[CP2K-user] [CP2K:19986] Re: Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Zac Smith
qingxinzhang6 at gmail.com
Mon Mar 4 03:02:39 UTC 2024
Dear Frederick,
I've attached the input, output files for your reference. BN__PBE.wfn is a
first guess to facilitate accelerated PBE0 calculations.
Have a good day
Zac
On Sunday, March 3, 2024 at 12:48:35 PM UTC-5 Frederick Stein wrote:
> Dear Zac,
> without providing your CP2K input file "BN.inp" and the respective output
> file (not the Slurm input/output files), we can only guess. Depending on
> the size of your system, you might be running out of memory in which case
> you need a larger number of compute nodes or less MPI ranks per node while
> increasing the number of OpenMP threads appropriately. It could also be a
> bug which we can only identify if you provide the CP2K input and output
> files.
> Best,
> Frederick
>
> Zac Smith schrieb am Sonntag, 3. März 2024 um 06:06:08 UTC+1:
>
>> Dear CP2K Community.
>> I'm running a job to optimize the calculation of excited states of a
>> periodic system and I encountered this error *Program received signal
>> SIGSEGV: Segmentation fault - invalid memory reference*. Do you have any
>> suggestions for changes to avoid this error? I am attaching the submitted
>> submit file and slurm.out file for your reference. Thanks.
>>
>
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DBCSR| CPU Multiplication driver SMM (U)
DBCSR| Multrec recursion limit 512 (U)
DBCSR| Multiplication stack size 1000 (D)
DBCSR| Maximum elements for images UNLIMITED (U)
DBCSR| Multiplicative factor virtual images 1 (U)
DBCSR| Use multiplication densification T (D)
DBCSR| Multiplication size stacks 3 (U)
DBCSR| Use memory pool for CPU allocation F (U)
DBCSR| Number of 3D layers SINGLE (U)
DBCSR| Use MPI memory allocation F (U)
DBCSR| Use RMA algorithm F (U)
DBCSR| Use Communication thread T (U)
DBCSR| Communication thread load 83 (D)
DBCSR| MPI: My process id 0
DBCSR| MPI: Number of processes 9
DBCSR| OMP: Current number of threads 2
DBCSR| OMP: Max number of threads 2
DBCSR| Split modifier for TAS multiplication algorithm 1.0E+00 (U)
**** **** ****** ** PROGRAM STARTED AT 2024-03-03 21:44:42.814
***** ** *** *** ** PROGRAM STARTED ON cpn-m23-26.compute.cbls.ccr.bu
** **** ****** PROGRAM STARTED BY
***** ** ** ** ** PROGRAM PROCESS ID 11959
**** ** ******* ** PROGRAM STARTED IN
CP2K| version string: CP2K version 2023.1 (Development Version)
CP2K| source code revision number: git:49cb240
CP2K| cp2kflags: omp libint fftw3 libxc parallel scalapack quip plumed2 spglib
CP2K| mkl libvdwxc
CP2K| is freely available from https://www.cp2k.org/
CP2K| Program compiled at Tue Mar 21 09:43:41 EDT 2023
CP2K| Program compiled on srv-p22-13.cbls.ccr.buffalo.edu
CP2K| Program compiled for local
CP2K| Data directory path /projects/academic/cyberwksp21/Software/cp2k-gnu/c
CP2K| Input file name BN.inp
GLOBAL| Force Environment number 1
GLOBAL| Basis set file name BASIS_MOLOPT
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 BN
GLOBAL| Run type GEO_OPT
GLOBAL| FFT library FFTW3
GLOBAL| Diagonalization library ScaLAPACK
GLOBAL| DGEMM library BLAS
GLOBAL| Orthonormality check for eigenvectors DISABLED
GLOBAL| Matrix multiplication library ScaLAPACK
GLOBAL| All-to-all communication in single precision F
GLOBAL| FFTs using library dependent lengths F
GLOBAL| Grid backend AUTO
GLOBAL| Global print level LOW
GLOBAL| MPI I/O enabled T
GLOBAL| Total number of message passing processes 9
GLOBAL| Number of threads for this process 2
GLOBAL| This output is from process 0
GLOBAL| Stack size for threads created by OpenMP (OMP_STACKSIZE) default
GLOBAL| CPU model name Intel(R) Xeon(R) CPU E5-2650 v4 @ 2.20GHz
MEMORY| system memory details [Kb]
MEMORY| rank 0 min max average
MEMORY| MemTotal 263861508 263861508 263861508 263861508
MEMORY| MemFree 259120016 259120016 259120016 259120016
MEMORY| Buffers 2280 2280 2280 2280
MEMORY| Cached 723504 723504 723504 723504
MEMORY| Slab 174072 174072 174072 174072
MEMORY| SReclaimable 95716 95716 95716 95716
MEMORY| MemLikelyFree 259941516 259941516 259941516 259941516
GENERATE| Preliminary Number of Bonds generated: 0
GENERATE| Achieved consistency in connectivity generation.
