<br><br><div class="gmail_quote">On Wed, Apr 20, 2011 at 9:46 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></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 "make" 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'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 <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> 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='-O3 -fomit-frame-pointer<br>
-finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops<br>
-std=gnu99 -D_POSIX_PTHREAD_SEMANTICS'<br>
<br>
<br>
I'm no compiler expert, but is it necessary to set all these CFLAGS<br>
here? Does the installation fail for some reason if they're not set?<br>
<br>
Also, how is Gromacs finding FFTW? You haven'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'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>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br></div></div><div><div></div><div class="h5">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> 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>
To: Discussion list for GROMACS users<br>
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Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote:<br>
> Hi,<br>
> I have installed the latest version of gromacs 4.5.4<br>
and the<br>
> installation went fine. When I run pdb2gmx I get<br>
Segmentation<br>
fault<br>
> even before I could select the force field options. I<br>
tried with<br>
> different pdb files and I get seg fault without any other<br>
error messages.<br>
> 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>
Ames, Iowa 50011-3260 USA<br>
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MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div></div>
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-- ****************************************<br>
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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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Department of Biochemistry<br>
Virginia Tech<br>
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****************************************<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>
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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>
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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>
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