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

[Chang Liu]

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()

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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