[CP2K-user] Quickstep crash after compilation with scalapack 2.0.0

ec2017... at gmail.com ec2017... at gmail.com
Thu Dec 6 18:42:54 CET 2018


Dear all,

I compiled cp2k 6.1 with Intel 17 and using scalapack 2.0.0 (
www.netlib.org/scalapack 
<https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=2ahUKEwiirvjc64vfAhXNjqQKHYSFAgQQFjAAegQIAxAC&url=http%3A%2F%2Fwww.netlib.org%2Fscalapack%2F&usg=AOvVaw28sXyMLOi_Eo_hxvsZ-hJJ>), 
that I compiled itself using Intel 17 but then Quickstep crashes at 
execution. Strangely, Quickstep runs smoothly for native Intel scalapack 
compilation. I attached both input, crash output and both the native Intel 
makefile that work well and the scalapack makefile generating the crash at 
execution. I tried reducing the optimization to -O0 but it did not solve 
the problem. Intel 18 either makes the same issue. Could you please advise ?

Thanks in advance,
Best regards
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20181206/19fc2dbe/attachment-0001.html>
-------------- next part --------------
&FORCE_EVAL
  METHOD QS
  &DFT
    BASIS_SET_FILE_NAME GTH_BASIS_SETS
    POTENTIAL_FILE_NAME POTENTIAL
    &MGRID
      CUTOFF 280
      REL_CUTOFF 30
    &END MGRID
    &QS
      EPS_DEFAULT 1.0E-12
      WF_INTERPOLATION PS
      EXTRAPOLATION_ORDER 3
    &END QS
    &SCF
      SCF_GUESS ATOMIC
      &OT ON
        MINIMIZER DIIS
      &END OT
    # SCF_GUESS        RESTART
    # EPS_SCF      1.0E-7
      &PRINT
        &RESTART OFF
        &END
      &END
    &END SCF
    &XC
      &XC_FUNCTIONAL Pade
      &END XC_FUNCTIONAL
    &END XC
  &END DFT
  &SUBSYS
    &CELL
      ABC 9.8528 9.8528 9.8528
    &END CELL
    # 32 H2O (TIP5P,1bar,300K) a = 9.8528
    &COORD
   O       2.280398       9.146539       5.088696
   O       1.251703       2.406261       7.769908
   O       1.596302       6.920128       0.656695
   O       2.957518       3.771868       1.877387
   O       0.228972       5.884026       6.532308
   O       9.023431       6.119654       0.092451
   O       7.256289       8.493641       5.772041
   O       5.090422       9.467016       0.743177
   O       6.330888       7.363471       3.747750
   O       7.763819       8.349367       9.279457
   O       8.280798       3.837153       5.799282
   O       8.878250       2.025797       1.664102
   O       9.160372       0.285100       6.871004
   O       4.962043       4.134437       0.173376
   O       2.802896       8.690383       2.435952
   O       9.123223       3.549232       8.876721
   O       1.453702       1.402538       2.358278
   O       6.536550       1.146790       7.609732
   O       2.766709       0.881503       9.544263
   O       0.856426       2.075964       5.010625
   O       6.386036       1.918950       0.242690
   O       2.733023       4.452756       5.850203
   O       4.600039       9.254314       6.575944
   O       3.665373       6.210561       3.158420
   O       3.371648       6.925594       7.476036
   O       5.287920       3.270653       6.155080
   O       5.225237       6.959594       9.582991
   O       0.846293       5.595877       3.820630
   O       9.785620       8.164617       3.657879
   O       8.509982       4.430362       2.679946
   O       1.337625       8.580920       8.272484
   O       8.054437       9.221335       1.991376
   H       1.762019       9.820429       5.528454
   H       3.095987       9.107088       5.588186
   H       0.554129       2.982634       8.082024
   H       1.771257       2.954779       7.182181
   H       2.112148       6.126321       0.798136
   H       1.776389       7.463264       1.424030
   H       3.754249       3.824017       1.349436
   H       3.010580       4.524142       2.466878
   H       0.939475       5.243834       6.571945
   H       0.515723       6.520548       5.877445
   H       9.852960       6.490366       0.393593
   H       8.556008       6.860063      -0.294256
