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README.md

Dynamite

Dynamite provides a simple interface to fast evolution of quantum dynamics and eigensolving. Behind the scenes, dynamite uses the PETSc/SLEPc implementations of Krylov subspace exponentiation and eigensolving.

Setting up Dynamite on the FASRC Cannon Cluster

Below steps outline how to setup Dynamite on the Cannon cluster in your environment.

(1) Load the required software modules

module load python/3.8.5-fasrc01
module load gcc/10.2.0-fasrc01   
module load openmpi/4.1.1-fasrc01

(2) Download dynamite and pull the development branch

mkdir ~/sw
cd sw/
git clone https://github.com/GregDMeyer/dynamite.git
cd dynamite/
git pull origin dev

(3) Download and install PETSc

cd ~/sw
git clone https://gitlab.com/petsc/petsc.git petsc
cd petsc
git checkout tags/v3.15.0

Note: You will need to modify the script ~/sw/dynamite/petsc_config/complex-opt.py to add the configure option --with-64-bit-indices=1. This is required, if PETSc is intended to be used for very large matrices. Then, you need to configure PETSc with the below commands:

cd ~/sw/petsc
python ../dynamite/petsc_config/complex-opt.py

If all goes well, configure will tell you to run a make command. Copy the command and run it. It should look like:

make PETSC_DIR=<your_petsc_directory> PETSC_ARCH=complex-opt all

(4) Download and install SLEPc

cd ~/sw
export PETSC_DIR=<your_petsc_directory> PETSC_ARCH=complex-opt
git clone https://gitlab.com/slepc/slepc.git slepc
cd slepc
git checkout tags/v3.15.0
./configure

If it configures correctly, it will output a make command to run. Copy and paste that, and run it. It should look like:

make SLEPC_DIR=$PWD PETSC_DIR=<petsc_dir> PETSC_ARCH=complex-opt

(5) Building Dynamite

Dynamite is best installed in a conda environment. After you create your environment, you will need to activate it, e.g.:

conda create -n dynamite python=3.8 pip wheel cython
source activate dynamite

You will need to make sure that these environmental variables are all set correctly:

export PETSC_DIR=<petsc_dir> 
export PETSC_ARCH=complex-opt
export SLEPC_DIR=<your_slepc_installation_directory>

Next, install the required Python packages from requirements.txt. Please, notice that here we use the instance from the release dynamite version.

cd ~/sw/dynamite
# Get the requirements.txt from the release version
wget https://raw.githubusercontent.com/GregDMeyer/dynamite/master/requirements.txt
pip install -r requirements.txt

Then build dynamite:

cd ~/sw/dynamite
pip install -e ./

Example Python Script:

import argparse 
import numpy as np
from time import time
from scipy.special import comb
from mpi4py import MPI

from dynamite import config
from dynamite.subspaces import SpinConserve
#from dynamite.subspaces import *
from dynamite.operators import sigmax, sigmay, sigmaz, op_sum, index_product
from dynamite.msc_tools import *
from dynamite.tools import *


# Run the Heisenberg model on the Kagome lattice
# Requires the number of spins and the number of up spins

# Saves the eigenvector as a binary file
def main():
    parser = argparse.ArgumentParser(description="Run Heisenberg on the kagome lattice.")
    # Set the default for the dataset argument
    parser.add_argument('--N', dest='N', default="12", type=str)
    parser.add_argument('--num_up_spins', dest='U', default=6, type=int)
    parser.add_argument('--shell', default=False, action='store_true')
    parser.add_argument('--spinflip', default='None', type=str)
    parser.add_argument('--monitor', default=False, action='store_true')
    args = parser.parse_args()

    N = int(''.join(i for i in args.N if i.isdigit()))
    num_up = args.U

    # Load the edges and the ground state energy
    dir_path = "/n/home06/pkrastev/rc_team/tests/dynamite_test/kagome/"
    edges_file_path = dir_path + "data/edges%s.txt"%(args.N)
    #gs_file_path = dir_path + "data/gs%s.txt"%(args.N)

    edges = np.loadtxt(edges_file_path, dtype=int)
    #gs = np.loadtxt(gs_file_path, dtype=float)

    # Whether to print iteration info using the PETSc monitor
    if args.monitor:
        config.initialize(['-eps_monitor'])#, '-eps_view', '-log_view'])
    
