def main_local():
args = _args()
time0 = time.time()
box, numframes, cmplx = _get_info(args)
if args.end == -1:
args.end = numframes
print('Box: {}'.format(box))
print('Frames: {}'.format(numframes))
if args.box_left and args.box_right:
x0, y0, z0 = map(float, args.box_left.split(','))
x1, y1, z1 = map(float, args.box_right.split(','))
pos_cons = ((x0, y0, z0), (x1, y1, z1))
else:
pos_cons = ((0.0, 0.0, 0.0), tuple(box))
# Prepare for MPI run
nt = MPI.COMM_WORLD.size
if nt > 1:
num_frames = args.end - args.begin
per_process = int(round(num_frames / float(nt)))
print 'per_process', per_process
frame_ranges = range(args.begin, args.end, per_process)
frame_range_list = [
(frame_ranges[i], frame_ranges[i+1]) for i in range(len(frame_ranges)-1)
]
frame_range_list.append((frame_ranges[-1], args.end+1)) # Because it is right open range
else:
frame_range_list = [(args.begin, args.end)]
print('Frame range: {}'.format(frame_range_list))
# Q
q_vector = np.array(replicate_list(args.vector, args.molecules, args.N, cmplx=cmplx))
# PMI run
import pmi
pmi.setup()
pmi.execfile_(__file__)
if (args.trj.endswith('trr') or args.trj.endswith('xtc')) and SUPPORT_GROMACS:
data = pmi.invoke(
'_gromacs_processing',
args, q_vector, frame_range_list, pos_cons)
elif args.trj.endswith('h5'):
data = pmi.invoke(
'_h5_processing',
args, q_vector, frame_range_list, pos_cons)
else:
raise RuntimeError('Wrong trajectory file')
# Collect datas
vectors = []
for node_data in data:
vectors.extend([v for v in node_data])
filename_prefix = '' if not args.prefix else args.prefix + '_'
file_template = '# Date: %s\n# Filename: %s\n' % (datetime.datetime.today(), args.trj)
print('Saving data...')
save_data('vector', vectors, args.vector, filename_prefix, file_template)
print('Processing time: {}s with {} CPUs'.format(time.time() - time0, nt))
if __name__ != 'pmi':
##################################################
## Serial code
##################################################
import pmi
pmi.setup()
pmi.execfile_(__file__)
# invoke the method on all workers and get the results
res = pmi.invoke('hello_parallel', 'Olaf')
print('\n'.join(res))
else:
##################################################
## Parallel code
##################################################
from mpi4py import MPI
def hello_parallel(name):
return 'Hello %s, this is MPI task %d!' % (name, MPI.COMM_WORLD.rank)
def main_local():
args = _args()
time0 = time.time()
box, numframes, cmplx, is_gromacs = _get_info(args)
if args.end == -1:
args.end = numframes
print('Box: {}'.format(box))
print('Frames: {}'.format(numframes))
print('Scalling factor: {}'.format(args.scalling))
if args.box_left and args.box_right:
x0, y0, z0 = map(lambda x: float(x)*args.scalling, args.box_left.split(','))
x1, y1, z1 = map(lambda x: float(x)*args.scalling, args.box_right.split(','))
pos_cons = ((x0, y0, z0), (x1, y1, z1))
else:
pos_cons = ((0.0, 0.0, 0.0), tuple(box))
print('Position constraints: {}'.format(pos_cons))
# Prepare for MPI run
nt = MPI.COMM_WORLD.size
if nt > 1:
num_frames = args.end - args.begin
per_process = int(round(num_frames / float(nt)))
print 'per_process', per_process
frame_ranges = range(args.begin, args.end, per_process)
frame_range_list = [
(frame_ranges[i], frame_ranges[i+1]) for i in range(len(frame_ranges)-1)
]
frame_range_list.append((frame_ranges[-1], args.end+1)) # Because it is right open range
else:
frame_range_list = [(args.begin, args.end)]
print('Frame range: {}'.format(frame_range_list))
# Q
q_bonds = np.array(replicate_list(args.bonds, args.molecules, args.N, cmplx=cmplx))
q_angles = np.array(replicate_list(args.angles, args.molecules, args.N, cmplx=cmplx))
q_torsions = np.array(replicate_list(args.torsions, args.molecules, args.N, cmplx=cmplx))
# PMI run
import pmi
pmi.setup()
pmi.execfile_(__file__)
if is_gromacs:
data = pmi.invoke(
'_gromacs_processing',
args, q_bonds, q_angles, q_torsions, frame_range_list, pos_cons, box)
else:
data = pmi.invoke(
'_h5_processing',
args, q_bonds, q_angles, q_torsions, frame_range_list, pos_cons, box)
# Collect datas
bonds = []
angles = []
torsions = []
for node_data in data:
bonds.extend([v for v in node_data[0]])
angles.extend([v for v in node_data[1]])
torsions.extend([v for v in node_data[2]])
filename_prefix = '' if not args.prefix else args.prefix + '_'
file_template = '# Date: %s\n# Filename: %s\n' % (datetime.datetime.today(), args.trj)
print('Saving data...')
save_data('bond', bonds, args.bonds, filename_prefix, file_template, args.timeseries)
save_data('angle', angles, args.angles, filename_prefix, file_template, args.timeseries)
save_data('torsion', torsions, args.torsions, filename_prefix, file_template, args.timeseries)
print('Processing time: {}s with {} CPUs'.format(time.time() - time0, nt))
##################################################
## Serial code
##################################################
import pmi
pmi.setup()
pmi.execfile_("hello_class.py")
# create a frontend class via the proxy
class Hello(object):
__metaclass__ = pmi.Proxy
pmiproxydefs = dict(cls="HelloLocal", pmiinvoke=["__call__"])
# use the class
hello = Hello("Olaf")
print("\n".join(hello()))