Memory allocation and optimal input settings when running calculations for large systems

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Memory allocation and optimal input settings when running calculations for large systems

Date: 2024/10/29 08:14
Name: Beniam: Dear OpenMX Developers,
I am trying to run an NVT-NH MD on an MoS2/H2O system consisting of 900 atoms. Currently, I can complete 34 MD steps in 04:28:56 (hr:min:sec) but the calculation is failing with the following error:

[c314-144:3523221:0:3523221] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x800000034)

I suspect that this is due to a lack of memory, but I am already requesting a large amount of nodes and cores. How can I select the optimal amount of nodes to perform this calculation? It is hard to do scaling tests as many nodes/cores are needed to get the calculation started (studying a large system). Secondly, are there any optimizations I can make to the input settings to make the calculation run faster (for example, I am running DC-LNO diagonalization, 1x1x1 kgrid, etc.)? Based on experience, is the md steps completed / time slow for such a system running on a HPC cluster?
Please let me know if I can provide any more information (such as cluster specific data, input and output files - don't know how to attach to this message) to solve this problem.

Thank you for your help!

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Re: Memory allocation and optimal input settings when running calculations for large systems ( No.1 )

Date: 2024/10/29 23:42
Name: Beniam

I am attaching the relevant input parameters here:

scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization Off # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 300.0 # default=150 (Ry)
scf.maxIter 100 # default=40
scf.EigenvalueSolver dc-lno # DC|GDC|Cluster|Band
scf.Kgrid 1 1 1
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.10 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.400 # default=0.40
scf.Mixing.History 30 # default=5
scf.Mixing.StartPulay 10 # default=6
scf.criterion 1.0e-6 # default=1.0e-6 (Hartree)

# SCF Order-N
orderN.HoppingRanges 7.0 # default = 7.0 (Ang.)
scf.dclno.threading on # Enable multi-threading for diagonalization
#orderN.LNO.buffer 0.2 # default = 0.3
scf.system.charge 0.0
scf.coulomb.cutoff off

# 4. MD - - - - - - - - - - - - - - -
MD.Type NVT_NH # Nomd|Opt|NVE|NVT_VS|NVT_NH
MD.maxIter 700 # default=1
MD.TimeStep 0.5 # default=0.5 (fs)
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (Hartree/bohr)
MD.Opt.DIIS_Mixing 0.5 # default=0.5
<MD.TempControl
8
1 1000.0
100 900.0
200 800.0
300 700.0
400 600.0
500 500.0
600 400.0
700 300.0
MD.TempControl>

NH.Mass.HeatBath 30.0 # default = 20.0

scf.dftD on # on|off, default=off
version.dftD 3 # 2|3, default=2
DFTD3.damp bj # zero|bj, default=bj
DFTD.Unit AU # Ang|AU
DFTD.rcut_dftD 100.0 # default=100 (DFTD.Unit)
DFTD.cncut_dftD 40 # default=40 (DFTD.Unit)
DFTD.IntDirection 1 1 1 # default=1 1 1 (1:on 0:off)

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