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Cannot allocate memory

Elk Users
Vj
2017-02-11
2018-05-31
  • Vj

    Vj - 2017-02-11

    I'm trying to calculate the force calculation in elk and this kind of error appears. Could you give some suggestions?
    Thank you.

    ERROR:
    Info(elk): current task : 0
    Info(checkmt): reduced muffin-tin radius of species 1 (Be) from 1.8000 to 0.8695
    Info(checkmt): reduced muffin-tin radius of species 2 (H) from 1.4000 to 0.6762
    Info(findsymcrys): atomic basis shift (lattice) :
    -0.2539360081E-02 0.000000000 0.000000000
    See GEOMETRY.OUT for new atomic positions
    Operating system error: Cannot allocate memory
    Allocation would exceed memory limit

    where the input file is elk.in.

    tasks
    0

    avec
    7.8760000000000003 0.0000000000000000 0.0000000000000000
    0.0000000000000000 7.8760000000000003 0.0000000000000000
    0.0000000000000000 0.0000000000000000 7.8760000000000003
    atoms
    2
    'Be.in'
    32
    0.0025393600812595 0.0000000000000000 0.0000000000000000
    0.5000000000000000 0.0000000000000000 0.0000000000000000
    0.0000000000000000 0.5000000000000000 0.0000000000000000
    0.5000000000000000 0.5000000000000000 0.0000000000000000
    0.0000000000000000 0.0000000000000000 0.5000000000000000
    0.5000000000000000 0.0000000000000000 0.5000000000000000
    0.0000000000000000 0.5000000000000000 0.5000000000000000
    0.5000000000000000 0.5000000000000000 0.5000000000000000
    0.2500000000000000 0.0000000000000000 0.2500000000000000
    0.7499999999999999 0.0000000000000000 0.2500000000000000
    0.2500000000000000 0.5000000000000000 0.2500000000000000
    0.7499999999999999 0.5000000000000000 0.2500000000000000
    0.2500000000000000 0.0000000000000000 0.7499999999999999
    0.7499999999999999 0.0000000000000000 0.7499999999999999
    0.2500000000000000 0.5000000000000000 0.7499999999999999
    0.7499999999999999 0.5000000000000000 0.7499999999999999
    0.2500000000000000 0.2500000000000000 0.0000000000000000
    0.7499999999999999 0.2500000000000000 0.0000000000000000
    0.2500000000000000 0.7499999999999999 0.0000000000000000
    0.7499999999999999 0.7499999999999999 0.0000000000000000
    0.2500000000000000 0.2500000000000000 0.5000000000000000
    0.7499999999999999 0.2500000000000000 0.5000000000000000
    0.2500000000000000 0.7499999999999999 0.5000000000000000
    0.7499999999999999 0.7499999999999999 0.5000000000000000
    0.0000000000000000 0.2500000000000000 0.2500000000000000
    0.5000000000000000 0.2500000000000000 0.2500000000000000
    0.0000000000000000 0.7499999999999999 0.2500000000000000
    0.5000000000000000 0.7499999999999999 0.2500000000000000
    0.0000000000000000 0.2500000000000000 0.7499999999999999
    0.5000000000000000 0.2500000000000000 0.7499999999999999
    0.0000000000000000 0.7499999999999999 0.7499999999999999
    0.5000000000000000 0.7499999999999999 0.7499999999999999
    'H.in'
    64
    0.1761000000000000 0.1761000000000000 0.1761000000000000
    0.6760999999999999 0.1761000000000000 0.1761000000000000
    0.1761000000000000 0.6760999999999999 0.1761000000000000
    0.6760999999999999 0.6760999999999999 0.1761000000000000
    0.1761000000000000 0.1761000000000000 0.6760999999999999
    0.6760999999999999 0.1761000000000000 0.6760999999999999
    0.1761000000000000 0.6760999999999999 0.6760999999999999
    0.6760999999999999 0.6760999999999999 0.6760999999999999
    0.0739000000000000 0.3239000000000000 0.4261000000000000
