[ase-users] Segmentation fault from minima hopping
Chang Liu
chang.liu at fysik.su.se
Tue Jan 10 07:05:38 CET 2017
Hello,
I am running a minima hopping test, which went well for a well but it ended with a 'segmentation fault' error.
python-ase/3.6.0.2515(27):ERROR:150: Module 'python-ase/3.6.0.2515' conflicts with the currently loaded module(s) 'python-ase/3.9.1'
python-ase/3.6.0.2515(27):ERROR:102: Tcl command execution failed: conflict python-ase
recv desc error, 128, 0x520c428
recv desc error, 128, 0x4f1bc78
recv desc error, 128, 0x2c1e280
recv desc error, 128, 0x5b32668
send desc error
recv desc error, 128, 0x5cbf978
send desc error
recv desc error, 128, 0x4d36358
send desc error
srun: error: t-cn0715: task 65: Segmentation fault
srun: error: t-cn1009: tasks 85-87,89-91,93-94: Segmentation fault
recv desc error, 128, 0x1fbe0c0
send desc error
recv desc error, 128, 0x28dbd58
recv desc error, 128, 0x3509b10
srun: error: t-cn0833: tasks 73-75,77: Segmentation fault
send desc error
send desc error
recv desc error, 128, 0x337e310
send desc error
send desc error
srun: error: t-cn0805: tasks 66-67,69-71: Segmentation fault
srun: First task exited 60s ago
srun: tasks 0-64,68,72,76,78-84,88,92,95: running
srun: tasks 65-67,69-71,73-75,77,85-87,89-91,93-94: exited abnormally
srun: Terminating job step 5871446.0
slurmstepd: error: *** STEP 5871446.0 CANCELLED AT 2017-01-10T05:18:15 *** on t-cn0124
srun: Job step aborted: Waiting up to 2 seconds for job step to finish.
srun: error: t-cn0805: task 68: Killed
srun: error: t-cn0833: tasks 72,76: Killed
srun: error: t-cn1009: tasks 84,88,92,95: Killed
srun: error: t-cn0715: tasks 60-64: Killed
srun: error: t-cn0210: tasks 12-23: Killed
srun: error: t-cn0706: tasks 48-59: Killed
srun: error: t-cn0309: tasks 36-47: Killed
srun: error: t-cn0220: tasks 24-35: Killed
srun: error: t-cn0124: tasks 0-11: Killed
srun: error: Timed out waiting for job step to complete
Usually the first 2 lines cause no problem and I do not think they did this time. The input file is
from ase import Atoms, Atom
from gpaw import *
from gpaw.utilities import h2gpts
from ase.constraints import *
from ase.lattice.surface import fcc100, add_adsorbate
from ase.optimize.minimahopping import MinimaHopping
from ase.optimize import *
from ase.io import *
from ase.visualize import view
import numpy as np
a0 = 3.670
a = a0+0.01
h = 2.05 #Cu-C
h_1 = 5.00 #Cu-O
l = 10 #Cell size
d = 1.13 #CO bond length
d_oh = 0.97
xc = 'RPBE'
surf = 'fcc100'
site = 'clean'
kpts = (3,4,1) #check the slab size!
task = site
name = 'mh'
ceng = 2
fix_depth = 4
slab = read('slab_pre.traj')
slab.pbc=1
#constraints
constraint=[]
yueshu_0 = FixAtoms(mask=[atom.symbol=='Cu' or (atom.index >= 96 and atom.index <= 99 ) for atom in slab])
constraint.append(yueshu_0)
for i in range(8):
yueshu_a = Hookean(a1=72+i*3,a2=73+i*3,rt=1.40, k=5.)
yueshu_b = Hookean(a1=72+i*3,a2=74+i*3,rt=1.40, k=5.)
yueshu_c = Hookean(a1=72+i*3,a2=(0,0,1,-22.8),k=10.)
constraint.extend([yueshu_a,yueshu_b,yueshu_c])
slab.set_constraint(constraint)
slab_masses=slab.get_masses()
#change m_H to deuterium, 2.01410
for i in range(len(slab)):
if slab[i].symbol == 'H':
slab_masses[i]=2.01410
slab.set_masses(slab_masses)
mixer = Mixer(0.1, 5, weight=100.0)
calc = GPAW(#mode=PW(500),
h = 0.2,
kpts=kpts, xc=xc,
txt='%s_%s_%s_gpaw.txt' % (name, surf,task),
poissonsolver=PoissonSolver(nn=3),
stencils = (3, 3),
usesymm=False,
#eigensolver='cg',
mixer=mixer,
maxiter=250,
width=0.1
#gpts=h2gpts(0.2,slab.get_cell(),idiv=16)
)
slab.set_calculator(calc)
hop = MinimaHopping(slab,Ediff0=0.75,T0=2000,logfile=name+'_'+surf+'_'+task+'.txt', minima_traj=name+'_'+surf+'_'+task+'.traj',fmax=0.05,timestep=1.0,optimizer=QuasiNewton)
hop(totalsteps=5)
e_f = slab.get_potential_energy()
#calc.write('%s_%s_%s.gpw' % (name,surf,task))
f = open('Energy_%s_%s_%s.txt' % (name,surf,task), 'w')
#f.write('Final energy: %.3f Adsorption energy: %.3f' % (e_f, -274.307952-14.640527-e_f))
f.write('%s for %s: %.3f eV' % (name, surf, e_f))
f.close()
if I change the slab_pre.traj into an xyz file it looks like:
