[gmx-users] pdb2gmx segmentation fault
Justin A. Lemkul
jalemkul at vt.edu
Wed Apr 20 15:33:27 CEST 2011
Ragothaman Yennamalli wrote:
> These were the exact commands used to install fftw 3.2.2
> ./configure --prefix=/export/home/raghu/fftw --enable-float
> --enable-shared CC=cc F77=f77
> make -j 48
> make install
>
> These were the exact commands used to install gromacs4.5.4
> ./configure --prefix=/export/home/raghu/gromacs --with-fft=fftw3
> --without-x --enable-float CC=gcc-4.3.2 CXX=g++-4.3.2 CFLAGS='-O3
> -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
> -funroll-all-loops -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS'
I'm no compiler expert, but is it necessary to set all these CFLAGS here? Does
the installation fail for some reason if they're not set?
Also, how is Gromacs finding FFTW? You haven't set the CPPFLAGS or LDFLAGS.
> make -j 48
> make install
>
> I had installed the gromacs version 4.5.3 earlier and encountered the
> same problem with pdb2gmx. Hence installed the latest version.
This would indicate to me that the problem is not necessarily in Gromacs, but
the way you're installing it, and as Mark suggested, is probably related to some
static/shared library issue.
-Justin
> Thanks and Regards,
> Raghu
>
>
> On Wed, Apr 20, 2011 at 7:39 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Ragothaman Yennamalli wrote:
>
> I had the issue of shared libraries while installing which I did
> troubleshoot and the installation went without any errors. I
> tried converting the pdb file to a new one using editconf and it
> runs perfectly fine. So, there is some issue with pdb2gmx, which
> I am not able to detect.
> Any hints will be appreciated.
>
>
> Please provide the exact commands that you used to install Gromacs.
> What exactly were the issues that you had to circumvent? Have you
> installed previous versions of Gromacs that have worked, such that
> this problem is specific to 4.5.4?
>
> -Justin
>
> Thanks and Regards,
> Raghu
>
> Subject: Re: [gmx-users] pdb2gmx segmentation fault
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>>
> Message-ID: <4DAE452B.3090905 at anu.edu.au
> <mailto:4DAE452B.3090905 at anu.edu.au>
> <mailto:4DAE452B.3090905 at anu.edu.au
> <mailto:4DAE452B.3090905 at anu.edu.au>>>
>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote:
> > Hi,
> > I have installed the latest version of gromacs 4.5.4 and the
> > installation went fine. When I run pdb2gmx I get Segmentation
> fault
> > even before I could select the force field options. I tried with
> > different pdb files and I get seg fault without any other
> error messages.
> > The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top
>
> Probably, no other GROMACS command works either, because of some
> shared
> library issue related to your new installation.
>
> Mark
>
>
>
>
> --
> ****************************************
> Ragothaman M Yennamalli, Ph.D.
> Postdoctoral Research Associate
> 1012 Crop Genome Informatics Laboratory
> Department of Genetics, Development and Cell Biology
> Iowa State University
> Ames, Iowa 50011-3260 USA
>
> +1 515-294-8971 <tel:%2B1%20515-294-8971> (Office)
> +1 515-294-8280 <tel:%2B1%20515-294-8280> (Fax)
> +1 515-851-1016 <tel:%2B1%20515-851-1016> (Mobile)
>
> "When you can do the common things of life in an uncommon way,
> you will command the attention of the world." -George Washington
> Carver
>
> http://www.public.iastate.edu/~raghu/
> <http://www.public.iastate.edu/%7Eraghu/>
> <http://www.public.iastate.edu/%7Eraghu/>
> http://www.artistrkrishnarao.com/
>
> ***************************************
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> <tel:%28540%29%20231-9080>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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>
>
> --
> ****************************************
> Ragothaman M Yennamalli, Ph.D.
> Postdoctoral Research Associate
> 1012 Crop Genome Informatics Laboratory
> Department of Genetics, Development and Cell Biology
> Iowa State University
> Ames, Iowa 50011-3260 USA
>
> +1 515-294-8971 (Office)
> +1 515-294-8280 (Fax)
> +1 515-851-1016 (Mobile)
>
> "When you can do the common things of life in an uncommon way, you will
> command the attention of the world." -George Washington Carver
>
> http://www.public.iastate.edu/~raghu/
> <http://www.public.iastate.edu/%7Eraghu/>
> http://www.artistrkrishnarao.com/
>
> ***************************************
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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