    0.5738999999999999 0.3239000000000000 0.4261000000000000
    0.0739000000000000 0.8239000000000001 0.4261000000000000
    0.5738999999999999 0.8239000000000001 0.4261000000000000
    0.0739000000000000 0.3239000000000000 0.9260999999999999
    0.5738999999999999 0.3239000000000000 0.9260999999999999
    0.0739000000000000 0.8239000000000001 0.9260999999999999
    0.5738999999999999 0.8239000000000001 0.9260999999999999
    0.4261000000000000 0.0739000000000000 0.3239000000000000
    0.9260999999999999 0.0739000000000000 0.3239000000000000
    0.4261000000000000 0.5738999999999999 0.3239000000000000
    0.9260999999999999 0.5738999999999999 0.3239000000000000
    0.4261000000000000 0.0739000000000000 0.8239000000000001
    0.9260999999999999 0.0739000000000000 0.8239000000000001
    0.4261000000000000 0.5738999999999999 0.8239000000000001
    0.9260999999999999 0.5738999999999999 0.8239000000000001
    0.3239000000000000 0.4261000000000000 0.0739000000000000
    0.8239000000000001 0.4261000000000000 0.0739000000000000
    0.3239000000000000 0.9260999999999999 0.0739000000000000
    0.8239000000000001 0.9260999999999999 0.0739000000000000
    0.3239000000000000 0.4261000000000000 0.5738999999999999
    0.8239000000000001 0.4261000000000000 0.5738999999999999
    0.3239000000000000 0.9260999999999999 0.5738999999999999
    0.8239000000000001 0.9260999999999999 0.5738999999999999
    0.3238500000000000 0.3238500000000000 0.3238500000000000
    0.8238500000000000 0.3238500000000000 0.3238500000000000
    0.3238500000000000 0.8238500000000000 0.3238500000000000
    0.8238500000000000 0.8238500000000000 0.3238500000000000
    0.3238500000000000 0.3238500000000000 0.8238500000000000
    0.8238500000000000 0.3238500000000000 0.8238500000000000
    0.3238500000000000 0.8238500000000000 0.8238500000000000
    0.8238500000000000 0.8238500000000000 0.8238500000000000
    0.4261499999999999 0.1761500000000000 0.0738500000000000
    0.9261500000000000 0.1761500000000000 0.0738500000000000
    0.4261499999999999 0.6761500000000000 0.0738500000000000
    0.9261500000000000 0.6761500000000000 0.0738500000000000
    0.4261499999999999 0.1761500000000000 0.5738500000000000
    0.9261500000000000 0.1761500000000000 0.5738500000000000
    0.4261499999999999 0.6761500000000000 0.5738500000000000
    0.9261500000000000 0.6761500000000000 0.5738500000000000
    0.0738500000000000 0.4261499999999999 0.1761500000000000
    0.5738500000000000 0.4261499999999999 0.1761500000000000
    0.0738500000000000 0.9261500000000000 0.1761500000000000
    0.5738500000000000 0.9261500000000000 0.1761500000000000
    0.0738500000000000 0.4261499999999999 0.6761500000000000
    0.5738500000000000 0.4261499999999999 0.6761500000000000
    0.0738500000000000 0.9261500000000000 0.6761500000000000
    0.5738500000000000 0.9261500000000000 0.6761500000000000
    0.1761500000000000 0.0738500000000000 0.4261499999999999
    0.6761500000000000 0.0738500000000000 0.4261499999999999
    0.1761500000000000 0.5738500000000000 0.4261499999999999
    0.6761500000000000 0.5738500000000000 0.4261499999999999
    0.1761500000000000 0.0738500000000000 0.9261500000000000
    0.6761500000000000 0.0738500000000000 0.9261500000000000
    0.1761500000000000 0.5738500000000000 0.9261500000000000
    0.6761500000000000 0.5738500000000000 0.9261500000000000

    mixtype
    3

    sppath
    '../../../species/'

    ngridk
    1 1 1

    vkloff
    0.5 0.5 0.5

    tforce
    .true.

