[gmx-users] pdb2gmx segmentation fault
Peter C. Lai
pcl at uab.edu
Thu Apr 21 00:56:51 CEST 2011
Also why the make -j 48, when you only have 8 cores?
I'm not even sure if the linker is ok with make -jN for building gromacs, it
is not listed as compatible for *BSD ports. Also, does your make (I imagine
this is Solaris make) have all the same semantics as gnu-make (gmake)?
And why did you switch your CC between fftw and gromacs configures?
Solaris 'cc' may or may not be gcc43. Also, do we know if gcc43 is stable
especially with -O3...Try removing -O3 or move it to -O2 at most...
To rule out a bad fftw library, you can set --with-fft to use the builtin
(slower) libfft instead of fftw (but fftw should not be affecting pdb2gmx
I don't think...).
I too have the questions of your CFLAGS, do you not require -m64 either?
On 2011-04-20 10:23:25AM -0500, Ragothaman Yennamalli wrote:
>
>
> On Wed, Apr 20, 2011 at 9:46 AM, Justin A. Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:
>
>
> 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.
>
>
> 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.
>
>
> 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> <mailto: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>>
> <mailto: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>>
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> 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>
> <tel:%2B1%20515-294-8971> (Office)
> +1 515-294-8280<tel:%2B1%20515-294-8280> <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>
> <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.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> <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
>
> ========================================
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>
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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<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>>
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> Please search the archive at
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> <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/
>
> ***************************************
>
> --
> gmx-users mailing list 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!
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--
===============================================================
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | BEC 257
Genetics, Div. of Research | 1150 10th Avenue South
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
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