Is this a memory problem?

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Posts 8
Hi everyone

I run a CCSD(T) calculation with AV5Z basis set for the F+H2 system,
the output is as follows.
Is this error caused by the memory limitation?

 argument  1 = fh2-uhf-ccsd_t-av5z-spherical-fc-c1-diis5.nw

             Northwest Computational Chemistry Package (NWChem) 6.1.1
             --------------------------------------------------------
 
                    Environmental Molecular Sciences Laboratory
                       Pacific Northwest National Laboratory
                                Richland, WA 99352
 
                              Copyright (c) 1994-2012
                       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      = compute-11-10.local
    program       = nwchem
    date          = Fri Dec  7 21:12:31 2012
 
    compiled      = Sun_Nov_18_14:18:02_2012
    source        = /state/partition1/share/chenjun/work2/nwchem-6.1.1-impi
    nwchem branch = 6.1.1
    input         = fh2-uhf-ccsd_t-av5z-spherical-fc-c1-diis5.nw
    prefix        = fh2.
    data base     = ./fh2.db
    status        = startup
    nproc         =      108
    time left     =     -1s
 
 
 
           Memory information
           ------------------
 
    heap     =  419430401 doubles =   3200.0 Mbytes
    stack    =  104857601 doubles =    800.0 Mbytes
    global   =  524288000 doubles =   4000.0 Mbytes (distinct from heap & stack)
    total    = 1048576002 doubles =   8000.0 Mbytes
    verify   = yes
    hardfail = no 
 
 
           Directory information
           ---------------------
 
  0 permanent = .
  0 scratch   = ./tmp
  
                                NWChem Input Module
                                -------------------
 
 Turning off AUTOSYM since
 SYMMETRY directive was detected!
  
                             Geometry "geometry" -> ""
                             -------------------------
 
 Output coordinates in a.u. (scale by  1.000000000 to convert to a.u.)
 
  No.       Tag          Charge          X              Y              Z
 ---- ---------------- ---------- -------------- -------------- --------------
    1 H1                   1.0000    -2.15042120     0.00000000    -2.33003060
    2 H2                   1.0000    -2.15042120     0.00000000    -0.87003060
    3 F                    9.0000     0.47787138     0.00000000     0.35556236
 
      Atomic Mass 
      ----------- 
 
      H1                 1.007825
      H2                 1.007825
      F                 18.998400
 
 
 Effective nuclear repulsion energy (a.u.)       6.1834600022
 
            Nuclear Dipole moment (a.u.) 
            ----------------------------
        X                 Y               Z
 ---------------- ---------------- ----------------
     0.0000000000     0.0000000000     0.0000000000
 
 
 
                                Z-matrix (user)
                                -------- 
 
 Units are Angstrom for bonds and degrees for angles
 
      Type          Name      I     J     K     L     M      Value
      ----------- --------  ----- ----- ----- ----- ----- ----------
    1 Stretch                  2     1                       0.77260
    2 Stretch                  3     2                       1.53461
    3 Bend                     3     2     1               115.00000
 
 
            XYZ format geometry
            -------------------
     3
 geometry
 H1                   -1.13795398     0.00000000    -1.23299918
 H2                   -1.13795398     0.00000000    -0.46040040
 F                     0.25287866     0.00000000     0.18815551
 
  library name resolved from: .nwchemrc
  library file name is: </home/chenjun/bin/NWchem_mvapich2/data/libraries/>
  
                                 NWChem SCF Module
                                 -----------------
 
 
 
  ao basis        = "ao basis"
  functions       =   287
  atoms           =     3
  alpha electrons =     6
  beta  electrons =     5
  charge          =   0.00
  wavefunction    = UHF 
  input vectors   = atomic
  output vectors  = ./fh2.movecs
  use symmetry    = F
  symmetry adapt  = F
 
 
 Summary of "ao basis" -> "ao basis" (spherical)
 ------------------------------------------------------------------------------
       Tag                 Description            Shells   Functions and Types
 ---------------- ------------------------------  ------  ---------------------
 F                        aug-cc-pv5z               27      127   7s6p5d4f3g2h
 H                        aug-cc-pv5z               20       80   6s5p4d3f2g
 
 
 
 Forming initial guess at       2.8s
 
 
 !! The overlap matrix has   1 vectors deemed linearly dependent with
    eigenvalues:
 6.23D-06
 