     
  • Markus

    Markus - 2017-02-12

    Hello,

    well, you are out of memory. Your problem has too many atoms. Reduce the number of atoms or look for a bigger computer.

    By the way... the reduced muffin tin sizes look fishy. Are you sure the coordinates and lattice constants are right?

    Regards
    Markus

     
  • Vj

    Vj - 2017-02-15

    Hello sir,
    I'm doing the same calculation and now this kind of error appears. The Input file is same, Could you give some suggestions?
    Thank you
    Regards

    Info(elk): current task : 0
    Info(checkmt): reduced muffin-tin radius of species 1 (Be) from 1.8000 to 0.8695
    Info(checkmt): reduced muffin-tin radius of species 2 (H) from 1.4000 to 0.6762
    Info(findsymcrys): atomic basis shift (lattice) :
    -0.2539360081E-02 0.000000000 0.000000000
    See GEOMETRY.OUT for new atomic positions

    Warning(occupy): minimum eigenvalue less than minimum linearisation energy : -2.321802372 0.000000000
    for s.c. loop 1

    Warning(rhonorm): total charge density incorrect for s.c. loop 1
    Calculated : 187.2091786
    Required : 192.0000000
    .
    .
    .
    Warning(rhonorm): total charge density incorrect for s.c. loop 15
    Calculated : 183.3885991
    Required : 192.0000000

    Warning(occupy): minimum eigenvalue less than minimum linearisation energy : -1.409226668 0.000000000
    for s.c. loop 16

    Warning(rhonorm): total charge density incorrect for s.c. loop 16
    Calculated : 183.3885991
    Required : 192.0000000
    Killed

     
  • Markus

    Markus - 2017-02-15

    ... there is a serious problem with the basis set. As I saaid, I think your structure is wrong - the muffin-tin radii are extremely small, i.e., the atoms are very close. You have a cubic lattice with a lattice constant of 4.14 Angstroms. And you are trying to stuff 96 atoms in there. I guess you are confusing the units. The lattice constants in elk are given in Bohr radii, not Angstroms. Elk uses atomic units everywhere.

    Regards,
    Markus

     
    • Vj

      Vj - 2017-02-21

      Thank you sir,
      You are right about lattice constant, I will change it and do it again.

      With Regards

      On Wed, Feb 15, 2017 at 7:50 PM, Markus markusmeinert@users.sf.net wrote:

      ... there is a serious problem with the basis set. As I saaid, I think
      your structure is wrong - the muffin-tin radii are extremely small, i.e.,
      the atoms are very close. You have a cubic lattice with a lattice constant
      of 4.14 Angstroms. And you are trying to stuff 96 atoms in there. I guess
      you are confusing the units. The lattice constants in elk are given in Bohr
      radii, not Angstroms. Elk uses atomic units everywhere.

      Regards,
      Markus


      Cannot allocate memory
      https://sourceforge.net/p/elk/discussion/897820/thread/f1760abd/?limit=25#64cc


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  • Vj

    Vj - 2018-05-20

    Hello,
    I'm facing the same problem with the less atoms when I was doing the lattice optimization.

    ERROR:
    Elk code version 4.3.06 started

    Info(readinput): parameters set by highq option
    rgkmax : 8.000000000
    gmaxvr : 20.00000000
    trimvg : T
    lmaxapw : 10
    lmaxmat : 8
    lmaxo : 8
    lmaxi : 4
    fracinr : 0.5000000000E-02
    nrmtscf : 1.500000000
    nxlo : 2
    radkpt : 50.00000000
    autokpt : T
    vkloff : 0.000000000 0.000000000 0.000000000
    nempty0 : 10.00000000
    epspot : 0.1000000000E-06
    epsengy : 0.1000000000E-04
    epsforce : 0.1000000000E-03
    autolinengy : T
    gmaxrf : 4.000000000

