[gmx-users] segfault(11) -- simulation blows up on first step
Inon Sharony
InonShar at TAU.ac.IL
Tue Jun 2 13:11:58 CEST 2009
Hi everyone!
I'm trying to run a simulation of a single diatomic Sulfur molecule. When I run an equilibration scheme (generating velocities from a 300K Maxwell-Boltzmann distribution) it runs fine, but when I take the equilibrated molecule and couple one atom to a 0K heat bath (using Stochastic Dynamics) the simulation segfaults at the first step.
I've enclosed as much information as I could. Notice (at the very bottom) that the md.log file shows an initial temperature of 17884.7K, but already in the report for step 0 the temperature, as well as many other thermodynamic quantities, are NaN.
I've encountered one reference to the same error I'm getting, but itjust said that there was some problem with the input files, but didn'tsay what was the problem...
I hope you will find some stupid mistake in the *.mdp file, or something easily remedied...
P.S.
I know GROMACS is not optimized for simulating tiny molecules, but I don't see why it should be such a critical problem...
A wholotta supplemental data:
MDRUN_MPI STD-I/O:
==================
step 0
[hydrogen:15285] *** Process received signal ***
[hydrogen:15285] Signal: Segmentation fault (11)
[hydrogen:15285] Signal code: Address not mapped (1)
[hydrogen:15285] Failing at address: 0xfffffffe16c50a90
[hydrogen:15285] [ 0] /lib64/libpthread.so.0 [0x355c00de80]
[hydrogen:15285] [ 1] mdrun_mpi(gmx_pme_do+0x28b2) [0x4b56f2]
[hydrogen:15285] [ 2] mdrun_mpi(do_force_lowlevel+0x1023) [0x47f6f3]
[hydrogen:15285] [ 3] mdrun_mpi(do_force+0xe6e) [0x4c99ce]
[hydrogen:15285] [ 4] mdrun_mpi(do_md+0x48f0) [0x42c4a0]
[hydrogen:15285] [ 5] mdrun_mpi(mdrunner+0x831) [0x42d771]
[hydrogen:15285] [ 6] mdrun_mpi(main+0x3c0) [0x42e6a0]
[hydrogen:15285] [ 7] /lib64/libc.so.6(__libc_start_main+0xf4) [0x355b41d8b4]
[hydrogen:15285] [ 8] mdrun_mpi [0x4131a9]
[hydrogen:15285] *** End of error message ***
./test-2-6-09.sh: line 16: 15285 Segmentation fault mdrun_mpi -c md -v
----------------------------------------------------------------------------------------------------------------
MD.MDP
======
integrator = sd ;stochastic dynamics (velocity Langevin) using a leap-frog algorithm
dt = 0.0001
nsteps = 10000 ; [steps] ==> total (nsteps*dt) ps.
nstxout = 1
nstvout = 1
nstfout = 1
; nstxtcout = 1
nstenergy = 1 ; write energies to energy file every 1000 steps (default 100)
nstlog = 1
energygrps = SL SR
ns_type = simple
periodic_molecules = no
coulombtype = PME
tc-grps = SL SR
tau_t = 0 1 ; mass/gamma
ref_t = 0 0 ; refference (bath) temperature
Pcoupl = no
gen_vel = no
gen_seed = -1 ; random seed based on computer clock
constraints = none
--------------------------------------------------------------------------------------------
1S2.itp
=======
[ atomtypes ]
;atomtype m (u) q (e) part.type V(cr) W(cr)
SX 32.0600 0.000 A 1E-03 1E-05
[ moleculetype ]
; Name nrexcl
1S2 2
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 SX 1 1S2 SL 1 0.000 32.0600
2 SX 1 1S2 SR 2 0.000 32.0600
[ bonds ]
; ai aj fu c0, c1, ...
