def main():
batch_dir = os.path.basename(__file__).replace(".py", "").replace("run_","flow_")
# intialize the BatchLauncher.
from pymatgen.io.abinit.launcher import BatchLauncher
batch = BatchLauncher(workdir=batch_dir)
# Build multiple flows and add them to the BatchLauncher.
for paral_kgb in range(2):
#flow_dir = os.path.join(batch.workdir, "flow_paral_kgb_%d" % paral_kgb)
# Get the SCF and the NSCF input and build the flow.
scf_input, nscf_input = make_scf_nscf_inputs(paral_kgb)
# Each flow will have a unique wordir inside batch.workdir.
# Note that we have to pass workdir=None and use set_name to specify the dir basename
flow = abilab.bandstructure_flow(None, scf_input, nscf_input, allocate=False)
flow.set_name("flow_paral_kgb_%d" % paral_kgb)
batch.add_flow(flow)
# Submit to the queue in batch mode.
# Use abibatch.py to inspect the status or resubmit.
job = batch.submit()
print("batch.submit() returned: ", job.retcode)
return job.retcode
def main():
batch_dir = os.path.basename(__file__).replace(".py", "").replace(
"run_", "flow_")
# intialize the BatchLauncher.
from pymatgen.io.abinit.launcher import BatchLauncher
batch = BatchLauncher(workdir=batch_dir)
# Build multiple flows and add them to the BatchLauncher.
for paral_kgb in range(2):
#flow_dir = os.path.join(batch.workdir, "flow_paral_kgb_%d" % paral_kgb)
# Get the SCF and the NSCF input and build the flow.
scf_input, nscf_input = make_scf_nscf_inputs(paral_kgb)
# Each flow will have a unique wordir inside batch.workdir.
# Note that we have to pass workdir=None and use set_name to specify the dir basename
flow = abilab.bandstructure_flow(None,
scf_input,
nscf_input,
allocate=False)
flow.set_name("flow_paral_kgb_%d" % paral_kgb)
batch.add_flow(flow)
# Submit to the queue in batch mode.
# Use abibatch.py to inspect the status or resubmit.
job = batch.submit()
print("batch.submit() returned: ", job.retcode)
return job.retcode
def make_electronic_structure_flow(ngkpts_for_dos=((2, 2, 2), (4, 4, 4), (6, 6, 6), (8, 8, 8))):
"""Band structure calculation."""
multi = abilab.MultiDataset(structure=abidata.cif_file("si.cif"),
pseudos=abidata.pseudos("14si.pspnc"), ndtset=2 + len(ngkpts_for_dos))
# Global variables
multi.set_vars(ecut=10)
# Dataset 1
multi[0].set_vars(tolvrs=1e-9)
multi[0].set_kmesh(ngkpt=[4, 4, 4], shiftk=[0, 0, 0])
# Dataset 2
multi[1].set_vars(tolwfr=1e-15)
multi[1].set_kpath(ndivsm=5)
# Dataset 3
for i, ngkpt in enumerate(ngkpts_for_dos):
multi[2+i].set_vars(tolwfr=1e-15)
multi[2+i].set_kmesh(ngkpt=ngkpt, shiftk=[0,0,0])
inputs = multi.split_datasets()
scf_input, nscf_input, dos_input = inputs[0], inputs[1], inputs[2:]
return abilab.bandstructure_flow(workdir="flow_dos_bands", scf_input=scf_input, nscf_input=nscf_input,
dos_inputs=dos_input)
def make_electronic_structure_flow(ngkpts_for_dos=[(2, 2, 2), (4, 4, 4), (6, 6, 6), (8, 8, 8)]):
"""Band structure calculation."""
multi = abilab.MultiDataset(structure=abidata.cif_file("si.cif"),
pseudos=abidata.pseudos("14si.pspnc"), ndtset=2 + len(ngkpts_for_dos))
# Global variables
multi.set_vars(ecut=10)
# Dataset 1
multi[0].set_vars(tolvrs=1e-9)
multi[0].set_kmesh(ngkpt=[4, 4, 4], shiftk=[0, 0, 0])
# Dataset 2
multi[1].set_vars(tolwfr=1e-15)
multi[1].set_kpath(ndivsm=5)
# Dataset 3
for i, ngkpt in enumerate(ngkpts_for_dos):
multi[2+i].set_vars(tolwfr=1e-15)
multi[2+i].set_kmesh(ngkpt=ngkpt, shiftk=[0,0,0])
inputs = multi.split_datasets()
scf_input, nscf_input, dos_input = inputs[0], inputs[1], inputs[2:]
return abilab.bandstructure_flow(workdir="flow_dos_bands", scf_input=scf_input, nscf_input=nscf_input,
dos_inputs=dos_input)
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
workdir = options.workdir
if not options.workdir:
workdir = os.path.basename(__file__).replace(".py", "").replace(
"run_", "flow_")
#pseudos = abidata.pseudos("12mg.pspnc", "5b.pspnc")
structure = abidata.structure_from_ucell("MgB2")
# Get pseudos from a table.
table = abilab.PseudoTable(abidata.pseudos("12mg.pspnc", "5b.pspnc"))
pseudos = table.get_pseudos_for_structure(structure)
nval = structure.num_valence_electrons(pseudos)
#print(nval)
inputs = make_scf_nscf_inputs(structure, pseudos)
scf_input, nscf_input, dos_inputs = inputs[0], inputs[1], inputs[2:]
#print(scf_input.pseudos)
return abilab.bandstructure_flow(workdir,
scf_input,
nscf_input,
dos_inputs=dos_inputs,
manager=options.manager)
def itest_bandstructure_schedflow(fwp, tvars):
"""
Run a bandstructure flow with the scheduler.
"""
print("tvars:\n %s" % str(tvars))
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs(tvars, pp_paths="Si.GGA_PBE-JTH-paw.xml")
# Build the flow and create the database.
flow = abilab.bandstructure_flow(fwp.workdir, fwp.manager, scf_input, nscf_input)
flow.build_and_pickle_dump()
fwp.scheduler.add_flow(flow)
print(fwp.scheduler)
# scheduler cannot handle more than one flow.
with pytest.raises(fwp.scheduler.Error):
fwp.scheduler.add_flow(flow)
fwp.scheduler.start()
assert fwp.scheduler.num_excs == 0
assert fwp.scheduler.nlaunch == 2
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
def itest_bandstructure_schedflow(fwp, tvars):
"""
Run a bandstructure flow with the scheduler.
"""
print("tvars:\n %s" % str(tvars))
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs(tvars, pp_paths="Si.GGA_PBE-JTH-paw.xml")
# Build the flow and create the database.
flow = abilab.bandstructure_flow(fwp.workdir, scf_input, nscf_input, manager=fwp.manager)
# Will remove output files (WFK)
flow.set_cleanup_exts()
flow.build_and_pickle_dump()
fwp.scheduler.add_flow(flow)
print(fwp.scheduler)
# scheduler cannot handle more than one flow.
with pytest.raises(fwp.scheduler.Error):
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start()
assert not fwp.scheduler.exceptions
assert fwp.scheduler.nlaunch == 2
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
# The WFK files should have been removed because we called set_cleanup_exts
for task in flow[0]:
assert not task.outdir.has_abiext("WFK")
def build_flow(workdir):
#workdir = "flow_test"
# Instantiate the TaskManager.
manager = abilab.TaskManager.from_user_config()
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs()
# Build the flow.
return abilab.bandstructure_flow(workdir, scf_input, nscf_input, manager=manager)
def build_bands_flow(workdir):
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs()
# Instantiate the TaskManager from `taskmanager.yml`.
manager = abilab.TaskManager.from_user_config()
# Build the flow.
flow = abilab.bandstructure_flow(workdir, manager, scf_input, nscf_input)
return flow.allocate()
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
workdir = options.workdir
if not options.workdir:
workdir = os.path.basename(__file__).replace(".py", "").replace("run_","flow_")
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs()
print(scf_input.to_string(sortmode="section"))
# Build the flow.
return abilab.bandstructure_flow(workdir, scf_input, nscf_input, manager=options.manager)
def itest_unconverged_scf(fwp, tvars):
"""Test the treatment of unconverged GS calculations."""
print("tvars:\n %s" % str(tvars))
# Build the SCF and the NSCF input (note nstep to have an unconverged run)
scf_input, nscf_input = make_scf_nscf_inputs(tvars, pp_paths="14si.pspnc", nstep=1)
# Build the flow and create the database.
flow = abilab.bandstructure_flow(fwp.workdir, fwp.manager, scf_input, nscf_input)
flow.allocate()
flow.build_and_pickle_dump()
t0 = flow[0][0]
t1 = flow[0][1]
# This run should not converge.
t0.start_and_wait()
t0.check_status()
