segmentation fault - hydrogen bonded system

m-ymgc m-y... at jcom.home.ne.jp
Thu Jul 25 01:03:27 CEST 2013


Dear cp2k group members,

Recently I got a problem with running MD simulations: I am using both 
locally compiled by gfortran and the OpenMP binary on linux x86-64 
machines. I am trying to do simulation of IR spectra of hydrogen bonded 
systems and the input files are based on the one listed in the recently 
uploaded document by Prof. Kirchner's group. The jobs stops after reaching 
certain geometries with segmentation fault. The error message also appears 
when I restart another MD run by setting the last geometry as an initial 
geometry in the input file.

This is an input file

&GLOBAL
  PROJECT t2w2
  PRINT_LEVEL LOW
  RUN_TYPE MD
&END GLOBAL
&FORCE_EVAL
  METHOD Quickstep
  &DFT
    BASIS_SET_FILE_NAME /home/yamaguti/cp2k-2.4/tests/QS/BASIS_MOLOPT
    POTENTIAL_FILE_NAME /home/yamaguti/cp2k-2.4/tests/QS/POTENTIAL
    &MGRID
      CUTOFF 280
      REL_CUTOFF 50
      NGRIDS 5
    &END MGRID
    &QS
      METHOD GAPW
      EPS_FILTER_MATRIX 1.0E-12
      EPS_PGF_ORB 1.0E-12
    &END QS
    &SCF
      SCF_GUESS ATOMIC
      MAX_SCF 200
      &OT
        MINIMIZER DIIS
        PRECONDITIONER FULL_ALL
      &END
      &PRINT
        &RESTART
          &EACH
            MD 0
          &END
        &END
      &END
    &END SCF
    &LOCALIZE
      METHOD JACOBI
      MAX_ITER 10000
      &PRINT
        &WANNIER_CENTERS 
          IONS+CENTERS
          FILENAME =t2w2_wannier.xyz
          &EACH
            MD 5
          &END
        &END
      &END
    &END
    &XC
      &XC_FUNCTIONAL PBE
      &END XC_FUNCTIONAL
      &XC_GRID
        XC_DERIV NN10_SMOOTH
        XC_SMOOTH_RHO NN10
      &END
      &VDW_POTENTIAL
        DISPERSION_FUNCTIONAL PAIR_POTENTIAL
        &PAIR_POTENTIAL
          TYPE DFTD3
          PARAMETER_FILE_NAME /home/yamaguti/cp2k-2.4/tests/QS/dftd3.dat
          REFERENCE_FUNCTIONAL PBE
        &END
      &END
    &END XC
  &END DFT
  &SUBSYS
    &CELL
      ABC 14.0 14.0 14.0
    &END
    &COORD
  S        -2.2142972451       -2.9301020672       -1.7868817159
  C        -4.1143788911       -2.9080311721       -1.6594602736
  O        -1.9603585719       -1.4223988788       -1.6100212352
  O        -1.9237112535       -3.4880179501       -3.1062952014
  O        -1.6837714859       -3.5669369762       -0.6059877320
  F        -4.6513022715       -4.0882072061       -1.9360349753
  F        -4.4128418293       -2.1216482404       -2.6635660253
  F        -4.5526869429       -2.4071250953       -0.5253867513
  S         1.3510503362        0.6035280707       -0.9906320418
  C         3.0771087088        1.2462159133       -0.7130631578
  O         0.6420948929        1.2841777235       -2.0646513289
  O         0.7294924782        0.5776620616        0.3056773055
  O         1.7707528694       -0.8416817161       -1.4049090763
  F         3.7739327792        0.5574724880        0.2158258484
  F         2.8850487080        2.5723123785       -0.2839271390
  F         3.8165588985        1.2238166764       -1.8889602835
  H        -1.5232549971       -0.1264383431       -4.2892222990
  O        -1.4908555749        0.2406897543       -3.4169473059
  H        -1.8478856441       -0.7667078085       -2.4042984017
  H        -0.6827635921        0.7757075991       -3.2751540434
  H         1.4792713316       -1.6202279080       -0.7424100509
  O         1.0009947110       -2.8892822226        0.0212840022
  H         1.5449312315       -3.7292092505        0.1226208428
  H         0.0649028840       -3.1917212778        0.0813336304
  &END
  &KIND H
   BASIS_SET DZVP-MOLOPT-SR-GTH
   POTENTIAL GTH-PBE-q1
  &END
  &KIND O
   BASIS_SET DZVP-MOLOPT-SR-GTH
   POTENTIAL GTH-PBE-q6
  &END
  &KIND C
   BASIS_SET DZVP-MOLOPT-SR-GTH
   POTENTIAL GTH-PBE-q4
  &END
  &KIND F
   BASIS_SET DZVP-MOLOPT-SR-GTH
   POTENTIAL GTH-PBE-q7
  &END
  &KIND S
   BASIS_SET DZVP-MOLOPT-SR-GTH
   POTENTIAL GTH-PBE-q6
  &END
  &END SUBSYS
&END FORCE_EVAL
&MOTION
 &MD
  ENSEMBLE NVT
  STEPS 20000
  TIMESTEP 0.25
  &THERMOSTAT
   REGION GLOBAL
   TYPE NOSE
   &NOSE
    TIMECON 100
   &END NOSE
  &END THERMOSTAT
  TEMPERATURE 300
 &END MD
 &PRINT
  &RESTART
   &EACH
    MD 1
   &END EACH
  &END RESTART
 &END PRINT
&END MOTION

Following error messages appeared after the job by the precompiled binary.

----

Program received signal SIGSEGV: Segmentation fault - invalid memory 
reference.

Backtrace for this error:
#0  0x1DB74DD in _gfortrani_show_backtrace at backtrace.c:260
#1  0x1D93CA6 in _gfortrani_backtrace_handler at compile_options.c:129
#2  0x40BAEF in _L_unlock_16 at bar.c:0
#3  0x18384D8 in dgemm_
#4  0xB12748 in __ai_moments_MOD_contract_cossin at ai_moments.F:83
#5  0x11D9834 in __qs_loc_utils_MOD_get_berry_operator at qs_loc_utils.F:889
#6  0x11DCB54 in __qs_loc_utils_MOD_qs_loc_env_init at qs_loc_utils.F:653
#7  0x11DDA40 in __qs_loc_utils_MOD_qs_loc_init at qs_loc_utils.F:1407
#8  0x7DFDEF in __qs_scf_post_gpw_MOD_scf_post_calculation_gpw at 
qs_scf_post_gpw.F:460
#9  0x7BB735 in __qs_scf_MOD_scf at qs_scf.F:419
#10  0x69B434 in __qs_energy_MOD_qs_energies_scf at qs_energy.F:148
#11  0x6BA417 in __qs_force_MOD_qs_forces at qs_force.F:233
#12  0x4740D9 in __force_env_methods_MOD_force_env_calc_energy_force at 
force_env_methods.F:244
#13  0x5AC7F5 in __md_run_MOD_qs_mol_dyn_low at md_run.F:366
#14  0x5ADAC6 in __md_run_MOD_qs_mol_dyn at md_run.F:152
#15  0x4133F3 in __cp2k_runs_MOD_cp2k_run at cp2k_runs.F:397
#16  0x416F6B in __cp2k_runs_MOD_run_input at cp2k_runs.F:1161
#17  0x40D7B7 in cp2k at cp2k.F:307

Best regards,

Makoto Yamaguchi
Fuel Cell Cutting-edge Research Center, Tokyo, Japan

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