[gpaw-users] Increase in process memory for single point calculations

[Ask Hjorth Larsen]

Dear Chang Liu,

2018-08-15 7:24 GMT-05:00 Chang Liu via gpaw-users
<gpaw-users at listserv.fysik.dtu.dk>:
> Hi GPAW users,
>
>
> I have encountered a strange problem of increasing process memory when I did
> a few single point calculations in loop. Here is my input file:
>
>
> from gpaw import *
> from ase.io import *
> from gpaw.utilities import h2gpts
> import numpy as np
>
>
> names = ['2co','6co']
> states = ['is','ts','fs']
> tsind = {'2co':6,'6co':4}
>
> mixer = Mixer(0.1, 5, weight = 100.0)
>
> def calc():
>     return GPAW(poissonsolver = {'dipolelayer':'xy','eps':1e-12},
>                 kpts = {'density':2},
>                 xc = 'RPBE',
>                 symmetry = {'point_group':False},
>                 mixer = mixer,
>                 eigensolver=Davidson(3),
>                 spinpol = False,
>                 occupations = FermiDirac(0.1),
>                 maxiter = 1000,
>
>     )
> for name in names:
>     neb_states = read('../%s/neb_all.traj@:'%name)
>     for state in states:
>         if state == 'is': slab = neb_states[0]
>         if state == 'fs': slab = neb_states[-1]
>         else: slab = neb_states[tsind[name]]
>         slab.center(vacuum=5.,axis=2)
>         slab.cell[2][2]+=10.
>         slab.pbc = (1,1,0)
>         slab.set_calculator(calc())
>         slab.calc.set(gpts = h2gpts(0.2, slab.get_cell(), idiv=8),txt =
> '%s_%s_gpaw.out' % (name,state))
>         e_f = slab.get_potential_energy()
>         f = open('Energy_%s_%s_gpaw.out' % (name,state), 'w')
>         f.write('%.3f\n' % e_f)
>         f.close()

There will be at least 3 coexisting calculators because neb_states
holds three atoms objects, each with a distinct calculator.  So the
increase in memory is not surprising.

In fact what I don't understand is why it does not increase *always*,
at least for the first three steps.  After that you would expect a few
small increases because it randomly claims a bit more heap space, but
should stabilize.

But the printouts do not disprove this.  The loops would need to be
much longer to see if there is a problem.

Best regards
Ask


>
> For GPAW-1.3.0, the output files for these calculations shows:
>
>
> b-an01 [~/pfs/co2rr/2018/180812/1.3.0]$ grep -r --include='*out' -i 'process
> memory' -A 1 $(ls -tr *)
> 2co_is_gpaw.out:  Process memory now: 80.45 MiB
> 2co_is_gpaw.out-  Calculator: 148.19 MiB
> --
> 2co_ts_gpaw.out:  Process memory now: 255.31 MiB
> 2co_ts_gpaw.out-  Calculator: 148.19 MiB
> --
> 2co_fs_gpaw.out:  Process memory now: 256.38 MiB
> 2co_fs_gpaw.out-  Calculator: 156.32 MiB
> --
> 6co_is_gpaw.out:  Process memory now: 414.14 MiB
> 6co_is_gpaw.out-  Calculator: 169.99 MiB
> --
> 6co_ts_gpaw.out:  Process memory now: 414.14 MiB
> 6co_ts_gpaw.out-  Calculator: 169.99 MiB
> --
> 6co_fs_gpaw.out:  Process memory now: 414.14 MiB
> 6co_fs_gpaw.out-  Calculator: 170.05 MiB
>
> For GPAW-1.4.0, it shows:
>
>
> b-an01 [~/pfs/co2rr/2018/180812/1.4.0]$ grep -r --include='*out' -i 'process
> memory' -A 1 $(ls -tr *)
> 2co_is_gpaw.out:  Process memory now: 103.06 MiB
> 2co_is_gpaw.out-  Calculator: 108.73 MiB
> --
> 2co_ts_gpaw.out:  Process memory now: 353.70 MiB
> 2co_ts_gpaw.out-  Calculator: 108.73 MiB
> --
> 2co_fs_gpaw.out:  Process memory now: 394.64 MiB
> 2co_fs_gpaw.out-  Calculator: 114.23 MiB
> --
> 6co_is_gpaw.out:  Process memory now: 589.16 MiB
> 6co_is_gpaw.out-  Calculator: 124.54 MiB
> --
> 6co_ts_gpaw.out:  Process memory now: 589.16 MiB
> 6co_ts_gpaw.out-  Calculator: 124.54 MiB
> --
> 6co_fs_gpaw.out:  Process memory now: 606.05 MiB
> 6co_fs_gpaw.out-  Calculator: 124.60 MiB
>
> It becomes a severe problem when I tried to do more single point
> calculations with different potentials with the Solvated Jellium Model
> calculator since in that case, the growth of process memory goes too fast so
> that the program crashes. Could you help me? Thank you very much!
>
>
> Best wishes,
> Chang Liu
> ----------------------------------------------------------
>                         Chang Liu
>                        PhD student
> Fysikum, Albanova, Stockholm University
>        S-106 91 Stockholm, Sweden
>                  +46 767159891
>     http://xsolasgroup.fysik.su.se/
>
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