StartDate: 2020-01-17 11:00:13+00:00 CpuId: 16x Intel Core i7-5000 Extreme Edition (Haswell R2) / Xeon E5-x600 / Xeon E5-4800 / Xeon E5-8800 v3 (Haswell-EP), 22nm CommitSHA: 7bf90922cbafbb3ac0585b47576f2ca24f0ace6b CommitTime: 2020-01-17 11:15:25 +0100 CommitAuthor: Ole Schütt CommitSubject: SIRIUS: Add LSAN suppressions Trying to pull image cp2k-toolchain-mpich... success :-) Trying to pull image cp2k-i-pi... success :-) #################### Running Image cp2k-i-pi #################### ========== Fetching Git Commit ========== CommitSHA: 7bf90922cbafbb3ac0585b47576f2ca24f0ace6b CommitTime: 2020-01-17 11:15:25 +0100 CommitAuthor: Ole Schütt CommitSubject: SIRIUS: Add LSAN suppressions ========== Running Test ========== ========== Compiling CP2K ========== Compiling cp2k... done. ========== Installing i-Pi ========== ========== Running i-Pi Tests ========== ____ ____ ____ ____ / \ / \ / \ / \ | ################################# | \__#_/ \____/ \____/ \_#__/ # _ _______ _____ # # (_) |_ __ \|_ _| # -*- v 2.0 -*- # __ ______ | |__) | | | # Y [ ||______|| ___/ | | # A Universal Force Engine 0 0 | | _| |_ _| |_ # # [___] |_____| |_____| # __#_ ____ ____ _#__ / # \ / \ / \ / # \ | ################################# | \____/ \____/ \____/ \____/ fetching ffsocket returning [] returning [] returning [] returning [] returning [ 0. 0. 0. 0. 0. 0. 0. 0. 0.] returning [ 1.] returning 0.0 returning 0.0023751114 returning -1.0 returning [-1. -0. -0. -0. -1. -0. -0. -0. -1.] returning 0.0 returning 20.6706865 returning 206.706865 returning 0.0 returning 2067.06865 returning 4134.1373 returning 206.706865 returning 0.0 returning 2067.06865 returning 4134.1373 returning 0.0 returning 0.0 returning 1.0 # Initializing system object # Initializing simulation object # Initializer (stage 1) parsing positions object. Initializing from file init.xyz. Dimension: length, units: automatic, cell_units: automatic Interpreting input with dimension length, units angstrom and cell units atomic_unit # Initializer (stage 1) parsing masses object. Initializing from file init.xyz. Dimension: length, units: automatic, cell_units: automatic Interpreting input with dimension length, units angstrom and cell units atomic_unit # Initializer (stage 1) parsing labels object. Initializing from file init.xyz. Dimension: length, units: automatic, cell_units: automatic Interpreting input with dimension length, units angstrom and cell units atomic_unit # Initializer (stage 1) parsing cell object. Initializing from file init.xyz. Dimension: length, units: automatic, cell_units: automatic Interpreting input with dimension length, units angstrom and cell units atomic_unit Initializing from file init.xyz. Dimension: length, units: automatic, cell_units: automatic Interpreting input with dimension length, units angstrom and cell units atomic_unit # Initializer (stage 1) parsing momenta object. # Resampling velocities at temperature 750.0 kelvin NOW BINDING THE FORCES.... # Initializer (stage 2) parsing positions object. # Initializer (stage 2) parsing masses object. # Initializer (stage 2) parsing labels object. # Initializer (stage 2) parsing cell object. # Initializer (stage 2) parsing momenta object. Created inet socket with address localhost and port number 21340 @ForceField: Starting the polling thread main loop. # i-PI loaded input file: input.xml --- begin input file content --- [step, time{femtosecond}, conserved, potential, kinetic_cv, pressure_cv, volume, temperature{kelvin}, kinetic_md, pressure_md ] x_centroid{atomic_unit} positions velocities forces 10 20222

localhost

21340 0.01 5000 init.xyz 750 750 ***** ** ** ** ** PROGRAM PROCESS ID 99658 **** ** ******* ** PROGRAM STARTED IN /opt/i-pi/examples/cp2k/nvt-cl/run_1 CP2K| version string: CP2K version 8.0 (Development Version) CP2K| source code revision number: git:7bf9092 CP2K| cp2kflags: omp libint fftw3 libxc pexsi elpa parallel mpi3 scalapack quip CP2K| smm_dnn smm xsmm plumed2 has_ieee_exceptions spglib sirius check_diag CP2K| is freely available from https://www.cp2k.org/ CP2K| Program compiled at Fri Jan 17 11:02:51 UTC 2020 CP2K| Program compiled on b2bcb6131f83 CP2K| Program compiled for local CP2K| Data directory path /workspace/cp2k/data CP2K| Input file name ../in.cp2k GLOBAL| Force Environment number 1 GLOBAL| Basis set file name ../../basis/GTH_BASIS_SETS GLOBAL| Potential file name ../../basis/GTH_POTENTIALS GLOBAL| MM Potential file name MM_POTENTIAL GLOBAL| Coordinate file name __STD_INPUT__ GLOBAL| Method name CP2K GLOBAL| Project name H2O GLOBAL| Preferred FFT library FFTW3 GLOBAL| Preferred diagonalization lib. ELPA GLOBAL| Run type DRIVER GLOBAL| All-to-all communication in single precision F GLOBAL| FFTs using library dependent lengths F GLOBAL| Global print level LOW GLOBAL| MPI I/O enabled T GLOBAL| Total number of message passing processes 2 GLOBAL| Number of threads for this process 16 GLOBAL| This output is from process 0 GLOBAL| CPU model name Intel(R) Xeon(R) CPU @ 2.30GHz GLOBAL| CPUID 1002 MEMORY| system memory details [Kb] MEMORY| rank 0 min max