nwchemgit / nwchem

NWChem: Open Source High-Performance Computational Chemistry
http://nwchemgit.github.io
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Non-deterministic runs #272

Closed marcindulak closed 3 years ago

marcindulak commented 3 years ago

Describe the bug

It seems like I'm able to trigger a non-converging scf from time to time (maybe every 50 runs).

Describe settings used

With the following Dockerfile, on an Ubuntu 18.04 host.

FROM fedora:33@sha256:fdf235fa167d2aa5d820fba274ec1d2edeb0534bd32d28d602a19b31bad79b80

RUN set -x \
    && dnf install -y https://kojipkgs.fedoraproject.org//packages/nwchem/7.0.2/3.fc33/x86_64/nwchem-7.0.2-3.fc33.x86_64.rpm  \
                      https://kojipkgs.fedoraproject.org//packages/nwchem/7.0.2/3.fc33/x86_64/nwchem-openmpi-7.0.2-3.fc33.x86_64.rpm \
                      https://kojipkgs.fedoraproject.org//packages/nwchem/7.0.2/3.fc33/noarch/nwchem-common-7.0.2-3.fc33.noarch.rpm \
    && dnf clean all

CMD ["/bin/bash"]

Attach log files

A typical results will converge in 10 steps:

 argument  1 = siosi3.nw

             Northwest Computational Chemistry Package (NWChem) 7.0.2
             --------------------------------------------------------

                    Environmental Molecular Sciences Laboratory
                       Pacific Northwest National Laboratory
                                Richland, WA 99352

                              Copyright (c) 1994-2020
                       Pacific Northwest National Laboratory
                            Battelle Memorial Institute

             NWChem is an open-source computational chemistry package
                        distributed under the terms of the
                      Educational Community License (ECL) 2.0
             A copy of the license is included with this distribution
                              in the LICENSE.TXT file

                                  ACKNOWLEDGMENT
                                  --------------

            This software and its documentation were developed at the
            EMSL at Pacific Northwest National Laboratory, a multiprogram
            national laboratory, operated for the U.S. Department of Energy
            by Battelle under Contract Number DE-AC05-76RL01830. Support
            for this work was provided by the Department of Energy Office
            of Biological and Environmental Research, Office of Basic
            Energy Sciences, and the Office of Advanced Scientific Computing.

           Job information
           ---------------

    hostname        = ac1b1a11b123
    program         = nwchem_openmpi
    date            = Mon Nov 23 20:22:13 2020

    compiled        = Sun_Nov_22_13:28:15_2020
    source          = /builddir/build/BUILD/nwchem-5d4a0e84c8f8d9656a0ac37e796a9a4eff8c5ad9
    nwchem branch   = 7.0.2
    nwchem revision = N/A
    ga revision     = 5.7.1
    use scalapack   = T
    input           = siosi3.nw
    prefix          = siosi3.
    data base       = ./siosi3.db
    status          = startup
    nproc           =        3
    time left       =     -1s

           Memory information
           ------------------

    heap     =   13107198 doubles =    100.0 Mbytes
    stack    =   13107195 doubles =    100.0 Mbytes
    global   =   26214400 doubles =    200.0 Mbytes (distinct from heap & stack)
    total    =   52428793 doubles =    400.0 Mbytes
    verify   = yes
    hardfail = no 

           Directory information
           ---------------------

  0 permanent = .
  0 scratch   = .

                                NWChem Input Module
                                -------------------

  library name resolved from: environment
  library file name is: </usr/share/nwchem/libraries/>

                      Basis "ao basis" -> "" (cartesian)
                      -----
  H (Hydrogen)
  ------------
            Exponent  Coefficients 
       -------------- ---------------------------------------------------------
  1 S  3.42525091E+00  0.154329
  1 S  6.23913730E-01  0.535328
  1 S  1.68855400E-01  0.444635

  O (Oxygen)
  ----------
            Exponent  Coefficients 
       -------------- ---------------------------------------------------------
  1 S  1.30709320E+02  0.154329
  1 S  2.38088610E+01  0.535328
  1 S  6.44360830E+00  0.444635

  2 S  5.03315130E+00 -0.099967
  2 S  1.16959610E+00  0.399513
  2 S  3.80389000E-01  0.700115

  3 P  5.03315130E+00  0.155916
  3 P  1.16959610E+00  0.607684
  3 P  3.80389000E-01  0.391957

  Si (Silicon)
  ------------
            Exponent  Coefficients 
       -------------- ---------------------------------------------------------
  1 S  4.07797551E+02  0.154329
  1 S  7.42808331E+01  0.535328
  1 S  2.01032923E+01  0.444635

  2 S  2.31936561E+01 -0.099967
  2 S  5.38970687E+00  0.399513
  2 S  1.75289995E+00  0.700115

  3 P  2.31936561E+01  0.155916
  3 P  5.38970687E+00  0.607684
  3 P  1.75289995E+00  0.391957

  4 S  1.47874062E+00 -0.219620
  4 S  4.12564880E-01  0.225595
  4 S  1.61475098E-01  0.900398

  5 P  1.47874062E+00  0.010588
  5 P  4.12564880E-01  0.595167
  5 P  1.61475098E-01  0.462001

 Summary of "ao basis" -> "" (cartesian)
 ------------------------------------------------------------------------------
       Tag                 Description            Shells   Functions and Types
 ---------------- ------------------------------  ------  ---------------------
 H                           STO-3G                  1        1   1s
 O                           STO-3G                  3        5   2s1p
 Si                          STO-3G                  5        9   3s2p