   H       7.886607       7.941321       6.234506
   H       7.793855       9.141028       5.315813
   H       4.467366       9.971162       0.219851
   H       5.758685      10.102795       0.998994
   H       6.652693       7.917443       3.036562
   H       6.711966       7.743594       4.539279
   H       7.751955       8.745180      10.150905
   H       7.829208       9.092212       8.679343
   H       8.312540       3.218330       6.528858
   H       8.508855       4.680699       6.189990
   H       9.742249       1.704975       1.922581
   H       8.799060       2.876412       2.095861
   H       9.505360       1.161677       6.701213
   H       9.920117      -0.219794       7.161006
   H       4.749903       4.186003      -0.758595
   H       5.248010       5.018415       0.403676
   H       3.576065       9.078451       2.026264
   H       2.720238       9.146974       3.273164
   H       9.085561       4.493058       9.031660
   H       9.215391       3.166305       9.749133
   H       1.999705       2.060411       1.927796
   H       1.824184       0.564565       2.081195
   H       7.430334       0.849764       7.438978
   H       6.576029       1.537017       8.482885
   H       2.415851       1.576460       8.987338
   H       2.276957       0.099537       9.289499
   H       1.160987       1.818023       4.140602
   H       0.350256       2.874437       4.860741
   H       5.768804       2.638450       0.375264
   H       7.221823       2.257514       0.563730
   H       3.260797       5.243390       5.962382
   H       3.347848       3.732214       5.988196
   H       5.328688       9.073059       5.982269
   H       5.007063       9.672150       7.334875
   H       4.566850       6.413356       3.408312
   H       3.273115       7.061666       2.963521
   H       3.878372       7.435003       6.843607
   H       3.884673       6.966316       8.283117
   H       5.918240       3.116802       5.451335
   H       5.355924       2.495093       6.711958
   H       5.071858       7.687254      10.185667
   H       6.106394       7.112302       9.241707
   H       1.637363       5.184910       4.169264
   H       0.427645       4.908936       3.301903
   H       9.971698       7.227076       3.709104
   H      10.647901       8.579244       3.629806
   H       8.046808       5.126383       2.213838
   H       7.995317       4.290074       3.474723
   H       1.872601       7.864672       7.930401
   H       0.837635       8.186808       8.987268
   H       8.314696      10.115534       2.212519
   H       8.687134       8.667252       2.448452
    &END COORD
    &KIND H
      BASIS_SET TZV2P-GTH
      POTENTIAL GTH-PADE-q1
    &END KIND
    &KIND O
      BASIS_SET TZV2P-GTH
      POTENTIAL GTH-PADE-q6
    &END KIND
  &END SUBSYS
&END FORCE_EVAL
&GLOBAL
  PROJECT H2O-32
  RUN_TYPE MD
  PRINT_LEVEL LOW
  &TIMINGS
     THRESHOLD 0.000001
  &END
&END GLOBAL
&MOTION
  &MD
    ENSEMBLE NVE
    STEPS 10
    TIMESTEP 0.5
    TEMPERATURE 300.0
  &END MD
&END MOTION
-------------- next part --------------
 DBCSR| Multiplication driver                                               BLAS
 DBCSR| Multrec recursion limit                                              512
 DBCSR| Multiplication stack size                                           1000
 DBCSR| Maximum elements for images                                    UNLIMITED
 DBCSR| Multiplicative factor virtual images                                   1
 DBCSR| Multiplication size stacks                                             3
 DBCSR| Number of 3D layers                                               SINGLE
 DBCSR| Use MPI memory allocation                                              T
 DBCSR| Use RMA algorithm                                                      F
 DBCSR| Use Communication thread                                               T
 DBCSR| Communication thread load                                             87


