[gmx-users] grompp segmentation error
Justin A. Lemkul
jalemkul at vt.edu
Tue Jan 5 19:24:51 CET 2010
ram bio wrote:
> 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.
Does grompp give any other output, or does it just seg fault? Do other
executables work on this system?
There are a whole host of issues that could be causing this, from 32/64 bit
mismatch, shared libraries being moved, etc, so it is very difficult to
diagnose. Was the whole package compiled with MPI (per the above command)? If
so, there is no point, since the only MPI-enabled executable is mdrun. It may
help to re-compile correctly if this is the case (a bit of a long shot, but
perhaps worth trying). Do you have gcc available on the cluster, to test and
see if it produces functioning code?
-Justin
>
> 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
>>
>> ========================================
>> --
>> gmx-users mailing list gmx-users at gromacs.org
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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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