                                 NWChem DFT Module
                                 -----------------

 Summary of "ao basis" -> "ao basis" (cartesian)
 ------------------------------------------------------------------------------
       Tag                 Description            Shells   Functions and Types
 ---------------- ------------------------------  ------  ---------------------
 H                           STO-3G                  1        1   1s
 O                           STO-3G                  3        5   2s1p
 Si                          STO-3G                  5        9   3s2p

  Caching 1-el integrals 

            General Information
            -------------------
          SCF calculation type: DFT
          Wavefunction type:  closed shell.
          No. of atoms     :    33
          No. of electrons :   186
           Alpha electrons :    93
            Beta electrons :    93
          Charge           :     0
          Spin multiplicity:     1
          Use of symmetry is: off; symmetry adaption is: off
          Maximum number of iterations:  30
          AO basis - number of functions:   125
                     number of shells:    79
          Convergence on energy requested:  1.00D-06
          Convergence on density requested:  1.00D-05
          Convergence on gradient requested:  5.00D-04

              XC Information
              --------------
                        Slater Exchange Functional  1.000 local    
                      VWN V Correlation Functional  1.000 local    

             Grid Information
             ----------------
          Grid used for XC integration:  medium    
          Radial quadrature: Mura-Knowles        
          Angular quadrature: Lebedev. 
          Tag              B.-S. Rad. Rad. Pts. Rad. Cut. Ang. Pts.
          ---              ---------- --------- --------- ---------
          O                   0.60       49          12.0       434
          Si                  1.10       88          13.0       590
          H                   0.35       45          13.0       434
          Grid pruning is: on 
          Number of quadrature shells:  1857
          Spatial weights used:  Erf1

          Convergence Information
          -----------------------
          Convergence aids based upon iterative change in 
          total energy or number of iterations. 
          Levelshifting, if invoked, occurs when the 
          HOMO/LUMO gap drops below (HL_TOL):  1.00D-02
          DIIS, if invoked, will attempt to extrapolate 
          using up to (NFOCK): 10 stored Fock matrices.

                    Damping(70%)  Levelshifting(0.5)       DIIS
                  --------------- ------------------- ---------------
          dE  on:    start            ASAP                start   
          dE off:    2 iters         30 iters            30 iters 

      Screening Tolerance Information
      -------------------------------
          Density screening/tol_rho:  1.00D-10
          AO Gaussian exp screening on grid/accAOfunc:  14
          CD Gaussian exp screening on grid/accCDfunc:  20
          XC Gaussian exp screening on grid/accXCfunc:  20
          Schwarz screening/accCoul:  1.00D-10

      Superposition of Atomic Density Guess
      -------------------------------------

 Sum of atomic energies:       -2808.45068874

      Non-variational initial energy
      ------------------------------

 Total energy =   -2808.711208
 1-e energy   =   -8554.867668
 2-e energy   =    3432.914083
 HOMO         =      -0.195706
 LUMO         =       0.302945

   Time after variat. SCF:      2.0
   Time prior to 1st pass:      2.0

 Integral file          = ./siosi3.aoints.0
 Record size in doubles =  65536        No. of integs per rec  =  43688
 Max. records in memory =    322        Max. records in file   =  40750
 No. of bits per label  =      8        No. of bits per value  =     64

 #quartets = 1.895D+06 #integrals = 1.051D+07 #direct =  0.0% #cached =100.0%

File balance: exchanges=     2  moved=    61  time=   0.0

 Grid_pts file          = ./siosi3.gridpts.0
 Record size in doubles =  12289        No. of grid_pts per rec  =   3070
 Max. records in memory =    132        Max. recs in file   =    217322

           Memory utilization after 1st SCF pass: 
           Heap Space remaining (MW):        0.00                  18
          Stack Space remaining (MW):       13.11            13105164

   convergence    iter        energy       DeltaE   RMS-Dens  Diis-err    time
 ---------------- ----- ----------------- --------- --------- ---------  ------
 d=70,ls=0.0,diis     1  -2805.2717589687 -5.12D+03  3.62D-02  3.91D+00    19.4
 d=70,ls=0.0,diis     2  -2805.4960457228 -2.24D-01  1.00D-02  8.88D-01    20.6
 d= 0,ls=0.0,diis     3  -2805.6123818091 -1.16D-01  5.05D-03  4.74D-01    21.9
 d= 0,ls=0.0,diis     4  -2805.8905491090 -2.78D-01  2.28D-03  4.71D-02    23.4
 d= 0,ls=0.0,diis     5  -2805.8977486187 -7.20D-03  7.15D-04  6.26D-03    24.3
  Resetting Diis
 d= 0,ls=0.0,diis     6  -2805.8985888292 -8.40D-04  1.77D-04  6.16D-04    25.6
 d= 0,ls=0.0,diis     7  -2805.8986838322 -9.50D-05  2.19D-04  7.77D-05    26.8
 d= 0,ls=0.0,diis     8  -2805.8986667160  1.71D-05  1.31D-04  1.80D-04    28.1
 d= 0,ls=0.0,diis     9  -2805.8986983155 -3.16D-05  1.42D-05  2.25D-06    29.3
 d= 0,ls=0.0,diis    10  -2805.8986986623 -3.47D-07  2.53D-06  8.35D-08    30.6

         Total DFT energy =    -2805.898698662279
      One electron energy =    -8538.131776044655
           Coulomb energy =     3641.119679437993
    Exchange-Corr. energy =     -222.128978829017
 Nuclear repulsion energy =     2313.242376773399

