[DFTB-Plus-User] Extremely slow MD
Abdullah Bin Faheem
abdullahbinfaheem at hotmail.com
Wed Apr 28 18:45:00 CEST 2021
Dear Bálint,
After compiling DFTB 20.2 and comparing the time taken for MD with the precompiled version using a box of water molecules and running the tests available in the source code, I confirmed that it is not a compilation problem. I also tried using a lower number threads (or MPI processes), but the system consisting of CaF2, graphene, and water takes too much time (a day for a few md steps). Is there perhaps something wrong with the input file? Any idea on how long a single md step should take (for 882 atoms, 3344 electrons), would be highly appreciated.
Thank you for your time.
Best Regard,
Abdullah
________________________________
From: DFTB-Plus-User <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de> on behalf of Bálint Aradi <aradi at uni-bremen.de>
Sent: Saturday, April 24, 2021 3:05 AM
To: dftb-plus-user at mailman.zfn.uni-bremen.de <dftb-plus-user at mailman.zfn.uni-bremen.de>
Subject: Re: [DFTB-Plus-User] Extremely slow MD
Dear Abdullah,
Even with the precompiled binary, check for the scaling. Your system is
of a moderate size, so 30 threads (or 30 MPI-processes with your
compilation) may be beyond the optimal scaling point. Start with a low
number and increase the nr. of threads / nr. of MPI-processes as long as
you experience wall-clock time benefits.
Best regards,
Bálint
On 23.04.21 19:54, Abdullah Bin Faheem wrote:
> Dear Bálint,
>
> Thank you for your response. I think it might be a compilation problem.
> I will look into it. I used MPI (OMP_NUM_THREADS=1 miprun -np 30) as I
> believed it would give better performance. This is because I observed
> that when I compiled without MPI, and set the OMP_NUM_THREADS
> environment variable to say 20, only 8 threads would actually be used.
>
> By slow, I meant taking one day just for 10-15 MD steps. I don't think
> it's a ram issue as 120GB of ram was available.
>
> As per your suggestion, I also downloaded the precompiled executables of
> dftb+ 20.2.1 and 19.1 from the website compared them to the performance
> of dftb+ 19.1 (it was compiled with MPI) compiled on my machine. I used
> OpenMP for this purpose (OMP_NUM_THREADS=30 for all three) and used a
> simple simulation box of water molecules (792 atoms) and found that a
> single MD step takes more than 10 times longer when using the dftb+
> compiled on my machine. For example, the precompiled executables take 18
> to 20 seconds, while the one on my machine takes 300 seconds.
>
> Best regards,
> Abdullah
>
> ------------------------------------------------------------------------
> *From:* DFTB-Plus-User
> <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de> on behalf of Bálint
> Aradi <aradi at uni-bremen.de>
> *Sent:* Friday, April 23, 2021 6:54 PM
> *To:* dftb-plus-user at mailman.zfn.uni-bremen.de
> <dftb-plus-user at mailman.zfn.uni-bremen.de>
> *Subject:* Re: [DFTB-Plus-User] Extremely slow MD
> Dear Abdullah,
>
> first of all, please use the most recent version. Download the binary
> directly from the website or install it via conda, to make sure, it is
> not a compilation problem.
>
> Otherwise, is hard to say. What do you mean by slow. Also, do you use
> parallelism? If yes, which one (OpenMP or MPI)? Does your machine has
> enough RAM? (Maybe the process is swapping?)
>
> Best regards,
>
> Bálint
>
> On 20.04.21 17:11, Abdullah Bin Faheem wrote:
>> Dear DFTB+ users,
>>
>> I am using DFTB+ 19.1 to run MD of a box of water molecules, with
>> graphene and CaF2 layers (882 atoms) and using the 3ob parameters for
>> DFTB3. However, it takes a very long time to finish even one MD step. I
>> have tried to use different Solvers (ELPA, NTPoly, OMM), but it does not
>> make a difference. I am using the MPI version of DFTB+ and have tried
>> out using 6, 12, 15, and 30 mpi processes, but it does not improve the
>> results. Changing the Mixer from Broyden to Anderson gives the same time
>> results.
