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# $Id$
#
# Copyright (C) 2009 Greg Landrum
# All rights reserved
#
# Demo for using boost.mpi with the RDKit
#
# run this with : mpirun -n 4 python rdkpympi.py
#
from __future__ import print_function
from boost import mpi
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.RDLogger import logger
logger = logger()
def dividetask(data, task, silent=True):
data = mpi.broadcast(mpi.world, data, 0)
nProcs = mpi.world.size
chunkSize = len(data) // nProcs
extraBits = len(data) % nProcs
res = []
allRes = []
# the root node handles the extra pieces:
if mpi.world.rank == 0:
for i in range(extraBits):
elem = data[i]
res.append(task(elem))
if not silent:
logger.info('task(%d) done %d' % (mpi.world.rank, i + 1))
pos = extraBits + mpi.world.rank * chunkSize
for i in range(chunkSize):
elem = data[pos]
pos += 1
res.append(task(elem))
if not silent:
logger.info('task(%d) done %d' % (mpi.world.rank, i + 1))
if mpi.world.rank == 0:
tmp = mpi.gather(mpi.world, res, 0)
for res in tmp:
allRes.extend(res)
else:
mpi.gather(mpi.world, res, 0)
return allRes
if __name__ == '__main__':
from rdkit import RDConfig
import os
fName = os.path.join(RDConfig.RDBaseDir, 'Projects', 'DbCLI', 'testData', 'bzr.sdf')
if mpi.world.rank == 0:
data = [x for x in Chem.SDMolSupplier(fName)][:50]
else:
data = None
def generateconformations(m):
m = Chem.AddHs(m)
ids = AllChem.EmbedMultipleConfs(m, numConfs=10)
for id in ids:
AllChem.UFFOptimizeMolecule(m, confId=id)
return m
cms = dividetask(data, generateconformations, silent=False)
# report:
if mpi.world.rank == 0:
for i, mol in enumerate(cms):
print(i, mol.GetNumConformers())
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