    # Parse spinflip option
    spinflip = None
    if args.spinflip == "+" or args.spinflip == "-":
        spinflip = args.spinflip
    elif args.spinflip != "None":
        raise ValueError("spinflip is either + or -")
    # Create hamiltonian
    config.L = int(N)
    h = 1/4*op_sum(sigmax(i)*sigmax(j) + \
               sigmay(i)*sigmay(j) + \
               sigmaz(i)*sigmaz(j) for i, j in edges)

    # Whether to use shell mode
    h.shell = args.shell
    tic = time()
    subspace = SpinConserve(config.L, num_up, spinflip=spinflip)
    toc = time()
    comm = MPI.COMM_WORLD
    rank = comm.Get_rank()
    if rank == 0:
        print("Subspace (s): ", toc - tic, flush=True)

    h.subspace = subspace
    
    #before = get_cur_memory_usage()
    tic = time()
    #energies, eigvecs = h.eigsolve(getvecs=True)
    energies = h.eigsolve()
    toc = time()
    #after = get_cur_memory_usage()
    '''
    from petsc4py import PETSc
    
    # Save the eigenvector
    eigvec_file_path = dir_path + "heis_%s_vec.dat"%(args.N)
    w_viewer = PETSc.Viewer().createBinary(eigvec_file_path, 'w',
               comm=PETSc.COMM_WORLD)
    eigvecs[0].vec.view(w_viewer)

    # Check 
    r_viewer = PETSc.Viewer().createBinary(eigvec_file_path, 'r',
               comm=PETSc.COMM_WORLD)
    u = PETSc.Vec().load(r_viewer)
    assert eigvecs[0].vec.equal(u)
    '''
    if rank == 0:
        print("Eigsolve (s): ", toc - tic)
        print("lowest energy: %f" %(energies[0]))
        #print("expected energy: %f" %(gs))
        #print("relative error: %.2e" %(np.abs((energies[0] - gs)/gs)))
        #print('matrix memory usage: %f Mb' % ((after-before)/1E6))
  
if __name__ == "__main__":
    main()

Example Batch-Job Submission Script:

#!/bin/bash -l
#SBATCH -J N36_U18_n512_shell
#SBATCH -t 2-00:00
#SBATCH -o n512_shell.out
#SBATCH -e n512_shell.err
#SBATCH -p shared
#SBATCH -n 512
#SBATCH -N 64
#SBATCH --ntasks-per-node=8
#SBATCH --mem-per-cpu=8G
#SBATCH -x holy2a19307

# Set up environment
module load python/3.8.5-fasrc01 
module load gcc/10.2.0-fasrc01
module load openmpi/4.1.1-fasrc01
source activate dynamite
export PETSC_DIR=<PETSC_LOCATION>/petsc 
export PETSC_ARCH=complex-opt
export SLEPC_DIR=<SLEPC_LOCATION>/slepc

# Run program
time srun -n 512 --mpi=pmix  python run_heis_kagome_spinconserve.py --N 36 --num_up_spins 18 --shell --monitor

Example Output:

