[DFTB-Plus-User] mpiprocs and ompthreads setting

[jsxz]

Hi Ben,


Thanks a lot for your reply.
I still have following questions. Can you please help me?
1. May I ask whether the precompilied executables dftb+ can run the larger system? What is difference bewteen the precompiled executables dftb+ and compiled dftb+ by source code? I try to compiled the source code, but found the compilation is very complex and can not be successfuly compiled.


2. Are there some specific example about Excitedstate calcution ? There is liittle information in the manual. Although there are some example in the website: https://github.com/dftbplus/dftbplus/tree/master/test/prog/dftb%2B/timedep, they are only scripts and geometrys. May I ask how to get the spectrum from the calcution results?


3. How to run the calculation of ExcitedState in the periodic boundary conditions?   I try to implement the excitedState calcution under the periodic boundary conditions, but can not run.                                                                          


4. StateOfInterest  Specifies the target excited state or states that should be calculated. 
I want to investigate the electronic excitation under external stimuli and I do not care about the state of interest, only care about number of electrons excited. May I ask how to set the parameter of Stateofinterest? Does this parameter setting depend on the number of atoms in system?


5. OscillatorWindow [Dipole moment] Screening cut-off below which single particle transitions are neglected in excitation spectra calculations. This selects from states above the top of the EnergyWindow(if present). Does this parameter setting depend on the number of atoms in system?


Thank you for your time.


Best Regards,
Chao




At 2020-06-22 19:38:10, "Ben Hourahine" <benjamin.hourahine at strath.ac.uk> wrote:

Hello Zhang,

yes, both of these can change calculation speed (both wall clock and also cpu time used). Have a look at


https://dftbplus-recipes.readthedocs.io/en/stable/parallel/index.html

for some discussion about openMP (most of the theory is relevant for MPI parallel as well)

OMP_NUM_THREADS is the shell variable for setting number of threads, while ompthreads is an instruction to the queueing system to set that variable as well as  management tasks over job scheduling. There are some more pbs examples at


https://www2.cisl.ucar.edu/resources/computational-systems/cheyenne/running-jobs/pbs-pro-job-script-examples


including a pure openMP parallel calculation. Depending on how you have compiled DFTB+, it may be parallelised with openMP, MPI or both. Generally, mixed openMP and MPI does not give good performance.

For 3x10^4 atoms you may get some memory limitations, as that will require ~1Tb of memory if you use an eigensolver. If your system is suitable you might want to explore using one of the alternative solvers from ELSI (these are only available for MPI parallel code and need to be enabled at compile time).

Regards

Ben





On 19/06/2020 13:53, jsxz wrote:

Hi All,


May I ask how to set the mpipros and ompthreads in the submission script? Do these two parameters affect the calculation speed?
Is the ompthreads the same as OMP_NUM_THREADS?
My system is about 30000 atoms.  I plan to calculate the molecular dynamics. The simulation time is aout 10 ps. 
The documentation below is my submission script. The select is the number of nodes. The number of CPU per node is 24.


#!/bin/bash
#PBS -N dftb
#PBS -q normal
#PBS -P 13101xxx
#PBS -l select=30:ncpus=24:mpiprocs=12:ompthreads=24:mem=96gb

#PBS -l walltime=24:00:00
#PBS -j oe


module load composerxe/2016.1.150
module load intelmpi
cd "$PBS_O_WORKDIR"
export OMP_NUM_THREADS=12

/home/users/xz/software/DFTB/18.2/bin/dftb+ <  dftb_in.hsd > out


Thanks a lot.


Best Regards,
Chao Zhang




 



_______________________________________________
DFTB-Plus-User mailing list
DFTB-Plus-User at mailman.zfn.uni-bremen.dehttps://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.zfn.uni-bremen.de%2Fcgi-bin%2Fmailman%2Flistinfo%2Fdftb-plus-user&data=02%7C01%7Cbenjamin.hourahine%40strath.ac.uk%7C4ba8cf7c18584f7e39d308d8145462e4%7C631e0763153347eba5cd0457bee5944e%7C0%7C0%7C637281700548282867&sdata=uOmltkQ7UwTbGCYNaI0SwneGDi6Wch8c2TlYBQSdrxc%3D&reserved=0
-- 
        Dr.  B.  Hourahine,  Senior  lecturer
            SUPA, Department  of  Physics,
             University  of  Strathclyde,
              John  Anderson  Building,
          107 Rottenrow, Glasgow G4 0NG, UK.                    
  +44 141 548 2325, benjamin.hourahine at strath.ac.uk

The  Department is  a partner  in SUPA,  the Scottish
            Universities Physics Alliance

The University  of Strathclyde  is a  charitable body,
       registered in Scotland, number SC015263
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.zfn.uni-bremen.de/pipermail/dftb-plus-user/attachments/20200623/f673bf51/attachment.htm>