 
      Superposition of Atomic Density Guess
      -------------------------------------
 
 Sum of atomic energies:        -100.42183068
 
      Non-variational initial energy
      ------------------------------
 
 Total energy =    -100.034876
 1-e energy   =    -152.412676
 2-e energy   =      46.194340
 HOMO         =      -0.433685
 LUMO         =       0.038067
 
 
 Starting SCF solution at       5.6s
 
 
 
 ----------------------------------------------
         Quadratically convergent UHF
 
 Convergence threshold     :          1.000E-08
 Maximum no. of iterations :          100
 Integral*density screening:          1.000E-10
 ----------------------------------------------
 
 
 Integral file          = ./tmp/fh2.aoints.000
 Record size in doubles =  65536        No. of integs per rec  =  32766
 Max. records in memory =    244        Max. records in file   =   1876
 No. of bits per label  =     16        No. of bits per value  =     64
 
 
 #quartets = 2.526D+06 #integrals = 3.856D+08 #direct =  0.0% #cached =100.0%
 
 
File balance: exchanges=   367  moved=  1012  time=   0.0
 
 
              iter       energy          gnorm     gmax       time
             ----- ------------------- --------- --------- --------
                 1     -100.4054162613  6.30D-01  3.10D-01      7.0
                 2     -100.4791309790  4.53D-01  7.74D-02      7.6
                 3     -100.5255008850  1.50D-01  5.40D-02      9.6
                 4     -100.5292889520  1.02D-02  1.97D-03     10.8
                 5     -100.5293902085  1.66D-03  2.61D-04     13.2
                 6     -100.5293903875  1.43D-06  2.87D-07     15.8
                 7     -100.5293903875  7.50D-10  1.32D-10     18.7
 
 
       Final UHF  results 
       ------------------ 
 
         Total SCF energy =   -100.529390387480
      One electron energy =   -152.702330124734
      Two electron energy =     45.989479735027
 Nuclear repulsion energy =      6.183460002228
 
                       Sz =      0.5000
                 Sz(Sz+1) =      0.7500
                      S^2 =      0.7619
 
        Time for solution =     15.3s
 
 
          Final alpha eigenvalues
          -----------------------
 
              1      
    1  -26.3944
    2   -1.6675
    3   -0.8633
    4   -0.7243
    5   -0.7233
    6   -0.5762
    7    0.0377
    8    0.0447
    9    0.0994
   10    0.1244
   11    0.1529
   12    0.1641
   13    0.1790
   14    0.1827
   15    0.1954
   16    0.2110
 
          Final beta eigenvalues
          ----------------------
 
              1      
    1  -26.3470
    2   -1.4832
    3   -0.6752
    4   -0.6728
    5   -0.5962
    6    0.0242
    7    0.0443
    8    0.0607
    9    0.1049
   10    0.1256
   11    0.1543
   12    0.1685
   13    0.1835
   14    0.1840
   15    0.2076
   16    0.2108
 
                    UHF Final Alpha Molecular Orbital Analysis
                    ------------------------------------------
 
 Vector    2  Occ=1.000000D+00  E=-1.667525D+00
              MO Center=  2.4D-01, -1.0D-15,  1.8D-01, r^2= 3.4D-01
   Bfn.  Coefficient  Atom+Function         Bfn.  Coefficient  Atom+Function  
  ----- ------------  ---------------      ----- ------------  ---------------
   165      0.531121  3 F  s                164      0.402001  3 F  s          
   162      0.351572  3 F  s                166      0.187190  3 F  s          

 ...(MOs skipped)

 Vector   24  Occ=0.000000D+00  E= 5.100678D-01
              MO Center= -1.2D+00,  6.3D-14, -8.6D-01, r^2= 5.6D+00
   Bfn.  Coefficient  Atom+Function         Bfn.  Coefficient  Atom+Function  
  ----- ------------  ---------------      ----- ------------  ---------------
   181      2.582629  3 F  py               206     -1.579173  3 F  d -2       
    38     -1.512709  1 H  d -1             100     -1.268777  2 H  py         
    37     -1.238952  1 H  d -2             137     -0.818594  2 H  f -2       
   117     -0.811993  2 H  d -2              20     -0.758035  1 H  py         
    17     -0.554887  1 H  py               184      0.551636  3 F  py         
 
 
 center of mass
 --------------
 x =   0.22576776 y =   0.00000000 z =   0.16798352
 
 moments of inertia (a.u.)
 ------------------
           8.043281968142           0.000000000000          -9.366440167364
           0.000000000000          20.631660905204           0.000000000000
          -9.366440167364           0.000000000000          12.588378937061
 
