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 <jalem...@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 (mockbu...@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 <jalem...@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@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-requ...@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@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-requ...@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@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Reply via email to