 Numeric. integr. density =      186.000109057542

     Total iterative time =     28.6s

 center of mass
 --------------
 x =  -0.00952295 y =   0.03028985 z =  -0.02257135

 moments of inertia (a.u.)
 ------------------
        6246.693956998223       -1350.867456527316         178.358701865298
       -1350.867456527316       10287.349148271958        -337.687957306077
         178.358701865298        -337.687957306077       10500.339172729240

 Parallel integral file used     242 records with       0 large values

 Task  times  cpu:       29.4s     wall:       30.6s

                                NWChem Input Module
                                -------------------

 Summary of allocated global arrays
-----------------------------------
  No active global arrays

                         GA Statistics for process    0
                         ------------------------------

       create   destroy   get      put      acc     scatter   gather  read&inc
calls:  162      162     4.15e+05  612     2.70e+05    0        0     4939     
number of processes/call 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
bytes total:             1.10e+08 1.59e+07 5.93e+07 0.00e+00 0.00e+00 3.95e+04
bytes remote:            1.52e+06 4.87e+05 1.70e+06 0.00e+00 0.00e+00 0.00e+00
Max memory consumed for GA by this process: 4500000 bytes

MA_summarize_allocated_blocks: starting scan ...
MA_summarize_allocated_blocks: scan completed: 0 heap blocks, 0 stack blocks
MA usage statistics:

    allocation statistics:
                          heap       stack
                          ----       -----
    current number of blocks             0           0
    maximum number of blocks            21          51
    current total bytes              0           0
    maximum total bytes      181863816    22525624
    maximum total K-bytes           181864       22526
    maximum total M-bytes              182          23

                                     CITATION
                                     --------
                Please cite the following reference when publishing
                           results obtained with NWChem:

          E. Aprà, E. J. Bylaska, W. A. de Jong, N. Govind, K. Kowalski,
       T. P. Straatsma, M. Valiev, H. J. J. van Dam, Y. Alexeev, J. Anchell,
       V. Anisimov, F. W. Aquino, R. Atta-Fynn, J. Autschbach, N. P. Bauman,
     J. C. Becca, D. E. Bernholdt, K. Bhaskaran-Nair, S. Bogatko, P. Borowski,
        J. Boschen, J. Brabec, A. Bruner, E. Cauët, Y. Chen, G. N. Chuev,
      C. J. Cramer, J. Daily, M. J. O. Deegan, T. H. Dunning Jr., M. Dupuis,
   K. G. Dyall, G. I. Fann, S. A. Fischer, A. Fonari, H. Früchtl, L. Gagliardi,
      J. Garza, N. Gawande, S. Ghosh, K. Glaesemann, A. W. Götz, J. Hammond,
       V. Helms, E. D. Hermes, K. Hirao, S. Hirata, M. Jacquelin, L. Jensen,
   B. G. Johnson, H. Jónsson, R. A. Kendall, M. Klemm, R. Kobayashi, V. Konkov,
      S. Krishnamoorthy, M. Krishnan, Z. Lin, R. D. Lins, R. J. Littlefield,
      A. J. Logsdail, K. Lopata, W. Ma, A. V. Marenich, J. Martin del Campo,
   D. Mejia-Rodriguez, J. E. Moore, J. M. Mullin, T. Nakajima, D. R. Nascimento,
    J. A. Nichols, P. J. Nichols, J. Nieplocha, A. Otero-de-la-Roza, B. Palmer,
    A. Panyala, T. Pirojsirikul, B. Peng, R. Peverati, J. Pittner, L. Pollack,
   R. M. Richard, P. Sadayappan, G. C. Schatz, W. A. Shelton, D. W. Silverstein,
   D. M. A. Smith, T. A. Soares, D. Song, M. Swart, H. L. Taylor, G. S. Thomas,
            V. Tipparaju, D. G. Truhlar, K. Tsemekhman, T. Van Voorhis,
     Á. Vázquez-Mayagoitia, P. Verma, O. Villa, A. Vishnu, K. D. Vogiatzis,
        D. Wang, J. H. Weare, M. J. Williamson, T. L. Windus, K. Woliński,
        A. T. Wong, Q. Wu, C. Yang, Q. Yu, M. Zacharias, Z. Zhang, Y. Zhao,
                                and R. J. Harrison
                        "NWChem: Past, present, and future
                         J. Chem. Phys. 152, 184102 (2020)
                               doi:10.1063/5.0004997

                                      AUTHORS
                                      -------
     E. Apra, E. J. Bylaska, N. Govind, K. Kowalski, M. Valiev, W. A. de Jong,
      T. P. Straatsma, H. J. J. van Dam, D. Wang, T. L. Windus, N. P. Bauman,
       A. Panyala, J. Hammond, J. Autschbach, K. Bhaskaran-Nair, J. Brabec,
    K. Lopata, S. A. Fischer, S. Krishnamoorthy, M. Jacquelin, W. Ma, M. Klemm,
       O. Villa, Y. Chen, V. Anisimov, F. Aquino, S. Hirata, M. T. Hackler,
           Eric Hermes, L. Jensen, J. E. Moore, J. C. Becca, V. Konjkov,
            D. Mejia-Rodriguez, T. Risthaus, M. Malagoli, A. Marenich,
   A. Otero-de-la-Roza, J. Mullin, P. Nichols, R. Peverati, J. Pittner, Y. Zhao,
        P.-D. Fan, A. Fonari, M. J. Williamson, R. J. Harrison, J. R. Rehr,
      M. Dupuis, D. Silverstein, D. M. A. Smith, J. Nieplocha, V. Tipparaju,
      M. Krishnan, B. E. Van Kuiken, A. Vazquez-Mayagoitia, M. Swart, Q. Wu,
   T. Van Voorhis, A. A. Auer, M. Nooijen, L. D. Crosby, E. Brown, G. Cisneros,
     G. I. Fann, H. Fruchtl, J. Garza, K. Hirao, R. A. Kendall, J. A. Nichols,
       K. Tsemekhman, K. Wolinski, J. Anchell, D. E. Bernholdt, P. Borowski,
       T. Clark, D. Clerc, H. Dachsel, M. J. O. Deegan, K. Dyall, D. Elwood,
      E. Glendening, M. Gutowski, A. C. Hess, J. Jaffe, B. G. Johnson, J. Ju,
        R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield, X. Long, B. Meng,
      T. Nakajima, S. Niu, L. Pollack, M. Rosing, K. Glaesemann, G. Sandrone,
      M. Stave, H. Taylor, G. Thomas, J. H. van Lenthe, A. T. Wong, Z. Zhang.