  Mulliken analysis of the total density
  --------------------------------------
 
    Atom       Charge   Shell Charges
 -----------   ------   -------------------------------------------------------
    1 H    1     0.98   0.03  0.14  0.36  0.35  0.07  0.00  0.00  0.00  0.01  0.01  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00
    2 H    1     0.98   0.03  0.14  0.36  0.33  0.07  0.00  0.00  0.00  0.02  0.02  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00
    3 F    9     9.04   1.91 -0.01  0.10  0.64  1.01  0.33  0.00  0.41  1.09  1.75  1.42  0.37  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00
  0.00  0.00
 
  Mulliken analysis of the alpha density
  --------------------------------------
 
    Atom       Charge   Shell Charges
 -----------   ------   -------------------------------------------------------
    1 H    1     0.56   0.02  0.08  0.21  0.20  0.04  0.00  0.00  0.00  0.01  0.01  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00
    2 H    1     0.47   0.02  0.07  0.17  0.15  0.04  0.00  0.00  0.00  0.01  0.01  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00
    3 F    9     4.98   0.96  0.00  0.05  0.33  0.51  0.15  0.00  0.25  0.66  1.06  0.82  0.18  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00
  0.00  0.00
 
   Mulliken analysis of the beta density
   -------------------------------------
 
    Atom       Charge   Shell Charges
 -----------   ------   -------------------------------------------------------
    1 H    1     0.42   0.01  0.06  0.15  0.15  0.03  0.00  0.00  0.00  0.01  0.01  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00
    2 H    1     0.51   0.02  0.07  0.19  0.18  0.03  0.00  0.00  0.00  0.01  0.01  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00
    3 F    9     4.06   0.96  0.00  0.05  0.31  0.50  0.18  0.00  0.16  0.42  0.69  0.60  0.19  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00
  0.00  0.00
 
   Mulliken analysis of the spin density
   -------------------------------------
 
    Atom       Charge   Shell Charges
 -----------   ------   -------------------------------------------------------
    1 H    1     0.13   0.00  0.02  0.06  0.05  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00
    2 H    1    -0.05   0.00  0.00 -0.03 -0.03  0.01  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00
    3 F    9     0.91   0.00  0.00  0.00  0.02  0.01 -0.03  0.00  0.09  0.24  0.37  0.22  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00
  0.00  0.00
 
       Multipole analysis of the density wrt the origin
       ------------------------------------------------
 
     L   x y z        total         alpha         beta         nuclear
     -   - - -        -----         -----         ----         -------
     0   0 0 0      0.000000     -6.000000     -5.000000     11.000000
 
     1   1 0 0     -0.078719     -0.142927      0.064208      0.000000
     1   0 1 0      0.000000      0.000000      0.000000      0.000000
     1   0 0 1     -0.054691     -0.048610     -0.006081      0.000000
 
     2   2 0 0     -4.718687     -8.770649     -7.251909     11.303872
     2   1 1 0      0.000000      0.000000      0.000000      0.000000
     2   1 0 1      0.315977     -4.690583     -3.404138      8.410697
     2   0 2 0     -5.164054     -2.657818     -2.506236      0.000000
     2   0 1 1      0.000000      0.000000      0.000000      0.000000
     2   0 0 2     -4.410992     -6.535592     -5.199218      7.323817
 
 
 Parallel integral file used   11821 records with       0 large values
 
                   NWChem Extensible Many-Electron Theory Module
                   ---------------------------------------------
 
              ======================================================
                   This portion of the program was automatically
                  generated by a Tensor Contraction Engine (TCE).
                  The development of this portion of the program
                 and TCE was supported by US Department of Energy,
                Office of Science, Office of Basic Energy Science.
                      TCE is a product of Battelle and PNNL.
              Please cite: S.Hirata, J.Phys.Chem.A 107, 9887 (2003).
              ======================================================
 
