[gmx-users] 4.0.3 goes off into la la land .... infinite loop

[Dallas B. Warren]

Alluded to this yesterday, GROMACS jobs don't finish on a SC.  I have some information back from one of the admins there, they want me to post details etc so we can work out what is going on.

It looks like with my input data, GROMACS going into an infinite loop in the nb_kernel100_ia64_single subroutine.

Can provide the tpr file assembled on the SC if / as required.

GROMACS 4.0.3 on the SC was compiled with intel-cc v.11.0.069 with fftw v.2.1.5 on itanium ia64.

Program works fine with generic kernel gmx_nb_generic_kernel but goes to infinite loop inside nb_kernel110_ia64_single.

Double precision version works exactly the same way: fine with generic kernel, infinite loop in nb_kernel110_ia64_double.

The details of the installation of double precision, single processor version:

setenv CC icc
setenv CFLAGS "-O3 -ip -ftz"
setenv CPPFLAGS "-I$FFTWDIR/include"
setenv CXX icpc
setenv MPI icc
setenv F77 ifort
setenv FFLAGS "-O3 -ip -ftz"
setenv LD ifort
setenv LDFLAGS "-L$FFTWDIR/lib"

./configure --prefix=/opt/gromacs/4.0.3 --exec-prefix=/opt/gromacs/4.0.3 --disable-nice --disable-float --program-suffix=_d --with-fft=fftw2

gmake
gmake install

My md.mdp file for these runs is (yes, I need to update a few things in this, but want to make some comparisons between versions etc first):

;       Run Control
integrator      =  md                           ; simulation algorithm
dt              =  0.005                        ; time step (ps)
nsteps          =  20000                        ; # steps
comm_mode       =  linear                       ; c.o.m. motion reset
nstcomm         =  1                            ; steps for c.o.m. motion reset
comm_grps       =  System                       ; groups for c.o.m. removal
;
;       Output Control
nstxout         =  5000                         ; write coordinates to .trr
nstvout         =  5000                         ; write velocities to .trr
nstlog          =  800                          ; write energies to .log
nstenergy       =  400                          ; write energies to .edr
nstxtcout       =  800                          ; write coordinates to .xtc
;
;       Neightbour Searching
nstlist         =  10                           ; update neighbour list
ns_type         =  grid                         ; neighbour list method
pbc             =  xyz                          ; periodic boundary conditions
rlist           =  1.0                          ; cut-off for short-range neighbour (nm)
;
;       Electrostatics and VdW
coulombtype     =  cut-off                      ; type of coulomb interaction
rcoulomb        =  1.5                          ; cut-off distance for coulomb (nm)
epsilon_r       =  1                            ; dielectric constant
vdwtype         =  cut-off                      ; type of VdW interaction
rvdw            =  1.0                          ; cut-off for vdw (nm)
DispCorr        =  EnerPres                     ; long range correction
;
;       Temperature Coupling
Tcoupl          =  berendsen                    ; type of temperature coupling
tc-grps         =  System                       ; coupled groups
tau_t           =  .05                          ; T-coupling time constant (ps)
ref_t           =  310                          ; reference temperature (K)
;
;       Pressure Coupling
Pcoupl          =  berendsen                    ; type of pressure coupling
Pcoupltype      =  anisotropic                  ; pressure coupling geometry
tau_p           =  4.0 4.0 4.0 4.0 4.0 4.0      ; p-coupling time constant (ps)
compressibility =  4.5e-5 4.5e-5 4.5e-5 0 0 0   ; compressibiity
ref_p           =  1.0 1.0 1.0 0 0 0            ; reference pressure (bar)
;
;       Velocity Generation
gen_vel         =  no                           ; generate initial velocities
;
;       Bonds
constraints     =  all-bonds                    ; which bonds to contrain
constraint_algorithm    =  lincs                ; algorithm to use
lincs_order     =  8                            ; highest order matrix expansion

Catch ya,

Dr Dallas Warren
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