    Info(elk): several copies of Elk may be running in this path
    (this could be intentional, or result from a previous crash,
    or arise from an incorrect MPI compilation)

    Info(elk): current task : 0
    Info(checkmt): reduced muffin-tin radius of species 1 (Nb) from 2.6000 to 1.5029
    Info(checkmt): reduced muffin-tin radius of species 2 (O) from 1.8000 to 1.0405
    Info(findsymcrys): atomic basis shift (lattice) :
    -0.1250000000 0.2500000000 -0.7500000000
    See GEOMETRY.OUT for new atomic positions

    Warning(linengy): could not find 8 linearisation energies in s.c. loop 1
    Operating system error: Cannot allocate memory
    Allocation would exceed memory limit


    In the input file there is not that much atoms, but it still giving the error. What should I do?
    Here I'm giving the input file so that you can help me out.
    Thank you in advance.
    With regards.

    ELK.IN
    avec
    0.000000000 0.000000000 11.30261000
    12.94102000 12.94102000 5.651305000
    12.94102000 -12.94102000 5.651305000

    atoms
    2 : nspecies
    'Nb.in' : spfname
    16 : natoms; atposl, bfcmt below
    0.37200000 0.23900000 0.99300000 0.00000000 0.00000000 0.00000000
    0.86100000 0.49300000 0.26100000 0.00000000 0.00000000 0.00000000
    0.60400000 0.76100000 0.00700000 0.00000000 0.00000000 0.00000000
    0.61500000 0.50700000 0.73900000 0.00000000 0.00000000 0.00000000
    0.87800000 0.26100000 0.50700000 0.00000000 0.00000000 0.00000000
    0.38900000 0.00700000 0.23900000 0.00000000 0.00000000 0.00000000
    0.64600000 0.73900000 0.49300000 0.00000000 0.00000000 0.00000000
    0.63500000 0.99300000 0.76100000 0.00000000 0.00000000 0.00000000
    0.89800000 0.25700000 0.00900000 0.00000000 0.00000000 0.00000000
    0.40500000 0.50900000 0.24300000 0.00000000 0.00000000 0.00000000
    0.16400000 0.74300000 0.99100000 0.00000000 0.00000000 0.00000000
    0.15700000 0.49100000 0.75700000 0.00000000 0.00000000 0.00000000
    0.35200000 0.24300000 0.49100000 0.00000000 0.00000000 0.00000000
    0.84500000 0.99100000 0.25700000 0.00000000 0.00000000 0.00000000
    0.08600000 0.75700000 0.50900000 0.00000000 0.00000000 0.00000000
    0.09300000 0.00900000 0.74300000 0.00000000 0.00000000 0.00000000
    'O.in' : spfname
    32 : natoms; atposl, bfcmt below
    0.00800000 0.12000000 0.85400000 0.00000000 0.00000000 0.00000000
    0.37800000 0.35400000 0.38000000 0.00000000 0.00000000 0.00000000
    0.98200000 0.88000000 0.14600000 0.00000000 0.00000000 0.00000000
    0.11200000 0.64600000 0.62000000 0.00000000 0.00000000 0.00000000
    0.24200000 0.38000000 0.64600000 0.00000000 0.00000000 0.00000000
    0.87200000 0.14600000 0.12000000 0.00000000 0.00000000 0.00000000
    0.26800000 0.62000000 0.35400000 0.00000000 0.00000000 0.00000000
    0.13800000 0.85400000 0.88000000 0.00000000 0.00000000 0.00000000
    0.50900000 0.10200000 0.85000000 0.00000000 0.00000000 0.00000000
    0.86100000 0.35000000 0.39800000 0.00000000 0.00000000 0.00000000
    0.46100000 0.89800000 0.15000000 0.00000000 0.00000000 0.00000000
    0.60900000 0.65000000 0.60200000 0.00000000 0.00000000 0.00000000
    0.74100000 0.39800000 0.65000000 0.00000000 0.00000000 0.00000000
    0.38900000 0.15000000 0.10200000 0.00000000 0.00000000 0.00000000
    0.78900000 0.60200000 0.35000000 0.00000000 0.00000000 0.00000000
    0.64100000 0.85000000 0.89800000 0.00000000 0.00000000 0.00000000
    0.71300000 0.39300000 0.15500000 0.00000000 0.00000000 0.00000000
    0.35600000 0.65500000 0.10700000 0.00000000 0.00000000 0.00000000
    0.26100000 0.60700000 0.84500000 0.00000000 0.00000000 0.00000000
    0.11800000 0.34500000 0.89300000 0.00000000 0.00000000 0.00000000
    0.53700000 0.10700000 0.34500000 0.00000000 0.00000000 0.00000000
    0.89400000 0.84500000 0.39300000 0.00000000 0.00000000 0.00000000
    0.98900000 0.89300000 0.65500000 0.00000000 0.00000000 0.00000000
    0.13200000 0.15500000 0.60700000 0.00000000 0.00000000 0.00000000
    0.24400000 0.39100000 0.13900000 0.00000000 0.00000000 0.00000000
    0.88500000 0.63900000 0.10900000 0.00000000 0.00000000 0.00000000
    0.77400000 0.60900000 0.86100000 0.00000000 0.00000000 0.00000000
    0.63300000 0.36100000 0.89100000 0.00000000 0.00000000 0.00000000
    0.00600000 0.10900000 0.36100000 0.00000000 0.00000000 0.00000000
    0.36500000 0.86100000 0.39100000 0.00000000 0.00000000 0.00000000
    0.47600000 0.89100000 0.63900000 0.00000000 0.00000000 0.00000000
    0.61700000 0.13900000 0.60900000 0.00000000 0.00000000 0.00000000