>>
>> The input file is as follows:
>>
>> Geometry = GenFormat {
>> 882 S
>> Ca F C O H
>> 1 1 0.7202443272E-01 0.7032980539E+01 0.4107560989E+01
>> 2 1 0.4004118083E+01 0.6999144781E+01 0.4161273297E+01
>> 3 1 0.7890550957E+01 0.7070604493E+01 0.4106813778E+01
>> 4 1 0.1168937823E+02 0.7005426600E+01 0.4039285473E+01
>> 5 1 0.9944288762E-01 0.2736434439E-01 0.4168457924E+01
>> .
>> .
>> .
>> 877 4 0.1421618759E+02 0.6309258063E+01 0.3225699778E+02
>> 878 5 0.1353106869E+02 0.6940379596E+01 0.3241309410E+02
>> 879 5 0.1509388546E+02 0.6646394136E+01 0.3226620183E+02
>> 880 4 0.7717108287E+00 0.7430108512E+01 0.4311866219E+02
>> 881 5 0.1500101168E+01 0.6928998668E+01 0.4275502506E+02
>> 882 5 0.4968721117E+00 0.7268172745E+01 0.4401107775E+02
>> 0.0000 0.0000 0.0000
>> 16.500 0.0000 0.0000
>> 0.0000 14.900 0.0000
>> 0.0000 0.0000 69.000
>> }
>> Driver = VelocityVerlet {
>> MovedAtoms = 1:-1
>> Steps = 1
>> TimeStep [Femtosecond] = 0.5
>> MDRestartFrequency = 1
>> Thermostat = NoseHoover {
>> Temperature [Kelvin] = 298.00
>> CouplingStrength [cm^-1] = 3200
>> }
>> OutputPrefix = "geo_end"
>> }
>>
>> Hamiltonian = DFTB {
>> Solver = ELPA {
>> Mode = 2
>> }
>> Mixer = Anderson {
>> MixingParameter = 0.2
>> }
>> SCCTolerance = 1.000E-004
>> ForceEvaluation = Dynamics
>> SCC = Yes
>> SlaterKosterFiles = Type2FileNames {
>> Separator = "-"
>> Suffix = ".skf"
>> }
>> Filling = Fermi {
>> Temperature [Kelvin] = 298
>> }
>> MaxSCCIterations = 300
>> ReadInitialCharges = No
>> MaxAngularMomentum {
>> O = "p"
>> H = "s"
>> C = "p"
>> F = "p"
>> Ca = "p"
>> }
>> ThirdOrder = Yes
>> HubbardDerivs {
>> O = -0.1575
>> H = -0.1857
>> C = -0.1492
>> F = -0.1623
>> Ca = -0.0340
>> }
>> Dispersion = DftD3 {
>> Damping = BeckeJohnson {
>> a1 = 0.746
>> a2 = 4.191
>> }
>> s6 = 1.0
>> s8 = 3.209
>> }
>> HCorrection = Damping {
>> Exponent = 4.00
>> }
>> KPointsAndWeights = {
>> 1 0 0
>> 0 1 0
>> 0 0 1
>> 0.5 0.5 0.5
>> }
>> }
>> Options {
>> WriteAutotestTag = Yes
>> WriteChargesAsText = Yes
>> }
>> Parallel {
>> UseOmpThreads = no
>> Groups = 3
>> }
>>
>> Is there perhaps something wrong with my approach? Any suggestions would
>> be greatly appreciated. Thank you for your time.
>>
>> Regards,
>> Abdullah
>>
>> _______________________________________________
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>>
>
>
> --
> Dr. Bálint Aradi
> Bremen Center for Computational Materials Science, University of Bremen
> http://www.bccms.uni-bremen.de/cms/people/b-aradi/
> <http://www.bccms.uni-bremen.de/cms/people/b-aradi/>
>
>
>
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>
--
Dr. Bálint Aradi
Bremen Center for Computational Materials Science, University of Bremen
http://www.bccms.uni-bremen.de/cms/people/b-aradi/
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