  **** **** ******  **  PROGRAM STARTED AT               2018-12-06 09:02:04.715
 ***** ** ***  *** **   PROGRAM STARTED ON                              nid00008
 **    ****   ******    PROGRAM STARTED BY                               user
 ***** **    ** ** **   PROGRAM PROCESS ID                                 31738
  **** **  *******  **  PROGRAM STARTED IN /lustre/project/k1228/testcp2k-lapack
                                           -QS-6.1-pg-H2O-4096-INtel17

 CP2K| version string:                                          CP2K version 6.1
 CP2K| source code revision number:                                    svn:18464
 CP2K| cp2kflags: libint fftw3 parallel mpi3 scalapack has_no_shared_glibc libde
 CP2K|            riv_max_am1=6 libint_max_am=7 mkl
 CP2K| is freely available from                            https://www.cp2k.org/
 CP2K| Program compiled at                          Sun Dec  2 15:02:17 +03 2018
 CP2K| Program compiled on                                                  cdl1
 CP2K| Program compiled for                                      CRAY-XC40-intel
 CP2K| Data directory path                /home/user/cp2k-6.1-pg-Intel17/data
 CP2K| Input file name                                                H2O-32.inp
 
 GLOBAL| Force Environment number                                              1
 GLOBAL| Basis set file name                                      GTH_BASIS_SETS
 GLOBAL| Potential file name                                           POTENTIAL
 GLOBAL| MM Potential file name                                     MM_POTENTIAL
 GLOBAL| Coordinate file name                                      __STD_INPUT__
 GLOBAL| Method name                                                        CP2K
 GLOBAL| Project name                                                     H2O-32
 GLOBAL| Preferred FFT library                                             FFTW3
 GLOBAL| Preferred diagonalization lib.                                       SL
 GLOBAL| Run type                                                             MD
 GLOBAL| All-to-all communication in single precision                          F
 GLOBAL| FFTs using library dependent lengths                                  F
 GLOBAL| Global print level                                                  LOW
 GLOBAL| Total number of message passing processes                            32
 GLOBAL| Number of threads for this process                                    1
 GLOBAL| This output is from process                                           0
 GLOBAL| CPU model name :  Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz

 MEMORY| system memory details [Kb]
 MEMORY|                        rank 0           min           max       average
 MEMORY| MemTotal            131899584     131899584     131899584     131899584
 MEMORY| MemFree             128685068     128685068     128685068     128685068
 MEMORY| Buffers                  5284          5284          5284          5284
 MEMORY| Cached                 342364        342364        342364        342364
 MEMORY| Slab                   285820        285820        285820        285820
 MEMORY| SReclaimable            16520         16520         16520         16520
 MEMORY| MemLikelyFree       129049236     129049236     129049236     129049236

 
 GENERATE|  Preliminary Number of Bonds generated:                             0
 GENERATE|  Achieved consistency in connectivity generation.

 *******************************************************************************
 *******************************************************************************
 **                                                                           **
 **     #####                         ##              ##                      **
 **    ##   ##            ##          ##              ##                      **
 **   ##     ##                       ##            ######                    **
 **   ##     ##  ##   ##  ##   #####  ##  ##   ####   ##    #####    #####    **
 **   ##     ##  ##   ##  ##  ##      ## ##   ##      ##   ##   ##  ##   ##   **
 **   ##  ## ##  ##   ##  ##  ##      ####     ###    ##   ######   ######    **
 **    ##  ###   ##   ##  ##  ##      ## ##      ##   ##   ##       ##        **
 **     #######   #####   ##   #####  ##  ##  ####    ##    #####   ##        **
 **           ##                                                    ##        **
 **                                                                           **
 **                                                ... make the atoms dance   **
 **                                                                           **
 **            Copyright (C) by CP2K developers group (2000 - 2018)           **
 **                                                                           **
 *******************************************************************************


