<br><br><div class="gmail_quote">On Wed, Apr 20, 2011 at 9:46 AM, Justin A. Lemkul <span dir="ltr">&lt;<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">

<div class="im"><br>
<br>
Ragothaman Yennamalli wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Justin,<br>
<br>
Thanks for the mail. Yes, without these CFLAGS the &quot;make&quot; was not successful. Yes I did set the CPPFLAGS and LDFLAGS before configuring gromacs. Since without it it would have stopped compiling. I want to agree with you that it is some issue with shared libraries, but i dont think it is the issue since I have used the flag --enable-shared. Also, <br>


</blockquote>
<br></div>
You did --enable-shared for FFTW, but not Gromacs.  Perhaps there is some mismatch there.<div class="im"><br></div></blockquote><div><br>Since configure did not have any such option, i did not use it. However, I tried compiling with --enable-shared to reinstall gromacs. It installed without any issues. But, the same segmentation fault.<br>

 </div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
if this was the case then editconf would not have worked as well.<br>
<br>
</blockquote>
<br></div>
I wouldn&#39;t rule it out just yet.  If the installation was successful, everything would work.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thanks and Regards,<br>
Raghu<div><div></div><div class="h5"><br>
<br>
On Wed, Apr 20, 2011 at 8:33 AM, Justin A. Lemkul &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt; wrote:<br>


<br>
<br>
<br>
    Ragothaman Yennamalli wrote:<br>
<br>
        These were the exact commands used to install fftw 3.2.2<br>
        ./configure  --prefix=/export/home/raghu/fftw --enable-float<br>
        --enable-shared CC=cc F77=f77<br>
        make -j 48<br>
        make install<br>
<br>
        These were the exact commands used to install gromacs4.5.4<br>
        ./configure  --prefix=/export/home/raghu/gromacs<br>
        --with-fft=fftw3 --without-x --enable-float CC=gcc-4.3.2<br>
        CXX=g++-4.3.2 CFLAGS=&#39;-O3 -fomit-frame-pointer<br>
        -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops<br>
        -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS&#39;<br>
<br>
<br>
    I&#39;m no compiler expert, but is it necessary to set all these CFLAGS<br>
    here?  Does the installation fail for some reason if they&#39;re not set?<br>
<br>
    Also, how is Gromacs finding FFTW?  You haven&#39;t set the CPPFLAGS or<br>
    LDFLAGS.<br>
<br>
<br>
        make -j 48<br>
        make install<br>
<br>
        I had installed the gromacs version 4.5.3 earlier and<br>
        encountered the same problem with pdb2gmx. Hence installed the<br>
        latest version.<br>
<br>
<br>
    This would indicate to me that the problem is not necessarily in<br>
    Gromacs, but the way you&#39;re installing it, and as Mark suggested, is<br>
    probably related to some static/shared library issue.<br>
<br>
    -Justin<br>
<br>
        Thanks and Regards,<br>
        Raghu<br>
<br>
<br>
<br>
        On Wed, Apr 20, 2011 at 7:39 AM, Justin A. Lemkul<br>
        &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;<br></div></div><div><div></div><div class="h5">
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;&gt; wrote:<br>
<br>
<br>
<br>
           Ragothaman Yennamalli wrote:<br>
<br>
               I had the issue of shared libraries while installing<br>
        which I did<br>
               troubleshoot and the installation went without any errors. I<br>
               tried converting the pdb file to a new one using editconf<br>
        and it<br>
               runs perfectly fine. So, there is some issue with<br>
        pdb2gmx, which<br>
               I am not able to detect.<br>
               Any hints will be appreciated.<br>
<br>
<br>
           Please provide the exact commands that you used to install<br>
        Gromacs.<br>
            What exactly were the issues that you had to circumvent?<br>
         Have you<br>
           installed previous versions of Gromacs that have worked, such<br>
        that<br>
           this problem is specific to 4.5.4?<br>
<br>
           -Justin<br>
<br>
               Thanks and Regards,<br>
               Raghu<br>
<br>
               Subject: Re: [gmx-users] pdb2gmx segmentation fault<br>
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<br>
               Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
               On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote:<br>
                &gt; Hi,<br>
                &gt; I have installed the latest version of gromacs 4.5.4<br>
        and the<br>
                &gt; installation went fine. When I run pdb2gmx I get<br>
        Segmentation<br>
               fault<br>
                &gt; even before I could select the force field options. I<br>
        tried with<br>
                &gt; different pdb files and I get seg fault without any other<br>
               error messages.<br>
                &gt; The command is: pdb2gmx -f new.pdb -o conf.gro -p<br>
        topol.top<br>
<br>
               Probably, no other GROMACS command works either, because<br>
        of some<br>
               shared<br>
               library issue related to your new installation.<br>
<br>
               Mark<br>
<br>
<br>
<br>
<br>
               --         ****************************************<br>
               Ragothaman M Yennamalli, Ph.D.<br>
               Postdoctoral Research Associate<br>
               1012 Crop Genome Informatics Laboratory<br>
               Department of Genetics, Development and Cell Biology<br>
               Iowa State University<br>
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           --     ========================================<br>
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           Ph.D. Candidate<br>
           ICTAS Doctoral Scholar<br>
           MILES-IGERT Trainee<br>
           Department of Biochemistry<br>
           Virginia Tech<br>
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        1012 Crop Genome Informatics Laboratory<br>
        Department of Genetics, Development and Cell Biology<br>
        Iowa State University<br>
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1012 Crop Genome Informatics Laboratory<br>
Department of Genetics, Development and Cell Biology<br>
Iowa State University<br>
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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> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><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>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>****************************************<br>Ragothaman M Yennamalli, Ph.D.<br>Postdoctoral Research Associate<br>1012 Crop Genome Informatics Laboratory<br>Department of Genetics, Development and Cell Biology<br>

Iowa State University<br>Ames, Iowa 50011-3260 USA<br><br>+1 515-294-8971 (Office)<br>+1 515-294-8280 (Fax)<br>+1 515-851-1016 (Mobile)<br><br>&quot;When
 you can do the common things of life in an uncommon way, you will 
command the attention of the world.&quot; -George Washington Carver<br><br><a href="http://www.public.iastate.edu/%7Eraghu/" target="_blank">http://www.public.iastate.edu/~raghu/</a><br><a href="http://www.artistrkrishnarao.com/" target="_blank">http://www.artistrkrishnarao.com/</a><br>

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