 Re: NEB memory and parallel problems ( No.1 ) |
- Date: 2020/01/25 13:35
- Name: T. Ozaki
- Hi,
>1- The memory increases largely from 5GB in SCF to 70 GB in NEB calculation (with MD.NEB.Parallel.Number=2)
I could not reproduce your problem.
Could you share your input file with us?
>2- For MD.NEB.Parallel.Number=1, the outputs are doubled!
This is acctually a bug.
We are going to release a patch for that after other bugs will be fixed.
Regards,
TO
|
| Re: NEB memory and parallel problems ( No.2 ) |
- Date: 2020/01/26 15:48
- Name: Reza
- Hi Prof. Ozaki,
Thank you for your reply, and very thanks for your very good code.We hope that it will be better and better from day to day.We will use it in our future publications.
This is my input for testing NEB calculation. It is one of the methanol decomposition steps on Pt-doped CN:
========================================================================
#
# File Name
#
DATA.PATH /home/reza/openmx3.8/DFT_DATA13
System.CurrrentDirectory ./ # default=./
System.Name CNT_Pt_COH
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (1-3)
#
# Definition of Atomic Species
#
Species.Number 4
<Definition.of.Atomic.Species
O O6.0-s2p2d1 O_PBE13
C C6.0-s2p2d1 C_PBE13
H H6.0-s2p1 H_PBE13
Pt Pt7.0-s2p2d2f1 Pt_PBE13
Definition.of.Atomic.Species>
#
# Atoms
#
Atoms.Number 75
Atoms.UnitVectors.Unit AU
<Atoms.UnitVectors
37.713166660517643 -21.773706923443072 0.0000000000000000
0.0000000000000000 43.547413846886158 0.0000000000000000
0.0000000000000000 0.0000000000000000 24.257279375123979
Atoms.UnitVectors>
Atoms.SpeciesAndCoordinates.Unit FRAC
<Atoms.SpeciesAndCoordinates
1 H 0.76902000000000 0.79589000000000 0.44668000000000 0.5 0.5
2 C 0.50827000000000 0.59972000000000 0.04604000000000 2 2
3 C 0.56056000000000 0.59461000000000 0.21197000000000 2 2
4 C 0.56196000000000 0.59642000000000 0.32077000000000 2 2
5 C 0.38813000000000 0.52118000000000 0.04471000000000 2 2
6 C 0.50825000000000 0.59969000000000 0.15530000000000 2 2
7 C 0.44544000000000 0.57133000000000 0.21105000000000 2 2
8 C 0.44612000000000 0.57127000000000 0.32138000000000 2 2
9 C 0.33753000000000 0.40000000000000 0.04499000000000 2 2
10 C 0.38817000000000 0.52080000000000 0.15576000000000 2 2
11 C 0.34846000000000 0.45894000000000 0.21194000000000 2 2
12 C 0.34906000000000 0.45906000000000 0.32247000000000 2 2
13 C 0.41288000000000 0.35499000000000 0.04487000000000 2 2
14 C 0.33730000000000 0.39967000000000 0.15492000000000 2 2
15 C 0.36082000000000 0.36039000000000 0.21166000000000 2 2
16 C 0.36075000000000 0.36026000000000 0.32143000000000 2 2
17 C 0.53277000000000 0.43251000000000 0.04520000000000 2 2
18 C 0.41259000000000 0.35470000000000 0.15521000000000 2 2
19 C 0.47521000000000 0.38164000000000 0.21207000000000 2 2
20 C 0.47524000000000 0.38202000000000 0.32280000000000 2 2
21 C 0.58324000000000 0.55408000000000 0.04635000000000 2 2
22 C 0.53229000000000 0.43252000000000 0.15598000000000 2 2
23 C 0.57099000000000 0.49464000000000 0.21136000000000 2 2
24 C 0.57055000000000 0.49496000000000 0.32146000000000 2 2
25 C 0.58298000000000 0.55418000000000 0.15559000000000 2 2