 TOTAL NUMBERS AND MAXIMUM NUMBERS

  Total number of            - Atomic kinds:                                   2
                             - Atoms:                                         96
                             - Shell sets:                                   192
                             - Shells:                                       576
                             - Primitive Cartesian functions:                672
                             - Cartesian basis functions:                   1344
                             - Spherical basis functions:                   1280

  Maximum angular momentum of- Orbital basis functions:                        2
                             - Local part of the GTH pseudopotential:          2
                             - Non-local part of the GTH pseudopotential:      0


 SCF PARAMETERS         Density guess:                                    ATOMIC
                        --------------------------------------------------------
                        max_scf:                                              50
                        max_scf_history:                                       0
                        max_diis:                                              4
                        --------------------------------------------------------
                        eps_scf:                                        1.00E-05
                        eps_scf_history:                                0.00E+00
                        eps_diis:                                       1.00E-01
                        eps_eigval:                                     1.00E-05
                        --------------------------------------------------------
                        level_shift [a.u.]:                                 0.00
                        --------------------------------------------------------
                        No outer SCF
 
 MD| Molecular Dynamics Protocol 
 MD| Ensemble Type                                                           NVE
 MD| Number of Time Steps                                                     10
 MD| Time Step [fs]                                                         0.50
 MD| Temperature [K]                                                      300.00
 MD| Temperature tolerance [K]                                              0.00
 MD| Print MD information every                                        1 step(s)
 MD| File type     Print frequency[steps]                             File names
 MD| Coordinates            1                                   H2O-32-pos-1.xyz
 MD| Velocities             1                                   H2O-32-vel-1.xyz
 MD| Energies               1                                      H2O-32-1.ener
 MD| Dump                  20                                   H2O-32-1.restart
 
 ROT| Rotational Analysis Info 
 ROT| Principal axes and moments of inertia in atomic units:
 ROT|                                1                 2                 3
 ROT| EIGENVALUES            0.604570193E+08   0.643469341E+08   0.682377067E+08
 ROT|      X                    -0.588050609       0.712427121       0.382941350
 ROT|      Y                    -0.316321633      -0.638315596       0.701779042
 ROT|      Z                     0.744403859       0.291548960       0.600717986
 ROT| Numer of Rotovibrational vectors:     6

 Calculation of degrees of freedom
                                                      Number of atoms:        96
                                 Number of Intramolecular constraints:         0
                                 Number of Intermolecular constraints:         0
                                  Invariants(translation + rotations):         3
                                                   Degrees of freedom:       285


 Restraints Information
                                  Number of Intramolecular restraints:         0
                                  Number of Intermolecular restraints:         0
 ************************** Velocities initialization **************************
 Initial Temperature                                                    300.00 K
 COM velocity:           -0.000000000000     -0.000000000000     -0.000000000000
 *******************************************************************************


 Number of electrons:                                                        256
 Number of occupied orbitals:                                                128
 Number of molecular orbitals:                                               128

 Number of orbital functions:                                               1280
 Number of independent orbital functions:                                   1280

 Extrapolation method: initial_guess


 SCF WAVEFUNCTION OPTIMIZATION

  ----------------------------------- OT ---------------------------------------
  Minimizer      : DIIS                : direct inversion
                                         in the iterative subspace
                                         using   7 DIIS vectors
                                         safer DIIS on
  Preconditioner : FULL_KINETIC        : inversion of T + eS
  Precond_solver : DEFAULT
  stepsize       :    0.15000000                  energy_gap     :    0.20000000
  eps_taylor     :   0.10000E-15                  max_taylor     :             4
  ----------------------------------- OT ---------------------------------------

  Step     Update method      Time    Convergence         Total energy    Change
  ------------------------------------------------------------------------------
     1 OT DIIS     0.15E+00    0.2     0.01909729      -529.3015728815 -5.29E+02

