Dear Mark,
I have overlook it. Sorry.
I have already added the following two sentences in .bashrc file in my home
directory (when I login as user).
export
CPPFLAGS="-I/home/softwares/fftw301/include"
export LDFLAGS="-L/home/softwares/fftw301/lib"
Should I type in another lines?
Did I do any common mistakes in using the command export with .bash shell?
Should I add these two lines at the root directory as it seems I have a role as
root during installation?
Please kindly give me some more guidance.
Many thanks,
Catherine
Date: Tue, 29 May 2012 18:48:15 +1000
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] How to install GROMACS in 64-bit?
On 29/05/2012 6:37 PM, a a wrote:
Dear Sir/Madam,
Thanks for the insightful comments from the experts.
Follows the steps, I found the source of error:
This what I have done:
====================================================
In the following directory /home/softwares/fftw-3.0.1:
./configure --enable-shared
--prefix=/home/softwares/fftw301
make
make install
In the .bash file:
export
CPPFLAGS="-I/home/softwares/fftw301/include"
export LDFLAGS="-L/home/softwares/fftw301/lib"
go to the following directory
/home/softwares/gromacs-4.5.5:
./configure --enable-shared --prefix=/home/softwares/g455
make
=============================================
==============
In the middle of the make, I found this error message:
==========================================================
/usr/bin/ld: /usr/local/lib/libfftw3f.a(alloc.o):
relocation R_X86_64_32 against `.rodata.str1.1' can not be
used when making a shared object; recompile with -fPIC
/usr/local/lib/libfftw3f.a: could not read symbols: Bad
value
collect2: ld returned 1 exit status
make[3]: *** [libmd.la] Error 1
make[3]: Leaving directory
`/home/softwares/gromacs-4.5.5/src/mdlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory
`/home/softwares/gromacs-4.5.5/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory
`/home/softwares/gromacs-4.5.5/src'
make: *** [all-recursive] Error 1
============================================================
It seems to be a problem of 64 and 32 bit, my workstation
is a 64 bit machine and the OS is also 64 bit, what should I
do to make sure both the fftw-3.0.1
library and GROMACS are compiled with 64 bit settings?
I would start by observing that those error messages pertain to an
installation of FFTW that configure found in /usr/local/lib, and not
the one in /home/softwares. You have to sort that out first, since
this error messages indicates the need to use FFTW configured with
--enable-shared, per the link I gave last time.
Mark
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