> Date: Fri, 3 May 2013 20:00:57 +0900 > From: Souilem Safa <safasouil...@gmail.com> > Subject: Re: [gmx-users] installation Gromacs-Fedora18 > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <cagkn4tm30mse2z0wcsqabwumeiswt-p+qbuo0wantgep9qf...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > many thanks to you all, > I did installation as root it works well If you have root rights, why don't you just install Fedora's gromacs package? $ yum install gromacs
Cheers, Christoph > 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 >> -- Christoph Junghans Web: http://www.compphys.de -- 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