[gmx-developers] uninitialized data

[Alexander Herz]

Hey,

so the latest news on this, simply running with the walls enabled gives
(unmodified gromacs4.0.4 on 64 bit intel core2 duo (non parallel run) on
ubuntu 8.10; valgrind --leak-check mdrun ...):

Back Off! I just backed up md.log to ./#md.log.2#
Reading file nvt.tpr, VERSION 4.0.4 (double precision)

Back Off! I just backed up nvt.trr to ./#nvt.trr.1#

Back Off! I just backed up ener.edr to ./#ener.edr.2#
starting mdrun 'Electrolyte on gold 111 surface in water'
5000 steps,     10.0 ps.
==9419== Conditional jump or move depends on uninitialised value(s)
==9419==    at 0x4C9222: do_walls (wall.c:148)
==9419==    by 0x46D428: do_force_lowlevel (force.c:1591)
==9419==    by 0x4A7D10: do_force (sim_util.c:562)
==9419==    by 0x42938E: do_md (md.c:1116)
==9419==    by 0x4269FA: mdrunner (md.c:426)
==9419==    by 0x42C579: main (mdrun.c:492)
==9419==
==9419== Conditional jump or move depends on uninitialised value(s)
==9419==    at 0x4C923A: do_walls (wall.c:148)
==9419==    by 0x46D428: do_force_lowlevel (force.c:1591)
==9419==    by 0x4A7D10: do_force (sim_util.c:562)
==9419==    by 0x42938E: do_md (md.c:1116)
==9419==    by 0x4269FA: mdrunner (md.c:426)
==9419==    by 0x42C579: main (mdrun.c:492)
==9419==
==9419== More than 10000000 total errors detected.  I'm not reporting
any more.
==9419== Final error counts will be inaccurate.  Go fix your program!
==9419== Rerun with --error-limit=no to disable this cutoff.  Note
==9419== that errors may occur in your program without prior warning from
==9419== Valgrind, because errors are no longer being displayed.
==9419==
^C==9419==
==9419== ERROR SUMMARY: 10000000 errors from 2 contexts (suppressed: 112
from 2)
==9419== malloc/free: in use at exit: 0 bytes in 0 blocks.
==9419== malloc/free: 0 allocs, 0 frees, 0 bytes allocated.
==9419== For counts of detected errors, rerun with: -v
==9419== All heap blocks were freed -- no leaks are possible.

mdp:

; RUN CONTROL PARAMETERS =
integrator               = sd
; start time and timestep in ps =
tinit                    = 0
dt                       = 0.002
nsteps                   = 5000
; number of steps for center of mass motion removal =
nstcomm                  = 100
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout                  = 1
nstvout                  = 500
nstfout                  = 0
; Output frequency for energies to log file and energy file =
nstlog                   = 500
nstenergy                = 500
; Output frequency and precision for xtc file =
nstxtcout                = 0
xtc-precision            = 1000
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
;xtc_grps                 =
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist                  = 10
; ns algorithm (simple or grid) =
ns_type                  = grid
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r                = 1
; Method for doing Van der Waals =
vdw-type                 = switch
; cut-off lengths        =
rvdw-switch              = 0.75
rvdw                     = 0.8
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr                  = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing           = 0.1
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
epsilon_surface          = 0
optimize_fft             = no
;restraints
dihre=no
dihre-fc=1
nstdihreout=1000
disre=simple
disre_fc=1
;OPTIONS FOR TEMPERATURE COUPLING
tc_grps                  = system
tau_t                    = 0.1
ref_t                    = 300
;OPTIONS FOR PRESSURE COUPLING
Pcoupl                   = No
tau_p                    = 0.5
compressibility          = 4.5e-05
ref_p                    = 1.0
; Free energy control stuff
free_energy              = no
init_lambda              = 0.0
delta_lambda             = 0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = -1
; OPTIONS FOR BONDS     =
constraints              = h-bonds

freezegrps               = GLD
energygrps                 = GLD SOL
energygrp_excl             = GLD GLD
freezedim                = Y Y Y

; Periodic boundary conditions: xyz or none =
pbc                      = xy
;rcoulomb-switch          = 0
rcoulomb                 = 0.8
; nblist cut-off         =
rlist                    = 0.8

; walls:
nwall                = 2
wall_type            = 9-3
wall_density        = 30 30
wall_atomtype        = OW OW           
wall_r_linpot        = -1

The valgrind error about the forcerec has vanished after I added the
memset mentioned in the other mail.

ALex