 Total times  cpu:       29.4s     wall:       30.6s

and a non-converging result may look like

 argument  1 = siosi3.nw

             Northwest Computational Chemistry Package (NWChem) 7.0.2
             --------------------------------------------------------

                    Environmental Molecular Sciences Laboratory
                       Pacific Northwest National Laboratory
                                Richland, WA 99352

                              Copyright (c) 1994-2020
                       Pacific Northwest National Laboratory
                            Battelle Memorial Institute

             NWChem is an open-source computational chemistry package
                        distributed under the terms of the
                      Educational Community License (ECL) 2.0
             A copy of the license is included with this distribution
                              in the LICENSE.TXT file

                                  ACKNOWLEDGMENT
                                  --------------

            This software and its documentation were developed at the
            EMSL at Pacific Northwest National Laboratory, a multiprogram
            national laboratory, operated for the U.S. Department of Energy
            by Battelle under Contract Number DE-AC05-76RL01830. Support
            for this work was provided by the Department of Energy Office
            of Biological and Environmental Research, Office of Basic
            Energy Sciences, and the Office of Advanced Scientific Computing.

           Job information
           ---------------

    hostname        = 53b2407e4c23
    program         = nwchem_openmpi
    date            = Mon Nov 23 20:17:46 2020

    compiled        = Sun_Nov_22_13:28:15_2020
    source          = /builddir/build/BUILD/nwchem-5d4a0e84c8f8d9656a0ac37e796a9a4eff8c5ad9
    nwchem branch   = 7.0.2
    nwchem revision = N/A
    ga revision     = 5.7.1
    use scalapack   = T
    input           = siosi3.nw
    prefix          = siosi3.
    data base       = ./siosi3.db
    status          = startup
    nproc           =        3
    time left       =     -1s

           Memory information
           ------------------

    heap     =   13107200 doubles =    100.0 Mbytes
    stack    =   13107197 doubles =    100.0 Mbytes
    global   =   26214400 doubles =    200.0 Mbytes (distinct from heap & stack)
    total    =   52428797 doubles =    400.0 Mbytes
    verify   = yes
    hardfail = no 

           Directory information
           ---------------------

  0 permanent = .
  0 scratch   = .

                                NWChem Input Module
                                -------------------

  library name resolved from: environment
  library file name is: </usr/share/nwchem/libraries/>

                      Basis "ao basis" -> "" (cartesian)
                      -----
  H (Hydrogen)
  ------------
            Exponent  Coefficients 
       -------------- ---------------------------------------------------------
  1 S  3.42525091E+00  0.154329
  1 S  6.23913730E-01  0.535328
  1 S  1.68855400E-01  0.444635

  O (Oxygen)
  ----------
            Exponent  Coefficients 
       -------------- ---------------------------------------------------------
  1 S  1.30709320E+02  0.154329
  1 S  2.38088610E+01  0.535328
  1 S  6.44360830E+00  0.444635

  2 S  5.03315130E+00 -0.099967
  2 S  1.16959610E+00  0.399513
  2 S  3.80389000E-01  0.700115

  3 P  5.03315130E+00  0.155916
  3 P  1.16959610E+00  0.607684
  3 P  3.80389000E-01  0.391957

  Si (Silicon)
  ------------
            Exponent  Coefficients 
       -------------- ---------------------------------------------------------
  1 S  4.07797551E+02  0.154329
  1 S  7.42808331E+01  0.535328
  1 S  2.01032923E+01  0.444635

  2 S  2.31936561E+01 -0.099967
  2 S  5.38970687E+00  0.399513
  2 S  1.75289995E+00  0.700115

  3 P  2.31936561E+01  0.155916
  3 P  5.38970687E+00  0.607684
  3 P  1.75289995E+00  0.391957

  4 S  1.47874062E+00 -0.219620
  4 S  4.12564880E-01  0.225595
  4 S  1.61475098E-01  0.900398

  5 P  1.47874062E+00  0.010588
  5 P  4.12564880E-01  0.595167
  5 P  1.61475098E-01  0.462001

 Summary of "ao basis" -> "" (cartesian)
 ------------------------------------------------------------------------------
       Tag                 Description            Shells   Functions and Types
 ---------------- ------------------------------  ------  ---------------------
 H                           STO-3G                  1        1   1s
 O                           STO-3G                  3        5   2s1p
 Si                          STO-3G                  5        9   3s2p