average MEMORY| MemTotal 14775656 14775656 14775656 14775656 MEMORY| MemFree 2305128 2305128 2305128 2305128 MEMORY| Buffers 181736 181736 181736 181736 MEMORY| Cached 9790896 9790896 9790896 9790896 MEMORY| Slab 903932 903932 903932 903932 MEMORY| SReclaimable 725456 725456 725456 725456 MEMORY| MemLikelyFree 13003216 13003216 13003216 13003216 GENERATE| Preliminary Number of Bonds generated: 0 GENERATE| Achieved consistency in connectivity generation. ******************************************************************************* ******************************************************************************* ** ** ** ##### ## ## ** ** ## ## ## ## ## ** ** ## ## ## ###### ** ** ## ## ## ## ## ##### ## ## #### ## ##### ##### ** ** ## ## ## ## ## ## ## ## ## ## ## ## ## ## ** ** ## ## ## ## ## ## ## #### ### ## ###### ###### ** ** ## ### ## ## ## ## ## ## ## ## ## ## ** ** ####### ##### ## ##### ## ## #### ## ##### ## ** ** ## ## ** ** ** ** ... make the atoms dance ** ** ** ** Copyright (C) by CP2K developers group (2000 - 2020) ** ** ** ******************************************************************************* TOTAL NUMBERS AND MAXIMUM NUMBERS Total number of - Atomic kinds: 2 - Atoms: 3 - Shell sets: 6 - Shells: 11 - Primitive Cartesian functions: 15 - Cartesian basis functions: 24 - Spherical basis functions: 23 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-03 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 @ i-PI DRIVER BEING LOADED @ INPUT DATA: localhost 21340 F @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: POSDATA Number of electrons: 8 Number of occupied orbitals: 4 Number of molecular orbitals: 4 Number of orbital functions: 23 Number of independent orbital functions: 23 Extrapolation method: initial_guess At line 316 of file /workspace/cp2k/src/atom_operators.F Fortran runtime warning: An array temporary was created for argument 'a' of procedure 'dgesv' At line 316 of file /workspace/cp2k/src/atom_operators.F Fortran runtime warning: An array temporary was created for argument 'b' of procedure 'dgesv' At line 316 of file /workspace/cp2k/src/atom_operators.F Fortran runtime warning: An array temporary was created for argument 'a' of procedure 'dgesv' At line 316 of file /workspace/cp2k/src/atom_operators.F Fortran runtime warning: An array temporary was created for argument 'b' of procedure 'dgesv' SCF WAVEFUNCTION OPTIMIZATION ----------------------------------- OT --------------------------------------- Minimizer : DIIS : direct inversion in the iterative subspace using 7 DIIS vectors safer DIIS on Preconditioner : FULL_ALL : diagonalization, state selective Precond_solver : DEFAULT stepsize : 0.15000000 energy_gap : 0.08000000 eps_taylor : 0.10000E-15 max_taylor : 4 ----------------------------------- OT --------------------------------------- Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ 1 OT DIIS 0.15E+00 158.2 0.32892337 -15.4822254377 -1.55E+01 2 OT DIIS 0.15E+00 134.5 0.39486127 -16.1247656715 -6.43E-01 3 OT DIIS 0.15E+00 133.7 0.24244684 -16.8124428592 -6.88E-01 4 OT DIIS 0.15E+00 131.9 0.16957469 -16.9303009851 -1.18E-01 5 OT DIIS 0.15E+00 138.5 0.29475415 -16.9473363785 -1.70E-02 6 OT DIIS 0.15E+00 139.0 0.14087870 -17.0945521394 -1.47E-01 7 OT DIIS 0.15E+00 138.2 0.07722276 -17.1214695120 -2.69E-02 8 OT DIIS 0.15E+00 83.2 0.07715980 -17.1237733474 -2.30E-03 9 OT DIIS 0.15E+00 82.9 0.03703268 -17.1356684897 -1.19E-02 10 OT DIIS 0.15E+00 81.0 0.01161628 -17.1383070740 -2.64E-03 11 OT DIIS 0.15E+00 82.7 0.00513907 -17.1386959255 -3.89E-04 12 OT DIIS 0.15E+00 82.4 0.00082925 -17.1387469207 -5.10E-05 *** SCF run converged in 12 steps *** Electronic density on regular grids: -7.9999991042 0.0000008958 Core density on regular grids: 8.0000000752 0.0000000752 Total charge density on r-space grids: 0.0000009710 Total charge density g-space grids: 0.0000009710 Overlap energy of the core charge distribution: 0.00000008696889 Self energy of the core charge distribution: -43.83289054591484 Core Hamiltonian energy: 13.00586552086632 Hartree energy: 17.86025730667268 Exchange-correlation energy: -4.17197928932877 Total energy: -17.13874692073572 ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -17.138750708359552 @ DRIVER MODE: Received positions @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: GETFORCE @ DRIVER MODE: Returning v,forces,stress @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: POSDATA Number of electrons: 8 Number of occupied orbitals: 4 Number of molecular orbitals: 4 Number of orbital functions: 23 Number of independent orbital functions: 23 Extrapolation method: ASPC SCF WAVEFUNCTION OPTIMIZATION ----------------------------------- OT --------------------------------------- Minimizer : DIIS : direct inversion in the iterative subspace using 7 DIIS vectors safer DIIS on Preconditioner : FULL_ALL : diagonalization, state selective Precond_solver : DEFAULT stepsize : 0.15000000 energy_gap : 0.08000000 eps_taylor : 0.10000E-15 max_taylor : 4 ----------------------------------- OT --------------------------------------- Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ 1 OT DIIS 0.15E+00 93.3 0.00361550 -17.1384145189 -1.71E+01 2 OT DIIS 0.15E+00 69.4 0.00143001 -17.1385385626 -1.24E-04 3 OT DIIS 0.15E+00 69.4 0.00043055 -17.1385604389 -2.19E-05 *** SCF run converged in 3 steps *** Electronic density on regular grids: -7.9999991298 0.0000008702 Core density on regular grids: 8.0000000549 0.0000000549 Total charge density on r-space grids: 0.0000009251 Total charge density g-space grids: 0.0000009251 Overlap energy of the core charge distribution: 0.00000009358732 Self energy of the core charge distribution: -43.83289054591484 Core Hamiltonian energy: 13.00899007158026 Hartree energy: 17.85824294289868 Exchange-correlation energy: -4.17290300106530 Total energy: -17.13856043891386 ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -17.138561289484969 @ DRIVER MODE: Received positions @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: GETFORCE @ DRIVER MODE: Returning v,forces,stress @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: POSDATA Number of electrons: 8 Number of occupied orbitals: 4 Number of molecular orbitals: 4 Number of orbital functions: 23 Number of independent orbital functions: 23 Extrapolation method: ASPC SCF WAVEFUNCTION OPTIMIZATION ----------------------------------- OT --------------------------------------- Minimizer : DIIS : direct inversion in the iterative subspace using 7 DIIS vectors safer DIIS on Preconditioner : FULL_ALL : diagonalization, state selective Precond_solver : DEFAULT stepsize : 0.15000000 energy_gap : 0.08000000 eps_taylor : 0.10000E-15 max_taylor : 4 ----------------------------------- OT --------------------------------------- Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ 1 OT DIIS 0.15E+00 94.3 0.00104570 -17.1382682000 -1.71E+01 2 OT DIIS 0.15E+00 70.1 0.00043133 -17.1382778712 -9.67E-06 *** SCF run converged in 2 steps *** Electronic density on regular grids: -7.9999991588 0.0000008412 Core density on regular grids: 8.0000000306 0.0000000306 Total charge density on r-space grids: 0.0000008719 Total charge density g-space grids: 0.0000008719 Overlap energy of the core charge distribution: 0.00000010753607 Self energy of the core charge distribution: -43.83289054591484 Core Hamiltonian energy: 13.02643418955750 Hartree energy: 17.84513186454562 Exchange-correlation energy: -4.17695348693429 Total energy: -17.13827787120995 ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -17.138279410507117 @ DRIVER MODE: Received positions @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: GETFORCE @ DRIVER MODE: Returning v,forces,stress @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: POSDATA Number of electrons: 8 Number of occupied orbitals: 4 Number of molecular orbitals: 4 Number of orbital functions: 23 Number of independent orbital functions: 23 Extrapolation method: ASPC SCF WAVEFUNCTION OPTIMIZATION ----------------------------------- OT --------------------------------------- Minimizer : DIIS : direct inversion in the iterative subspace using 7 DIIS vectors safer DIIS on Preconditioner : FULL_ALL : diagonalization, state selective Precond_solver : DEFAULT stepsize : 0.15000000 energy_gap : 0.08000000 eps_taylor : 0.10000E-15 max_taylor : 4 ----------------------------------- OT --------------------------------------- Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ 1 OT DIIS 0.15E+00 92.6 0.00142683 -17.1378825471 -1.71E+01 2 OT DIIS 0.15E+00 69.6 0.00066346 -17.1378975856 -1.50E-05 *** SCF run converged in 2 steps *** Electronic density on regular grids: -7.9999991937 0.0000008063 Core density on regular grids: 8.0000000183 0.0000000183 Total charge density on r-space grids: 0.0000008246 Total charge density g-space grids: 0.0000008246 Overlap energy of the core charge distribution: 0.00000012703346 Self energy of the core charge distribution: -43.83289054591484 Core Hamiltonian energy: 13.04532793371978 Hartree energy: 17.83143231107428 Exchange-correlation energy: -4.18176741147303 Total energy: -17.13789758556036 ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -17.137900221690821 @ DRIVER MODE: Received positions @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: GETFORCE @ DRIVER MODE: Returning v,forces,stress @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: POSDATA Number of electrons: 8 Number of occupied orbitals: 4 Number of molecular orbitals: 4 Number of orbital functions: 23 Number of independent orbital functions: 23 Extrapolation method: ASPC SCF WAVEFUNCTION OPTIMIZATION ----------------------------------- OT --------------------------------------- Minimizer : DIIS : direct inversion in the iterative subspace using 7 DIIS vectors safer DIIS on Preconditioner : FULL_ALL : diagonalization, state selective Precond_solver : DEFAULT stepsize : 0.15000000 energy_gap : 0.08000000 eps_taylor : 0.10000E-15 max_taylor : 4 ----------------------------------- OT --------------------------------------- Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ 1 OT DIIS 0.15E+00 92.4 0.00079794 -17.1374528915 -1.71E+01 *** SCF run converged in 1 steps *** Electronic density on regular grids: -7.9999992231 0.0000007769 Core density on regular grids: 7.9999999889 -0.0000000111 Total charge density on r-space grids: 0.0000007658 Total charge density g-space grids: 0.0000007658 Overlap energy of the core charge distribution: 0.00000015375008 Self energy of the core charge distribution: -43.83289054591484 Core Hamiltonian energy: 13.05388690084406 Hartree energy: 17.82668637156258 Exchange-correlation energy: -4.18513577170223 Total energy: -17.13745289146035 ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -17.137457233979305 @ DRIVER MODE: Received positions @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: GETFORCE @ DRIVER MODE: Returning v,forces,stress @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: POSDATA Number of electrons: 8 Number of occupied orbitals: 4 Number of molecular orbitals: 4 Number of orbital functions: 23 Number of independent orbital functions: 23 Extrapolation method: ASPC SCF WAVEFUNCTION OPTIMIZATION ----------------------------------- OT --------------------------------------- Minimizer : DIIS : direct inversion in the iterative subspace using 7 DIIS vectors safer DIIS on Preconditioner : FULL_ALL : diagonalization, state selective Precond_solver : DEFAULT stepsize : 0.15000000 energy_gap : 0.08000000 eps_taylor : 0.10000E-15 max_taylor : 4 ----------------------------------- OT --------------------------------------- Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ 1 OT DIIS 0.15E+00 91.5 0.00291753 -17.1374911298 -1.71E+01 2 OT DIIS 0.15E+00 70.2 0.00144467 -17.1375466879 -5.56E-05 3 OT DIIS 0.15E+00 69.3 0.00053320 -17.1375579440 -1.13E-05 *** SCF run converged in 3 steps *** Electronic density on regular grids: -7.9999992307 0.0000007693 Core density on regular grids: 7.9999999584 -0.0000000416 Total charge density on r-space grids: 0.0000007277 Total charge density g-space grids: 0.0000007277 Overlap energy of the core charge distribution: 0.00000014944517 Self energy of the core charge distribution: -43.83289054591484 Core Hamiltonian energy: 13.06054216716829 Hartree energy: 17.82080523367042 Exchange-correlation energy: -4.18601494836448 Total energy: -17.13755794399544 ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -17.137560516457366 @ DRIVER MODE: Received positions @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: GETFORCE @ DRIVER MODE: Returning v,forces,stress @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: POSDATA Number of electrons: 8 Number of occupied orbitals: 4 Number of molecular orbitals: 4 Number of orbital functions: 23 Number of independent orbital functions: 23 Extrapolation method: ASPC SCF WAVEFUNCTION OPTIMIZATION ----------------------------------- OT --------------------------------------- Minimizer : DIIS : direct inversion in the iterative subspace using 7 DIIS vectors safer DIIS on Preconditioner : FULL_ALL : diagonalization, state selective Precond_solver : DEFAULT stepsize : 0.15000000 energy_gap : 0.08000000 eps_taylor : 0.10000E-15 max_taylor : 4 ----------------------------------- OT --------------------------------------- Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ 1 OT DIIS 0.15E+00 93.2 0.00128795 -17.1378312178 -1.71E+01 2 OT DIIS 0.15E+00 70.3 0.00048801 -17.1378468687 -1.57E-05 *** SCF run converged in 2 steps *** Electronic density on regular grids: -7.9999992288 0.0000007712 Core density on regular grids: 7.9999999465 -0.0000000535 Total charge density on r-space grids: 0.0000007176 Total charge density g-space grids: 0.0000007176 Overlap energy of the core charge distribution: 0.00000013632602 Self energy of the core charge distribution: -43.83289054591484 Core Hamiltonian energy: 13.04677601766230 Hartree energy: 17.83087006214686 Exchange-correlation energy: -4.18260253893253 Total energy: -17.13784686871218 ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -17.137849525372193 @ DRIVER MODE: Received positions @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: GETFORCE @ DRIVER MODE: Returning v,forces,stress @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: POSDATA Number of electrons: 8 Number of occupied orbitals: 4 Number of molecular orbitals: 4 Number of orbital functions: 23 Number of independent orbital functions: 23 Extrapolation method: ASPC SCF WAVEFUNCTION OPTIMIZATION ----------------------------------- OT --------------------------------------- Minimizer : DIIS : direct inversion in the iterative subspace using 7 DIIS vectors safer DIIS on Preconditioner : FULL_ALL : diagonalization, state selective Precond_solver : DEFAULT stepsize : 0.15000000 energy_gap : 0.08000000 eps_taylor : 0.10000E-15 max_taylor : 4 ----------------------------------- OT --------------------------------------- Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ 1 OT DIIS 0.15E+00 91.1 0.00053726 -17.1380636228 -1.71E+01 *** SCF run converged in 1 steps *** Electronic density on regular grids: -7.9999992328 0.0000007672 Core density on regular grids: 7.9999999343 -0.0000000657 Total charge density on r-space grids: 0.0000007015 Total charge density g-space grids: 0.0000007015 Overlap energy of the core charge distribution: 0.00000012117957 Self energy of the core charge distribution: -43.83289054591484 Core Hamiltonian energy: 13.03728556917877 Hartree energy: 17.83725548950424 Exchange-correlation energy: -4.17971425673779 Total energy: -17.13806362279004 ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -17.138066090911497 @ DRIVER MODE: Received positions @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: GETFORCE @ DRIVER MODE: Returning v,forces,stress @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: POSDATA Number of electrons: 8 Number of occupied orbitals: 4 Number of molecular orbitals: 4 Number of orbital functions: 23 Number of independent orbital functions: 23 Extrapolation method: ASPC SCF WAVEFUNCTION OPTIMIZATION ----------------------------------- OT --------------------------------------- Minimizer : DIIS : direct inversion in the iterative subspace using 7 DIIS vectors safer DIIS on Preconditioner : FULL_ALL : diagonalization, state selective Precond_solver : DEFAULT stepsize : 0.15000000 energy_gap : 0.08000000 eps_taylor : 0.10000E-15 max_taylor : 4 ----------------------------------- OT --------------------------------------- Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ 1 OT DIIS 0.15E+00 93.3 0.00086217 -17.1381620449 -1.71E+01 *** SCF run converged in 1 steps *** Electronic density on regular grids: -7.9999992423 0.0000007577 Core density on regular grids: 7.9999999438 -0.0000000562 Total charge density on r-space grids: 0.0000007015 Total charge density g-space grids: 0.0000007015 Overlap energy of the core charge distribution: 0.00000010599394 Self energy of the core charge distribution: -43.83289054591484 Core Hamiltonian energy: 13.01946070115003 Hartree energy: 17.85046552022744 Exchange-correlation energy: -4.17519782633419 Total energy: -17.13816204487761 ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -17.138168592625423 @ DRIVER MODE: Received positions @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: GETFORCE @ DRIVER MODE: Returning v,forces,stress @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: POSDATA Number of electrons: 8 Number of occupied orbitals: 4 Number of molecular orbitals: 4 Number of orbital functions: 23 Number of independent orbital functions: 23 Extrapolation method: ASPC SCF WAVEFUNCTION OPTIMIZATION ----------------------------------- OT --------------------------------------- Minimizer : DIIS : direct inversion in the iterative subspace using 7 DIIS vectors safer DIIS on Preconditioner : FULL_ALL : diagonalization, state selective Precond_solver : DEFAULT stepsize : 0.15000000 energy_gap : 0.08000000 eps_taylor : 0.10000E-15 max_taylor : 4 ----------------------------------- OT --------------------------------------- Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ 1 OT DIIS 0.15E+00 93.0 0.00155649 -17.1378942844 -1.71E+01 2 OT DIIS 0.15E+00 71.1 0.00067134 -17.1379144014 -2.01E-05 *** SCF run converged in 2 steps *** Electronic density on regular grids: -7.9999992743 0.0000007257 Core density on regular grids: 7.9999999849 -0.0000000151 Total charge density on r-space grids: 0.0000007106 Total charge density g-space grids: 0.0000007106 Overlap energy of the core charge distribution: 0.00000011202381 Self energy of the core charge distribution: -43.83289054591484 Core Hamiltonian energy: 13.02963069568126 Hartree energy: 17.84265083798006 Exchange-correlation energy: -4.17730550121646 Total energy: -17.13791440144617 ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -17.137917596421016 @ DRIVER MODE: Received positions @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: GETFORCE @ DRIVER MODE: Returning v,forces,stress @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: POSDATA Number of electrons: 8 Number of occupied orbitals: 4 Number of molecular orbitals: 4 Number of orbital functions: 23 Number of independent orbital functions: 23 Extrapolation method: ASPC SCF WAVEFUNCTION OPTIMIZATION ----------------------------------- OT --------------------------------------- Minimizer : DIIS : direct inversion in the iterative subspace using 7 DIIS vectors safer DIIS on Preconditioner : FULL_ALL : diagonalization, state selective Precond_solver : DEFAULT stepsize : 0.15000000 energy_gap : 0.08000000 eps_taylor : 0.10000E-15 max_taylor : 4 ----------------------------------- OT --------------------------------------- Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ 1 OT DIIS 0.15E+00 92.4 0.00153313 -17.1377189891 -1.71E+01 2 OT DIIS 0.15E+00 70.2 0.00062835 -17.1377383096 -1.93E-05 *** SCF run converged in 2 steps *** Electronic density on regular grids: -7.9999993221 0.0000006779 Core density on regular grids: 8.0000000282 0.0000000282 Total charge density on r-space grids: 0.0000007061 Total charge density g-space grids: 0.0000007061 Overlap energy of the core charge distribution: 0.00000010851210 Self energy of the core charge