26 C 0.50909000000000 0.60277000000000 0.37690000000000 2 2
27 C 0.56916000000000 0.60359000000000 0.66758000000000 2 2
28 C 0.38984000000000 0.52097000000000 0.37846000000000 2 2
29 C 0.51035000000000 0.61133000000000 0.48530000000000 2 2
30 C 0.44935000000000 0.57444000000000 0.54324000000000 2 2
31 C 0.44923000000000 0.57359000000000 0.65486000000000 2 2
32 C 0.33731000000000 0.39943000000000 0.37860000000000 2 2
33 C 0.39211000000000 0.52142000000000 0.48930000000000 2 2
34 C 0.35149000000000 0.45986000000000 0.54477000000000 2 2
35 C 0.35124000000000 0.46020000000000 0.65492000000000 2 2
36 C 0.41248000000000 0.35469000000000 0.37849000000000 2 2
37 C 0.33763000000000 0.39961000000000 0.48831000000000 2 2
38 C 0.36061000000000 0.36014000000000 0.54543000000000 2 2
39 C 0.36104000000000 0.36062000000000 0.65498000000000 2 2
40 C 0.53229000000000 0.43380000000000 0.37886000000000 2 2
41 C 0.41266000000000 0.35524000000000 0.48868000000000 2 2
42 C 0.47549000000000 0.38453000000000 0.54493000000000 2 2
43 C 0.47588000000000 0.38434000000000 0.65529000000000 2 2
44 C 0.58523000000000 0.55555000000000 0.37608000000000 2 2
45 C 0.53219000000000 0.43589000000000 0.48933000000000 2 2
46 C 0.57292000000000 0.49898000000000 0.54407000000000 2 2
47 C 0.57251000000000 0.49826000000000 0.65594000000000 2 2
48 C 0.59371000000000 0.55825000000000 0.48426000000000 2 2
49 C 0.51113000000000 0.60167000000000 0.71454000000000 2 2
50 C 0.56067000000000 0.59417000000000 0.88160000000000 2 2
51 C 0.56011000000000 0.59374000000000 0.99032000000000 2 2
52 C 0.39203000000000 0.52224000000000 0.71028000000000 2 2
53 C 0.50917000000000 0.59991000000000 0.82469000000000 2 2
54 C 0.44619000000000 0.57233000000000 0.87920000000000 2 2
55 C 0.44553000000000 0.57218000000000 0.98972000000000 2 2
56 C 0.33813000000000 0.40032000000000 0.71178000000000 2 2
57 C 0.39012000000000 0.52165000000000 0.82182000000000 2 2
58 C 0.34950000000000 0.45981000000000 0.87750000000000 2 2
59 C 0.34886000000000 0.45947000000000 0.98826000000000 2 2
60 C 0.41324000000000 0.35576000000000 0.71163000000000 2 2
61 C 0.33785000000000 0.40015000000000 0.82136000000000 2 2
62 C 0.36144000000000 0.36112000000000 0.87839000000000 2 2
63 C 0.36143000000000 0.36111000000000 0.98816000000000 2 2
64 C 0.53311000000000 0.43586000000000 0.71089000000000 2 2
65 C 0.41311000000000 0.35550000000000 0.82173000000000 2 2
66 C 0.47593000000000 0.38271000000000 0.87774000000000 2 2
67 C 0.47568000000000 0.38204000000000 0.98861000000000 2 2
68 C 0.58545000000000 0.55690000000000 0.71618000000000 2 2
69 C 0.53306000000000 0.43415000000000 0.82223000000000 2 2
70 C 0.57248000000000 0.49517000000000 0.87997000000000 2 2
71 C 0.57216000000000 0.49473000000000 0.99025000000000 2 2
72 C 0.58415000000000 0.55484000000000 0.82553000000000 2 2
73 C 0.69221000000000 0.71610000000000 0.49216000000000 2 2
74 O 0.75496000000000 0.76208000000000 0.50252000000000 3 3
75 Pt 0.60945000000000 0.64935000000000 0.53907000000000 8 8
Atoms.SpeciesAndCoordinates>
# SCF Convergence
#
scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW
scf.SpinPolarization on # On|Off
scf.ElectronicTemperature 1000.0 # default=300 (K)
scf.energycutoff 200.0 # default=150 (Ry)
scf.maxIter 400 # default=40
scf.EigenvalueSolver band # Recursion|Cluster|Band
scf.Kgrid 1 1 4
scf.Mixing.Type Rmm-Diis # Simple|Rmm-Diis|Gr-Pulay
scf.Init.Mixing.Weight 0.60 # default=0.30
scf.Min.Mixing.Weight 0.1 # default=0.001
scf.Max.Mixing.Weight 0.70 # default=0.40
scf.Mixing.History 15 # default=5
scf.Mixing.StartPulay 6 # default=6
scf.criterion 6.0e-6 # default=1.0e-6 (Hartree)
#
# MD or Geometry Optimization
#
MD.Type neb # Nomd|Opt|DIIS|NVE|NVT_VS|NVT_NH
MD.Opt.DIIS.History 10 # default=7
MD.Opt.StartDIIS 5 # default=5
MD.Opt.EveryDIIS 6 # default=10
MD.maxIter 400 # default=1
MD.Opt.criterion 1.0e-3
MD.NEB.Number.Images 10 # default=10
MD.NEB.Parallel.Number 2
<NEB.Atoms.SpeciesAndCoordinates
1 H 0.68710000000000 0.66671000000000 0.55789000000000 0.5 0.5
2 C 0.51016000000000 0.60107000000000 0.04251000000000 2 2
3 C 0.56162000000000 0.59429000000000 0.20828000000000 2 2
4 C 0.56310000000000 0.59631000000000 0.31688000000000 2 2
5 C 0.38999000000000 0.52340000000000 0.04094000000000 2 2
6 C 0.51011000000000 0.60098000000000 0.15172000000000 2 2
7 C 0.44723000000000 0.57375000000000 0.20717000000000 2 2
8 C 0.44739000000000 0.57322000000000 0.31712000000000 2 2
9 C 0.34092000000000 0.40235000000000 0.04066000000000 2 2
10 C 0.39003000000000 0.52295000000000 0.15142000000000 2 2
11 C 0.35162000000000 0.46097000000000 0.20787000000000 2 2
12 C 0.35133000000000 0.46096000000000 0.31839000000000 2 2
13 C 0.41323000000000 0.35384000000000 0.04096000000000 2 2
14 C 0.34053000000000 0.40198000000000 0.15093000000000 2 2
15 C 0.36245000000000 0.36168000000000 0.20735000000000 2 2
16 C 0.36206000000000 0.36159000000000 0.31740000000000 2 2
17 C 0.53327000000000 0.43088000000000 0.04144000000000 2 2
18 C 0.41277000000000 0.35353000000000 0.15107000000000 2 2
19 C 0.47538000000000 0.37958000000000 0.20834000000000 2 2
20 C 0.47517000000000 0.38007000000000 0.31850000000000 2 2
21 C 0.58279000000000 0.55251000000000 0.04257000000000 2 2
22 C 0.53253000000000 0.43089000000000 0.15196000000000 2 2
23 C 0.57048000000000 0.49320000000000 0.20764000000000 2 2
24 C 0.56975000000000 0.49346000000000 0.31789000000000 2 2
25 C 0.58260000000000 0.55263000000000 0.15202000000000 2 2
26 C 0.51026000000000 0.60325000000000 0.37257000000000 2 2
27 C 0.56851000000000 0.60204000000000 0.66716000000000 2 2
28 C 0.39096000000000 0.52320000000000 0.37465000000000 2 2
29 C 0.51063000000000 0.61062000000000 0.48018000000000 2 2
30 C 0.45062000000000 0.57666000000000 0.53946000000000 2 2
31 C 0.45082000000000 0.57628000000000 0.65113000000000 2 2
32 C 0.34012000000000 0.40183000000000 0.37437000000000 2 2
33 C 0.39314000000000 0.52372000000000 0.48508000000000 2 2
34 C 0.35481000000000 0.46203000000000 0.54121000000000 2 2
35 C 0.35426000000000 0.46244000000000 0.65121000000000 2 2
36 C 0.41241000000000 0.35414000000000 0.37452000000000 2 2
37 C 0.34074000000000 0.40202000000000 0.48459000000000 2 2
38 C 0.36210000000000 0.36141000000000 0.54116000000000 2 2
