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

[David van der Spoel]

Diane Fournier wrote:
> 
> 
> -----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

Have you enabled fortran at the compilation stage? In that case try it 
without, otherwise please file a bugzilla, such that we can document 
this problem (and try to fix it of course).

> 
> 
> 
>> 
>>
>>
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> 
> 
> 
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-- 
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
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