Thanks again J, is that compulsory each time one installs something new?<br><br><div class="gmail_quote">On Fri, Dec 24, 2010 at 2:50 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">Quoting Sergio Manzetti <<a href="mailto:sergio.manzetti@vestforsk.no">sergio.manzetti@vestforsk.no</a>>:<br>
<br>
</div><div class="im">> Thanks J, I think I will install Ubuntu entirely first, because I just tried<br>
> to install FFTW now, and managed only to get to make install, then I got<br>
> permission denied messages, so even though I thought I was the admin, I am<br>
> seemingly not.<br>
><br>
<br>
</div>Before blowing away your system, use "sudo make install," which will prompt you<br>
for your password and should work if you actually are an admin.<br>
<font color="#888888"><br>
-Justin<br>
</font><div><div></div><div class="h5"><br>
> On Fri, Dec 24, 2010 at 2:44 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
><br>
> > Quoting Sergio Manzetti <<a href="mailto:sergio.manzetti@vestforsk.no">sergio.manzetti@vestforsk.no</a>>:<br>
> ><br>
> > > Thanks Justin, here is it the copy-out:<br>
> > ><br>
> > > sergio@sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure<br>
> > > checking build system type... i686-pc-linux-gnu<br>
> > > checking host system type... i686-pc-linux-gnu<br>
> > > checking for a BSD-compatible install... /usr/bin/install -c<br>
> > > checking whether build environment is sane... yes<br>
> > > checking for a thread-safe mkdir -p... /bin/mkdir -p<br>
> > > checking for gawk... gawk<br>
> > > checking whether make sets $(MAKE)... yes<br>
> > > checking how to create a ustar tar archive... gnutar<br>
> > > checking for cc... cc<br>
> > > checking for C compiler default output file name... a.out<br>
> > > checking whether the C compiler works... yes<br>
> > > checking whether we are cross compiling... no<br>
> > > checking for suffix of executables...<br>
> > > checking for suffix of object files... o<br>
> > > checking whether we are using the GNU C compiler... yes<br>
> > > checking whether cc accepts -g... yes<br>
> > > checking for cc option to accept ISO C89... none needed<br>
> > > checking for style of include used by make... GNU<br>
> > > checking dependency style of cc... gcc3<br>
> > > checking dependency style of cc... gcc3<br>
> > > checking how to run the C preprocessor... cc -E<br>
> > > checking for grep that handles long lines and -e... /bin/grep<br>
> > > checking for egrep... /bin/grep -E<br>
> > > checking whether ln -s works... yes<br>
> > > checking whether cc accepts -O3... yes<br>
> > > checking whether cc accepts -msse2... yes<br>
> > > checking whether cc accepts -funroll-all-loops... yes<br>
> > > checking whether cc accepts -std=gnu99... yes<br>
> > > checking whether cc accepts -fexcess-precision=fast... no<br>
> > > checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions<br>
> > > -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes<br>
> > > checking for ANSI C header files... yes<br>
> > > checking for sys/types.h... yes<br>
> > > checking for sys/stat.h... yes<br>
> > > checking for stdlib.h... yes<br>
> > > checking for string.h... yes<br>
> > > checking for memory.h... yes<br>
> > > checking for strings.h... yes<br>
> > > checking for inttypes.h... yes<br>
> > > checking for stdint.h... yes<br>
> > > checking for unistd.h... yes<br>
> > > checking for unistd.h... (cached) yes<br>
> > > checking sys/time.h usability... yes<br>
> > > checking sys/time.h presence... yes<br>
> > > checking for sys/time.h... yes<br>
> > > checking sched.h usability... yes<br>
> > > checking sched.h presence... yes<br>
> > > checking for sched.h... yes<br>
> > > checking for sysconf... yes<br>
> > > checking for the pthreads library -lpthreads... no<br>
> > > checking whether pthreads work without any flags... no<br>
> > > checking whether pthreads work with -Kthread... no<br>
> > > checking whether pthreads work with -kthread... no<br>
> > > checking for the pthreads library -llthread... no<br>
> > > checking whether pthreads work with -pthread... yes<br>
> > > checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE<br>
> > > checking if more special flags are required for pthreads... no<br>
> > > checking for cc_r... cc<br>
> > > checking if atomic operations are supported... yes<br>
> > > checking whether byte ordering is bigendian... no<br>
> > > checking that size_t can hold pointers... yes<br>
> > > checking for SIGUSR1... yes<br>
> > > checking for pipes... yes<br>
> > > checking floating-point format... IEEE754 (little-endian byte and word<br>
> > > order)<br>
> > > checking whether ln -s works... yes<br>
> > > checking whether make sets $(MAKE)... (cached) yes<br>
> > > checking for a sed that does not truncate output... /bin/sed<br>
