A strange problem when running CP2K

yoman gogo... at gmail.com
Wed Mar 16 12:28:24 CET 2011


Hi everyone!

I have a problem that the job will stop writing output file when the cluster 
server shows the job is still running. Moreover, there is no error message. 
Is this the way CP2K told me the job is dead? Let me describe this problem 
in detail. I run a Molecular dynamics simulation of iceIh using BLYP or PBE 
functional for 30 ps.( timestep = 0.5 fs) The BLYP job would run well in 
certain nodes and cores. The best combination is 8nodes and each node has 8 
cpus. When I increase the number of nodes to 12 (each has 8 cpus) the job 
will have the problem I have mentioned within 500 steps. Moreover, 
restarting the job will have the same problem. Besides, when I try to use 
the same setting (same nodes with the same cores) to run the PBE job. It has 
the problem again. Did anyone has the same problem? The following is my 
input file of the job.

Thanks in advance for any reply


Yu-ming Hung


Institute of Atomic and Molecular Sciences, Academia Sinica


&FORCE_EVAL
  METHOD QS
  STRESS_TENSOR ANALYTICAL

  &DFT
    BASIS_SET_FILE_NAME ./GTH_BASIS_SETS
    POTENTIAL_FILE_NAME ./POTENTIAL

    &MGRID
      CUTOFF 300
      NGRIDS 4
    &END MGRID

    &QS
      EPS_DEFAULT 1.0E-12
      EXTRAPOLATION PS
      EXTRAPOLATION_ORDER 3
    &END QS

    &SCF
      SCF_GUESS ATOMIC
      EPS_SCF      1.0E-6
      MAX_SCF      300

      &OT ON
        MINIMIZER DIIS
        PRECONDITIONER  FULL_KINETIC
      &END OT

      &PRINT
        &RESTART OFF
        &END
      &END

    &END SCF

    &XC
      &XC_FUNCTIONAL PBE
      &END XC_FUNCTIONAL
    &END XC

    &LOCALIZE
      EPS_LOCALIZATION 1E-7
      METHOD  JACOBI
    &END LOCALIZE

    &PRINT
      &LOCALIZATION
        &WANNIER_CENTERS
          IONS+CENTERS  TRUE
          FILENAME ./96_iceIh_150_NPT
          COMMON_ITERATION_LEVELS 1

          &EACH
          &END EACH

        &END WANNIER_CENTERS


        &MOLECULAR_DIPOLES
          FILENAME ./96_iceIh_150_NPT
          COMMON_ITERATION_LEVELS 1

          &EACH
          &END EACH
        &END MOLECULAR_DIPOLES


        &TOTAL_DIPOLE
          FILENAME ./96_iceIh_150_NPT
          COMMON_ITERATION_LEVELS 1

          &EACH
          &END EACH
        &END TOTAL_DIPOLE

      &END LOCALIZATION
    &END PRINT

  &END DFT

I skip the coordinate and velocity of atoms

    &KIND H
      BASIS_SET TZV2P-GTH
      POTENTIAL GTH-PBE-q1
      MASS 2.0
      ELEMENT H
    &END KIND

    &KIND O
      BASIS_SET TZV2P-GTH
      POTENTIAL GTH-PBE-q6
    &END KIND

  &END SUBSYS

&END FORCE_EVAL

&GLOBAL
  PROJECT 96_iceIh_NPT
  RUN_TYPE MD
  PRINT_LEVEL LOW
&END GLOBAL

&MOTION
  &MD
    ENSEMBLE NPT_F
    STEPS 60000
    TIMESTEP 0.5
    TEMPERATURE 150.0
    &THERMOSTAT
      REGION MASSIVE

      &NOSE
        LENGTH 3
        YOSHIDA 3
        TIMECON 100
        MTS 2
      &END NOSE
    &END THERMOSTAT

    &BAROSTAT
        PRESSURE 1.0
    &END BAROSTAT

  &END MD

  &PRINT
   &VELOCITIES
   &END

   &RESTART
     BACKUP_COPIES 1
   &END RESTART
  &END PRINT

&END MOTION

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