def diffraction_pattern_calculation(params):
number_channels, min_dist_fr_sample_center = params
create_collimator_geometry(coll_length=min_dist_fr_sample_center,
number_channels=int(number_channels),
channel_length=min_dist_fr_sample_center,
detector_angles=[-45, -135],
outputfile=outputfile)
simdir = os.path.join(
parentpath, "out/optimization-NC_%s-dist_%s" %
(number_channels, min_dist_fr_sample_center))
run_script.run_mpi(instr,
simdir,
beam=scattered,
ncount=ncount,
nodes=nodes,
sample=sample,
sourceTosample=sourceTosample,
detector_size=detector_size,
overwrite_datafiles=True)
dcs, I_d, error = reduction.reduce_all(simdir,
conf,
l1=14.699,
l2=0.3,
l3=0.5,
bins=np.arange(0, 4, 0.01))
return (dcs, I_d, error)
def test_run_mpi():
run_script.run_mpi(script,
workdir=workdir,
ncount=ncount,
buffer_size=int(5e5),
nodes=nodes,
use_gpu=False,
overwrite_datafiles=True)
return
def test_run_collimator():
run_script.run_mpi(instr,
output,
beam=scattered,
ncount=ncount,
nodes=nodes,
angleMon1=-50.,
angleMon2=105.,
sample=sample,
sourceTosample_x=sourceTosample,
sourceTosample_y=sourceTosample,
sourceTosample_z=sourceTosample,
detector_size=detector_size,
overwrite_datafiles=True)
def run(instrument_script,
ncount,
niters,
mpi=False,
nodes=1,
acc_run=False,
skip_ncounts=[],
**kwds):
outdir = 'out.debug-check-speed'
if os.path.exists(outdir):
shutil.rmtree(outdir)
# TODO: this stdout file gets overwritten on each call, move or use append?
stdout = open("./check-speed-stdout.txt", "w")
sys.stderr = stdout
avg_times = []
for n in ncount:
if n in skip_ncounts:
# insert element to preserve ordering
avg_times.append(np.nan)
continue
print(" Running '{}' with n={}".format(instrument_script, n))
times = []
# redirect script output to reduce terminal clutter
for iter in range(niters + 1):
sys.stdout = stdout
buffer_size = int(n) if n > 1e6 else int(1e6)
if buffer_size > 1e9:
buffer_size = int(1e9)
# get the runtime for the script. Note: this probably isn't the
# best timing, since it will include the overhead of launching the
# script and any file IO done inside the script, but there is no
# current way to time individual components.
# TODO: the stdout could be parsed to pull the process timings for acc components
# TODO: there is still mcvine component output, likely from a subprocess in which this redirection has no effect
if mpi:
# run script in MPI mode
# NOTE: with mcvine=0.44, pyyaml 5.3 must be used to avoid yaml load error. This is fixed in newer versions of mcvine.
time_before = time.time_ns()
run_script.run_mpi(instrument_script,
outdir,
nodes=nodes,
buffer_size=buffer_size,
ncount=n,
overwrite_datafiles=True,
**kwds)
time_after = time.time_ns()
elif acc_run:
# use accelerated run script
time_before = time.time_ns()
run_acc_script.run(instrument_script,
outdir,
buffer_size=buffer_size,
ncount=n,
overwrite_datafiles=True,
**kwds)
time_after = time.time_ns()
else:
# use default run script (mcvine, single node)
time_before = time.time_ns()
run_script.run1(instrument_script,
outdir,
buffer_size=buffer_size,
ncount=n,
overwrite_datafiles=True,
**kwds)
time_after = time.time_ns()
# skip first run
if iter < 1:
continue
delta = time_after - time_before
times.append(delta)
sys.stdout = sys.__stdout__
time_avg = np.sum(np.asarray(times)) / len(times)
avg_times.append(time_avg)
print(" TIME = {} ms ({} s)".format(time_avg * 1e-6, time_avg * 1e-9))
sys.stdout = sys.__stdout__
sys.stderr = sys.__stderr__
stdout.close()
return avg_times
#!/usr/bin/env python
from mcvine import run_script
run_script.run_mpi('./sss.py',
'out',
ncount=8e6,
nodes=8,
overwrite_datafiles=True)
def diffraction_pattern_calculation(self, params=[20, 20]):
max_coll_len, chann_size = params
if self.coll_sim:
create_collimator_geometry(channel_size=chann_size,
max_coll_len=max_coll_len,
Snap_angle=self.Snap_angle,
detector_angles=[-45])
name = "length_%s-dist_%s" % (max_coll_len, chann_size)
else:
name = self.sampleassembly_fileName
simdir = os.path.join(parent_dir, "out/%s" % (name))
instr = os.path.join(libpath, 'myinstrument.py')
# scattered_neutrons ='clampcellSi_scattered-neutrons_1e9_det-50_105_new'
# scatterer = {(sampleassembly_fileName, 'shapeColl', 'coll_geometry', 'H', 'xyz'),
# }
#
# sa.makeSAXML(sampleassembly_fileName, scatterer)
# sample= 'collimator_plastic'
run_script.run_mpi(instr,
simdir,
beam=self.source_neutrons(),
ncount=self.ncount,
nodes=20,
angleMon1=-50.,
angleMon2=105.,
sample=self.sampleassembly_fileName,
sourceTosample_x=self.sourceTosample_x,
sourceTosample_y=self.sourceTosample_y,
sourceTosample_z=self.sourceTosample_z,
detector_size=0.45,
overwrite_datafiles=True)
template = os.path.join(mantid_path, 'template.nxs')
nexus_file_path = os.path.join(mantid_path, '{}.nxs'.format(name))
det2nxs.create_nexus(simdir, nexus_file_path, template)
SNAP_definition_file = os.path.join(mantid_path,
'SNAP_virtual_Definition.xml')
nexus_file_correctDet_path = os.path.join(
mantid_path, '{}_correctDet.nxs'.format(name))
rot.detector_position_for_reduction(nexus_file_path, conf,
SNAP_definition_file,
nexus_file_correctDet_path)
if self.masking:
masked_file_path = os.path.join(mantid_path,
'{}_masked.nxs'.format(name))
masked_template_path = os.path.join(
mantid_path, '{}'.format(self.masked_template))
mask.masking(nexus_file_correctDet_path, masked_template_path,
masked_file_path)
else:
masked_file_path = nexus_file_correctDet_path
binning = [0.5, 0.01, 4.]