*******************************************************************************
*******************************************************************************
** **
** ##### ## ## **
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** ## ## ## ## ## ##### ## ## #### ## ##### ##### **
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** ## ### ## ## ## ## ## ## ## ## ## ## **
** ####### ##### ## ##### ## ## #### ## ##### ## **
** ## ## **
** **
** ... make the atoms dance **
** **
** Copyright (C) by CP2K developers group (2000-2023) **
** J. Chem. Phys. 152, 194103 (2020) **
** **
*******************************************************************************
TOTAL NUMBERS AND MAXIMUM NUMBERS
Total number of - Atomic kinds: 2
- Atoms: 20
- Shell sets: 20
- Shells: 100
- Primitive Cartesian functions: 90
- Cartesian basis functions: 280
- Spherical basis functions: 260
Maximum angular momentum of- Orbital basis functions: 2
- Local part of the GTH pseudopotential: 2
- Non-local part of the GTH pseudopotential: 0
AUX_FIT ADMM-Basis:
Total number of - Shell sets: 100
- Shells: 100
- Primitive Cartesian functions: 140
- Cartesian basis functions: 280
- Spherical basis functions: 260
Maximum angular momentum 2
SCF PARAMETERS Density guess: RESTART
--------------------------------------------------------
max_scf: 128
max_scf_history: 0
max_diis: 4
--------------------------------------------------------
eps_scf: 1.00E-06
eps_scf_history: 0.00E+00
eps_diis: 1.00E-01
eps_eigval: 1.00E-05
--------------------------------------------------------
level_shift [a.u.]: 0.000000
--------------------------------------------------------
Mixing method: BROYDEN_MIXING
charge density mixing in g-space
--------------------------------------------------------
No outer SCF
BFGS| Use rational function optimization for step estimation: NO
BFGS| Use model Hessian for initial guess: YES
BFGS| Restart Hessian: NO
BFGS| Trust radius: 0.378
*******************************************************************************
*** STARTING GEOMETRY OPTIMIZATION ***
*** BFGS ***
*******************************************************************************
Number of electrons: 80
Number of occupied orbitals: 40
Number of molecular orbitals: 40
Number of orbital functions: 260
Number of independent orbital functions: 260
Extrapolation method: initial_guess
SCF WAVEFUNCTION OPTIMIZATION
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 NoMix/Diag. 0.40E+00 32.9 1.39160466 -121.4917303389 -1.21E+02
2 Broy./Diag. 0.40E+00 2.6 0.08176984 -132.9576340524 -1.15E+01
3 Broy./Diag. 0.40E+00 2.5 0.05298748 -128.1726759312 4.78E+00
4 Broy./Diag. 0.40E+00 2.6 0.01803165 -126.9766978679 1.20E+00
5 Broy./Diag. 0.40E+00 2.5 0.00321983 -126.9941736830 -1.75E-02
6 Broy./Diag. 0.40E+00 2.6 0.00197974 -126.9787137351 1.55E-02
7 Broy./Diag. 0.40E+00 2.6 0.00082445 -126.9871287939 -8.42E-03
8 Broy./Diag. 0.40E+00 2.6 0.00016356 -127.0043319097 -1.72E-02
9 Broy./Diag. 0.40E+00 2.5 0.00005964 -127.0046986817 -3.67E-04
10 Broy./Diag. 0.40E+00 2.6 0.00002329 -127.0045113020 1.87E-04
11 Broy./Diag. 0.40E+00 2.6 0.00001367 -127.0046802104 -1.69E-04
12 Broy./Diag. 0.40E+00 2.6 0.00000295 -127.0045590379 1.21E-04
13 Broy./Diag. 0.40E+00 2.5 0.00000093 -127.0045362146 2.28E-05
*** SCF run converged in 13 steps ***
Electronic density on regular grids: -80.0000000000 0.0000000000
Core density on regular grids: 79.9999999999 -0.0000000001
Total charge density on r-space grids: -0.0000000000
Total charge density g-space grids: -0.0000000000
Overlap energy of the core charge distribution: 0.00001188676083
Self energy of the core charge distribution: -309.10057823440422
Core Hamiltonian energy: 97.27593870362261
