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On 30/05/2012 1:50 AM, a a wrote:
<blockquote cite="mid:COL118-W1028BECD4295D9151DA8D2A3050@phx.gbl"
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Dear Mark,<br>
<br>
I have overlook it. Sorry.<br>
<br>
I have already added the following two sentences in .bashrc file
in my home directory (when I login as user).<br>
<br>
<div><span style="font-size: 10pt;">export
CPPFLAGS="-I/home/softwares/fftw301/include"</span></div>
<div>export LDFLAGS="-L/home/softwares/fftw301/lib"<br>
<br>
Should I type in another lines?<br>
</div>
</div>
</blockquote>
<br>
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.<br>
<br>
<blockquote cite="mid:COL118-W1028BECD4295D9151DA8D2A3050@phx.gbl"
type="cite">
<div dir="ltr">
<div><br>
Did I do any common mistakes in using the command export with
.bash shell?<br>
<br>
Should I add these two lines at the root directory as it seems
I have a role as root during installation?<br>
</div>
</div>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:COL118-W1028BECD4295D9151DA8D2A3050@phx.gbl"
type="cite">
<div dir="ltr">
<div><br>
Please kindly give me some more guidance.<br>
<br>
Many thanks,<br>
<br>
Catherine<br>
</div>
<br>
<br>
<div>
<hr id="stopSpelling">Date: Tue, 29 May 2012 18:48:15 +1000<br>
From: <a class="moz-txt-link-abbreviated" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a><br>
To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Subject: Re: [gmx-users] How to install GROMACS in 64-bit?<br>
<br>
On 29/05/2012 6:37 PM, a a wrote:
<blockquote
cite="mid:COL118-W591D8740DC2110F95CF87AA3050@phx.gbl">
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<div dir="ltr"> Dear Sir/Madam,
<div><br>
</div>
<div>Thanks for the insightful comments from the experts.
Follows the steps, I found the source of error:</div>
<div><br>
</div>
<div>This what I have done:</div>
<div><br>
</div>
<div>
<div>====================================================</div>
<div>In the following directory
/home/softwares/fftw-3.0.1:</div>
<div>./configure --enable-shared
--prefix=/home/softwares/fftw301</div>
<div>make</div>
<div>make install</div>
<div><span style="font-size: 10pt;"><br>
</span></div>
<div><span style="font-size: 10pt;">In the .bash file:</span></div>
<div><span style="font-size: 10pt;">export
CPPFLAGS="-I/home/softwares/fftw301/include"</span></div>
<div>export LDFLAGS="-L/home/softwares/fftw301/lib"</div>
<div><br>
</div>
<div>go to the following directory
/home/softwares/gromacs-4.5.5:</div>
<div>./configure --enable-shared
--prefix=/home/softwares/g455</div>
<div>make</div>
<div><span style="font-size: 10pt;">=============================================
==============</span></div>
<div><br>
</div>
<div>In the middle of the make, I found this error
message:</div>
<div><br>
</div>
<div>==========================================================</div>
<div><br>
</div>
<div>/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</div>
<div>/usr/local/lib/libfftw3f.a: could not read symbols:
Bad value</div>
<div>collect2: ld returned 1 exit status</div>
<div>make[3]: *** [libmd.la] Error 1</div>
<div>make[3]: Leaving directory
`/home/softwares/gromacs-4.5.5/src/mdlib'</div>
<div>make[2]: *** [all-recursive] Error 1</div>
<div>make[2]: Leaving directory
`/home/softwares/gromacs-4.5.5/src'</div>
<div>make[1]: *** [all] Error 2</div>
<div>make[1]: Leaving directory
`/home/softwares/gromacs-4.5.5/src'</div>
<div>make: *** [all-recursive] Error 1</div>
</div>
<div><br>
</div>
<div>============================================================</div>
<div><br>
</div>
<div>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 <span
style="font-size: 10pt;">fftw-3.0.1 library and
GROMACS are compiled with 64 bit settings?</span></div>
</div>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
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