[gmx-users] installation Gromacs-Fedora18

[Souilem Safa]

Dear Gromacs users,
I m aiming to install gromacs 4.5.5 package in in linux Fedora 18. I have
updated the needed compilers and downloaded the fftw-3.3.2.tar.gz and
gromacs4.5.5.tar.gz

I have followed these commands to install:
$ tar -zxvf fftw-3.3.2/
$ cd fftw-3.3.2/
$ ./configure --prefix /home/safa/programs/fftw-3.3.2 --enable-threads
--enable-sse2 --enable-shared
$ make
$ make install
$ cd
$ tar zxvf gromacs-4.5.5.tar.gz
$ cd gromac-4.5.5/
$../configure --prefix /home/safa/programs/gromacs-4.5.5
LDFLAGS="-L/home/safa/fftw-3.3.2/lib"
CPPFLAGS="-I/home/safa/programs/fftw-3.3.2/include" --disable-float
When I wrote the last command I got this error.
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking for cc... cc
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 cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of cc... gcc3
checking dependency style of cc... gcc3
checking how to run the C preprocessor... cc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking whether ln -s works... yes
checking whether cc accepts -O3... yes
checking whether cc accepts -msse2... yes
checking whether cc accepts -funroll-all-loops... yes
checking whether cc accepts -std=gnu99... yes
checking whether cc accepts -fexcess-precision=fast... yes
checking whether cc accepts  -O3 -fomit-frame-pointer -finline-functions
-Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99
-fexcess-precision=fast... yes
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 for unistd.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sched.h usability... yes
checking sched.h presence... yes
checking for sched.h... yes
checking for sysconf... yes
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for cc_r... cc
checking if atomic operations are supported... yes
checking if pthread_setaffinity_np is available... yes
checking whether byte ordering is bigendian... no
checking that size_t can hold pointers... yes
checking for SIGUSR1... yes
checking for pipes... yes
checking floating-point format... IEEE754 (little-endian byte and word
order)
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for a sed that does not truncate output... /usr/bin/sed
checking for ld used by cc ... /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 how to recognise dependent libraries... pass_all
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking how to run the C++ preprocessor... g++ -E
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from cc  object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if cc  supports -fno-rtti -fno-exceptions... no
checking for cc  option to produce PIC... -fPIC
checking if cc  PIC flag -fPIC works... yes
checking if cc  static flag -static works... no
checking if cc  supports -c -o file.o... yes
checking whether the cc  linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking for g++ option to produce PIC... -fPIC
checking if g++ PIC flag -fPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
appending configuration tag "F77" to libtool
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for sqrt in -lm... yes
checking for fftw3.h... yes
checking for main in -lfftw3... no
configure: error: Cannot find fftw3 library
 Please can you advise me what should I do to solve this error
thanks