[gmx-users] MPI segmentation Fault
Xu Dong Huang
xudongh at eden.rutgers.edu
Wed Jan 2 21:42:16 CET 2013
@Justin, here are the details of my NVT and NPT .mdp, (All ran without position restraint) , + details of the NVT run
For NVT.mdp:
integrator = md
tinit = 0.0
dt = 0.02
nsteps = 10000
nstcomm = 1
comm-grps =
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
xtc_precision = 100
xtc-grps =
energygrps = system
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = V-rescale
tc-grps = system
tau_t = 1.0
ref_t = 300
Pcoupl = no
Pcoupltype = isotropic
tau_p = 1.0
compressibility = 3e-4
ref_p = 1.0
gen_vel = yes
gen_temp = 300
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
For NPT.mdp
integrator = md
tinit = 0.0
dt = 0.02
nsteps = 1000000
nstcomm = 1
comm-grps =
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
xtc_precision = 100
xtc-grps =
energygrps = system
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = V-rescale
tc-grps = system
tau_t = 1.0
ref_t = 300
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
tau_p = 5.0
compressibility = 3e-4
ref_p = 1.0
gen_vel = no
gen_temp = 300
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
OUTPUT log FOR NVT RUN:
Writing checkpoint, step 9760 at Wed Jan 2 06:43:55 2013
Step Time Lambda
10000 200.00000 0.00000
Writing checkpoint, step 10000 at Wed Jan 2 06:56:58 2013
Energies (kJ/mol)
Bond LJ (SR) Coulomb (SR) Potential Kinetic En.
1.27815e+03 -2.21982e+07 0.00000e+00 -2.21969e+07 2.99756e+06
Total Energy Conserved En. Temperature Pressure (bar)
-1.91994e+07 -2.18426e+07 2.99676e+02 7.09077e+02
<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>
Statistics over 10001 steps using 1001 frames
Energies (kJ/mol)
Bond LJ (SR) Coulomb (SR) Potential Kinetic En.
1.33393e+03 -2.22049e+07 0.00000e+00 -2.22036e+07 2.98604e+06
Total Energy Conserved En. Temperature Pressure (bar)
-1.92176e+07 -2.18431e+07 2.98524e+02 7.06152e+02
Total Virial (kJ/mol)
-9.41186e+05 7.05498e+01 6.65566e+02
7.05612e+01 -9.40675e+05 -3.05521e+00
6.65543e+02 -3.06027e+00 -9.44794e+05
Pressure (bar)
7.05835e+02 -4.93053e-02 -2.47918e-01
-4.93095e-02 7.05573e+02 -4.79105e-03
-2.47909e-01 -4.78920e-03 7.07047e+02
Total Dipole (D)
0.00000e+00 0.00000e+00 0.00000e+00
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudongh at eden.rutgers.edu
On Jan 2, 2013, at 3:20 PM, Xu Dong Huang <xudongh at eden.rutgers.edu> wrote:
> Dear gromac users,
>
> after examining my nvt run outcome, I see that my molecule has half of the arm stuck outside of the box (I guess my run wasn't very successful). But I thought the jumping outside of the box would be corrected by periodic boundary? Should I run my nvt for longer since the structure itself did not seem to change much in the solute? (My initial
> Xu Dong Huangnvt nstep=10000, should I increase it to resolve the problem? if that resolves the problem at all that is)
>
> Thanks for any input,
>
> Chemical & Biochemical Engineering
> Rutgers School of Engineering
> xudongh at eden.rutgers.edu
>
> On Jan 2, 2013, at 3:08 PM, Xu Dong Huang <xudongh at eden.rutgers.edu> wrote:
>
>> Dear gromac users,
>>
>> after running a successful NVT, I was going to run NPT. (All ran with MPI), however when I attempt to run the NPT, I get the following segmentation error:
>>
>> Getting Loaded...
>> Reading file npt.tpr, VERSION 4.5.3 (single precision)
>> Loaded with Money
>>
>>
>> WARNING: This run will generate roughly 3890 Mb of data
>>
>> starting mdrun 'star'
>> 1000000 steps, 20000.0 ps.
>>
>> step 0[Ultranode02:26884] *** Process received signal ***
>> [Ultranode02:26884] Signal: Segmentation fault (11)
>> [Ultranode02:26884] Signal code: Address not mapped (1)
>> [Ultranode02:26884] Failing at address: 0x1f5acf020
>> [Ultranode02:26884] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x2b21605168f0]
>> [Ultranode02:26884] [ 1] mdrun_mpi() [0x745509]
>> [Ultranode02:26884] *** End of error message ***
>> /usr/local/SGE/default/spool/Ultranode02/job_scripts/39346: line 38: 26884 Segmentation fault mdrun_mpi -v -deffnm npt
>>
>>
>> -----Is my system blowing up? Or there is something wrong with MPI ? (I requested 4 processors)
>>
>> Xu Dong Huang
>> Chemical & Biochemical Engineering
>> Rutgers School of Engineering
>> xudongh at eden.rutgers.edu
>>
>> --
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