[gpaw-users] Increase in process memory for single point calculations
Jens Jørgen Mortensen
jjmo at dtu.dk
Fri Aug 17 10:26:08 CEST 2018
Den 17-08-2018 kl. 10:05 skrev Chang Liu via gpaw-users:
>
> Hi,
>
>
> I have reinstalled GPAW-1.4.0 with MPI/2.1.1 and did a test with a
> trajectory file of 22 images. The input is:
>
>
> from gpaw import *
> from ase.io import *
> from gpaw.utilities import h2gpts
> import numpy as np
>
>
> 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,
> )
> neb_states = read('neb_2co.traj@:')
>
> for slab in neb_states:
> 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
> = '2co_%d_gpaw.out' % neb_states.index(slab))
> e_f = slab.get_potential_energy()
> f = open('Energy_2co_%d_gpaw.out' % neb_states.index(slab), 'w')
> f.write('%.3f\n' % e_f)
> f.close()
Try to add "slab.calc = None" as the last line of the loop.
Jens Jørgen
>
> The memory usage for 1.3.0 is:
>
>
> b-an01 [~/pfs/co2rr/2018/180815/1.3.0]$ grep -r --include='*out' -i
> 'process memory' -A 1 $(ls -tr *)
> 2co_0_gpaw.out: Process memory now: 80.99 MiB
> 2co_0_gpaw.out- Calculator: 257.25 MiB
> --
> 2co_1_gpaw.out: Process memory now: 361.00 MiB
> 2co_1_gpaw.out- Calculator: 257.25 MiB
> --
> 2co_2_gpaw.out: Process memory now: 619.15 MiB
> 2co_2_gpaw.out- Calculator: 273.71 MiB
> --
> 2co_3_gpaw.out: Process memory now: 889.65 MiB
> 2co_3_gpaw.out- Calculator: 273.69 MiB
> --
> 2co_4_gpaw.out: Process memory now: 1167.81 MiB
> 2co_4_gpaw.out- Calculator: 273.71 MiB
> --
> 2co_5_gpaw.out: Process memory now: 1441.73 MiB
> 2co_5_gpaw.out- Calculator: 273.70 MiB
> --
> 2co_6_gpaw.out: Process memory now: 1717.00 MiB
> 2co_6_gpaw.out- Calculator: 257.25 MiB
> --
> 2co_7_gpaw.out: Process memory now: 1977.18 MiB
> 2co_7_gpaw.out- Calculator: 257.25 MiB
> --
> 2co_8_gpaw.out: Process memory now: 2222.76 MiB
> 2co_8_gpaw.out- Calculator: 273.58 MiB
> --
> 2co_9_gpaw.out: Process memory now: 2495.62 MiB
> 2co_9_gpaw.out- Calculator: 273.46 MiB
> --
> 2co_10_gpaw.out: Process memory now: 2769.93 MiB
> 2co_10_gpaw.out- Calculator: 273.43 MiB
> --
> 2co_11_gpaw.out: Process memory now: 3049.25 MiB
> 2co_11_gpaw.out- Calculator: 273.42 MiB
> --
> 2co_12_gpaw.out: Process memory now: 3323.22 MiB
> 2co_12_gpaw.out- Calculator: 273.51 MiB
> --
> 2co_13_gpaw.out: Process memory now: 3599.27 MiB
> 2co_13_gpaw.out- Calculator: 273.43 MiB
> --
> 2co_14_gpaw.out: Process memory now: 3876.67 MiB
> 2co_14_gpaw.out- Calculator: 273.38 MiB
> --
> 2co_15_gpaw.out: Process memory now: 4150.99 MiB
> 2co_15_gpaw.out- Calculator: 281.86 MiB
> --
> 2co_16_gpaw.out: Process memory now: 4434.88 MiB
> 2co_16_gpaw.out- Calculator: 281.85 MiB
> --
> 2co_18_gpaw.out: Process memory now: 5011.75 MiB
> 2co_18_gpaw.out- Calculator: 281.85 MiB
> --
> 2co_17_gpaw.out: Process memory now: 4722.66 MiB
> 2co_17_gpaw.out- Calculator: 281.84 MiB
>
> For 1.4.0, it is:
>
>
> b-an01 [~/pfs/co2rr/2018/180815/1.4.0]$ grep -r --include='*out' -i
> 'process memory' -A 1 $(ls -tr *)
> 2co_0_gpaw.out: Process memory now: 94.30 MiB
> 2co_0_gpaw.out- Calculator: 183.75 MiB
> --