 *******************************************************************************
 *   ___                                                                       *
 *  /   \                                                                      *
 * [ABORT]                                                                     *
 *  \___/                KS energy is an abnormal value (NaN/Inf).             *
 *    |                                                                        *
 *  O/|                                                                        *
 * /| |                                                                        *
 * / \                                                     qs_ks_methods.F:866 *
 *******************************************************************************


 ===== Routine Calling Stack ===== 

            9 qs_ks_build_kohn_sham_matrix
            8 rebuild_ks_matrix
            7 qs_ks_update_qs_env
            6 scf_env_do_scf_inner_loop
            5 scf_env_do_scf
            4 qs_energies
            3 qs_forces
            2 qs_mol_dyn_low
            1 CP2K
-------------- next part --------------
CC       = cc
CPP      =
FC       = ftn
LD       = ftn
AR       = ar -r
CPPFLAGS =
DFLAGS   = -D__MKL -D__FFTW3 -D__parallel -D__SCALAPACK -D__LIBXC2 -D__HAS_NO_SHARED_GLIBC -D__LIBINT -D__LIBINT_MAX_AM=7 -D__LIBDERIV_MAX_AM1=6
CFLAGS   = ${DFLAGS} -xSSE4.2 -pg -O2
FCFLAGS  = ${DFLAGS} -xSSE4.2 -pg -O2 \
           -pad -qopt-prefetch -funroll-loops -fpp -free \
           -nogen-interfaces \
           -I${MKLROOT}/include -I${MKLROOT}/include/fftw
LDFLAGS  = ${FCFLAGS}
MKL_LIB  = ${MKLROOT}/lib/intel64
LIBS     = ${LIBXC_HOME}/lib/libxcf90.a ${LIBXC_HOME}/lib/libxc.a
LIBS    += -Wl,--start-group ${MKL_LIB}/libmkl_scalapack_lp64.a \
           ${MKL_LIB}/libmkl_intel_lp64.a ${MKL_LIB}/libmkl_sequential.a \
           ${MKL_LIB}/libmkl_core.a \
           ${MKL_LIB}/libmkl_blacs_intelmpi_lp64.a -Wl,--end-group \
           $(LIBINT_HOME)/lib/libderiv.a \
           $(LIBINT_HOME)/lib/libint.a -lstdc++

-------------- next part --------------
CC       = cc
CPP      =
FC       = ftn -nofor-main
LD       = ftn -nofor-main
AR       = ar -r
CPPFLAGS =
DFLAGS   = -D__MKL -D__FFTW3 -D__parallel -D__SCALAPACK -D__LIBXC2 -D__HAS_NO_SHARED_GLIBC -D__LIBINT -D__LIBINT_MAX_AM=7 -D__LIBDERIV_MAX_AM1=6
CFLAGS   = ${DFLAGS} -xSSE4.2 -pg -O2
FCFLAGS  = ${DFLAGS} -xSSE4.2 -pg -O2 \
           -pad -qopt-prefetch -funroll-loops -fpp -free \
           -nogen-interfaces \
           -I${MKLROOT}/include -I${MKLROOT}/include/fftw 
LDFLAGS  = ${FCFLAGS}
MKL_LIB  = -mkl=sequential
LIBS     = /home/user/libxc-3.0.0-Intel17/build/lib/libxcf90.a /home/chermae/libxc-3.0.0-Intel17/build/lib/libxc.a
LIBS    += -Wl,--start-group -L/project/k1228/scalapack_installer-intel17/install/lib -lscalapack \
           -L/project/k1228/lapack-3.8.0-intel17 -llapack  -mkl=sequential \
           /home/user/libint-1.1.5-Intel17/lib/libderiv.a \
           /home/user/libint-1.1.5-Intel17/lib/libint.a -lstdc++



More information about the CP2K-user mailing list