                                 NWChem DFT Module
                                 -----------------

 Summary of "ao basis" -> "ao basis" (cartesian)
 ------------------------------------------------------------------------------
       Tag                 Description            Shells   Functions and Types
 ---------------- ------------------------------  ------  ---------------------
 H                           STO-3G                  1        1   1s
 O                           STO-3G                  3        5   2s1p
 Si                          STO-3G                  5        9   3s2p

  Caching 1-el integrals 

            General Information
            -------------------
          SCF calculation type: DFT
          Wavefunction type:  closed shell.
          No. of atoms     :    33
          No. of electrons :   186
           Alpha electrons :    93
            Beta electrons :    93
          Charge           :     0
          Spin multiplicity:     1
          Use of symmetry is: off; symmetry adaption is: off
          Maximum number of iterations:  30
          AO basis - number of functions:   125
                     number of shells:    79
          Convergence on energy requested:  1.00D-06
          Convergence on density requested:  1.00D-05
          Convergence on gradient requested:  5.00D-04

              XC Information
              --------------
                        Slater Exchange Functional  1.000 local    
                      VWN V Correlation Functional  1.000 local    

             Grid Information
             ----------------
          Grid used for XC integration:  medium    
          Radial quadrature: Mura-Knowles        
          Angular quadrature: Lebedev. 
          Tag              B.-S. Rad. Rad. Pts. Rad. Cut. Ang. Pts.
          ---              ---------- --------- --------- ---------
          O                   0.60       49          12.0       434
          Si                  1.10       88          13.0       590
          H                   0.35       45          13.0       434
          Grid pruning is: on 
          Number of quadrature shells:  1857
          Spatial weights used:  Erf1

          Convergence Information
          -----------------------
          Convergence aids based upon iterative change in 
          total energy or number of iterations. 
          Levelshifting, if invoked, occurs when the 
          HOMO/LUMO gap drops below (HL_TOL):  1.00D-02
          DIIS, if invoked, will attempt to extrapolate 
          using up to (NFOCK): 10 stored Fock matrices.

                    Damping(70%)  Levelshifting(0.5)       DIIS
                  --------------- ------------------- ---------------
          dE  on:    start            ASAP                start   
          dE off:    2 iters         30 iters            30 iters 

      Screening Tolerance Information
      -------------------------------
          Density screening/tol_rho:  1.00D-10
          AO Gaussian exp screening on grid/accAOfunc:  14
          CD Gaussian exp screening on grid/accCDfunc:  20
          XC Gaussian exp screening on grid/accXCfunc:  20
          Schwarz screening/accCoul:  1.00D-10

      Superposition of Atomic Density Guess
      -------------------------------------

 Sum of atomic energies:       -2808.45068874

      Non-variational initial energy
      ------------------------------

 Total energy =   -2808.711208
 1-e energy   =   -8554.867668
 2-e energy   =    3432.914083
 HOMO         =      -0.195706
 LUMO         =       0.302945

   Time after variat. SCF:      1.5
   Time prior to 1st pass:      1.5

 Integral file          = ./siosi3.aoints.0
 Record size in doubles =  65536        No. of integs per rec  =  43688
 Max. records in memory =    322        Max. records in file   =  40760
 No. of bits per label  =      8        No. of bits per value  =     64

 #quartets = 1.895D+06 #integrals = 1.051D+07 #direct =  0.0% #cached =100.0%

File balance: exchanges=     2  moved=    71  time=   0.0

 Grid_pts file          = ./siosi3.gridpts.0
 Record size in doubles =  12289        No. of grid_pts per rec  =   3070
 Max. records in memory =    132        Max. recs in file   =    217373

           Memory utilization after 1st SCF pass: 
           Heap Space remaining (MW):        0.00                  18
          Stack Space remaining (MW):       13.11            13105172

