[gmx-users] segmentation fault in mdrun when using PME

[Diane Fournier]

-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of David van der Spoel
Sent: Sat 4/29/2006 2:25 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] segmentation fault in mdrun when using PME
 
Diane Fournier wrote:
> Hi, I'm new to Gromacs and I'm trying to run a enzyme-ligand complex 
> molecular dynamics simulation. I have tried doing John 
> Kerrigan's Drug-Enzyme tutorial and mdrun crashes with segmentation 
> fault and core dump at the steepest descents minimization step. However, 
> mdrun works fine when using cutoff instead of PME. 
>  
> I'm working with Gromacs v. 3.3.1 on a SGI altix 3700 with 32 Intel 
> Itanium 2 processors (but I'm currently using a single node, so it's not 
> a MPI problem) under Red Hat Enterprise Linux AS release 3 with Intel 
> Math Kernel Librarary (MKL) v. 8.0.1 as FFT library (which is optimized 
> for Itanium 2).
>  
> the em.mdp file looks like:
>  
> title               =  drg_trp
> cpp                 =  /usr/bin/cpp
> define              =  -DFLEX_SPC
> constraints         =  none
> integrator          =  steep
> dt                  =  0.002    ; ps !
> nsteps              =  500
> nstlist             =  10
> ns_type             =  grid
> rlist               =  0.9
> coulombtype             =  PME
> rcoulomb            =  0.9
> rvdw                =  0.9
> fourierspacing          =  0.12
> fourier_nx              =  0
> fourier_ny              =  0
> fourier_nz              =  0
> pme_order               =  4
> ewald_rtol              =  1e-5
> optimize_fft            =  yes
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  1000.0
> emstep              =  0.01
> Is it possible this could be related to insufficient memory allocation ? 
> How demanding is this PME calculation ?
Not likely a memory problem. It could be a compiler issue but we need 
more info! Where does it crash? Is it reproducible? DOes the same tpr 
file cause a crash on another architecture (e.g. your desktop)?

I installed gromacs 3.3.1 on my desktop (Pentium 4 under linux fedora core 4 and using the fftw3 fourier transform library). I used the .tpr file generated on the altix in mdrun and it worked fine. 

When I run that same file on the altix, it crashes every time without any iteration in the .log file:

Removing pbc first time
Done rmpbc
Initiating Steepest Descents
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest, initial mass: 14580
Started Steepest Descents on node 0 Mon May  1 11:47:39 2006

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------


After that the file ends. There is no other error message than segmentation fault with core dump.

The compilers that are used on the altix are:
           C++ Version 9                9.0-023 -> 9.0-031
           C++ Version 8                8.1-033 -> 8.1-036
           Fortran 9                    9.0-021 -> 9.0-032
           Fortran 8                    8.1-029 -> 8.1-033
           IPP                          4.1 -> 5.0


>  
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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

-------------- next part --------------
A non-text attachment was scrubbed...
Name: winmail.dat
Type: application/ms-tnef
Size: 5083 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060501/725d57a3/attachment.bin>