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On 29/05/2012 3:09 PM, a a wrote:
<blockquote cite="mid:COL118-W625892DB2B509AB318608A3050@phx.gbl"
type="cite">
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<div>Dear Sir/Madam,</div>
<div><br>
</div>
<div>Follow the steps below, I have installed fftw library and
gromacs as a root.</div>
<div><br>
</div>
<div>(1) tar -xzvf fftw-3.0.1.tar.gz</div>
<div>(2) cd fftw-3.0.1</div>
<div>(3) ./configure --enable-float --enable-threads
--enable-shared</div>
</div>
</div>
</blockquote>
<br>
Here you enabled threads for fftw, which is not recommended here <a
href="http://www.gromacs.org/Documentation/Installation_Instructions#Details_for_building_the_FFTW_prerequisite">http://www.gromacs.org/Documentation/Installation_Instructions#Details_for_building_the_FFTW_prerequisite</a>.
I don't know whether that's a problem, but certainly it will not
help.<br>
<br>
<blockquote cite="mid:COL118-W625892DB2B509AB318608A3050@phx.gbl"
type="cite">
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<div>(4) make</div>
<div>(5) make install</div>
<div>(6) tar -xzvf gromacs-4.5.5.tar.gz</div>
<div>(7) cd gromacs-4.5.5</div>
<div>(8) ./configure</div>
<div>(9) make</div>
<div>(10) make install</div>
<div>(11) I have also add "<span style="font-size: 10pt; ">PATH=/usr/local/gromacs:$PATH;
export PATH" to my .bashrc file in my directory.</span></div>
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</blockquote>
<br>
See
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Installation_Instructions#Getting_access_to_GROMACS_after_installation">http://www.gromacs.org/Documentation/Installation_Instructions#Getting_access_to_GROMACS_after_installation</a>
for the recommended procedure.<br>
<br>
<blockquote cite="mid:COL118-W625892DB2B509AB318608A3050@phx.gbl"
type="cite">
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<div><span style="font-size: 10pt; "><br>
</span></div>
<div><span style="font-size: 10pt; ">However, I have problem
to do the following comments:</span></div>
<div><span style="font-size: 10pt; "><br>
</span></div>
<div><span style="font-size: 10pt;">
<div>/usr/local/gromacs/bin/g_covar -s test.pdb -f
test.netcdf -o -v</div>
<div><br>
< /div>
<div>The follow error message appears:</div>
<div><br>
</div>
<div>/usr/local/gromacs/bin/g_covar: error while loading
shared libraries: libfftw3f.so.3: cannot open shared
object file: No such file or directory</div>
<div><br>
</div>
<div>I found the following libraries in my <span
style="font-size: 10pt; ">/usr/local/lib directory:</span><span
style="font-size: 10pt; "></span></div>
<div><span style="font-size: 10pt; "><br>
</span></div>
<div><span style="font-size: 10pt; ">libfftw3f.a
libfftw3f.so.3.0.1 libfftw3f_threads.so.3</span><br>
<div>libfftw3f.la libfftw3f_threads.a
libfftw3f_threads.so.3.0.1</div>
<div>libfftw3f.so libfftw3f_threads.la pkgconfig</div>
<div>libfftw3f.so.3 libfftw3f_threads.so</div>
<div><br>
</div>
<div>Thus, it seems to me that <span style="font-size:
10pt; ">libfftw3f.so.3 is already installed,
whats' wrong with this? Could you mind to help.</span></div>
</div>
</div>
</span></div>
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</blockquote>
<br>
Your system apparently doesn't have this location in the search path
for shared libraries. Maybe following
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Installation_Instructions#Getting_access_to_GROMACS_after_installation">http://www.gromacs.org/Documentation/Installation_Instructions#Getting_access_to_GROMACS_after_installation</a>
will fix that.<br>
<br>
Mark<br>
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