     
  • Vj

    Vj - 2018-05-22

    I'm facing the same problem with the less atom in NbO2. There is 400GB data storage is empty. I don't understand how to solve it, please halp me find the problem. Here is the error:

    ERROR:

    Info(elk): current task : 0
    Info(checkmt): reduced muffin-tin radius of species 1 (Nb) from 2.6000 to 1.5029
    Info(checkmt): reduced muffin-tin radius of species 2 (O) from 1.8000 to 1.0405
    Info(findsymcrys): atomic basis shift (lattice) :
    -0.1250000000 0.2500000000 -0.7500000000
    See GEOMETRY.OUT for new atomic positions

    Warning(linengy): could not find 8 linearisation energies in s.c. loop 1
    Killed

    The above error is came when I was doing the geometry optimization of NbO2 . I'm adding the input file ELK.IN, so that you can find problem.
    Thank you
    With regards

    ElK.in
    tasks
    0 : generate the ground-state

    autolinengy
    .true.

    mixtype
    3

    ngridk
    4 4 4

    sppath
    '../../species/'

    avec
    0.000000000 0.000000000 11.30261000
    12.94102000 12.94102000 5.651305000
    12.94102000 -12.94102000 5.651305000

    atoms
    2 : nspecies
    'Nb.in' : spfname
    16 : natoms; atposl, bfcmt below
    0.37200000 0.23900000 0.99300000 0.00000000 0.00000000 0.00000000
    0.86100000 0.49300000 0.26100000 0.00000000 0.00000000 0.00000000
    0.60400000 0.76100000 0.00700000 0.00000000 0.00000000 0.00000000
    0.61500000 0.50700000 0.73900000 0.00000000 0.00000000 0.00000000
    0.87800000 0.26100000 0.50700000 0.00000000 0.00000000 0.00000000
    0.38900000 0.00700000 0.23900000 0.00000000 0.00000000 0.00000000
    0.64600000 0.73900000 0.49300000 0.00000000 0.00000000 0.00000000
    0.63500000 0.99300000 0.76100000 0.00000000 0.00000000 0.00000000
    0.89800000 0.25700000 0.00900000 0.00000000 0.00000000 0.00000000
    0.40500000 0.50900000 0.24300000 0.00000000 0.00000000 0.00000000
    0.16400000 0.74300000 0.99100000 0.00000000 0.00000000 0.00000000
    0.15700000 0.49100000 0.75700000 0.00000000 0.00000000 0.00000000
    0.35200000 0.24300000 0.49100000 0.00000000 0.00000000 0.00000000
    0.84500000 0.99100000 0.25700000 0.00000000 0.00000000 0.00000000
    0.08600000 0.75700000 0.50900000 0.00000000 0.00000000 0.00000000
    0.09300000 0.00900000 0.74300000 0.00000000 0.00000000 0.00000000
