[gmx-users] need help with mdrun

[Dodi Heryadi]

Hello,

One of our Gromacs users at NCSA reported that his Gromacs job was aborted 
after a few seconds of
running mdrun. The Gromacs he used was compiled with MPI on SGI IRIX 6.5.14 
using MIPSPro 7.3.1.3m
compiler. Similar behavior was also observed when I ran the same tpr file 
on MPI Gromacs compiled on
our IA32 Linux Cluster using Intel Compiler.

I'm new to Gromacs. Nevertheless, using dbx on the SGI Origin I tried to 
find out what might cause the error.
At the end of this  note, I  am including the last few lines from running 
mdrun and the first few lines from running dbx.
We'd really  appreciate it if someone could look at this problem and shed 
us some light. I'll be happy to send you the input files.

thanks,
--Dodi
-------------------------------------------------------------------------
Dodi Heryadi, PhD
NCSA @ University of Illinois at Urbana-Champaign
Phone:(217)-333-6078 Fax: (217)-244-2909
--------------------------------------------------------------------------

================ start of running mdrun ==============================

Back Off! I just backed up md.log to ./#md.log.2#
Reading file dppc128c.tpr, VERSION 3.1.4 (single precision)
Reading file dppc128c.tpr, VERSION 3.1.4 (single precision)

Back Off! I just backed up ener.edr to ./#ener.edr.2#
starting mdrun 'dppc in water'
250000 steps, 500.0 ps.

MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
MPI: aborting job

================== end of running mdrun =============================


=================== start of running dbx 
=========================================
modi4 167% dbx 
/usr/apps/chemistry/gromacs-3.1.4/mips-sgi-irix6.5/r10000/bin/mdrun 
core.43780720
dbx version 7.3.1 68542_Oct26 MR Oct 26 2000 17:50:34
Core from signal SIGBUS: Bus error
(dbx) where
 > 0 inl3100(0x107fd804, 0x11181178, 0x111cc1a8, 0x1149b2c0, 0x111b3198, 
0x102262a0, 0x102263f0, 0x1119a188) 
["/usr/apps/chemistry/gromacs-3.1.4/gromacs-3.1.4/src/gmxlib/innerf.f":16460, 
0x1011e470]
  1 do_fnbf(log = 0xdb33e50, cr = 0x10227148, fr = 0x107fd710, x = 0x107977f8,
f = 0x10b489f0, mdatoms = 0x10226fa0, egnb = 0x10223748, egcoul = 
0x102236d0, box_size = 0xffffff2668, nrnb = 0xffffff2980, lambda = 0.0, 
dvdlambda = 0x10223850, bLR = 0, eNL = -1) 
["/usr/apps/chemistry/gromacs-3.1.4/gromacs-3.1.4/src/gmxlib/fnbf.c":729, 
0x100cacd8]
  2 force(fp = 0xdb33e50, step = 0, fr = 0x107fd710, ir = 0x10224da0, idef 
= 0x1078b3a0, nsb = 0x10223d78, cr = 0x10227148, mcr = (nil), nrnb = 
0xffffff2980, grps = 0x10222290, md = 0x10226fa0, ngener = 2, opts = 
0x10224f20, x = 0x107977f8, f = 0x10b489f0, epot = 0x102237a8, fcd = 
0x10226e98, bVerbose = 0, box = 0x10224ff0, lambda = 0.0, graph = 
0x10222248, excl = 0x107966c8, bNBFonly = 0, lr_vir = 0xffffff2dd0, mu_tot =
0xffffff2e20, qsum = 1.1444091796875e-05, bGatherOnly
= 0) 
["/usr/apps/chemistry/gromacs-3.1.4/gromacs-3.1.4/src/mdlib/force.c":880, 
0x1005df7c]
  3 do_force(log = 0xdb33e50, cr = 0x10227148, mcr = (nil), parm = 0x10224da0,
nsb = 0x10223d78, vir_part = 0xffffff2da8, pme_vir = 0xffffff2dd0, step = 
0, nrnb = 0xffffff2980, top = 0x1078b398, grps = 0x10222290, x = 
0x107977f8, v = 0x107ca600, f = 0x10b489f0, buf = 0x10b15be8, mdatoms = 
0x10226fa0, ener = 0x102237a8, fcd = 0x10226e98, bVerbose = 0, lambda = 
0.0, graph = 0x10222248, bNS = 1, bNBFonly = 0, fr = 0x107fd710, mu_tot = 
0xffffff2e20, bGatherOnly = 0) 
["/usr/apps/chemistry/gromacs-3.1.4/gromacs-3.1.4/src/mdlib/sim_util.c":282, 
0x10054d00]

======================= end of running dbx 
================================================