[gmx-users] Re: installation Gromacs-Fedora18

[Christoph Junghans]

> Date: Fri, 3 May 2013 20:00:57 +0900
> From: Souilem Safa <safasouilem1 at gmail.com>
> Subject: Re: [gmx-users] installation Gromacs-Fedora18
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>         <CAGkn4TM30mSE2z0wCSqABwumeisWT-p+qBuO0waNtgEp9qFfTw at 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 <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
>>

--
Christoph Junghans
Web: http://www.compphys.de