39 C 0.36238000000000 0.36186000000000 0.65106000000000 2 2
40 C 0.53216000000000 0.43213000000000 0.37502000000000 2 2
41 C 0.41256000000000 0.35408000000000 0.48450000000000 2 2
42 C 0.47550000000000 0.38202000000000 0.54122000000000 2 2
43 C 0.47575000000000 0.38211000000000 0.65101000000000 2 2
44 C 0.58441000000000 0.55388000000000 0.37295000000000 2 2
45 C 0.53208000000000 0.43381000000000 0.48526000000000 2 2
46 C 0.57230000000000 0.49683000000000 0.53979000000000 2 2
47 C 0.57193000000000 0.49639000000000 0.65155000000000 2 2
48 C 0.59226000000000 0.55633000000000 0.48120000000000 2 2
49 C 0.51309000000000 0.60446000000000 0.71146000000000 2 2
50 C 0.56101000000000 0.59340000000000 0.87775000000000 2 2
51 C 0.56054000000000 0.59280000000000 0.98688000000000 2 2
52 C 0.39396000000000 0.52492000000000 0.70679000000000 2 2
53 C 0.51114000000000 0.60206000000000 0.82176000000000 2 2
54 C 0.44793000000000 0.57527000000000 0.87600000000000 2 2
55 C 0.44745000000000 0.57479000000000 0.98609000000000 2 2
56 C 0.34132000000000 0.40286000000000 0.70757000000000 2 2
57 C 0.39214000000000 0.52424000000000 0.81808000000000 2 2
58 C 0.35242000000000 0.46199000000000 0.87349000000000 2 2
59 C 0.35229000000000 0.46148000000000 0.98399000000000 2 2
60 C 0.41300000000000 0.35461000000000 0.70778000000000 2 2
61 C 0.34115000000000 0.40263000000000 0.81755000000000 2 2
62 C 0.36331000000000 0.36265000000000 0.87410000000000 2 2
63 C 0.36341000000000 0.36253000000000 0.98427000000000 2 2
64 C 0.53295000000000 0.43434000000000 0.70686000000000 2 2
65 C 0.41326000000000 0.35441000000000 0.81759000000000 2 2
66 C 0.47625000000000 0.38069000000000 0.87395000000000 2 2
67 C 0.47613000000000 0.38008000000000 0.98440000000000 2 2
68 C 0.58496000000000 0.55543000000000 0.71147000000000 2 2
69 C 0.53304000000000 0.43277000000000 0.81818000000000 2 2
70 C 0.57208000000000 0.49382000000000 0.87601000000000 2 2
71 C 0.57188000000000 0.49337000000000 0.98641000000000 2 2
72 C 0.58324000000000 0.55342000000000 0.82176000000000 2 2
73 C 0.62849000000000 0.73834000000000 0.57530000000000 2 2
74 O 0.64061000000000 0.79067000000000 0.60307000000000 3 3
75 Pt 0.60912000000000 0.64707000000000 0.53433000000000 8 8
NEB.Atoms.SpeciesAndCoordinates>
==========================================================================
Please change "MD.NEB.Parallel.Number" and track the memory usage. I tested it for both 3.8 and 3.9 versions with intel-cluster-studio-2015 compiler (mpiicc+mkl+....).
very thanks,
Reza
 |
| Re: NEB memory and parallel problems ( No.3 ) |
- Date: 2020/01/27 01:40
- Name: T. Ozaki
- Hi,
This problem seems to happen in case of Atoms.SpeciesAndCoordinates.Unit = FRAC.
Could you try the following modified codes?
http://www.openmx-square.org/bugfixed/20Jan27/neb.c
http://www.openmx-square.org/bugfixed/20Jan27/neb_run.c
If your problem is resolved by the modification, I will release a patch.
Regards,
TO
|
| Re: NEB memory and parallel problems ( No.4 ) |
- Date: 2020/01/27 17:14
- Name: Reza
- Hi,
Recompilation with these files doesn't help. Memory usage is still too high.