Subspace (s):  0.0006227493286132812
  1 EPS nconv=0 first unconverged value (error) -15.032+0i (6.15452408e-02)
  2 EPS nconv=0 first unconverged value (error) -15.5044+0i (3.26595719e-02)
  3 EPS nconv=0 first unconverged value (error) -15.6523+0i (1.95111880e-02)
  4 EPS nconv=0 first unconverged value (error) -15.7129+0i (1.32490815e-02)
  5 EPS nconv=0 first unconverged value (error) -15.7409+0i (9.81638414e-03)
  6 EPS nconv=0 first unconverged value (error) -15.7595+0i (9.74307026e-03)
  7 EPS nconv=0 first unconverged value (error) -15.7772+0i (8.85957623e-03)
  8 EPS nconv=0 first unconverged value (error) -15.7913+0i (7.75999297e-03)
  9 EPS nconv=0 first unconverged value (error) -15.8019+0i (6.26800697e-03)
 10 EPS nconv=0 first unconverged value (error) -15.8085+0i (4.76529153e-03)
 11 EPS nconv=0 first unconverged value (error) -15.8117+0i (3.22744776e-03)
 12 EPS nconv=0 first unconverged value (error) -15.813+0i (2.26363678e-03)
 13 EPS nconv=0 first unconverged value (error) -15.8136+0i (1.51102158e-03)
 14 EPS nconv=0 first unconverged value (error) -15.8138+0i (1.09526205e-03)
 15 EPS nconv=0 first unconverged value (error) -15.814+0i (8.28988692e-04)
 16 EPS nconv=0 first unconverged value (error) -15.8141+0i (7.24207126e-04)
 17 EPS nconv=0 first unconverged value (error) -15.8141+0i (6.42843428e-04)
 18 EPS nconv=0 first unconverged value (error) -15.8142+0i (6.10340814e-04)
 19 EPS nconv=0 first unconverged value (error) -15.8142+0i (5.51641730e-04)
 20 EPS nconv=0 first unconverged value (error) -15.8143+0i (4.98788862e-04)
 21 EPS nconv=0 first unconverged value (error) -15.8143+0i (4.06420038e-04)
 22 EPS nconv=0 first unconverged value (error) -15.8143+0i (3.30687878e-04)
 23 EPS nconv=0 first unconverged value (error) -15.8143+0i (2.52598133e-04)
 24 EPS nconv=0 first unconverged value (error) -15.8143+0i (1.99440039e-04)
 25 EPS nconv=0 first unconverged value (error) -15.8143+0i (1.49571026e-04)
 26 EPS nconv=0 first unconverged value (error) -15.8143+0i (1.16663354e-04)
 27 EPS nconv=0 first unconverged value (error) -15.8143+0i (8.77298592e-05)
 28 EPS nconv=0 first unconverged value (error) -15.8143+0i (6.99765242e-05)
 29 EPS nconv=0 first unconverged value (error) -15.8143+0i (5.43091765e-05)
 30 EPS nconv=0 first unconverged value (error) -15.8143+0i (4.43432245e-05)
 31 EPS nconv=0 first unconverged value (error) -15.8143+0i (3.45173686e-05)
 32 EPS nconv=0 first unconverged value (error) -15.8143+0i (2.76235524e-05)
 33 EPS nconv=0 first unconverged value (error) -15.8143+0i (2.07241727e-05)
 34 EPS nconv=0 first unconverged value (error) -15.8143+0i (1.59162617e-05)
 35 EPS nconv=0 first unconverged value (error) -15.8143+0i (1.15626945e-05)
 36 EPS nconv=0 first unconverged value (error) -15.8143+0i (8.74722215e-06)
 37 EPS nconv=0 first unconverged value (error) -15.8143+0i (6.37374691e-06)
 38 EPS nconv=0 first unconverged value (error) -15.8143+0i (4.90428302e-06)
 39 EPS nconv=0 first unconverged value (error) -15.8143+0i (3.66103867e-06)
 40 EPS nconv=0 first unconverged value (error) -15.8143+0i (2.88797896e-06)
 41 EPS nconv=0 first unconverged value (error) -15.8143+0i (2.20003865e-06)
 42 EPS nconv=0 first unconverged value (error) -15.8143+0i (1.75736741e-06)
 43 EPS nconv=0 first unconverged value (error) -15.8143+0i (1.34336587e-06)
 44 EPS nconv=0 first unconverged value (error) -15.8143+0i (1.06738181e-06)
 45 EPS nconv=0 first unconverged value (error) -15.8143+0i (8.05849515e-07)
 46 EPS nconv=0 first unconverged value (error) -15.8143+0i (6.29479843e-07)
 47 EPS nconv=0 first unconverged value (error) -15.8143+0i (4.66446864e-07)
 48 EPS nconv=0 first unconverged value (error) -15.8143+0i (3.57980820e-07)
 49 EPS nconv=0 first unconverged value (error) -15.8143+0i (2.61422701e-07)
 50 EPS nconv=0 first unconverged value (error) -15.8143+0i (1.98564902e-07)
 51 EPS nconv=0 first unconverged value (error) -15.8143+0i (1.44179370e-07)
 52 EPS nconv=0 first unconverged value (error) -15.8143+0i (1.09379673e-07)
 53 EPS nconv=0 first unconverged value (error) -15.8143+0i (7.96447419e-08)
 54 EPS nconv=0 first unconverged value (error) -15.8143+0i (6.07999903e-08)
 55 EPS nconv=0 first unconverged value (error) -15.8143+0i (4.46717754e-08)
 56 EPS nconv=0 first unconverged value (error) -15.8143+0i (3.44850292e-08)
 57 EPS nconv=0 first unconverged value (error) -15.8143+0i (2.56610271e-08)
 58 EPS nconv=0 first unconverged value (error) -15.8143+0i (2.00827677e-08)
 59 EPS nconv=0 first unconverged value (error) -15.8143+0i (1.51564930e-08)
 60 EPS nconv=0 first unconverged value (error) -15.8143+0i (1.20295852e-08)
 61 EPS nconv=1 first unconverged value (error) -15.8025+0i (7.10033299e-07)
Eigsolve (s):  91833.94949650764
lowest energy: -15.814334

References: