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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;"><font size="6"><span style="font-family: Times New Roman; font-weight: bold;">fftw-3.3 installation:</span></font><br>
<span style="font-weight: bold;">first gone to the fftw3.3 folder</span><br>
<br>
<font size="3">./configure --enable-threads --enable-float --enable-sse --enable-shared --prefix /home/ganguly/Gromacs/fftw3.3<br>
.<br>
.<br>
.<br>
make<br>
.<br>
.<br>
.<br>
make install</font><br>
<br>
Then gromacs 4.5.5 is being installed.<br>
installation:<br>
<span style="font-weight: bold;">first gone to the gromacs-4.5.5 folder</span><br>
<br>
<font size="3">./configure --disable-shared [also done for ./configure --enable-shared]<br>
.<br>
.<br>
.<br>
make<br>
.<br>
.<br>
.<br>
make install</font><br>
<br>
same error is coming. The error is given below:<br>
<br>
<font size="4"><span style="font-weight: bold;">After make command, the last few lines are this type:::--</span></font><br>
<br>
<p class="Standard">make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html'</p>
<p class="Standard">Making all in images</p>
<p class="Standard">make[3]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html/images'</p>
<p class="Standard">make[3]: Nothing to be done for `all'.</p>
<p class="Standard">make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html/images'</p>
<p class="Standard">Making all in online</p>
<p class="Standard">make[3]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html/online'</p>
<p class="Standard">make[3]: Nothing to be done for `all'.</p>
<p class="Standard">make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html/online'</p>
<p class="Standard">make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html'</p>
<p class="Standard">make[2]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/share'</p>
<p class="Standard">make[2]: Nothing to be done for `all-am'.</p>
<p class="Standard">make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share'</p>
<p class="Standard">make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share'</p>
<p class="Standard">Making all in man</p>
<p class="Standard">make[1]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/man'</p>
<p class="Standard">Making all in man1</p>
<p class="Standard">make[2]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/man/man1'</p>
<p class="Standard">make[2]: Nothing to be done for `all'.</p>
<p class="Standard">make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/man/man1'</p>
<p class="Standard">Making all in man7</p>
<p class="Standard">make[2]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/man/man7'</p>
<p class="Standard">make[2]: Nothing to be done for `all'.</p>
<p class="Standard">make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/man/man7'</p>
<p class="Standard">make[2]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/man'</p>
<p class="Standard">make[2]: Nothing to be done for `all-am'.</p>
<p class="Standard">make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/man'</p>
<p class="Standard">make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/man'</p>
<p class="Standard">make[1]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5'</p>
<p class="Standard">make[1]: Nothing to be done for `all-am'.</p>
<p class="Standard">make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5'</p>
<p class="Standard" style="font-weight: bold;"><font size="4"><br>
</font></p>
<p class="Standard"><font style="font-weight: bold;" size="4">Then after the make install command :-</font></p>
<p class="Standard"><br>
</p>
<p class="Standard">[ganguly@localhost gromacs-4.5.5]$ make install</p>
<p class="Standard">Making install in include</p>
.<br>
.<br>
.<br>
.<br>
.<br>
<p class="Standard">/usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/futil.h': Permission denied</p>
<p class="Standard">/usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gbutil.h': Permission denied</p>
<p class="Standard">/usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gen_ad.h': Permission denied</p>
<p class="Standard">/usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/genborn.h': Permission denied</p>
<p class="Standard">/usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_ana.h': Permission denied</p>
<p class="Standard">/usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_arpack.h': Permission denied</p>
<p class="Standard">/usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_blas.h': Permission denied</p>
<p class="Standard">/usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_cyclecounter.h': Permission denied</p>
<p class="Standard">/usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_fatal.h': Permission denied</p>
<p class="Standard">/usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_fft.h': Permission denied</p>
<p class="Standard">/usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_ga2la.h': Permission denied</p>
<p class="Standard">/usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_lapack.h': Permission denied</p>
<p class="Standard">/usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_matrix.h': Permission denied</p>
<p class="Standard">/usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_parallel_3dfft.h': Permission denied</p>
