[gmx-users] (no subject)

[Anik Sen]

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]$

________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Javier Cerezo [jcb1 at um.es]
Sent: Wednesday, January 11, 2012 5:12 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] (no subject)

You need to post how did you exactly installed fftw and gromacs in order to get more help. It seems to me that the problem is related to the shared fftw libraries. Could you compile the gromacs binaries with --disable-shared?

Javier

El 11/01/12 12:07, Anik Sen escribió:
I have already done that but the problem persisits.

________________________________
From: gmx-users-bounces at gromacs.org<mailto:gmx-users-bounces at gromacs.org> [gmx-users-bounces at gromacs.org<mailto:gmx-users-bounces at gromacs.org>] on behalf of Javier Cerezo [jcb1 at um.es<mailto:jcb1 at um.es>]
Sent: Wednesday, January 11, 2012 1:56 PM
To: gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>
Subject: Re: [gmx-users] (no subject)

Hi

You should compile your fftw with --enable-shared if you want to link your gromacs installation to shared libraries (which is the default in the latest versions). Check the installation instructions in the website.

Javier

El 11/01/12 08:20, Anik Sen escribió:
Im having problems installing Gromacs. I followed the GROMACS installation instructions as suggested by justin. But in vain. The same error is coming again and again. Please suggest.

The error file is given below:



/usr/bin/ld: /usr/local/lib/libfftw3.a(plan-dft-r2c-3d.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC

/usr/local/lib/libfftw3.a: could not read symbols: Bad value

collect2: ld returned 1 exit status

make[3]: *** [libmd_d.la<http://libmd_d.la/>] Error 1

make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/src/mdlib'

make[2]: *** [all-recursive] Error 1

make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/src'

make[1]: *** [all] Error 2

make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/src'

make: *** [all-recursive] Error 1



Thanx in advance
Anik
========================================================
Anik Sen
Student
CSIR-Central Salt & Marine Chemicals Research Institute,
Gijubhai Badheka Marg.
Bhavnagar, Gujarat 364002
[www.csmcri.org]
========================================================




--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Phone: (+34)868887434




--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Phone: (+34)868887434
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