[gmx-users] Installation GROMACS UBUNTU

Fri Dec 24 14:50:20 CET 2010

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

> Thanks J, I think I will install Ubuntu entirely first, because I just tried
> to install FFTW now, and managed only to get to make install, then I got
> permission denied messages, so even though I thought I was the admin, I am
> seemingly not.
>

Before blowing away your system, use "sudo make install," which will prompt you
for your password and should work if you actually are an admin.

-Justin

> On Fri, Dec 24, 2010 at 2:44 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> > 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.
> > >
> >
> >
> > ========================================
> >
> > 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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>

========================================

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

========================================