<p class="Standard">make[3]: *** [install-pkgincludeHEADERS] Error 1</p>
<p class="Standard">make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/include'</p>
<p class="Standard">make[2]: *** [install-am] Error 2</p>
<p class="Standard">make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/include'</p>
<p class="Standard">make[1]: *** [install-recursive] Error 1</p>
<p class="Standard">make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/include'</p>
<p class="Standard">make: *** [install-recursive] Error 1</p>
<p class="Standard">[ganguly@localhost gromacs-4.5.5]$</p>
<div style="font-family: Times New Roman; color: rgb(0, 0, 0); font-size: 16px;">
<hr tabindex="-1">
<div style="direction: ltr;" id="divRpF708455"><font color="#000000" face="Tahoma" size="2"><b>From:</b> gmx-users-bounces@gromacs.org [gmx-users-bounces@gromacs.org] on behalf of Javier Cerezo [jcb1@um.es]<br>
<b>Sent:</b> Wednesday, January 11, 2012 5:12 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> Re: [gmx-users] (no subject)<br>
</font><br>
</div>
<div></div>
<div>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?<br>
<br>
Javier<br>
<br>
El 11/01/12 12:07, Anik Sen escribió:
<blockquote type="cite">
<div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 10pt;">
I have already done that but the problem persisits.<br>
<br>
<div style="font-family: Times New Roman; color: rgb(0, 0, 0); font-size: 16px;">
<hr tabindex="-1">
<div id="divRpF880567" style="direction: ltr;"><font color="#000000" face="Tahoma" size="2"><b>From:</b>
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users-bounces@gromacs.org" target="_blank">
gmx-users-bounces@gromacs.org</a> [<a class="moz-txt-link-abbreviated" href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>] on behalf of Javier Cerezo [<a class="moz-txt-link-abbreviated" href="mailto:jcb1@um.es" target="_blank">jcb1@um.es</a>]<br>
<b>Sent:</b> Wednesday, January 11, 2012 1:56 PM<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org" target="_blank">
gmx-users@gromacs.org</a><br>
<b>Subject:</b> Re: [gmx-users] (no subject)<br>
</font><br>
</div>
<div>Hi<br>
<br>
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.<br>
<br>
Javier<br>
<br>
El 11/01/12 08:20, Anik Sen escribió:
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<font size="3"><span style="font-family: Times New Roman;">Im having problems installing Gromacs. I followed the GROMACS installation instructions as suggested by justin</span></font>. But in vain. The same error is coming again and again. Please suggest.<br>
<br>
The error file is given below:<br style="font-family: Times New Roman;">
<font size="4"><br>
<br style="font-family: Times New Roman;">
</font>
<p style="text-align: left; font-family: Times New Roman;"><font size="4"><b><font>/usr/bin/ld: /usr/local/lib/libfftw3.a(<wbr>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</font></b></font></p>
<p style="text-align: left; font-family: Times New Roman;"><font size="4"><b><font>/usr/local/lib/libfftw3.a: could not read symbols: Bad value</font></b></font></p>
<p style="text-align: left; font-family: Times New Roman;"><font size="4"><b><font>collect2: ld returned 1 exit status</font></b></font></p>
<p style="text-align: left; font-family: Times New Roman;"><font size="4"><b><font>make[3]: *** [<a href="http://libmd_d.la/" target="_blank">libmd_d.la</a>] Error 1</font></b></font></p>
<p style="text-align: left; font-family: Times New Roman;"><font size="4"><b><font>make[3]: Leaving directory `/home/ganguly/Gromacs/<wbr>gromacs-4.5.5/src/mdlib'</font></b></font></p>
<p style="text-align: left; font-family: Times New Roman;"><font size="4"><b><font>make[2]: *** [all-recursive] Error 1</font></b></font></p>
<p style="text-align: left; font-family: Times New Roman;"><font size="4"><b><font>make[2]: Leaving directory `/home/ganguly/Gromacs/<wbr>gromacs-4.5.5/src'</font></b></font></p>
<p style="text-align: left; font-family: Times New Roman;"><font size="4"><b><font>make[1]: *** [all] Error 2</font></b></font></p>
<p style="text-align: left; font-family: Times New Roman;"><font size="4"><b><font>make[1]: Leaving directory `/home/ganguly/Gromacs/<wbr>gromacs-4.5.5/src'</font></b></font></p>
<p style="text-align: left; font-family: Times New Roman;"><font size="4"><b><font>make: *** [all-recursive] Error 1</font></b></font></p>
<p style="text-align: left;"><br>
</p>
<p style="text-align: left;"><br>
</p>
Thanx in advance<br>
Anik<br>
</div>
<div style="font-size: 9pt; font-family: 'Calibri',sans-serif;">========================================================<br>
Anik Sen<br>
Student<br>
CSIR-Central Salt & Marine Chemicals Research Institute,<br>
Gijubhai Badheka Marg.<br>
Bhavnagar, Gujarat 364002<br>
<div><img alt="www.csmcri.org" src="http://www.csmcri.org/images/logo.png"></div>
========================================================</div>
<br>
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<br>
<pre class="moz-signature" cols="72">--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Phone: (+34)868887434</pre>
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<br>
<pre class="moz-signature" cols="72">--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Phone: (+34)868887434</pre>
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