1 2 2 0.2040 5.3E+6 0.2040 5.3E+6 ; SL SR
--------------------------------------------------------------------------------------------
TRAJ.TRR
========
traj.trr frame 0:
natoms= 2 step= 0 time=0.0000000e+00 lambda= 0
box (3x3):
box[ 0]={ 6.37511e+00, 0.00000e+00, 0.00000e+00}
box[ 1]={ 0.00000e+00, 6.37511e+00, 0.00000e+00}
box[ 2]={ 0.00000e+00, 0.00000e+00, 6.37511e+00}
x (2x3):
x[ 0]={ 3.19756e+00, 3.20532e+00, 3.18725e+00}
x[ 1]={ 3.03044e+00, 3.21568e+00, 3.08875e+00}
v (2x3):
v[ 0]={ 2.22763e+00, -2.56083e-01, 1.38905e+00}
v[ 1]={-2.22763e+00, 2.56083e-01, -1.38905e+00}
f (2x3):
f[ 0]={ 3.43615e+03, -2.13216e+02, 2.02509e+03}
f[ 1]={-3.43615e+03, 2.13216e+02, -2.02509e+03}
--------------------------------------------------------------------------------------------
MD.LOG
======
Input Parameters:
integrator = sd
nsteps = 10000
init_step = 0
ns_type = Simple
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstlog = 1
nstxout = 1
nstvout = 1
nstfout = 1
nstenergy = 1
nstxtcout = 0
init_t = 0
delta_t = 0.0001
xtcprec = 1000
nkx = 54
nky = 54
nkz = 54
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = No
epc = No
epctype = Isotropic
tau_p = 1
ref_p (3x3):
ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress (3x3):
compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.00000e+00
posres_com[1]= 0.00000e+00
posres_com[2]= 0.00000e+00
posres_comB (3):
posres_comB[0]= 0.00000e+00
posres_comB[1]= 0.00000e+00
posres_comB[2]= 0.00000e+00
andersen_seed = 815131
rlist = 1
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
epsilon_r = 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = No
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall = 0
wall_type = 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre = No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 10
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 0.0001
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel = 0
deform (3x3):
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 1.5 1.5
ref_t: 0 0
tau_t: 0 1
anneal: No No
ann_npoints: 0 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0 0
energygrp_flags[ 1]: 0 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Will do PME sum in reciprocal space.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Cut-off's: NS: 1 Coulomb: 1 LJ: 1
System total charge: 0.000
Generated table with 4000 data points for Ewald.
Tabscale = 2000 points/nm
Generated table with 4000 data points for LJ6.
Tabscale = 2000 points/nm
Generated table with 4000 data points for LJ12.
Tabscale = 2000 points/nm
Configuring nonbonded kernels...
Testing x86_64 SSE2 support... present.
Removing pbc first time
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
There are: 2 Atoms
Max number of connections per atom is 1
Total number of connections is 2
Max number of graph edges per atom is 1
Total number of graph edges is 2
Initial temperature: 17884.7 K
Started mdrun on node 0 Tue Jun 2 13:38:03 2009
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
G96Bond LJ (SR) Coulomb (SR) Coul. recip. Potential
1.99416e+01 0.00000e+00 0.00000e+00 0.00000e+00 1.99416e+01
Kinetic En. Total Energy Temperature Pressure (bar)
nan nan nan nan
Step Time Lambda
1 0.00010 0.00000
--
Inon Sharony
ינון שרוני
+972(3)6407634
atto.TAU.ac.IL/~inonshar
Please consider your environmental responsibility before printing this e-mail.
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MDRUN_MPI STD-I/O:
==================
step 0
[hydrogen:15285] *** Process received signal ***
[hydrogen:15285] Signal: Segmentation fault (11)
[hydrogen:15285] Signal code: Address not mapped (1)
[hydrogen:15285] Failing at address: 0xfffffffe16c50a90
[hydrogen:15285] [ 0] /lib64/libpthread.so.0 [0x355c00de80]
[hydrogen:15285] [ 1] mdrun_mpi(gmx_pme_do+0x28b2) [0x4b56f2]
[hydrogen:15285] [ 2] mdrun_mpi(do_force_lowlevel+0x1023) [0x47f6f3]
[hydrogen:15285] [ 3] mdrun_mpi(do_force+0xe6e) [0x4c99ce]
[hydrogen:15285] [ 4] mdrun_mpi(do_md+0x48f0) [0x42c4a0]
[hydrogen:15285] [ 5] mdrun_mpi(mdrunner+0x831) [0x42d771]
[hydrogen:15285] [ 6] mdrun_mpi(main+0x3c0) [0x42e6a0]
[hydrogen:15285] [ 7] /lib64/libc.so.6(__libc_start_main+0xf4) [0x355b41d8b4]
[hydrogen:15285] [ 8] mdrun_mpi [0x4131a9]
[hydrogen:15285] *** End of error message ***
./test-2-6-09.sh: line 16: 15285 Segmentation fault mdrun_mpi -c md -v
----------------------------------------------------------------------------------------------------------------
MD.MDP
======
integrator = sd ;stochastic dynamics (velocity Langevin) using a leap-frog algorithm
dt = 0.0001
nsteps = 10000 ; [steps] ==> total (nsteps*dt) ps.
