[gmx-users] Installation GROMACS UBUNTU

[Justin A. Lemkul]

Quoting Sergio Manzetti <sergio.manzetti at vestforsk.no>:

> Thanks Justin, here is it the copy-out:
>
> sergio at sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure
> checking build system type... i686-pc-linux-gnu
> checking host system type... i686-pc-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... /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... /bin/grep
> checking for egrep... /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... no
> checking whether cc accepts  -O3 -fomit-frame-pointer -finline-functions
> -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... 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 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... /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++... no
> checking for c++... no
> checking for gpp... no
> checking for aCC... no
> checking for CC... no
> checking for cxx... no
> checking for cc++... no
> checking for cl.exe... no
> checking for FCC... no
> checking for KCC... no
> checking for RCC... no
> checking for xlC_r... no
> checking for xlC... no
> checking whether we are using the GNU C++ compiler... no
> checking whether g++ accepts -g... no
> checking dependency style of g++... none
> checking the maximum length of command line arguments... 32768
> checking command to parse /usr/bin/nm -B output from cc  object... failed
> 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... yes
> checking if cc  supports -c -o file.o... yes
> checking whether the cc  linker (/usr/bin/ld) supports shared libraries...
> yes
> 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... no
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... no
> checking whether to build static libraries... yes
> configure: creating libtool
> appending configuration tag "CXX" to libtool
> 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... 64
> checking for _LARGEFILE_SOURCE value needed for large files... no
> checking for sqrt in -lm... yes
> checking for fftw3.h... configure: error: Cannot find the default external

Here's an error...

> FFT library (fftw3).
> Other alternatives are 'fftw2', or 'mkl' for Intel MKL.
> You are STRONGLY recommended to use one of these - fftw is free.
>
> Use CPPFLAGS and LDFLAGS if the library is installed in a
> non-standard location. (see FAQ at http://www.gromacs.org)

...and the possible solution. Custom installation options are discussed in the
installation instructions. If you have FFTW installed, you'll have to specify
header and library locations with CPPFLAGS and LDFLAGS, respectively. If you
didn't install FFTW, start over and read about the prerequisites before trying
to configure again.

-Justin

>
> If you dont care about performance you can also specify 'fftpack'
> to use a slower set of FFTs built into Gromacs.
> (Just install FFTW3 unless you really know what you are doing).
>
> sergio at sergio-laptop:~/Desktop/gromacs-4.5.3$ make
> make: *** No targets specified and no makefile found.  Stop.
>


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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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