   convergence    iter        energy       DeltaE   RMS-Dens  Diis-err    time
 ---------------- ----- ----------------- --------- --------- ---------  ------
 d=70,ls=0.0,diis     1  -2805.2717593838 -5.12D+03  3.62D-02  3.91D+00    14.5
 d=70,ls=0.0,diis     2  -2805.2963851236 -2.46D-02  2.51D-02  7.65D+01    16.0
 d= 0,ls=0.0,diis     3  -2805.7183552117 -4.22D-01  1.04D-02  7.01D+01    18.1
 d= 0,ls=0.0,diis     4  -2806.8538370890 -1.14D+00  1.69D-03  7.24D+01    20.3
 d= 0,ls=0.0,diis     5  -2806.9643064277 -1.10D-01  2.99D-03  7.19D+01    22.5
 d= 0,ls=0.0,diis     6  -2806.8531330078  1.11D-01  3.00D-03  7.03D+01    24.7
 d= 0,ls=0.0,diis     7  -2806.7579420483  9.52D-02  2.21D-03  7.00D+01    26.9
 d= 0,ls=0.0,diis     8  -2806.8084727178 -5.05D-02  3.66D-03  6.97D+01    28.8
 d= 0,ls=0.0,diis     9  -2806.5021991093  3.06D-01  2.66D-03  7.23D+01    30.0
 d= 0,ls=0.0,diis    10  -2806.3561605692  1.46D-01  1.11D-03  7.22D+01    31.3
 d= 0,ls=0.0,diis    11  -2806.2766178862  7.95D-02  9.77D-02  7.29D+01    32.7
 d= 0,ls=0.5,diis    12  -2813.9945292877 -7.72D+00  6.11D-02  2.57D+01    34.9
 d= 0,ls=0.5,diis    13  -2816.8399068611 -2.85D+00  3.75D-02  1.38D+01    36.3
 d= 0,ls=0.5,diis    14  -2818.7617192672 -1.92D+00  2.09D-02  4.23D+00    37.6
 d= 0,ls=0.5,diis    15  -2819.3942365930 -6.33D-01  1.16D-02  2.40D+00    38.9
 d= 0,ls=0.5,diis    16  -2819.5078304355 -1.14D-01  7.17D-03  2.40D+00    40.1
 d= 0,ls=0.5,diis    17  -2819.6063348821 -9.85D-02  8.97D-03  1.96D+00    41.8
 d= 0,ls=0.5,diis    18  -2819.8839854449 -2.78D-01  7.62D-03  5.01D-01    43.1
 d= 0,ls=0.5,diis    19  -2820.0012749915 -1.17D-01  6.11D-03  1.13D-01    44.5
 d= 0,ls=0.5,diis    20  -2820.0629149421 -6.16D-02  6.17D-03  6.60D-02    46.0
 d= 0,ls=0.5,diis    21  -2820.1184848158 -5.56D-02  6.96D-03  1.05D-01    48.3
 d= 0,ls=0.5,diis    22  -2820.1732246559 -5.47D-02  6.57D-03  2.26D-01    50.5
  Resetting Diis
 d= 0,ls=0.5,diis    23  -2820.2219780187 -4.88D-02  5.88D-03  3.79D-01    52.7
 d= 0,ls=0.5,diis    24  -2820.2711975180 -4.92D-02  9.08D-03  4.84D-01    55.0
 d= 0,ls=0.5,diis    25  -2820.4147142318 -1.44D-01  6.59D-03  1.51D-01    57.2
 d= 0,ls=0.5,diis    26  -2820.4886173218 -7.39D-02  5.72D-03  9.11D-02    59.4
 d= 0,ls=0.5,diis    27  -2820.5418679642 -5.33D-02  5.43D-03  5.53D-02    61.7
 d= 0,ls=0.5,diis    28  -2820.5812371376 -3.94D-02  4.57D-03  3.40D-02    63.9
 d= 0,ls=0.5,diis    29  -2820.6081023633 -2.69D-02  4.21D-03  2.29D-02    66.1
 d= 0,ls=0.5,diis    30  -2820.6283738236 -2.03D-02  3.90D-03  1.71D-02    68.4

      Calculation failed to converge
      ------------------------------

         Total DFT energy =    -2820.643572585439
      One electron energy =    -8530.040840079822
           Coulomb energy =     3618.538701065680
    Exchange-Corr. energy =     -222.383810344694
 Nuclear repulsion energy =     2313.242376773399

 Numeric. integr. density =      186.000125974326

     Total iterative time =     69.2s

 center of mass
 --------------
 x =  -0.00952295 y =   0.03028985 z =  -0.02257135

 moments of inertia (a.u.)
 ------------------
        6246.693956998223       -1350.867456527316         178.358701865298
       -1350.867456527316       10287.349148271958        -337.687957306077
         178.358701865298        -337.687957306077       10500.339172729240

 Parallel integral file used     242 records with       0 large values

 ------------------------------------------------------------------------
 dft energy failed                                                                                  0
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
  current input line : 
    55: task dft
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
 This type of error is most commonly associated with calculations not reaching convergence criteria
 ------------------------------------------------------------------------
 For more information see the NWChem manual at https://github.com/nwchemgit/nwchem/wiki

 For further details see manual section:                                                                                                                                                                                                                                                                
0:dft energy failed:Received an Error in Communication
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3 DUP FROM 0
with errorcode -1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------

To Reproduce

docker build -t f33.nondeterminism .
/usr/bin/time -p docker run --name f33.nondeterminism --memory 512m --rm -it -v "$(pwd):/mnt" f33.nondeterminism bash -c '. /etc/profile.d/modules.sh&& module use /usr/share/modulefiles&& module load mpi/openmpi-x86_64&& cd /mnt&& . /etc/profile.d/nwchem.sh&& mpiexec --allow-run-as-root --oversubscribe -np 3 nwchem_openmpi siosi3.nw'
start siosi3
geometry units au noautoz noautosym noprint
O 0.000000 0.000000 0.000000 
Si 3.014576 0.000000 0.000000 
Si -2.508676 -1.669137 0.090355 
O 3.981166 -1.323122 -2.508935 
O 3.870273 2.910825 0.000000 
O 4.041116 -1.465033 2.376888 
O -2.655663 -3.328781 -2.400368 
O -2.480544 -3.435889 2.483573 
O -4.832471 0.280842 0.142363 
Si 5.637169 -3.319181 -4.029830 
Si 5.930953 4.953101 0.791790 
Si 5.468246 -2.250324 4.885188 
Si -7.654391 0.847590 1.014023 
Si -3.158194 -4.857247 5.026302 
Si -2.974151 -5.921535 -3.888964 
H 5.270061 -6.079998 -2.949279 
H 8.494671 -2.562004 -3.822741 
H 4.688562 -3.250915 -6.887353 
H 4.114112 -1.013523 7.254688 
H 5.390639 -5.229699 5.239395 
H 8.311107 -1.375146 4.719652 
H 5.236878 7.507709 -0.616368 
H 5.938739 5.355645 3.732678 
H 8.621652 4.058320 -0.087848 
H -1.107625 -8.007345 -2.844945 
H -5.765149 -6.871347 -3.589463 
H -2.308182 -5.365343 -6.772894 
H -2.645080 -3.056162 7.365261 
H -1.433339 -7.291917 5.351028 
H -6.013502 -5.704069 4.953988 
H -8.533456 3.346292 -0.391100 
H -7.795607 1.205101 3.957357 
H -9.424475 -1.395251 0.207369 
end

basis
H library STO-3G
O library STO-3G
Si library STO-3G
end
dft
noio
noprint "final vectors analysis" multipole
tolerances acccoul 10
convergence damp 70 ncydp 2
end
set tolguess 1d-5
#uncomment the following line in a cluster environment
#set dft:xcreplicated t

task dft

Expected behavior

Small differences in results between repeated runs.