Hartree energy: 120.96545171286176
Exchange-correlation energy: -29.23215704690666
Hartree-Fock Exchange energy: -6.91320323654282
Total energy: -127.00453621460849
*******************************************************************************
** **
** ######## ####### ####### ######## ####### ######## **
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** ## ## ## ## ## ###### ####### ## **
** ## ## ## ## ## ## ## ## **
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** **
*******************************************************************************
KERNEL| FULL
FUNCTIONAL| PBE:
FUNCTIONAL| J.P.Perdew, K.Burke, M.Ernzerhof, Phys. Rev. Letter, vol. 77, n 18,
FUNCTIONAL| pp. 3865-3868, (1996)sx=0.750sc=1.000{spin unpolarized}
KERNEL| ADMM Exact Exchange
KERNEL| Apply ADMM Kernel XC
KERNEL| Symmetric ADMM Kernel
KERNEL| Spin symmetry of excitations Singlet
TDDFPT| Number of states calculated 3
TDDFPT| Number of Davidson iterations 50
TDDFPT| Davidson iteration convergence 0.367E-07
TDDFPT| Max. number of Krylov space vectors 5000
TDDFPT| Molecular Orbitals: Spin AOs Occ Virt Total
TDDFPT| 1 260 40 220 260
-------------------------------------------------------------------------------
- TDDFPT Initial Guess -
-------------------------------------------------------------------------------
State Occupied -> Virtual Excitation
number orbital orbital energy (eV)
-------------------------------------------------------------------------------
1 40 41 7.13500
2 40 42 7.13501
3 39 41 7.13502
Number of active states: 8800
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
- TDDFPT WAVEFUNCTION OPTIMIZATION -
-------------------------------------------------------------------------------
Step Time Convergence Conv. states
-------------------------------------------------------------------------------
1 9.1 2.3916E-02 0
2 9.1 1.0563E-02 0
3 9.0 4.4438E-03 0
4 9.0 5.0473E-03 0
5 9.1 2.3549E-04 0
6 9.1 5.2288E-06 0
7 9.1 1.6286E-07 2
8 8.8 4.2672E-09 3
------------------------- Restart Davidson iterations -------------------------
9 8.8 1.1102E-16 3
-------------------------------------------------------------------------------
- TDDFPT run converged in 9 iteration(s)
-------------------------------------------------------------------------------
R-TDDFPT states of multiplicity 1
Transition dipoles calculated using velocity formulation
State Excitation Transition dipole (a.u.) Oscillator
number energy (eV) x y z strength (a.u.)
------------------------------------------------------------------------
TDDFPT| 1 7.09094 6.4752E-04 3.7305E-04 1.7700E-09 9.70164E-08
TDDFPT| 2 7.11663 2.1222E+00 1.2253E+00 5.1938E-09 1.04703E+00
TDDFPT| 3 7.37168 2.3757E-05 1.5960E-05 -1.0800E-08 1.47935E-10
TDDFPT : CheckSum = 0.457923E+00
-------------------------------------------------------------------------------
- Excitation analysis -
-------------------------------------------------------------------------------
State Occupied Virtual Excitation
number orbital orbital amplitude
-------------------------------------------------------------------------------
1 7.09094 eV
40 41 0.702741
39 42 -0.702683
40 42 0.050127
39 41 0.050127
37 45 0.031981
33 41 0.031482
34 42 0.031482
39 44 -0.025355
40 43 -0.025351
36 59 -0.017438
35 60 -0.017356
38 61 -0.013504
37 62 0.012146
32 69 0.010645
31 70 -0.010644
2 7.11663 eV
40 42 -0.699273
39 41 -0.699251
40 44 0.082541
39 43 -0.082541
40 41 0.049880
39 42 -0.049878
38 45 0.036469
33 42 0.014103
34 41 -0.014101
33 44 0.012859
34 43 0.012857
26 54 -0.011369
3 7.37168 eV
39 41 -0.693874
40 42 0.693852
34 43 0.077136
33 44 -0.077135
39 43 -0.072336
40 44 -0.072333
40 50 -0.027658
39 51 0.027658
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