[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 UTC 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
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&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
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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
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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++
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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++
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