Screenshots

Additional context

edoapra commented 3 years ago

Could you add the keyword direct to the dft input section and try again? This way we would rule out I/O issues

edoapra commented 3 years ago

I wonder if making OpenBLAS less efficient (as discussed in https://github.com/edoapra/fedpkg/issues/10#issuecomment-732484560), might fix the issue. For example, you could set

OPENBLAS_CORETYPE=CORE2
marcindulak commented 3 years ago

I was not able to trigger a non-converging scf or a crash after several hundreds of "direct" runs.

When the "direct" setting is not used, with -e OPENBLAS_CORETYPE=CORE2 (or even -e OPENBLAS_CORETYPE=Haswell) on the docker cli, still there are non-converging scf or crashes.

From the processor specification it looks like it's an old Skylake.

An example output of a crash early in scf is included below.

 argument  1 = siosi3.nw

             Northwest Computational Chemistry Package (NWChem) 7.0.2
             --------------------------------------------------------

                    Environmental Molecular Sciences Laboratory
                       Pacific Northwest National Laboratory
                                Richland, WA 99352

                              Copyright (c) 1994-2020
                       Pacific Northwest National Laboratory
                            Battelle Memorial Institute

             NWChem is an open-source computational chemistry package
                        distributed under the terms of the
                      Educational Community License (ECL) 2.0
             A copy of the license is included with this distribution
                              in the LICENSE.TXT file

                                  ACKNOWLEDGMENT
                                  --------------

            This software and its documentation were developed at the
            EMSL at Pacific Northwest National Laboratory, a multiprogram
            national laboratory, operated for the U.S. Department of Energy
            by Battelle under Contract Number DE-AC05-76RL01830. Support
            for this work was provided by the Department of Energy Office
            of Biological and Environmental Research, Office of Basic
            Energy Sciences, and the Office of Advanced Scientific Computing.

           Job information
           ---------------

    hostname        = a4e962d0e957
    program         = nwchem_openmpi
    date            = Tue Nov 24 20:26:46 2020

    compiled        = Sun_Nov_22_13:28:15_2020
    source          = /builddir/build/BUILD/nwchem-5d4a0e84c8f8d9656a0ac37e796a9a4eff8c5ad9
    nwchem branch   = 7.0.2
    nwchem revision = N/A
    ga revision     = 5.7.1
    use scalapack   = T
    input           = siosi3.nw
    prefix          = siosi3.
    data base       = ./siosi3.db
    status          = startup
    nproc           =        3
    time left       =     -1s

           Memory information
           ------------------

    heap     =   13107194 doubles =    100.0 Mbytes
    stack    =   13107199 doubles =    100.0 Mbytes
    global   =   26214400 doubles =    200.0 Mbytes (distinct from heap & stack)
    total    =   52428793 doubles =    400.0 Mbytes
    verify   = yes
    hardfail = no 

           Directory information
           ---------------------

  0 permanent = .
  0 scratch   = .

                                NWChem Input Module
                                -------------------

  library name resolved from: environment
  library file name is: </usr/share/nwchem/libraries/>

                      Basis "ao basis" -> "" (cartesian)
                      -----
  H (Hydrogen)
  ------------
            Exponent  Coefficients 
       -------------- ---------------------------------------------------------
  1 S  3.42525091E+00  0.154329
  1 S  6.23913730E-01  0.535328
  1 S  1.68855400E-01  0.444635

  O (Oxygen)
  ----------
            Exponent  Coefficients 
       -------------- ---------------------------------------------------------
  1 S  1.30709320E+02  0.154329
  1 S  2.38088610E+01  0.535328
  1 S  6.44360830E+00  0.444635

  2 S  5.03315130E+00 -0.099967
  2 S  1.16959610E+00  0.399513
  2 S  3.80389000E-01  0.700115

  3 P  5.03315130E+00  0.155916
  3 P  1.16959610E+00  0.607684
  3 P  3.80389000E-01  0.391957

  Si (Silicon)
  ------------
            Exponent  Coefficients 
       -------------- ---------------------------------------------------------
  1 S  4.07797551E+02  0.154329
  1 S  7.42808331E+01  0.535328
  1 S  2.01032923E+01  0.444635

  2 S  2.31936561E+01 -0.099967
  2 S  5.38970687E+00  0.399513
  2 S  1.75289995E+00  0.700115

  3 P  2.31936561E+01  0.155916
  3 P  5.38970687E+00  0.607684
  3 P  1.75289995E+00  0.391957

  4 S  1.47874062E+00 -0.219620
  4 S  4.12564880E-01  0.225595
  4 S  1.61475098E-01  0.900398

  5 P  1.47874062E+00  0.010588
  5 P  4.12564880E-01  0.595167
  5 P  1.61475098E-01  0.462001

 Summary of "ao basis" -> "" (cartesian)
 ------------------------------------------------------------------------------
       Tag                 Description            Shells   Functions and Types
 ---------------- ------------------------------  ------  ---------------------
 H                           STO-3G                  1        1   1s
 O                           STO-3G                  3        5   2s1p
 Si                          STO-3G                  5        9   3s2p

