Hi everyone.<br><br>I followed the steps in <a href="http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites" target="_blank">http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites</a> for my problem, but I obtained problems at the moment to perform "make".<br>
<br>So, as mention the web page of gromacs... <br><br><span style="background-color: rgb(255, 255, 0);">If you get errors during GROMACS compilation (the "make" step) that
suggest that you "recompile with -fPIC," then you should return to this
FFTW stage and configure with </span><code style="background-color: rgb(255, 255, 0);">--enable-shared</code><span style="background-color: rgb(255, 255, 0);"> or </span><code style="background-color: rgb(255, 255, 0);">--with-pic</code><span style="background-color: rgb(255, 255, 0);">.</span><br>
<br>By the way, previously I performed "make" with FFTW version 3.2.2 (default version in rocks cluster 5.4)<br><br>I did:<br><br>root@bioinfocluster fftw-3.2.2]# ./configure --enable-threads --prefix=/share/apps/opt/fftw<div>
<br>Without errors, and then:<br></div><div><br></div><div>[root@bioinfocluster fftw-3.2.2]# make</div><div><br></div><div>make[3]: Leaving directory `/share/apps/src/fftw-3.2.2/tools'</div>
<div>make[2]: Leaving directory `/share/apps/src/fftw-3.2.2/tools'</div><div>Making all in m4</div><div>make[2]: Entering directory `/share/apps/src/fftw-3.2.2/m4'</div><div>make[2]: Nothing to be done for `all'.</div>
<div>make[2]: Leaving directory `/share/apps/src/fftw-3.2.2/m4'</div><div>make[1]: Leaving directory `/share/apps/src/fftw-3.2.2'</div><div><br>What could be the problem? please advices.<br><br>Miguel Quiliano.<br>
</div><br><div class="gmail_quote"><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
Miguel Quiliano Meza wrote:<br>
> Dear community.<br>
><br>
> Justin was right.<br>
><br>
> I did not want to make the explanation so long, but you're right I have<br>
> to put those details. As you will see I had to redirect the "outputs"<br>
> after perform "*./configure*" and "*make*" (these files are attach to<br>
> this mail).<br>
><br>
> I sincerely hope you can give their opinions and help.<br>
><br>
> Thanks in advance.<br>
><br>
> Miguel Quiliano.<br>
><br>
> Here are the general procedure:<br>
><br>
> root@bioinfocluster src]# tar xf gromacs-4.5.4.tar.gz<br>
> [root@bioinfocluster src]# export LDFLAGS="-L/opt/rocks/lib"<br>
> [root@bioinfocluster src]# export CPPFLAGS="-I/opt/rocks/include"<br>
> [root@bioinfocluster gromacs-4.5.4]# ./configure --enable-mpi<br>
> --prefix=/share/apps/opt/gromacs > output<br>
> [root@bioinfocluster gromacs-4.5.4]# make >output2<br>
> mempool.c: In function '_gmx_sel_mempool_alloc_group':<br>
> mempool.c:201: warning: dereferencing type-punned pointer will break<br>
> strict-aliasing rules<br>
> selelem.c: In function '_gmx_selelem_mempool_reserve':<br>
> selelem.c:203: warning: dereferencing type-punned pointer will break<br>
> strict-aliasing rules<br>
> selelem.c:208: warning: dereferencing type-punned pointer will break<br>
> strict-aliasing rules<br>
> checkpoint.c: In function 'do_cpt_state':<br>
> checkpoint.c:852: warning: dereferencing type-punned pointer will break<br>
> strict-aliasing rules<br>
> /usr/bin/ld: /opt/rocks/lib/libfftw3f.a(plan-guru-dft-c2r.o): relocation<br>
> R_X86_64_32 against `a local symbol' can not be used when making a<br>
> shared object; recompile with -fPIC<br>
<br>
This issue and its resolution are specifically described in the installation<br>
instructions:<br>
<br>
<a href="http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites" target="_blank">http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites</a><br>
<br>
(Under the "a few tips" heading)<br>
<br>
-Justin<br>
<br>
> /opt/rocks/lib/libfftw3f.a: could not read symbols: Bad value<br>
> collect2: ld returned 1 exit status<br>
> make[3]: *** [<a href="http://libmd_mpi.la" target="_blank">libmd_mpi.la</a> <<a href="http://libmd_mpi.la/" target="_blank">http://libmd_mpi.la/</a>>] Error 1<br>
> make[2]: *** [all-recursive] Error 1<br>
> make[1]: *** [all] Error 2<br>
> make: *** [all-recursive] Error 1<br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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