[gmx-users] grompp segmentation error

Justin A. Lemkul jalemkul at vt.edu
Mon Jan 4 13:47:34 CET 2010



ram bio wrote:
> Dear Justin,
> 
> Thanks for the response.
> 
> I am using gromacs 4.0.3 version on my PC and 4.0.5 on cluster, I have
> asked my system admin to provide the details regarding the cluster,
> whereas for my PC:
> 
> The info is as follows:
> 
> 1. The Gromacs version you are using. - 4.0.3
> 2. The compilers used in installing Gromacs.- gcc
> gcc -v
> Using built-in specs.
> Target: i386-redhat-linux
> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
> --infodir=/usr/share/info --enable-shared --enable-threads=posix
> --enable-checking=release --with-system-zlib --enable-__cxa_atexit
> --disable-libunwind-exceptions --enable-libgcj-multifile
> --enable-languages=c,c++,objc,obj-c++,java,fortran,ada
> --enable-java-awt=gtk --disable-dssi --enable-plugin
> --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre
> --with-cpu=generic --host=i386-redhat-linux
> Thread model: posix
> gcc version 4.1.2 20080704 (Red Hat 4.1.2-44)
> 

The gcc 4.1.x is well-known to be buggy, and as advised on the Gromacs source 
code download site:

"WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These 
compilers come with recent Linux distrubutions like Fedora 5/6 etc."

I would suggest updating to the latest version of Gromacs (4.0.7), using a more 
reliable compiler (other versions of gcc, i.e. 4.0.x and older, and 4.2.x and 
newer, are fine).

>  3. Options specified during configuration.
> 
> I didnot get this, can you please elaborate...
> 

Things like --enable-shared, --disable-(whatever), but I don't know that any of 
this is relevant.  I think the compiler is the problem.

-Justin

> 
> 4. Specifications of your hardware.
> 
> processor       : 0
> vendor_id       : GenuineIntel
> cpu family      : 6
> model           : 13
> model name      : Intel(R) Pentium(R) M processor 1.70GHz
> stepping        : 6
> cpu MHz         : 600.000
> cache size      : 2048 KB
> fdiv_bug        : no
> hlt_bug         : no
> f00f_bug        : no
> coma_bug        : no
> fpu             : yes
> fpu_exception   : yes
> cpuid level     : 2
> wp              : yes
> flags           : fpu vme de pse tsc msr mce cx8 mtrr pge mca cmov pat
> clflush dts acpi mmx fxsr sse sse2 ss tm pbe up est tm2
> bogomips        : 1196.53
> 
> Linux version 2.6.18-8.el5 (mockbuild at builder4.centos.org) (gcc
> version 4.1.1 20070105 (Red Hat 4.1.1-52)) #1 SMP Thu Mar 15 19:57:35
> EDT 2007
> 
> Build Operating System: Linux 2.6.18-53.1.14.el5PAE i686 Red Hat, Inc.
> Current Operating System: Linux localhost.localdomain 2.6.18-8.el5 #1
> SMP Thu Mar 15 19:57:35 EDT 2007 i686
> Build Date: 21 June 2008
> Build ID: xorg-x11-server 1.1.1-48.41.el5_2.1
> 
> 
> I would be providing the info about the cluster, once I receive it,
> mean please let me know if any info is missing and help me.
> 
> Thanks,
> 
> Ram
> 
> 
> 
> 
> 
> On Thu, Dec 31, 2009 at 11:49 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> ram bio wrote:
>>> Dear Gromacs Users,
>>>
>>> Iam following Drug/Enzyme complex solvation tutorial by John E.
>>> Kerrigan, I am unable to execute the grompp step as per the tutorial,
>>> the output of grompp command is as follows:
>>>
>>> grompp -f minim.mdp -c trp_b4ion.gro -p trp.top -o trp_b4ion.tpr
>>>
>>>
>>>                               :-)  grompp  (-:
>>>
>>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.11#
>>> checking input for internal consistency...
>>> processing topology...
>>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp
>>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp
>>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6bon.itp
>>> Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
>>> Segmentation fault
>>>
>>> what i have done is as per the tutorial, that is
>>> 1) generated the drg.itp using prodrug beta
>>> 2) executed pdb2gmx using 4 that is ff53a6 ff
>>> 3) edit the drg.itp by removing the lines redundant as per trp.top
>>> 4) edit trp.gro by adding drg coordinates and chainging the numbers
>>>
>>> please help me to overcome this error, for your convenience I have
>>> attached the drg.itp, trp.top, trp.gro and trp_b4ion.gro files.
>>>
>> I doubt any of these files will be useful.  Better information would
>> include:
>>
>> 1. The Gromacs version you are using.
>> 2. The compilers used in installing Gromacs.
>> 3. Options specified during configuration.
>> 4. Specifications of your hardware.
>>
>> A segmentation fault is a memory error and can have numerous causes.  The
>> above information may be useful.
>>
>> -Justin
>>
>>> Thanks,
>>>
>>> Ram
>>> 4 attachments —
>> --
>> ========================================
>>
>> 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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> 

-- 
========================================

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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