[gmx-users] grompp segmentation error
ram bio
rmbio861 at gmail.com
Wed Jan 6 10:34:10 CET 2010
Dear Justin,
I am having grompp segmentation error only for the drug-enzyme complex
tutorial, all other executables are ok, can this occur due to the any
other reasons like following the tutorial improperly.
Thanks,
Ram
On Tue, Jan 5, 2010 at 1:24 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>>>>>
>>>>> ========================================
>>>>> --
>>>>> 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/search before
>>>>> posting!
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>>>>> interface
>>>>> or send it to gmx-users-request at gromacs.org.
>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>
>>> --
>>> ========================================
>>>
>>> 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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>>> Please search the archive at http://www.gromacs.org/search before
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>>> or send it to gmx-users-request 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
>
> ========================================
> --
> 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/search before posting!
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