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add memmap to avoid storing 2e-integ in DRAM

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Abdallah Ammar 2024-12-06 15:53:14 +01:00
parent 97932b9c33
commit ba5da9536a
1 changed files with 32 additions and 14 deletions
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46
PyDuck.py
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@ -6,6 +6,8 @@ import pyscf
from pyscf import gto from pyscf import gto
import numpy as np import numpy as np
import subprocess import subprocess
import time
#Find the value of the environnement variable QUACK_ROOT. If not present we use the current repository #Find the value of the environnement variable QUACK_ROOT. If not present we use the current repository
if "QUACK_ROOT" not in os.environ: if "QUACK_ROOT" not in os.environ:
@ -23,6 +25,7 @@ parser.add_argument('--bohr', default='Angstrom', action='store_const', const='B
parser.add_argument('-c', '--charge', type=int, default=0, help='Total charge of the molecule. Specify negative charges with "m" instead of the minus sign, for example m1 instead of -1. Default is 0') parser.add_argument('-c', '--charge', type=int, default=0, help='Total charge of the molecule. Specify negative charges with "m" instead of the minus sign, for example m1 instead of -1. Default is 0')
parser.add_argument('--cartesian', default=False, action='store_true', help='Add this option if you want to use cartesian basis functions.') parser.add_argument('--cartesian', default=False, action='store_true', help='Add this option if you want to use cartesian basis functions.')
parser.add_argument('--print_2e', default=False, action='store_true', help='Add this option if you want to print 2e-integrals.') parser.add_argument('--print_2e', default=False, action='store_true', help='Add this option if you want to print 2e-integrals.')
parser.add_argument('--mmap_2e', default=False, action='store_true', help='If True, avoid using DRAM when generating 2e-integrals.')
parser.add_argument('-fc', '--frozen_core', type=bool, default=False, help='Freeze core MOs. Default is false') parser.add_argument('-fc', '--frozen_core', type=bool, default=False, help='Freeze core MOs. Default is false')
parser.add_argument('-m', '--multiplicity', type=int, default=1, help='Spin multiplicity. Default is 1 therefore singlet') parser.add_argument('-m', '--multiplicity', type=int, default=1, help='Spin multiplicity. Default is 1 therefore singlet')
parser.add_argument('--working_dir', type=str, default=QuAcK_dir, help='Set a working directory to run the calculation.') parser.add_argument('--working_dir', type=str, default=QuAcK_dir, help='Set a working directory to run the calculation.')
@ -38,6 +41,7 @@ multiplicity=args.multiplicity
xyz=args.xyz + '.xyz' xyz=args.xyz + '.xyz'
cartesian=args.cartesian cartesian=args.cartesian
print_2e=args.print_2e print_2e=args.print_2e
mmap_2e=args.mmap_2e
working_dir=args.working_dir working_dir=args.working_dir
#Read molecule #Read molecule
@ -129,33 +133,47 @@ write_matrix_to_file(y,norb,working_dir+'/int/y.dat')
subprocess.call(['rm', '-f', working_dir + '/int/z.dat']) subprocess.call(['rm', '-f', working_dir + '/int/z.dat'])
write_matrix_to_file(z,norb,working_dir+'/int/z.dat') write_matrix_to_file(z,norb,working_dir+'/int/z.dat')
eri_ao = mol.intor('int2e') def write_tensor_to_file(tensor,size,file_name,cutoff=1e-15):
f = open(file_name, 'w')
def write_tensor_to_file(tensor,size,file,cutoff=1e-15):
f = open(file, 'w')
for i in range(size): for i in range(size):
for j in range(i,size): for j in range(i,size):
for k in range(i,size): for k in range(i,size):
for l in range(j,size): for l in range(j,size):
if abs(tensor[i][k][j][l]) > cutoff: if abs(tensor[i][k][j][l]) > cutoff:
#f.write(str(i+1)+' '+str(j+1)+' '+str(k+1)+' '+str(l+1)+' '+"{:.16E}".format(tensor[i][k][j][l]))
f.write(str(i+1)+' '+str(j+1)+' '+str(k+1)+' '+str(l+1)+' '+"{:.16E}".format(tensor[i][k][j][l])) f.write(str(i+1)+' '+str(j+1)+' '+str(k+1)+' '+str(l+1)+' '+"{:.16E}".format(tensor[i][k][j][l]))
f.write('\n') f.write('\n')
f.close() f.close()
# Write two-electron integrals # Write two-electron integrals to HD
ti_2e = time.time()
if print_2e: if print_2e:
# (formatted) # (formatted)
subprocess.call(['rm', '-f', working_dir + '/int/ERI.dat']) output_file_path = working_dir + '/int/ERI.dat'
write_tensor_to_file(eri_ao, norb, working_dir + '/int/ERI.dat') subprocess.call(['rm', '-f', output_file_path])
eri_ao = mol.intor('int2e')
write_tensor_to_file(eri_ao, norb, output_file_path)
else: else:
# (binary) # (binary)
subprocess.call(['rm', '-f', working_dir + '/int/ERI.bin']) output_file_path = working_dir + '/int/ERI.bin'
# chem -> phys notation subprocess.call(['rm', '-f', output_file_path])
eri_ao = eri_ao.transpose(0, 2, 1, 3) if(mmap_2e):
f = open(working_dir + '/int/ERI.bin', 'w') # avoid using DRAM
eri_ao.tofile(working_dir + '/int/ERI.bin') eri_shape = (norb, norb, norb, norb)
f.close() eri_mmap = np.memmap(output_file_path, dtype='float64', mode='w+', shape=eri_shape)
mol.intor('int2e', out=eri_mmap)
for i in range(norb):
transposed_chunk = eri_mmap[i, :, :, :].transpose(1, 0, 2)
eri_mmap[i, :, :, :] = transposed_chunk
eri_mmap.flush()
del eri_mmap
else:
eri_ao = mol.intor('int2e').transpose(0, 2, 1, 3) # chem -> phys
f = open(output_file_path, 'w')
eri_ao.tofile(output_file_path)
f.close()
te_2e = time.time()
print("Wall time for writing 2e-integrals (physicist notation) to disk: {:.3f} seconds".format(te_2e - ti_2e))
#Execute the QuAcK fortran program #Execute the QuAcK fortran program