[gmx-users] pdb2gmx segmentation fault
Justin A. Lemkul
jalemkul at vt.edu
Wed Apr 20 16:46:29 CEST 2011
Ragothaman Yennamalli wrote:
> Dear Justin,
>
> 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,
You did --enable-shared for FFTW, but not Gromacs. Perhaps there is some
mismatch there.
> if this was the case then editconf would not have worked as well.
>
I wouldn't rule it out just yet. If the installation was successful, everything
would work.
-Justin
> Thanks and Regards,
> Raghu
>
> On Wed, Apr 20, 2011 at 8:33 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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>
> <mailto: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>> <mailto: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>>
> <mailto: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>
> <tel:%2B1%20515-294-8971> (Office)
> +1 515-294-8280 <tel:%2B1%20515-294-8280>
> <tel:%2B1%20515-294-8280> (Fax)
> +1 515-851-1016 <tel:%2B1%20515-851-1016>
> <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.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> <http://vt.edu> | (540)
> 231-9080 <tel:%28540%29%20231-9080>
> <tel:%28540%29%20231-9080>
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> -- gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>.
>
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> --
> ****************************************
> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> --
> ****************************************
> 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
========================================
More information about the gromacs.org_gmx-users
mailing list