[gmx-users] grompp segmentation error

ram bio rmbio861 at gmail.com
Tue Jan 5 16:57:21 CET 2010


Dear Justin,

Thanks for the response.

Here is the info regarding the cluster where gromacs version 4.0.5 is
installed with icc compliers.

 $ ./configure --prefix=/usr/local/gromacs --enable-mpi --with-fft=fftw2
uname -m = x86_64
uname -r = 2.6.18-128.7.1.el5
uname -s = Linux
uname -v = #1 SMP Mon Aug 24 08:21:56 EDT 2009
compilers: C and fortran Intel 10.1

Please suggest me as the grompp command also donot work with this configuration.

Thanks,

Ram

On Mon, Jan 4, 2010 at 6:17 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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