nstxout = 1
nstvout = 1
nstfout = 1
; nstxtcout = 1
nstenergy = 1 ; write energies to energy file every 1000 steps (default 100)
nstlog = 1
energygrps = SL SR
ns_type = simple
periodic_molecules = no
coulombtype = PME
tc-grps = SL SR
tau_t = 0 1 ; mass/gamma
ref_t = 0 0 ; refference (bath) temperature
Pcoupl = no
gen_vel = no
gen_seed = -1 ; random seed based on computer clock
constraints = none
--------------------------------------------------------------------------------------------
1S2.itp
=======
[ atomtypes ]
;atomtype m (u) q (e) part.type V(cr) W(cr)
SX 32.0600 0.000 A 1E-03 1E-05
[ moleculetype ]
; Name nrexcl
1S2 2
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 SX 1 1S2 SL 1 0.000 32.0600
2 SX 1 1S2 SR 2 0.000 32.0600
[ bonds ]
; ai aj fu c0, c1, ...
1 2 2 0.2040 5.3E+6 0.2040 5.3E+6 ; SL SR
--------------------------------------------------------------------------------------------
TRAJ.TRR
========
traj.trr frame 0:
natoms= 2 step= 0 time=0.0000000e+00 lambda= 0
box (3x3):
box[ 0]={ 6.37511e+00, 0.00000e+00, 0.00000e+00}
box[ 1]={ 0.00000e+00, 6.37511e+00, 0.00000e+00}
box[ 2]={ 0.00000e+00, 0.00000e+00, 6.37511e+00}
x (2x3):
x[ 0]={ 3.19756e+00, 3.20532e+00, 3.18725e+00}
x[ 1]={ 3.03044e+00, 3.21568e+00, 3.08875e+00}
v (2x3):
v[ 0]={ 2.22763e+00, -2.56083e-01, 1.38905e+00}
v[ 1]={-2.22763e+00, 2.56083e-01, -1.38905e+00}
f (2x3):
f[ 0]={ 3.43615e+03, -2.13216e+02, 2.02509e+03}
f[ 1]={-3.43615e+03, 2.13216e+02, -2.02509e+03}
--------------------------------------------------------------------------------------------
MD.LOG
======
Input Parameters:
integrator = sd
nsteps = 10000
init_step = 0
ns_type = Simple
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstlog = 1
nstxout = 1
nstvout = 1
nstfout = 1
nstenergy = 1
nstxtcout = 0
init_t = 0
delta_t = 0.0001
xtcprec = 1000
nkx = 54
nky = 54
nkz = 54
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = No
epc = No
epctype = Isotropic
tau_p = 1
ref_p (3x3):
ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress (3x3):
compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.00000e+00
posres_com[1]= 0.00000e+00
posres_com[2]= 0.00000e+00
posres_comB (3):
posres_comB[0]= 0.00000e+00
posres_comB[1]= 0.00000e+00
posres_comB[2]= 0.00000e+00
andersen_seed = 815131
rlist = 1
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
epsilon_r = 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = No
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall = 0
wall_type = 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre = No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 10
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 0.0001
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel = 0
deform (3x3):
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 1.5 1.5
ref_t: 0 0
tau_t: 0 1
anneal: No No
ann_npoints: 0 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0 0
energygrp_flags[ 1]: 0 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Will do PME sum in reciprocal space.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Cut-off's: NS: 1 Coulomb: 1 LJ: 1
System total charge: 0.000
Generated table with 4000 data points for Ewald.
Tabscale = 2000 points/nm
Generated table with 4000 data points for LJ6.
Tabscale = 2000 points/nm
Generated table with 4000 data points for LJ12.
Tabscale = 2000 points/nm
Configuring nonbonded kernels...
Testing x86_64 SSE2 support... present.
Removing pbc first time
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
There are: 2 Atoms
Max number of connections per atom is 1
Total number of connections is 2
Max number of graph edges per atom is 1
Total number of graph edges is 2
Initial temperature: 17884.7 K
Started mdrun on node 0 Tue Jun 2 13:38:03 2009
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
G96Bond LJ (SR) Coulomb (SR) Coul. recip. Potential
1.99416e+01 0.00000e+00 0.00000e+00 0.00000e+00 1.99416e+01
Kinetic En. Total Energy Temperature Pressure (bar)
nan nan nan nan
Step Time Lambda
1 0.00010 0.00000
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