[gmx-users] pdb2gmx segmentation fault
Ragothaman Yennamalli
ragothaman at gmail.com
Wed Apr 20 17:23:25 CEST 2011
On Wed, Apr 20, 2011 at 9:46 AM, Justin A. Lemkul <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>> 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>
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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> (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
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>> <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
>
> ========================================
> --
> 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!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to 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.artistrkrishnarao.com/
***************************************
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