Thanks.
|
| Re: NEB memory and parallel problems ( No.5 ) |
- Date: 2020/01/28 00:44
- Name: Reza
- Please check above comment by following input:
DATA.PATH /home/reza/openmx3.9/DFT_DATA19
System.CurrrentDirectory ./
System.Name TS_B_1
level.of.stdout 1
level.of.fileout 0
Atoms.Number 78
Atoms.SpeciesAndCoordinates.Unit FRAC
Atoms.UnitVectors.Unit Ang
Species.Number 4
<Definition.of.Atomic.Species
H H6.0-s2p2 H_PBE19
B B7.0-s2p2 B_PBE19
C C6.0-s2p2 C_PBE19
O O6.0-s2p2 O_PBE19
Definition.of.Atomic.Species>
<Atoms.UnitVectors
19.95696653 -11.52216000 0.00000000
0.00000000 23.04432000 0.00000000
0.00000000 0.00000000 12.83645000
Atoms.UnitVectors>
<Atoms.SpeciesAndCoordinates
1 H 0.6536092000000000 0.7411318000000000 0.6415650300000000 0.5 0.5
2 H 0.7112028600000000 0.7845552000000000 0.5355494300000000 0.5 0.5
3 H 0.6223204100000000 0.7477868200000000 0.5162517000000000 0.5 0.5
4 H 0.6911769700000000 0.6743512100000000 0.5514726900000000 0.5 0.5
5 B 0.5802618400000000 0.6048457800000000 0.5404577900000000 1.5 1.5
6 C 0.5181076300000000 0.6027360500000000 0.0434990100000000 2.0 2.0
7 C 0.5649783400000000 0.5891183600000000 0.2094889800000000 2.0 2.0
8 C 0.5660868200000000 0.5902694500000000 0.3181558000000000 2.0 2.0
9 C 0.3960371900000000 0.5404298500000000 0.0426114800000000 2.0 2.0
10 C 0.5181057900000000 0.6026871200000000 0.1531895200000000 2.0 2.0
11 C 0.4568212200000000 0.5839869800000000 0.2087393300000000 2.0 2.0
12 C 0.4573034300000000 0.5838991600000000 0.3192211400000000 2.0 2.0
13 C 0.3329442200000000 0.4189289100000000 0.0423800600000000 2.0 2.0
14 C 0.3960849500000000 0.5400241500000000 0.1531471800000000 2.0 2.0
15 C 0.3499672300000000 0.4798560400000000 0.2095870800000000 2.0 2.0
16 C 0.3503705300000000 0.4799004200000000 0.3195421600000000 2.0 2.0
17 C 0.3961792100000000 0.3603897200000000 0.0420040500000000 2.0 2.0
18 C 0.3326585000000000 0.4186123900000000 0.1523122000000000 2.0 2.0
19 C 0.3499943000000000 0.3746124200000000 0.2088110900000000 2.0 2.0
20 C 0.3497955500000000 0.3743974200000000 0.3190506700000000 2.0 2.0
21 C 0.5178596100000000 0.4220914500000000 0.0425571500000000 2.0 2.0
22 C 0.3958935900000000 0.3600938000000000 0.1526394000000000 2.0 2.0
23 C 0.4568403800000000 0.3775669100000000 0.2092265600000000 2.0 2.0
24 C 0.4569142400000000 0.3779756000000000 0.3198507300000000 2.0 2.0
25 C 0.5811267900000000 0.5439091100000000 0.0436963200000000 2.0 2.0
26 C 0.5174922700000000 0.4221615600000000 0.1531130800000000 2.0 2.0
27 C 0.5627901199999999 0.4824970700000000 0.2089494500000000 2.0 2.0
28 C 0.5626295500000000 0.4830486500000000 0.3189508200000000 2.0 2.0
29 C 0.5810696400000001 0.5439400200000000 0.1530153200000000 2.0 2.0
30 C 0.5190575400000000 0.6045925400000000 0.3746516700000000 2.0 2.0
31 C 0.5694735200000000 0.5937887800000000 0.6596576700000000 2.0 2.0
32 C 0.3971292900000000 0.5401278000000000 0.3759996500000000 2.0 2.0
33 C 0.5211224500000000 0.6089216700000000 0.4836914600000000 2.0 2.0