    'O.in' : spfname
    32 : natoms; atposl, bfcmt below
    0.00800000 0.12000000 0.85400000 0.00000000 0.00000000 0.00000000
    0.37800000 0.35400000 0.38000000 0.00000000 0.00000000 0.00000000
    0.98200000 0.88000000 0.14600000 0.00000000 0.00000000 0.00000000
    0.11200000 0.64600000 0.62000000 0.00000000 0.00000000 0.00000000
    0.24200000 0.38000000 0.64600000 0.00000000 0.00000000 0.00000000
    0.87200000 0.14600000 0.12000000 0.00000000 0.00000000 0.00000000
    0.26800000 0.62000000 0.35400000 0.00000000 0.00000000 0.00000000
    0.13800000 0.85400000 0.88000000 0.00000000 0.00000000 0.00000000
    0.50900000 0.10200000 0.85000000 0.00000000 0.00000000 0.00000000
    0.86100000 0.35000000 0.39800000 0.00000000 0.00000000 0.00000000
    0.46100000 0.89800000 0.15000000 0.00000000 0.00000000 0.00000000
    0.60900000 0.65000000 0.60200000 0.00000000 0.00000000 0.00000000
    0.74100000 0.39800000 0.65000000 0.00000000 0.00000000 0.00000000
    0.38900000 0.15000000 0.10200000 0.00000000 0.00000000 0.00000000
    0.78900000 0.60200000 0.35000000 0.00000000 0.00000000 0.00000000
    0.64100000 0.85000000 0.89800000 0.00000000 0.00000000 0.00000000
    0.71300000 0.39300000 0.15500000 0.00000000 0.00000000 0.00000000
    0.35600000 0.65500000 0.10700000 0.00000000 0.00000000 0.00000000
    0.26100000 0.60700000 0.84500000 0.00000000 0.00000000 0.00000000
    0.11800000 0.34500000 0.89300000 0.00000000 0.00000000 0.00000000
    0.53700000 0.10700000 0.34500000 0.00000000 0.00000000 0.00000000
    0.89400000 0.84500000 0.39300000 0.00000000 0.00000000 0.00000000
    0.98900000 0.89300000 0.65500000 0.00000000 0.00000000 0.00000000
    0.13200000 0.15500000 0.60700000 0.00000000 0.00000000 0.00000000
    0.24400000 0.39100000 0.13900000 0.00000000 0.00000000 0.00000000
    0.88500000 0.63900000 0.10900000 0.00000000 0.00000000 0.00000000
    0.77400000 0.60900000 0.86100000 0.00000000 0.00000000 0.00000000
    0.63300000 0.36100000 0.89100000 0.00000000 0.00000000 0.00000000
    0.00600000 0.10900000 0.36100000 0.00000000 0.00000000 0.00000000
    0.36500000 0.86100000 0.39100000 0.00000000 0.00000000 0.00000000
    0.47600000 0.89100000 0.63900000 0.00000000 0.00000000 0.00000000
    0.61700000 0.13900000 0.60900000 0.00000000 0.00000000 0.00000000

     

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