[gmx-users] (no subject)

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jan 12 07:56:45 CET 2012


On 12/01/2012 5:44 PM, Anik Sen wrote:
> fftw-3.3 installation:
> first gone to the fftw3.3 folder
>
> ./configure --enable-threads --enable-float --enable-sse 
> --enable-shared --prefix /home/ganguly/Gromacs/fftw3.3
> .
> .
> .
> make
> .
> .
> .
> make install
>
> Then gromacs 4.5.5 is being installed.
> installation:
> first gone to the gromacs-4.5.5 folder
>
> ./configure --disable-shared [also done for ./configure --enable-shared]
> .
> .
> .
> make
> .
> .
> .
> make install
>
> same error is coming. The error is given below:
>
> After make command, the last few lines are this type:::--
>
> make[3]: Leaving directory 
> `/home/ganguly/Gromacs/gromacs-4.5.5/share/html'
>
> Making all in images
>
> make[3]: Entering directory 
> `/home/ganguly/Gromacs/gromacs-4.5.5/share/html/images'
>
> make[3]: Nothing to be done for `all'.
>
> make[3]: Leaving directory 
> `/home/ganguly/Gromacs/gromacs-4.5.5/share/html/images'
>
> Making all in online
>
> make[3]: Entering directory 
> `/home/ganguly/Gromacs/gromacs-4.5.5/share/html/online'
>
> make[3]: Nothing to be done for `all'.
>
> make[3]: Leaving directory 
> `/home/ganguly/Gromacs/gromacs-4.5.5/share/html/online'
>
> make[2]: Leaving directory 
> `/home/ganguly/Gromacs/gromacs-4.5.5/share/html'
>
> make[2]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/share'
>
> make[2]: Nothing to be done for `all-am'.
>
> make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share'
>
> make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share'
>
> Making all in man
>
> make[1]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/man'
>
> Making all in man1
>
> make[2]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/man/man1'
>
> make[2]: Nothing to be done for `all'.
>
> make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/man/man1'
>
> Making all in man7
>
> make[2]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/man/man7'
>
> make[2]: Nothing to be done for `all'.
>
> make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/man/man7'
>
> make[2]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/man'
>
> make[2]: Nothing to be done for `all-am'.
>
> make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/man'
>
> make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/man'
>
> make[1]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5'
>
> make[1]: Nothing to be done for `all-am'.
>
> make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5'
>
>
> Then after the make install command :-
>
>
> [ganguly at localhost gromacs-4.5.5]$ make install
>
> Making install in include
>
> .
> .
> .
> .
> .
>
> /usr/bin/install: cannot remove 
> `/usr/local/gromacs/include/gromacs/futil.h': Permission denied
>
> /usr/bin/install: cannot remove 
> `/usr/local/gromacs/include/gromacs/gbutil.h': Permission denied
>
> /usr/bin/install: cannot remove 
> `/usr/local/gromacs/include/gromacs/gen_ad.h': Permission denied
>
> /usr/bin/install: cannot remove 
> `/usr/local/gromacs/include/gromacs/genborn.h': Permission denied
>
> /usr/bin/install: cannot remove 
> `/usr/local/gromacs/include/gromacs/gmx_ana.h': Permission denied
>
> /usr/bin/install: cannot remove 
> `/usr/local/gromacs/include/gromacs/gmx_arpack.h': Permission denied
>
> /usr/bin/install: cannot remove 
> `/usr/local/gromacs/include/gromacs/gmx_blas.h': Permission denied
>
> /usr/bin/install: cannot remove 
> `/usr/local/gromacs/include/gromacs/gmx_cyclecounter.h': Permission denied
>
> /usr/bin/install: cannot remove 
> `/usr/local/gromacs/include/gromacs/gmx_fatal.h': Permission denied
>
> /usr/bin/install: cannot remove 
> `/usr/local/gromacs/include/gromacs/gmx_fft.h': Permission denied
>
> /usr/bin/install: cannot remove 
> `/usr/local/gromacs/include/gromacs/gmx_ga2la.h': Permission denied
>
> /usr/bin/install: cannot remove 
> `/usr/local/gromacs/include/gromacs/gmx_lapack.h': Permission denied
>
> /usr/bin/install: cannot remove 
> `/usr/local/gromacs/include/gromacs/gmx_matrix.h': Permission denied
>
> /usr/bin/install: cannot remove 
> `/usr/local/gromacs/include/gromacs/gmx_parallel_3dfft.h': Permission 
> denied
>
> make[3]: *** [install-pkgincludeHEADERS] Error 1
>
> make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/include'
>
> make[2]: *** [install-am] Error 2
>
> make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/include'
>
> make[1]: *** [install-recursive] Error 1
>
> make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/include'
>
> make: *** [install-recursive] Error 1
>
> [ganguly at localhost gromacs-4.5.5]$
>

I updated 
http://www.gromacs.org/Downloads/Installation_Instructions#Final_Installation 
to address this issue.

Mark
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