34 C 0.4597477600000000 0.5853183100000000 0.5408925100000000 2.0 2.0
35 C 0.4597522200000000 0.5857242499999999 0.6527723400000000 2.0 2.0
36 C 0.3327142800000000 0.4185530300000000 0.3759660200000000 2.0 2.0
37 C 0.3983849900000000 0.5402380800000000 0.4864763000000000 2.0 2.0
38 C 0.3517994000000000 0.4803595600000000 0.5425898000000000 2.0 2.0
39 C 0.3520744300000000 0.4807822600000000 0.6522619100000000 2.0 2.0
40 C 0.3957756200000000 0.3600997100000000 0.3756285700000000 2.0 2.0
41 C 0.3329146600000000 0.4186238300000000 0.4858092100000000 2.0 2.0
42 C 0.3497981800000000 0.3744159300000000 0.5423674200000000 2.0 2.0
43 C 0.3502111300000000 0.3748351700000000 0.6524557700000000 2.0 2.0
44 C 0.5175255000000000 0.4232581200000000 0.3759756900000000 2.0 2.0
45 C 0.3958781900000000 0.3603328400000000 0.4861251700000000 2.0 2.0
46 C 0.4573621100000000 0.3795255900000000 0.5422352300000000 2.0 2.0
47 C 0.4577970600000000 0.3798432700000000 0.6525773900000000 2.0 2.0
48 C 0.5828827000000000 0.5449098999999999 0.3747636900000000 2.0 2.0
49 C 0.5177064600000000 0.4246287100000000 0.4864804100000000 2.0 2.0
50 C 0.5638956300000000 0.4856312500000000 0.5411331900000000 2.0 2.0
51 C 0.5643094200000000 0.4856673800000000 0.6525064500000000 2.0 2.0
52 C 0.5871497000000000 0.5471554100000000 0.4835181700000000 2.0 2.0
53 C 0.5210086800000000 0.6047921200000000 0.7120504200000000 2.0 2.0
54 C 0.5646362500000000 0.5887250500000000 0.8784348400000001 2.0 2.0
55 C 0.5643051300000000 0.5884172300000000 0.9879094899999999 2.0 2.0
56 C 0.3991710400000000 0.5411971900000000 0.7081760000000000 2.0 2.0
57 C 0.5188621000000000 0.6031910100000000 0.8224080400000000 2.0 2.0
58 C 0.4574798100000000 0.5850004400000000 0.8769422700000000 2.0 2.0
59 C 0.4569440700000000 0.5846437600000000 0.9874795300000000 2.0 2.0
60 C 0.3336123500000000 0.4193741300000000 0.7090789800000000 2.0 2.0
61 C 0.3976918500000000 0.5407787700000000 0.8193852700000001 2.0 2.0
62 C 0.3510053200000000 0.4806748500000000 0.8753981199999999 2.0 2.0
63 C 0.3504859700000000 0.4803419300000000 0.9855966800000000 2.0 2.0
64 C 0.3966287500000000 0.3611385200000000 0.7087245900000000 2.0 2.0
65 C 0.3333639800000000 0.4191687000000000 0.8188176700000001 2.0 2.0
66 C 0.3506546500000000 0.3752966800000000 0.8753806700000000 2.0 2.0
67 C 0.3505368400000000 0.3751434300000000 0.9857463900000000 2.0 2.0
68 C 0.5186224300000000 0.4253619300000000 0.7081936500000000 2.0 2.0
69 C 0.3964869800000000 0.3609141100000000 0.8191621600000000 2.0 2.0
70 C 0.4576909000000000 0.3786915800000000 0.8750814600000000 2.0 2.0
71 C 0.4573574600000000 0.3780869300000000 0.9859146500000000 2.0 2.0
72 C 0.5832204300000000 0.5469897700000000 0.7123175500000000 2.0 2.0
73 C 0.5182925500000000 0.4238759800000000 0.8193679400000000 2.0 2.0
74 C 0.5638972600000000 0.4832129700000000 0.8771483900000000 2.0 2.0
75 C 0.5635225400000000 0.4826737800000000 0.9871958800000000 2.0 2.0
76 C 0.5818054000000000 0.5447977500000000 0.8222293600000000 2.0 2.0
