[gmx-users] installation Gromacs-Fedora18

[Souilem Safa]

many thanks to you all,
I did installation as root it works well
I like gromacs users discussion. It is very useful :)


On 3 May 2013 19:10, Francesco <fracarb at myopera.com> wrote:

> this is what I do to install gromacs 4.5.5 on fedora 18
>
> fftw libraries
>
> cd fftw-3.3.3_folder
> ./configure --enable-threads --enable-shared --enable-float
> --prefix=/usr/local/fftw
> make
> make install
> make clean
>
> in this way I install single precision (--enable-float) fftw libraries
> in /usr/local/fftw (you can put it where you want)
> be sure to enable shared because gromacs seems need it
>
> if you want double precision remove --enable-float
>
> gromacs 4.5.5
>
> cd to folder
> ./configure CPPFLAGS="-I/usr/local/fftw/include"
> LDFLAGS="-L/usr/localfftw/lib" --with-fft=fftw3
> make
> make install
> make clean
>
> --disable-float for double precision and --enable-mpi if you need mpi
>
> remember that fftw and gromacs must have the same precision.
>
> hope this helps you
>
> cheers
>
> Francesco
>
> On Fri, 3 May 2013, at 09:39 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
> > thanks
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
>   Francesco
>   fracarb at myopera.com
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>