> 2co_1_gpaw.out: Process memory now: 415.34 MiB
> 2co_1_gpaw.out- Calculator: 183.75 MiB
> --
> 2co_2_gpaw.out: Process memory now: 675.71 MiB
> 2co_2_gpaw.out- Calculator: 194.96 MiB
> --
> 2co_3_gpaw.out: Process memory now: 954.99 MiB
> 2co_3_gpaw.out- Calculator: 194.95 MiB
> --
> 2co_4_gpaw.out: Process memory now: 1222.41 MiB
> 2co_4_gpaw.out- Calculator: 194.96 MiB
> --
> 2co_5_gpaw.out: Process memory now: 1493.82 MiB
> 2co_5_gpaw.out- Calculator: 194.96 MiB
> --
> 2co_6_gpaw.out: Process memory now: 1760.62 MiB
> 2co_6_gpaw.out- Calculator: 183.75 MiB
> --
> 2co_7_gpaw.out: Process memory now: 2018.56 MiB
> 2co_7_gpaw.out- Calculator: 183.75 MiB
> --
> 2co_8_gpaw.out: Process memory now: 2280.84 MiB
> 2co_8_gpaw.out- Calculator: 194.83 MiB
> --
> 2co_9_gpaw.out: Process memory now: 2553.50 MiB
> 2co_9_gpaw.out- Calculator: 194.71 MiB
> --
> 2co_10_gpaw.out: Process memory now: 2827.13 MiB
> 2co_10_gpaw.out- Calculator: 194.69 MiB
> --
> 2co_11_gpaw.out: Process memory now: 3105.79 MiB
> 2co_11_gpaw.out- Calculator: 194.68 MiB
> --
> 2co_12_gpaw.out: Process memory now: 3385.24 MiB
> 2co_12_gpaw.out- Calculator: 194.76 MiB
> --
> 2co_13_gpaw.out: Process memory now: 3664.50 MiB
> 2co_13_gpaw.out- Calculator: 194.69 MiB
> --
> 2co_14_gpaw.out: Process memory now: 3937.29 MiB
> 2co_14_gpaw.out- Calculator: 194.64 MiB
> --
> 2co_15_gpaw.out: Process memory now: 4212.07 MiB
> 2co_15_gpaw.out- Calculator: 200.50 MiB
> --
> 2co_16_gpaw.out: Process memory now: 4498.34 MiB
> 2co_16_gpaw.out- Calculator: 200.49 MiB
> --
> 2co_17_gpaw.out: Process memory now: 4786.58 MiB
> 2co_17_gpaw.out- Calculator: 200.48 MiB
> --
> 2co_18_gpaw.out: Process memory now: 5068.21 MiB
> 2co_18_gpaw.out- Calculator: 200.49 MiB
> --
> 2co_19_gpaw.out: Process memory now: 5344.71 MiB
> 2co_19_gpaw.out- Calculator: 200.49 MiB
> --
> 2co_20_gpaw.out: Process memory now: 5614.39 MiB
> 2co_20_gpaw.out- Calculator: 200.49 MiB
>
> The calculation crashes when the memory use grows to the maximum in
> both cases.
>
>
> Could I avoid this by reading in one image into "slab" each time in
> the loop instead? Thanks.
>
>
> Best wishes,
> Chang Liu
> ----------------------------------------------------------
> Chang Liu
> PhD student
> Fysikum, Albanova, Stockholm University
> S-106 91 Stockholm, Sweden
> +46 767159891
> http://xsolasgroup.fysik.su.se/
> ------------------------------------------------------------------------
> *From:* Ask Hjorth Larsen <asklarsen at gmail.com>
> *Sent:* Wednesday, August 15, 2018 10:45:10 PM
> *To:* Chang Liu
> *Cc:* gpaw-users at listserv.fysik.dtu.dk
> *Subject:* Re: [gpaw-users] Increase in process memory for single
> point calculations
> 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/
> >
> > _______________________________________________
> > gpaw-users mailing list
> > gpaw-users at listserv.fysik.dtu.dk
> > https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>
>
> _______________________________________________
> gpaw-users mailing list
> gpaw-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
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