77 C 0.6615561599999999 0.7432396500000000 0.5570267000000000 2.0 2.0
78 O 0.6561783300000000 0.6803742699999999 0.5190536300000000 3.0 3.0
Atoms.SpeciesAndCoordinates>
######## SCF Parameters #############
scf.stress.tensor on
#scf.restart on
scf.XcType GGA-PBE
scf.SpinPolarization on
scf.ElectronicTemperature 500.0
scf.energycutoff 300.0
#scf.Ngrid 32 32 32
scf.maxIter 1000
scf.EigenvalueSolver band
scf.Kgrid 1 1 4
scf.Mixing.Type rmm-diisk
scf.Init.Mixing.Weight 0.20
scf.Min.Mixing.Weight 0.001
scf.Max.Mixing.Weight 0.400
scf.Mixing.History 50
scf.Mixing.EveryPulay 1
scf.Mixing.StartPulay 15
#scf.Kerker.factor xxx
scf.criterion 1.0e-6
######## MD or Geometry Optimization #############
scf.ExtCharge.History 2
MD.Type NEB
MD.Opt.Init.Hessian Schlegel
MD.Opt.DIIS.History 3
MD.Opt.StartDIIS 10
MD.Opt.EveryDIIS 500
MD.maxIter 400
MD.Opt.criterion 1.0e-3
MD.NEB.Number.Images 10
MD.NEB.Parallel.Number 2
<NEB.Atoms.SpeciesAndCoordinates
1 H 0.5704895200000000 0.7190122700000000 0.5750021300000000 0.5 0.5
2 H 0.6089581800000000 0.7277609200000000 0.4517951400000000 0.5 0.5
3 H 0.5258234400000000 0.7157571300000000 0.4589858900000000 0.5 0.5
4 H 0.6905073100000000 0.6542238600000000 0.5420370900000000 0.5 0.5
5 B 0.5889612400000001 0.6062309100000000 0.5441090600000000 1.5 1.5
6 C 0.5207594300000000 0.6013837200000000 0.0463368400000000 2.0 2.0
7 C 0.5643937100000000 0.5842600100000001 0.2124458100000000 2.0 2.0
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NEB.Atoms.SpeciesAndCoordinates>
|
| Re: NEB memory and parallel problems ( No.6 ) |
- Date: 2020/01/29 01:49
- Name: T. Ozaki
- Hi,
I tested your input file using 112 MPI processes which were assigned by 28 processes/node times 4 nodes,
and monitored the memory usage by top command, resulting in the following required memory size per node.
MD.NEB.Parallel.Number Memory (GB/node)
0 81.0 (estimated, since the code encountered segmentation fault due to memory shortage)
1 19.4
2 26.8
3 35.1
4 42.5
5 48.0
Please note that the required memory size increases after the first MD step corresponding to the calculations
of terminal structures, and keeps almost constant during the proceeding MD steps. Thus, I took the values above
during the SCF calculation in the 2nd MD step.
As expected ( http://www.openmx-square.org/openmx_man3.9/node161.html ),
the required memory size is the lowest in case of MD.NEB.Parallel.Number=1,
and the memory size increases gradually with the increase of MD.NEB.Parallel.Number.
This is the intended behavior of OpenMX indeed.
Even at MD.NEB.Parallel.Number=2, no erratic behavior was observed.
How did you get the memory size, 5 GB?
>The memory increases largely from 5GB in SCF to 70 GB in NEB calculation (with MD.NEB.Parallel.Number=2)
My calculations suggest that the memory size of 5 GB you showed us is unlikely for the calculation.
Please check carefully the required memory size depending on MD.NEB.Parallel.Number.
Regards,
TO
|
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NEB memory and parallel problems