            General Information
            -------------------
      Number of processors :   108
         Wavefunction type : Unrestricted Hartree-Fock
          No. of electrons :    11
           Alpha electrons :     6
            Beta electrons :     5
           No. of orbitals :   572
            Alpha orbitals :   286
             Beta orbitals :   286
        Alpha frozen cores :     1
         Beta frozen cores :     1
     Alpha frozen virtuals :     0
      Beta frozen virtuals :     0
         Spin multiplicity : doublet 
    Number of AO functions :   287
       Number of AO shells :    67
        Use of symmetry is : off
      Symmetry adaption is : off
         Schwarz screening : 0.10D-09
 
  !! WARNING !! The number of MO is less than the number of AO
 
          Correlation Information
          -----------------------
          Calculation type : Coupled-cluster singles & doubles w/ perturbation           
   Perturbative correction : (T)                                                         
            Max iterations :      100
        Residual threshold : 0.10D-04
     T(0) DIIS level shift : 0.00D+00
     L(0) DIIS level shift : 0.00D+00
     T(1) DIIS level shift : 0.00D+00
     L(1) DIIS level shift : 0.00D+00
     T(R) DIIS level shift : 0.00D+00
     T(I) DIIS level shift : 0.00D+00
   CC-T/L Amplitude update :  5-th order DIIS
                I/O scheme : Global Array Library
        L-threshold : 0.10D-04
        EOM-threshold : 0.10D-04
 no EOMCCSD initial starts read in
 TCE RESTART OPTIONS
 READ_INT:   F
 WRITE_INT:  F
 READ_TA:    F
 WRITE_TA:   F
 READ_XA:    F
 WRITE_XA:   F
 READ_IN3:   F
 WRITE_IN3:  F
 
            Memory Information
            ------------------
          Available GA space size is    ********** doubles
          Available MA space size is     524279648 doubles
 
 Maximum block size        20 doubles
 
 tile_dim =     20
 
 Block   Spin    Irrep     Size     Offset   Alpha
 -------------------------------------------------
   1    alpha     a      5 doubles       0       1
   2    beta      a      4 doubles       5       2
   3    alpha     a     20 doubles       9       3
   4    alpha     a     20 doubles      29       4
   5    alpha     a     20 doubles      49       5
   6    alpha     a     20 doubles      69       6
   7    alpha     a     20 doubles      89       7
   8    alpha     a     20 doubles     109       8
   9    alpha     a     20 doubles     129       9
  10    alpha     a     20 doubles     149      10
  11    alpha     a     20 doubles     169      11
  12    alpha     a     20 doubles     189      12
  13    alpha     a     20 doubles     209      13
  14    alpha     a     20 doubles     229      14
  15    alpha     a     20 doubles     249      15
  16    alpha     a     20 doubles     269      16
  17    beta      a     18 doubles     289      17
  18    beta      a     19 doubles     307      18
  19    beta      a     19 doubles     326      19
  20    beta      a     18 doubles     345      20
  21    beta      a     19 doubles     363      21
  22    beta      a     19 doubles     382      22
  23    beta      a     19 doubles     401      23
  24    beta      a     18 doubles     420      24
  25    beta      a     19 doubles     438      25
  26    beta      a     19 doubles     457      26
  27    beta      a     19 doubles     476      27
  28    beta      a     18 doubles     495      28
  29    beta      a     19 doubles     513      29
  30    beta      a     19 doubles     532      30
  31    beta      a     19 doubles     551      31
 
 Global array virtual files algorithm will be used
 
 Parallel file system coherency ......... OK
 
 Integral file          = ./tmp/fh2.aoints.000
 Record size in doubles =  65536        No. of integs per rec  =  32766
 Max. records in memory =    244        Max. records in file   =   1876
 No. of bits per label  =     16        No. of bits per value  =     64
 