distribution: -43.83289054591484 Core Hamiltonian energy: 13.03237236243272 Hartree energy: 17.84068345213519 Exchange-correlation energy: -4.17790368673090 Total energy: -17.13773830956573 ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -17.137741099338193 @ DRIVER MODE: Received positions @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: GETFORCE @ DRIVER MODE: Returning v,forces,stress @ DRIVER MODE: Message from server: STATUS @ DRIVER MODE: Message from server: EXIT @DRIVER MODE: Socket disconnected, time to exit. ------------------------------------------------------------------------------- - - - DBCSR STATISTICS - - - ------------------------------------------------------------------------------- COUNTER TOTAL BLAS SMM ACC flops 4 x 4 x 4 22528 0.0% 100.0% 0.0% flops 13 x 5 x 4 27560 0.0% 100.0% 0.0% flops 5 x 13 x 4 27560 0.0% 100.0% 0.0% flops 5 x 5 x 4 31800 0.0% 100.0% 0.0% flops 4 x 4 x 10 43200 0.0% 100.0% 0.0% flops 5 x 4 x 4 53120 0.0% 100.0% 0.0% flops 4 x 4 x 13 56160 0.0% 100.0% 0.0% flops 5 x 4 x 10 67200 0.0% 100.0% 0.0% flops 13 x 4 x 4 69056 0.0% 100.0% 0.0% flops 13 x 13 x 4 71656 0.0% 100.0% 0.0% flops 13 x 4 x 10 87360 0.0% 100.0% 0.0% flops 5 x 4 x 5 120000 0.0% 100.0% 0.0% flops 13 x 4 x 5 156000 0.0% 100.0% 0.0% flops 5 x 4 x 13 243360 0.0% 100.0% 0.0% flops 13 x 4 x 13 316368 0.0% 100.0% 0.0% flops inhomo. stacks 0 0.0% 0.0% 0.0% flops total 1.392928E+06 0.0% 100.0% 0.0% flops max/rank 849.888000E+03 0.0% 100.0% 0.0% matmuls inhomo. stacks 0 0.0% 0.0% 0.0% matmuls total 3116 0.0% 100.0% 0.0% number of processed stacks 2745 0.0% 100.0% 0.0% average stack size 0.0 1.1 0.0 marketing flops 1.466744E+06 ------------------------------------------------------------------------------- # multiplications 775 max memory usage/rank 166.412288E+06 # max total images/rank 2 # max 3D layers 1 # MPI messages exchanged 1550 MPI messages size (bytes): total size 354.368000E+03 min size 0.000000E+00 max size 736.000000E+00 average size 228.624512E+00 MPI breakdown and total messages size (bytes): size <= 128 759 43776 128 < size <= 8192 791 310592 8192 < size <= 32768 0 0 32768 < size <= 131072 0 0 131072 < size <= 4194304 0 0 4194304 < size <= 16777216 0 0 16777216 < size 0 0 ------------------------------------------------------------------------------- *** WARNING in dbcsr_mm.F:295 :: Using a non-square number of MPI ranks *** *** might lead to poor performance. Used ranks: 2 Suggested: 1 4 *** ------------------------------------------------------------------------------- - - - DBCSR MESSAGE PASSING PERFORMANCE - - - ------------------------------------------------------------------------------- ROUTINE CALLS AVE VOLUME [Bytes] MP_Group 178 MP_Bcast 16 12. MP_Allreduce 3915 8. MP_Alltoall 5046 246. MP_Wait 21700 MP_ISend 4990 109. MP_IRecv 5366 89. MP_Memory 38294 ------------------------------------------------------------------------------- MEMORY| Estimated peak process memory [MiB] 159 ------------------------------------------------------------------------------- - - - MESSAGE PASSING PERFORMANCE - - - ------------------------------------------------------------------------------- ROUTINE CALLS AVE VOLUME [Bytes] MP_Group 8 MP_Bcast 472 387854. MP_Allreduce 1534 50. MP_Sync 190 MP_Alltoall 431 684172. MP_ISendRecv 358 64868. MP_Wait 358 MP_Send 57 4. ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- - - - R E F E R E N C E S - - - ------------------------------------------------------------------------------- CP2K version 8.0 (Development Version), the CP2K developers group (2019). CP2K is freely available from https://www.cp2k.org/ . Kapil, V; VandeVondele, J; Ceriotti, M. JOURNAL OF CHEMICAL PHYSICS, 144 (5), 054111 (2016). Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods. https://dx.doi.org/10.1063/1.4941091 Schuett, Ole; Messmer, Peter; Hutter, Juerg; VandeVondele, Joost. Electronic Structure Calculations on Graphics Processing Units, John Wiley & Sons, Ltd, 173-190 (2016). GPU-Accelerated Sparse Matrix-Matrix Multiplication for Linear Scaling Density Functional Theory. https://dx.doi.org/10.1002/9781118670712.ch8 Borstnik, U; VandeVondele, J; Weber, V; Hutter, J. PARALLEL COMPUTING, 40 (5-6), 47-58 (2014). Sparse matrix multiplication: The distributed block-compressed sparse row library. https://dx.doi.org/10.1016/j.parco.2014.03.012 Ceriotti, M; More, J; Manolopoulos, DE. COMPUTER PHYSICS COMMUNICATIONS, 185 (3), 1019-1026 (2014). i-PI: A Python interface for ab initio path integral molecular dynamics simulations. https://dx.doi.org/10.1016/j.cpc.2013.10.027 Hutter, J; Iannuzzi, M; Schiffmann, F; VandeVondele, J. WIREs Comput Mol Sci., 4 (1), 15-25 (2014). CP2K: atomistic simulations of condensed matter systems. https://dx.doi.org/10.1002/wcms.1159 Marek, A; Blum, V; Johanni, R; Havu, V; Lang, B; Auckenthaler, T; Heinecke, A; Bungartz, H; Lederer, H. Journal of Physics: Condensed Matter, 26 (21), (2014). The ELPA library: scalable parallel eigenvalue solutions for electronic structure theory and computational science. https://dx.doi.org/10.1088/0953-8984/26/21/213201 