> > > checking for ld used by cc ... /usr/bin/ld<br>
> > > checking if the linker (/usr/bin/ld) is GNU ld... yes<br>
> > > checking for /usr/bin/ld option to reload object files... -r<br>
> > > checking for BSD-compatible nm... /usr/bin/nm -B<br>
> > > checking how to recognise dependent libraries... pass_all<br>
> > > checking dlfcn.h usability... yes<br>
> > > checking dlfcn.h presence... yes<br>
> > > checking for dlfcn.h... yes<br>
> > > checking for g++... no<br>
> > > checking for c++... no<br>
> > > checking for gpp... no<br>
> > > checking for aCC... no<br>
> > > checking for CC... no<br>
> > > checking for cxx... no<br>
> > > checking for cc++... no<br>
> > > checking for cl.exe... no<br>
> > > checking for FCC... no<br>
> > > checking for KCC... no<br>
> > > checking for RCC... no<br>
> > > checking for xlC_r... no<br>
> > > checking for xlC... no<br>
> > > checking whether we are using the GNU C++ compiler... no<br>
> > > checking whether g++ accepts -g... no<br>
> > > checking dependency style of g++... none<br>
> > > checking the maximum length of command line arguments... 32768<br>
> > > checking command to parse /usr/bin/nm -B output from cc object... failed<br>
> > > checking for objdir... .libs<br>
> > > checking for ar... ar<br>
> > > checking for ranlib... ranlib<br>
> > > checking for strip... strip<br>
> > > checking if cc supports -fno-rtti -fno-exceptions... no<br>
> > > checking for cc option to produce PIC... -fPIC<br>
> > > checking if cc PIC flag -fPIC works... yes<br>
> > > checking if cc static flag -static works... yes<br>
> > > checking if cc supports -c -o file.o... yes<br>
> > > checking whether the cc linker (/usr/bin/ld) supports shared<br>
> > libraries...<br>
> > > yes<br>
> > > checking dynamic linker characteristics... GNU/Linux ld.so<br>
> > > checking how to hardcode library paths into programs... immediate<br>
> > > checking whether stripping libraries is possible... yes<br>
> > > checking for shl_load... no<br>
> > > checking for shl_load in -ldld... no<br>
> > > checking for dlopen... no<br>
> > > checking for dlopen in -ldl... yes<br>
> > > checking whether a program can dlopen itself... yes<br>
> > > checking whether a statically linked program can dlopen itself... no<br>
> > > checking if libtool supports shared libraries... yes<br>
> > > checking whether to build shared libraries... no<br>
> > > checking whether to build static libraries... yes<br>
> > > configure: creating libtool<br>
> > > appending configuration tag "CXX" to libtool<br>
> > > appending configuration tag "F77" to libtool<br>
> > > checking for special C compiler options needed for large files... no<br>
> > > checking for _FILE_OFFSET_BITS value needed for large files... 64<br>
> > > checking for _LARGEFILE_SOURCE value needed for large files... no<br>
> > > checking for sqrt in -lm... yes<br>
> > > checking for fftw3.h... configure: error: Cannot find the default<br>
> > external<br>
> ><br>
> > Here's an error...<br>
> ><br>
> > > FFT library (fftw3).<br>
> > > Other alternatives are 'fftw2', or 'mkl' for Intel MKL.<br>
> > > You are STRONGLY recommended to use one of these - fftw is free.<br>
> > ><br>
> > > Use CPPFLAGS and LDFLAGS if the library is installed in a<br>
> > > non-standard location. (see FAQ at <a href="http://www.gromacs.org" target="_blank">http://www.gromacs.org</a>)<br>
> ><br>
> > ...and the possible solution. Custom installation options are discussed in<br>
> > the<br>
> > installation instructions. If you have FFTW installed, you'll have to<br>
> > specify<br>
> > header and library locations with CPPFLAGS and LDFLAGS, respectively. If<br>
> > you<br>
> > didn't install FFTW, start over and read about the prerequisites before<br>
> > trying<br>
> > to configure again.<br>
> ><br>
> > -Justin<br>
> ><br>
> > ><br>
> > > If you dont care about performance you can also specify 'fftpack'<br>
> > > to use a slower set of FFTs built into Gromacs.<br>
> > > (Just install FFTW3 unless you really know what you are doing).<br>
> > ><br>
> > > sergio@sergio-laptop:~/Desktop/gromacs-4.5.3$ make<br>
> > > make: *** No targets specified and no makefile found. Stop.<br>
> > ><br>
> ><br>
> ><br>
> > ========================================<br>
> ><br>
> > Justin A. Lemkul<br>
> > Ph.D. Candidate<br>
> > ICTAS Doctoral Scholar<br>
> > MILES-IGERT Trainee<br>
> > Department of Biochemistry<br>
> > Virginia Tech<br>
> > Blacksburg, VA<br>
> > jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
> > <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
> ><br>
> > ========================================<br>
> > --<br>
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><br>
<br>
<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</div></div></blockquote></div><br>