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 <frac...@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@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-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > Francesco > frac...@myopera.com > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
