Segmentation fault after several structural optimization steps

Asked by Yuefei Huang on 2020-08-18

Hello SIESTA developers,
I am running an structural optimization in SIESTA 4.1-b4. It could run for several (1 to 10, depends) steps, but after that, it terminates and a segmentation fault occurs.
This is the head of my output file:
'''
Siesta Version : v4.1-b4
Architecture : unknown
Compiler version: ifort (IFORT) 18.0.5 20180823
Compiler flags : mpiifort -fPIC -O3 -xHost -fp-speculation=strict -fp-model strict
PP flags : -DFC_HAVE_ABORT -DMPI -DSIESTA__MRRR -DCDF -DNCDF -DNCDF_4 -DNCDF_PARALLEL -II/opt/apps/software/MPI/intel/2018.4.274-GCC-7.3.0/impi/2018.4.274/netCDF-Fortran/4.4.4/include -DSIESTA__ELPA -I/opt/apps/software/MPI/intel/2018.4.274-GCC-7.3.0/impi/2018.4.274/ELPA/2017.05.003/include/elpa-2017.05.003/modules
Libraries : libncdf.a libfdict.a -Wl,-Bstatic -Wl,--start-group -lmkl_scalapack_lp64 -lmkkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -Wl,-Bdynamic -lnetcdff -lelpa
PARALLEL version
NetCDF support
NetCDF-4 support
NetCDF-4 MPI-IO support

* Running on 100 nodes in parallel
'''

The end of output file is like this:
'''
                     ====================================
                        Begin CG opt. move = 1
                     ====================================

################# Omitting ~300 lines

Setting up quadratic distribution...
ExtMesh (bp) on 0 = 139 x 132 x 130 = 2385240
'''

The error file is like this:
'''
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
siesta 0000000002727CAD for__signal_handl Unknown Unknown
libpthread-2.17.s 00007FE0625015D0 Unknown Unknown Unknown
siesta 000000000065C678 Unknown Unknown Unknown
siesta 0000000000751719 Unknown Unknown Unknown
siesta 000000000050A8F0 Unknown Unknown Unknown
siesta 000000000048F8CD Unknown Unknown Unknown
siesta 0000000000722871 Unknown Unknown Unknown
siesta 00000000005EB577 Unknown Unknown Unknown
siesta 0000000000B92A20 Unknown Unknown Unknown
siesta 000000000042AE0E Unknown Unknown Unknown
libc-2.17.so 00007FE061E453D5 __libc_start_main Unknown Unknown
siesta 000000000042AD29 Unknown Unknown Unknown
'''

It is quite strange to me that it could run up to 10 steps, but raise such error. What do you think could be possible reason for this? I will attach my input file in the reply. Thank you!

Question information

Language:
English Edit question
Status:
Solved
For:
Siesta Edit question
Assignee:
No assignee Edit question
Solved by:
Yuefei Huang
Solved:
2020-08-20
Last query:
2020-08-20
Last reply:
Yuefei Huang (yh46) said : #1

SolutionMethod Diagon

SystemName PTCDA
SystemLabel PTCDA

==================================================
==================================================
# SPECIES AND BASIS

# Number of species
NumberOfSpecies 5
%block ChemicalSpeciesLabel
  1 1 H
  2 5 B
  3 6 C
  4 7 N
  5 8 O
%endblock ChemicalSpeciesLabel

PAO.BasisSize SZP
PAO.EnergyShift 0.005 Ry
XC.functional GGA
XC.authors PBE

==================================================
==================================================
# K-points

%block kgrid_Monkhorst_Pack
 1 0 0 0.0
 0 2 0 0.0
 0 0 1 0.0
%endblock kgrid_Monkhorst_Pack

==================================================
==================================================
UseStructFile .false.
# Structure
NumberOfAtoms 230
LatticeConstant 1.000 Ang
%block LatticeVectors
  48.443352627 0.000000000 0.000000000
  0.000000000 17.795130594 0.000000000
  0.000000000 0.000000000 20.000000000
%endblock LatticeVectors
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
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0.996649079 8.148793806 9.965555763 2 #1 th layer
0.996649079 14.080504004 9.965555763 2 #1 th layer
0.996649079 17.046359103 9.965555763 2 #1 th layer
0.996649079 2.217083608 9.965555763 2 #1 th layer
0.996649079 5.182938707 9.965555763 2 #1 th layer
1.908261610 0.734741855 9.965555763 2 #1 th layer
1.908261610 12.598162251 9.965555763 2 #1 th layer
1.908261610 6.666452053 9.965555763 2 #1 th layer
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%endblock AtomicCoordinatesAndAtomicSpecies

==================================================
==================================================

Diag.ParallelOverK .true.
Diag.DivideAndConquer False
# SCF variables

DM.MixSCF1 T
MaxSCFIterations 300 # Maximum number of SCF iter
SCFMustConverge .true. # Must Converge
DM.MixingWeight 0.02 # New DM amount for next SCF cycle
DM.Tolerance 1.d-3 # Tolerance in maximum difference
DM.UseSaveDM true # to use continuation files
DM.NumberPulay 5
SCF.H.Tolerance 5.d-3 eV
TS.MixH yes

==================================================
==================================================
# MD variables

MD.FinalTimeStep 1
MD.TypeOfRun CG
MD.NumCGsteps 300
MD.VariableCell .true.
MD.UseSaveXV .true.

==================================================
==================================================
# Output variables

WriteMullikenPop 1
WriteBands .false.
SaveRho .true.
SaveDeltaRho .false.
SaveHS .false.
SaveElectrostaticPotential True
SaveTotalPotential .true.
WriteCoorXmol .true.
WriteMDXmol .true.
WriteMDhistory .true.
WriteEigenvalues yes

%block Geometry.Constraints
#cell-vector B
#cell-angle alpha
cell-vector C
#atom [89 -- 120 step 1]
%endblock Geometry.Constraints

Yuefei Huang (yh46) said : #2

By adding ' ulimit -u unlimited', the problem is solved.