 
 #quartets = 2.526D+06 #integrals = 3.856D+08 #direct =  0.0% #cached =100.0%
 
 
File balance: exchanges=   315  moved=  1070  time=   0.0
 
 
 Fock matrix recomputed
 1-e file size   =           162450
 1-e file name   = ./tmp/fh2.f1        
 Cpu & wall time / sec            3.3            3.6
 
 tce_ao2e: fast2e=1
 half-transformed integrals in memory
 
 2-e (intermediate) file size =     13830084576
 2-e (intermediate) file name = ./tmp/fh2.v2i
 Cpu & wall time / sec           50.4           55.0
 
 tce_mo2e: fast2e=1
 2-e integrals stored in memory
 
 2-e file size   =      10354139766
 2-e file name   = ./tmp/fh2.v2        
 Cpu & wall time / sec          945.9          967.4
 do_pt =  F
 do_lam_pt =  F
 do_cr_pt =  F
 do_lcr_pt =  F
 do_2t_pt =  F
 T1-number-of-tasks                    29
 
 t1 file size   =             2524
 t1 file name   = ./tmp/fh2.t1        
 t1 file handle =       -998
 T2-number-of-boxes                   435
 
 t2 file size   =          3297424
 t2 file name   = ./tmp/fh2.t2        
 t2 file handle =       -995
 
 CCSD iterations
 -----------------------------------------------------------------
 Iter          Residuum       Correlation     Cpu    Wall    V2*C2
 -----------------------------------------------------------------
Last System Error Message from Task 44:: Operation now in progress
44:Segmentation Violation error, status=: 11
(rank:44 hostname:compute-11-13.local pid:3953):ARMCI DASSERT fail. ../../ga-5-1/armci/src/common/signaltrap.c:SigSegvHandler():310 cond:0
107:Segmentation Violation error, status=: 11
(rank:107 hostname:compute-11-15.local pid:3513):ARMCI DASSERT fail. ../../ga-5-1/armci/src/common/signaltrap.c:SigSegvHandler():310 cond:0
Last System Error Message from Task 107:: No such file or directory
application called MPI_Abort(comm=0x84000001, 11) - process 44
application called MPI_Abort(comm=0x84000001, 11) - process 107
rank 107 in job 6  i11-10_50649   caused collective abort of all ranks
  exit status of rank 107: killed by signal 9 
rank 44 in job 6  i11-10_50649   caused collective abort of all ranks
  exit status of rank 44: killed by signal 9

Forum Vet
Threads 10
Posts 1584
It could be a memory problem.
Have you defined ARMCI_DEFAULT_SHMMAX?

Clicked A Few Times
Threads 2
Posts 8
Quote:Edoapra Dec 7th 2:17 pm
It could be a memory problem.
Have you defined ARMCI_DEFAULT_SHMMAX?


Hi Edo,

Yes, I set ARMCI_DEFAULT_SHMMAX to 4096.

I have completed this job with more cores.

I still have problem with memory settings and reducing memory requirements. This job need a great mount of memory, as can be seen from the output file. Can this job be done with less memory, if the input file is properly modified?

 Fock matrix recomputed
 1-e file size   =           162450
 1-e file name   = ./tmp/fh2.f1
 Cpu & wall time / sec            1.5            1.9
 
 tce_ao2e: fast2e=1
 half-transformed integrals in memory
 
 2-e (intermediate) file size =     [color=red]13830084576[/color]
 2-e (intermediate) file name = ./tmp/fh2.v2i
 Cpu & wall time / sec           18.4           18.6
 
 tce_mo2e: fast2e=1
 2-e integrals stored in memory
 
 2-e file size   =      [color=red]10354139766[/color]
 2-e file name   = ./tmp/fh2.v2
 Cpu & wall time / sec          305.6          309.2
 do_pt =  F
 do_lam_pt =  F
 do_cr_pt =  F
 do_lcr_pt =  F
 do_2t_pt =  F
 T1-number-of-tasks                    29
 
 t1 file size   =             2524
 t1 file name   = ./tmp/fh2.t1
 t1 file handle =       -998
 T2-number-of-boxes                   435
 
 t2 file size   =          3297424
 t2 file name   = ./tmp/fh2.t2
 t2 file handle =       -995
 
Edited On 7:21:49 PM PST - Sat, Dec 8th 2012 by Psd

  • Karol Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Clicked A Few Times
Threads 1
Posts 36
Fir the uhf case the 4-index transformation is more memory thirsty. For the system compose of 300 basis set functions I would recommend using larger number of cores (around 256 should be OK).
Another way our is to use for doublet states ROHF reference instead of UHF one.
In this case we have specialized 4-index transfromation with much smaller memory requirements (compared to the UHF case).
For ROHF please use

tce
...
2eorb
2emet
tilesize 20
attilesize 40
...
end

With the ROHF reference 100 core should be more than enough.

Best,
Karol


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