[gmx-developers] Re: [gmx-users] grompp segmentation error
Justin A. Lemkul
jalemkul at vt.edu
Wed Jan 6 13:00:21 CET 2010
On 1/6/10 4:34 AM, ram bio wrote:
> 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.
>
So using grompp on other systems works fine? This would have been good to know
early on. I know you said you were working on the drug-enzyme tutorial, but not
that it was the *only* system that gives you problems.
If this is the case, start over to make sure you haven't made any mistakes. I
don't know why grompp would be doing this for only one system but not others.
-Justin
> 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!
>>>>>> 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/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
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/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/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
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/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/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
========================================
More information about the gromacs.org_gmx-developers
mailing list