[gmx-users] installation Gromacs-Fedora18

[Justin Lemkul]

On 5/3/13 5:39 AM, Souilem Safa wrote:
> 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

Specify LDFLAGS correctly.  What you have used is inconsistent with the 
installed location.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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