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.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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Received on Sun Jun 08 2008 - 06:07:35 PDT