100
Lattice="10.3803275478 0.0 0.0 0.0 7.78524566086 0.0 0.0 0.0 23.175" Properties=species:S:1:pos:R:3 pbc="T T T"
Cu 1.29754094 1.29754094 7.00000000
Cu 3.89262283 1.29754094 7.00000000
Cu 6.48770472 1.29754094 7.00000000
Cu 9.08278660 1.29754094 7.00000000
Cu 1.29754094 3.89262283 7.00000000
Cu 3.89262283 3.89262283 7.00000000
Cu 6.48770472 3.89262283 7.00000000
Cu 9.08278660 3.89262283 7.00000000
Cu 1.29754094 6.48770472 7.00000000
Cu 3.89262283 6.48770472 7.00000000
Cu 6.48770472 6.48770472 7.00000000
Cu 9.08278660 6.48770472 7.00000000
Cu 0.00000000 0.00000000 8.83500000
Cu 2.59508189 0.00000000 8.83500000
Cu 5.19016377 0.00000000 8.83500000
Cu 7.78524566 0.00000000 8.83500000
Cu 0.00000000 2.59508189 8.83500000
Cu 2.59508189 2.59508189 8.83500000
Cu 5.19016377 2.59508189 8.83500000
Cu 7.78524566 2.59508189 8.83500000
Cu 0.00000000 5.19016377 8.83500000
Cu 2.59508189 5.19016377 8.83500000
Cu 5.19016377 5.19016377 8.83500000
Cu 7.78524566 5.19016377 8.83500000
Cu 1.28224680 1.28149207 10.68866377
Cu 3.87913301 1.28469031 10.69028525
Cu 6.47679474 1.28325504 10.68805852
Cu 9.06995505 1.28369436 10.69021997
Cu 1.26591371 3.89025187 10.70323163
Cu 3.86271812 3.89213638 10.70430889
Cu 6.45845265 3.89163999 10.70281987
Cu 9.05102794 3.88838157 10.70989188
Cu 1.28050730 6.49452685 10.68627727
Cu 3.87855029 6.49796799 10.68808595
Cu 6.47588587 6.49672727 10.68669197
Cu 9.06769006 6.48428004 10.68782068
Cu -0.04655838 -0.01291519 12.55131768
Cu 2.54710225 -0.00946111 12.54595244
Cu 5.15254213 -0.00474901 12.54441218
Cu 7.74481854 -0.01079509 12.54949301
Cu -0.03908295 2.58294638 12.55216751
Cu 2.54853548 2.58462749 12.54337004
Cu 5.15784347 2.58535306 12.54463988
Cu 7.74654846 2.58329448 12.55135511
Cu -0.03888046 5.19428723 12.55463238
Cu 2.54906976 5.19964106 12.54357203
Cu 5.15670810 5.20037463 12.54467186
Cu 7.74707251 5.19538184 12.55325919
Cu 1.24052834 1.30935807 14.41757418
Cu 3.83950947 1.30999797 14.36346006
Cu 6.44080036 1.31230722 14.41687332
Cu 9.03070126 1.29801450 14.42553600
Cu 1.25938052 3.89520276 14.43830394
Cu 3.84250325 3.90756241 14.35035141
Cu 6.43217840 3.89593987 14.43272232
Cu 9.03495849 3.87832210 14.42471015
Cu 1.24651371 6.46600323 14.42286892
Cu 3.84108568 6.47681481 14.38767517
Cu 6.43645978 6.47225840 14.42009280
Cu 9.02982789 6.47526920 14.42309215
Cu -0.04770831 -0.01777802 16.22166272
Cu 2.54119845 -0.00350958 16.14711780
Cu 5.14443662 0.01570809 16.14568581
Cu 7.73569985 -0.01544871 16.22356925
Cu -0.04216257 2.58087808 16.22493261
Cu 2.56173384 2.57131549 16.23934756
Cu 5.13600462 2.57694104 16.22963200
Cu 7.74007574 2.58162240 16.22537861
Cu -0.04279201 5.19530742 16.22430141
Cu 2.56032436 5.21866505 16.31500570
Cu 5.13293715 5.22099623 16.25188377
Cu 7.74090228 5.19488200 16.22216730
O -0.35106962 -2.43572402 22.78012132
H 0.39415104 -1.89083038 22.45176693
H -0.26042300 -3.26676705 22.23902713
O 1.86118262 -1.12637823 21.04468994
H 2.11169082 -1.98391069 20.64374720
H 1.41474905 -0.65587826 20.31470858
O 0.11410988 3.11555532 21.07381847
H 0.76205905 2.52930065 21.53115292
H -0.69243345 2.55846813 20.92207446
O 2.29940300 1.56496351 22.42944792
H 2.33500312 0.63391172 22.13219454
H 3.20731796 1.90499532 22.24668618
O 5.02884910 2.58915613 21.58011209
H 4.69130386 2.58587500 20.65769641
H 5.08661753 3.54780277 21.79780374
O 8.08141227 1.60653847 20.47998415
H 8.07289544 0.71970786 20.93292623
H 7.29583253 2.04474391 20.86837798
O 5.20578835 5.57397831 21.74221098
H 4.64839291 6.12274297 22.32750551
H 4.83868344 5.73697425 20.84844712
O 7.93339368 6.95685708 21.84836686
H 8.63475750 6.34429048 22.20400599
H 7.10549046 6.43362249 21.83734447
C 3.84314233 3.10101931 17.81996321
C 3.87681619 4.63509324 17.85295230
O 3.85600466 2.40081203 18.83494680
O 3.91578435 5.27490424 18.91101785
I ran the test with 96 CPUs. Could you please tell me where it went wrong? Thanks.
Best wishes,
Chang Liu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.fysik.dtu.dk/pipermail/ase-users/attachments/20170110/9b11ad2a/attachment-0001.html>
More information about the ase-users
mailing list