld
   checking if the linker (/usr/bin/ld) is GNU ld... yes
   checking for /usr/bin/ld option to reload object files... -r
   checking for BSD-compatible nm... /usr/bin/nm -B
   checking whether ln -s works... yes
   checking how to recognize dependent libraries... pass_all
   checking how to run the C preprocessor... mpicc -E
   checking for ANSI C header files... yes
   checking for sys/types.h... yes
   checking for sys/stat.h... yes
   checking for stdlib.h... yes
   checking for string.h... yes
   checking for memory.h... yes
   checking for strings.h... yes
   checking for inttypes.h... yes
   checking for stdint.h... yes
   checking for unistd.h... yes
   checking dlfcn.h usability... yes
   checking dlfcn.h presence... yes
   checking for dlfcn.h... yes
   checking how to run the C++ preprocessor... /lib/cpp
   configure: error: C++ preprocessor "/lib/cpp" fails sanity check
   See `config.log' for more details.

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