On 30/05/2012 1:50 AM, a a wrote:
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?
They won't help until you start a new shell. Or, instead, use them on
the command line like the installation instructions suggest - since you
don't need these settings on an ongoing basis.
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?
Definitely not. "make install" is the only command for which you should
be root, and only then if the installation location requires it. Unless
you like pain from risking needing to reinstall your trashed system.
Mark
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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