                                 NWChem DFT Module
                                 -----------------

 Summary of "ao basis" -> "ao basis" (cartesian)
 ------------------------------------------------------------------------------
       Tag                 Description            Shells   Functions and Types
 ---------------- ------------------------------  ------  ---------------------
 H                           STO-3G                  1        1   1s
 O                           STO-3G                  3        5   2s1p
 Si                          STO-3G                  5        9   3s2p

  Caching 1-el integrals 

            General Information
            -------------------
          SCF calculation type: DFT
          Wavefunction type:  closed shell.
          No. of atoms     :    33
          No. of electrons :   186
           Alpha electrons :    93
            Beta electrons :    93
          Charge           :     0
          Spin multiplicity:     1
          Use of symmetry is: off; symmetry adaption is: off
          Maximum number of iterations:  30
          AO basis - number of functions:   125
                     number of shells:    79
          Convergence on energy requested:  1.00D-06
          Convergence on density requested:  1.00D-05
          Convergence on gradient requested:  5.00D-04

              XC Information
              --------------
                        Slater Exchange Functional  1.000 local    
                      VWN V Correlation Functional  1.000 local    

             Grid Information
             ----------------
          Grid used for XC integration:  medium    
          Radial quadrature: Mura-Knowles        
          Angular quadrature: Lebedev. 
          Tag              B.-S. Rad. Rad. Pts. Rad. Cut. Ang. Pts.
          ---              ---------- --------- --------- ---------
          O                   0.60       49          12.0       434
          Si                  1.10       88          13.0       590
          H                   0.35       45          13.0       434
          Grid pruning is: on 
          Number of quadrature shells:  1857
          Spatial weights used:  Erf1

          Convergence Information
          -----------------------
          Convergence aids based upon iterative change in 
          total energy or number of iterations. 
          Levelshifting, if invoked, occurs when the 
          HOMO/LUMO gap drops below (HL_TOL):  1.00D-02
          DIIS, if invoked, will attempt to extrapolate 
          using up to (NFOCK): 10 stored Fock matrices.

                    Damping(70%)  Levelshifting(0.5)       DIIS
                  --------------- ------------------- ---------------
          dE  on:    start            ASAP                start   
          dE off:    2 iters         30 iters            30 iters 

      Screening Tolerance Information
      -------------------------------
          Density screening/tol_rho:  1.00D-10
          AO Gaussian exp screening on grid/accAOfunc:  14
          CD Gaussian exp screening on grid/accCDfunc:  20
          XC Gaussian exp screening on grid/accXCfunc:  20
          Schwarz screening/accCoul:  1.00D-10

      Superposition of Atomic Density Guess
      -------------------------------------

 Sum of atomic energies:       -2808.45068874

      Non-variational initial energy
      ------------------------------

 Total energy =   -2808.711208
 1-e energy   =   -8554.867668
 2-e energy   =    3432.914083
 HOMO         =      -0.195706
 LUMO         =       0.302945

   Time after variat. SCF:      1.2
   Time prior to 1st pass:      1.2

 Integral file          = ./siosi3.aoints.0
 Record size in doubles =  65536        No. of integs per rec  =  43688
 Max. records in memory =    322        Max. records in file   =  40756
 No. of bits per label  =      8        No. of bits per value  =     64

 #quartets = 1.895D+06 #integrals = 1.051D+07 #direct =  0.0% #cached =100.0%

File balance: exchanges=     2  moved=    59  time=   0.0

 Grid_pts file          = ./siosi3.gridpts.0
 Record size in doubles =  12289        No. of grid_pts per rec  =   3070
 Max. records in memory =    132        Max. recs in file   =    217352

           Memory utilization after 1st SCF pass: 
           Heap Space remaining (MW):        0.00                  18
          Stack Space remaining (MW):       13.11            13105172

   convergence    iter        energy       DeltaE   RMS-Dens  Diis-err    time
 ---------------- ----- ----------------- --------- --------- ---------  ------
 d=70,ls=0.0,diis     1  -2805.2717610822 -5.12D+03  3.62D-02  3.91D+00    19.0
                    0                  170                  167                    0                    1                43687   0.0000000000000000     
 int2e_buf_cntr_unpack: invalid count                   0
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
  current input line : 
     0: 
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
 This error has not yet been assigned to a category
 ------------------------------------------------------------------------
 For more information see the NWChem manual at https://github.com/nwchemgit/nwchem/wiki

 For further details see manual section: No section for this category                                                                                                                                                                                                                                   
2:int2e_buf_cntr_unpack: invalid count:Received an Error in Communication
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 2 in communicator MPI COMMUNICATOR 3 DUP FROM 0
with errorcode -1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
edoapra commented 3 years ago

The last output seems a clear indication of an I/O issue. Not sure what the exact source of the problems is. I am often compiling with the setting USE_NOIO=1 (this environment variable triggers the removal of I/O based algorithms). I might be a good idea to set it for building RPMs, too.

marcindulak commented 3 years ago

For reference the mention of this parameter is in https://nwchemgit.github.io/Special_AWCforum/st/id2288.html

The fedora/epel rpms use now export USE_NOIO=TRUE during the compilation https://src.fedoraproject.org/rpms/nwchem/c/a466fc32984cbdd607127285ee8211875ad5c878?branch=master. With this setting I tried several hundreds of runs without encountering the problems mentioned in this issue.

edoapra commented 3 years ago

Yes, this change make sense. The only problem is that people might still want to use the I/O based algorithms. Let's see if we get any feedback about it. Unfortunately, there is probably not an easy way to re-enable I/O based algorithms from the input file at this moment.