d_sim, I_sim, error = red.mantid_reduction(masked_file_path, binning)
plt.figure()
plt.errorbar(d_sim, I_sim, error)
plt.xlabel('d_spacing ()')
plt.show()
np.save(
os.path.join(result_path, 'I_d_{sample}.npy'.format(sample=name)),
[d_sim, I_sim, error])
return (d_sim, I_sim, error)
def diffraction_pattern_calculation(self, params=[501.9, 444.5]):
channel_len, coll_front_end_from_center = params
if self.coll_sim:
create_collimator_geometry(
coll_front_end_from_center=coll_front_end_from_center,
chanel_length=channel_len,
Snap_angle=self.Snap_angle,
detector_angles=[150]) #150
name = "length_%s-dist_%s" % (channel_len,
coll_front_end_from_center)
else:
name = self.sampleassembly_fileName
simdir = os.path.join(parent_dir, "out/%s" % (name))
# instr = os.path.join(libpath, 'myinstrument_multipleDet.py')
instr = os.path.join(libpath, 'myinstrument.py')
# scattered_neutrons ='clampcellSi_scattered-neutrons_1e9_det-50_105_new'
# scatterer = {(sampleassembly_fileName, 'shapeColl', 'coll_geometry', 'H', 'xyz'),
# }
#
# sa.makeSAXML(sampleassembly_fileName, scatterer)
# sample= 'collimator_plastic'
import shutil
if os.path.exists(simdir):
shutil.rmtree(simdir)
# run_script.run_mpi(instr, simdir,
# beam=self.source_neutrons(), ncount=self.ncount,
# nodes=20, angleMons=self.angleMons,
# sample=self.sampleassembly_fileName,
# sourceTosample_x=self.sourceTosample_x, sourceTosample_y=self.sourceTosample_y,
# sourceTosample_z=self.sourceTosample_z, sampleTodetector_z=self.sampleTodetector_z,
# detector_width=self.detector_width, detector_height=self.detector_height,
# number_pixels_in_height=self.number_pixels_in_height,
# number_of_box_in_height=self.number_of_box_in_height,
# number_pixels_in_width=self.number_pixels_in_width,
# number_of_box_in_width= self.number_of_box_in_width,
# number_detectors=self.number_of_detectors,
# overwrite_datafiles=True)
run_script.run_mpi(
instr,
simdir,
beam=self.source_neutrons(),
ncount=self.ncount,
nodes=20,
angleMon1=150,
sample=self.sampleassembly_fileName,
sourceTosample_x=self.sourceTosample_x,
sourceTosample_y=self.sourceTosample_y,
sourceTosample_z=self.sourceTosample_z,
sampleTodetector_z=self.sampleTodetector_z,
detector_width=self.detector_width,
detector_height=self.detector_height,
number_pixels_in_height=self.number_pixels_in_height,
number_of_box_in_height=self.number_of_box_in_height,
number_pixels_in_width=self.number_pixels_in_width,
number_of_box_in_width=self.number_of_box_in_width,
multiple_detectors=False,
overwrite_datafiles=True)
SNAP_definition_file = os.path.join(mantid_path,
'SNAPOneDet_virtual_definition.xml'
) # Vulcan_virtual_Definition.xml
template = os.path.join(
mantid_path, 'template_snapOneDet.nxs') # vulcan_template.nxs
nxs_template.create(SNAP_definition_file,
ntotpixels=self.number_of_total_DetectorPixels,
outpath=template,
pulse_time_end=1e5)
nexus_file_path = os.path.join(mantid_path, '{}.nxs'.format(name))
det2nxs.create_nexus(simdir,
nexus_file_path,
template,
N=self.number_of_total_DetectorPixels)
nexus_file_correctDet_path = os.path.join(
mantid_path, '{}_correctDet.nxs'.format(name))
conf = Conf(self.moderatorTosample_z, self.angleMons,
self.sampleTodetector_z)
rot.detector_position_for_reduction(nexus_file_path, conf,
SNAP_definition_file,
nexus_file_correctDet_path)
if self.masking:
masked_file_path = os.path.join(mantid_path,
'{}_masked.nxs'.format(name))
masked_template_path = os.path.join(
mantid_path, '{}'.format(self.masked_template))
mask.masking(nexus_file_correctDet_path, masked_template_path,
masked_file_path)
else:
masked_file_path = nexus_file_correctDet_path
binning = [0.5, 0.01, 4.]
d_sim, I_sim, error = red.mantid_reduction(masked_file_path, binning)
plt.figure()
plt.errorbar(d_sim, I_sim, error)
plt.xlabel('d_spacing ()')
plt.show()
np.save(
os.path.join(result_path, 'I_d_{sample}.npy'.format(sample=name)),
[d_sim, I_sim, error])
return (d_sim, I_sim, error)
#!/usr/bin/env python
from mcvine import run_script
run_script.run_mpi('./ARCS_10_25_2008_mcvine_revised.py',
'out',
ncount=8e7,
nodes=8,
overwrite_datafiles=True)