Krack, M. THEORETICAL CHEMISTRY ACCOUNTS, 114 (1-3), 145-152 (2005). Pseudopotentials for H to Kr optimized for gradient-corrected exchange-correlation functionals. https://dx.doi.org/10.1007/s00214-005-0655-y VandeVondele, J; Krack, M; Mohamed, F; Parrinello, M; Chassaing, T; Hutter, J. COMPUTER PHYSICS COMMUNICATIONS, 167 (2), 103-128 (2005). QUICKSTEP: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach. https://dx.doi.org/10.1016/j.cpc.2004.12.014 Frigo, M; Johnson, SG. PROCEEDINGS OF THE IEEE, 93 (2), 216-231 (2005). The design and implementation of FFTW3. https://dx.doi.org/10.1109/JPROC.2004.840301 Kolafa, J. JOURNAL OF COMPUTATIONAL CHEMISTRY, 25 (3), 335-342 (2004). Time-reversible always stable predictor-corrector method for molecular dynamics of polarizable molecules. https://dx.doi.org/10.1002/jcc.10385 VandeVondele, J; Hutter, J. JOURNAL OF CHEMICAL PHYSICS, 118 (10), 4365-4369 (2003). An efficient orbital transformation method for electronic structure calculations. https://dx.doi.org/10.1063/1.1543154 Hartwigsen, C; Goedecker, S; Hutter, J. PHYSICAL REVIEW B, 58 (7), 3641-3662 (1998). Relativistic separable dual-space Gaussian pseudopotentials from H to Rn. https://dx.doi.org/10.1103/PhysRevB.58.3641 Lippert, G; Hutter, J; Parrinello, M. MOLECULAR PHYSICS, 92 (3), 477-487 (1997). A hybrid Gaussian and plane wave density functional scheme. https://dx.doi.org/10.1080/002689797170220 Goedecker, S; Teter, M; Hutter, J. PHYSICAL REVIEW B, 54 (3), 1703-1710 (1996). Separable dual-space Gaussian pseudopotentials. https://dx.doi.org/10.1103/PhysRevB.54.1703 ------------------------------------------------------------------------------- - - - T I M I N G - - - ------------------------------------------------------------------------------- SUBROUTINE CALLS ASD SELF TIME TOTAL TIME MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM CP2K 1 1.0 0.089 0.110 3321.135 3321.148 run_driver 1 2.0 1.354 2.679 3320.341 3320.368 qs_forces 11 3.0 0.002 0.002 3317.379 3317.407 qs_energies 11 4.0 0.003 0.003 3230.253 3230.795 scf_env_do_scf 11 5.0 0.023 0.044 2990.202 2990.313 dbcsr_multiply_generic 775 11.6 29.668 30.009 2437.333 2467.908 scf_env_do_scf_inner_loop 31 6.0 0.048 0.093 2462.160 2462.166 qs_scf_new_mos 31 7.0 0.001 0.001 2184.102 2185.847 qs_scf_loop_do_ot 31 8.0 0.001 0.001 2184.101 2185.847 ot_scf_mini 31 9.0 0.002 0.002 2075.161 2075.217 ot_mini 31 10.0 0.004 0.007 1448.049 1448.404 make_m2s 1550 12.6 0.335 0.338 1127.892 1134.142 qs_ot_get_derivative 31 11.0 0.002 0.002 1115.126 1115.594 dbcsr_create_new 11573 13.8 517.607 527.573 924.871 942.688 multiply_cannon 775 12.6 185.891 186.896 644.825 685.128 make_images 1550 13.6 205.639 206.287 590.157 619.701 init_scf_loop 11 6.0 0.001 0.001 521.215 521.250 dbcsr_finalize 2125 12.0 116.779 125.530 473.017 490.678 qs_ot_get_derivative_diag 11 12.0 0.002 0.002 437.806 437.882 dbcsr_make_index_exist 11573 14.8 406.547 414.341 406.999 414.863 qs_ot_get_p 42 9.5 0.001 0.001 378.643 387.223 dbcsr_merge_all 1679 13.6 319.539 327.173 349.216 357.552 ot_diis_step 31 11.0 0.009 0.014 331.065 331.067 dbcsr_make_images_dense 1228 14.0 0.170 0.189 275.688 327.601 rebuild_ks_matrix 42 7.2 0.000 0.000 320.395 320.704 qs_ks_build_kohn_sham_matrix 42 8.2 0.025 0.037 320.395 320.704 prepare_preconditioner 11 7.0 0.000 0.000 319.488 319.844 apply_preconditioner_dbcsr 42 12.0 0.001 0.001 296.038 296.914 apply_all 42 13.0 0.011 0.019 296.038 296.913 dbcsr_make_dense_low 2403 14.9 0.169 0.201 193.265 267.479 make_dense_data 2403 15.9 47.982 66.582 192.985 267.128 qs_ot_get_derivative_taylor 20 12.0 0.002 0.002 250.948 251.231 qs_ks_update_qs_env 42 7.0 0.001 0.001 242.898 242.920 pw_transfer 515 10.7 0.110 0.127 220.306 220.565 qs_ot_get_orbitals 31 10.0 0.001 0.001 209.955 218.321 fft_wrap_pw1pw2 431 11.9 0.016 0.022 217.139 217.335 subspace_eigenvalues_ks_dbcsr 22 8.5 0.009 0.014 212.558 213.022 dbcsr_iterator_start 9061 14.6 147.797 199.739 147.990 199.974 make_preconditioner 11 8.0 0.000 0.001 181.743 182.084 setup_buffer_matrices 1550 13.6 0.133 0.153 173.235 174.622 sum_up_and_integrate 42 9.2 0.026 0.039 172.484 172.729 integrate_v_rspace_low 42 10.2 7.253 7.264 172.457 172.690 init_scf_run 11 5.0 0.022 0.043 165.853 165.929 scf_env_initial_rho_setup 11 6.0 0.016 0.031 165.831 165.929 cp_dbcsr_sm_fm_multiply 44 9.5 0.004 0.004 161.958 162.230 fft3d_ps 431 13.9 103.571 104.719 160.568 160.685 calculate_dm_sparse 42 8.7 0.001 0.001 150.224 152.718 dbcsr_add_d 356 12.3 0.014 0.025 124.135 151.349 dbcsr_add_anytype 356 13.3 11.414 13.925 124.120 151.323 qs_rho_update_rho 42 7.2 0.001 0.001 142.317 145.082 calculate_rho_elec 42 8.2 19.278 19.334 142.316 145.081 dbcsr_make_index_list 2325 13.6 127.149 134.633 127.162 134.651 wfi_extrapolate 11 7.0 0.002 0.003 131.001 131.021 make_images_sizes 1550 14.6 0.074 0.091 77.247 122.511 mp_alltoall_i44 1550 15.6 77.173 122.419 77.173 122.419 make_images_data 1550 14.6 0.213 0.247 93.764 120.620 hybrid_alltoall_any 1727 15.2 89.562 116.140 93.198 119.973 dbcsr_make_undense 561 13.3 13.998 19.828 97.459 119.582 density_rs2pw 42 9.2 0.013 0.020 116.478 119.338 dbcsr_make_dense 561 13.3 0.036 0.043 98.867 116.240 qs_ot_p2m_diag 12 11.0 1.045 1.079 114.709 115.176 ot_scf_init 11 7.0 0.028 0.032 114.202 114.277 copy_dbcsr_to_fm 177 9.9 0.057 0.071 111.013 112.297 mp_sum_l 3602 12.7 70.173 104.894 70.173 104.894 cp_dbcsr_sm_fm_multiply_core 44 10.5 0.000 0.000 103.195 104.515 dbcsr_complete_redistribute 344 11.1 0.088 0.090 103.447 103.767 setup_rec_index_2d 1550 13.6 96.728 98.828 96.728 98.828 dbcsr_iterator_stop 9061 14.6 72.106 97.445 72.123 97.469 make_full_all 11 9.0 0.002 0.003 94.152 94.219 potential_pw2rs 42 11.2 0.010 0.013 93.328 93.435 fft_wrap_pw1pw2_100 179 12.3 13.847 13.917 91.181 91.808 buffer_matrices_ensure_size 1550 13.6 60.642 90.073 60.952 90.549 cp_dbcsr_plus_fm_fm_t_native 22 8.0 0.014 0.014 86.032 87.269 qs_ot_p2m_taylor 30 10.3 0.002 0.002 79.544 87.123 mp_allgather_i34 775 13.6 57.009 79.470 57.009 79.470 qs_ks_update_qs_env_forces 11 4.0 0.000 0.000 77.773 77.989 copy_fm_to_dbcsr 167 10.2 0.011 0.019 77.514 77.698 dbcsr_copy 913 10.9 18.374 21.567 64.122 67.741 ------------------------------------------------------------------------------- The number of warnings for this run is : 3 ------------------------------------------------------------------------------- **** **** ****** ** PROGRAM ENDED AT 2020-01-17 12:12:08.899 ***** ** *** *** ** PROGRAM RAN ON b2bcb6131f83 ** **** ****** PROGRAM RAN BY ***** ** ** ** ** PROGRAM PROCESS ID 99658 **** ** ******* ** PROGRAM STOPPED IN /opt/i-pi/examples/cp2k/nvt-cl/run_1 e='dynamics'> 5 50 100 0.5 True --- end input file content --- @SOCKET: Client asked for connection from ('127.0.0.1', 57402). Now hand-shaking. @SOCKET: Handshaking was successful. Added to the client list. @SOCKET: 20/01/17-11:16:48 Assigning [ none] request id 0 to client with last-id None ( 0/ 1 : ('127.0.0.1', 57402)) !W! @SOCKET: Timeout in getforce, trying again! @SOCKET: 20/01/17-11:40:46 Assigning [match] request id 0 to client with last-id 0 ( 0/ 1 : ('127.0.0.1', 57402)) !W! @SOCKET: Timeout in getforce, trying again! ThermoCL inherent dissipation time scale: 2068.71556013 # Average timings at MD step 0. t/step: 2.62079e+02 @SOCKET: 20/01/17-11:45:08 Assigning [match] request id 0 to client with last-id 0 ( 0/ 1 : ('127.0.0.1', 57402)) !W! @SOCKET: Timeout in getforce, trying again! ThermoCL inherent dissipation time scale: 2070.61652664 # Average timings at MD step 1. t/step: 1.97108e+02 @SOCKET: 20/01/17-11:48:25 Assigning [match] request id 0 to client with last-id 0 ( 0/ 1 : ('127.0.0.1', 57402)) !W! @SOCKET: Timeout in getforce, trying again! ThermoCL inherent dissipation time scale: 2072.36456385 # Average timings at MD step 2. t/step: 1.94807e+02 @SOCKET: 20/01/17-11:51:40 Assigning [match] request id 0 to client with last-id 0 ( 0/ 1 : ('127.0.0.1', 57402)) !W! @SOCKET: Timeout in getforce, trying again! ThermoCL inherent dissipation time scale: 2072.11076702 # Average timings at MD step 3. t/step: 1.25112e+02 @SOCKET: 20/01/17-11:53:45 Assigning [match] request id 0 to client with last-id 0 ( 0/ 1 : ('127.0.0.1', 57402)) !W! @SOCKET: Timeout in getforce, trying again! ThermoCL inherent dissipation time scale: 2070.2067217 # Average timings at MD step 4. t/step: 2.63771e+02 @SOCKET: 20/01/17-11:58:09 Assigning [match] request id 0 to client with last-id 0 ( 0/ 1 : ('127.0.0.1', 57402)) !W! @SOCKET: Timeout in getforce, trying again! ThermoCL inherent dissipation time scale: 2066.93117488 # Average timings at MD step 5. t/step: 1.96505e+02 @SOCKET: 20/01/17-12:01:25 Assigning [match] request id 0 to client with last-id 0 ( 0/ 1 : ('127.0.0.1', 57402)) !W! @SOCKET: Timeout in getforce, trying again! ThermoCL inherent dissipation time scale: 2065.11813751 # Average timings at MD step 6. t/step: 1.24451e+02 @SOCKET: 20/01/17-12:03:30 Assigning [match] request id 0 to client with last-id 0 ( 0/ 1 : ('127.0.0.1', 57402)) !W! @SOCKET: Timeout in getforce, trying again! ThermoCL inherent dissipation time scale: 2063.30653831 # Average timings at MD step 7. t/step: 1.26111e+02 @SOCKET: 20/01/17-12:05:36 Assigning [match] request id 0 to client with last-id 0 ( 0/ 1 : ('127.0.0.1', 57402)) !W! @SOCKET: Timeout in getforce, trying again! ThermoCL inherent dissipation time scale: 2064.42189647 # Average timings at MD step 8. t/step: 1.96726e+02 @SOCKET: 20/01/17-12:08:53 Assigning [match] request id 0 to client with last-id 0 ( 0/ 1 : ('127.0.0.1', 57402)) !W! @SOCKET: Timeout in getforce, trying again! ThermoCL inherent dissipation time scale: 2063.98127867 # Average timings at MD step 9. t/step: 1.95626e+02 SOFTEXIT CALLED FROM THREAD <_MainThread(MainThread, started 140264296840064)> @ SIMULATION: Exiting cleanly. !W! Soft exit has been requested with message: ' @ SIMULATION: Exiting cleanly.'. Cleaning up. @SOCKET: Shutting down the driver interface. SOFTEXIT: Saving the latest status at the end of the step CP2K exit code: 0 i-Pi exit code: 0 Summary: i-Pi commit 2fe3025 works fine. Status: OK EndDate: 2020-01-17 12:12:10+00:00