assert t0.status == t0.S_UNCONVERGED
# Remove nstep from the input so that we use the default value.
# Then restart the GS task and test that GS is OK.
assert not t1.can_run
t0.strategy.remove_extra_abivars(["nstep"])
assert t0.num_restarts == 0
t0.restart()
t0.wait()
assert t0.num_restarts == 1
t0.check_status()
assert t0.status == t1.S_OK
# Now we can start the NSCF step
assert t1.can_run
t1.start_and_wait()
t1.check_status()
assert t1.status == t0.S_UNCONVERGED
assert not flow.all_ok
# Restart (same trick as the one used for the GS run)
t1.strategy.remove_extra_abivars(["nstep"])
assert t1.num_restarts == 0
assert t1.restart()
t1.wait()
assert t1.num_restarts == 1
assert t1.status == t1.S_DONE
t1.check_status()
assert t1.status == t1.S_OK
flow.show_status()
assert flow.all_ok
def build_flow(workdir):
#workdir = "flow_test"
# Instantiate the TaskManager.
manager = abilab.TaskManager.from_user_config()
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs()
# Build the flow.
return abilab.bandstructure_flow(workdir,
scf_input,
nscf_input,
manager=manager)
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
workdir = options.workdir
if not options.workdir:
workdir = os.path.basename(__file__).replace(".py", "").replace("run_","flow_")
# Instantiate the TaskManager.
manager = abilab.TaskManager.from_user_config() if not options.manager else \
abilab.TaskManager.from_file(options.manager)
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs()
# Build the flow.
return abilab.bandstructure_flow(workdir, manager, scf_input, nscf_input)
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
workdir = options.workdir
if not options.workdir:
workdir = os.path.basename(__file__).replace(".py", "").replace(
"run_", "flow_")
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs()
print(scf_input.to_string(sortmode="section"))
# Build the flow.
return abilab.bandstructure_flow(workdir,
scf_input,
nscf_input,
manager=options.manager)
def build_bands_flow(workdir="tmp_mgb2_edoses"):
pseudos = data.pseudos("12mg.pspnc", "05b.soft_tm")
structure = data.structure_from_ucell("MgB2")
nval = structure.calc_nvalence(pseudos)
print(nval)
inputs = make_scf_nscf_inputs(structure, pseudos)
scf_input, nscf_input, dos_inputs = inputs[0], inputs[1], inputs[2:]
print(scf_input.pseudos)
manager = abilab.TaskManager.from_user_config()
flow = abilab.bandstructure_flow(workdir, manager, scf_input, nscf_input, dos_inputs=dos_inputs)
return flow.allocate()
def itest_bandstructure_schedflow(fwp, tvars):
"""
Testing bandstructure flow with the scheduler.
"""
print("tvars:\n %s" % str(tvars))
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs(
tvars, pp_paths="Si.GGA_PBE-JTH-paw.xml")
# Build the flow and create the database.
flow = abilab.bandstructure_flow(fwp.workdir,
scf_input,
nscf_input,
manager=fwp.manager)
# Will remove output files (WFK)
flow.set_garbage_collector()
flow.build_and_pickle_dump(abivalidate=True)
fwp.scheduler.add_flow(flow)
print(fwp.scheduler)
# scheduler cannot handle more than one flow.
with pytest.raises(fwp.scheduler.Error):
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start() == 0
assert not fwp.scheduler.exceptions
assert fwp.scheduler.nlaunch == 2
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
# The WFK files should have been removed because we called set_garbage_collector
for task in flow[0]:
assert not task.outdir.has_abiext("WFK")
# Test if GSR files are produced and are readable.
for i, task in enumerate(flow[0]):
with task.open_gsr() as gsr:
print(gsr)
assert gsr.nsppol == 1
#assert gsr.structure == structure
ebands = gsr.ebands
def make_ebands_flow():
"""Band structure calculation."""
multi = abilab.MultiDataset(structure=abidata.cif_file("si.cif"),
pseudos=abidata.pseudos("14si.pspnc"), ndtset=2)
# Global variables
multi.set_vars(ecut=10)
# Dataset 1
multi[0].set_vars(tolvrs=1e-9)
multi[0].set_kmesh(ngkpt=[4,4,4], shiftk=[0,0,0])
# Dataset 2
multi[1].set_vars(tolwfr=1e-15)
multi[1].set_kpath(ndivsm=5)
scf_input, nscf_input = multi.split_datasets()
return abilab.bandstructure_flow(workdir="flow_base3_ebands", scf_input=scf_input, nscf_input=nscf_input)
def eh_convergence_study():
"""
"""
scf_input, nscf_input, bse_template = make_inputs()
workdir = "flow_bse_bands"
if not os.path.exists(workdir):
print("Calling the scheduler")
bands_flow = abilab.bandstructure_flow(workdir, scf_input, nscf_input)
bands_flow.make_scheduler().start()
else:
print("Initializing flow from %s" % workdir)
bands_flow = abilab.Flow.pickle_load(workdir)
if not bands_flow.all_ok:
raise RuntimeError("bands_flow must have reached all_ok")
wfk_file = bands_flow.nscf_task.outdir.has_abiext("WFK")
if not wfk_file:
raise RuntimeError("WFK file does not exist")
work = abilab.Work()
#for inp in bse_template.generate(ecuteps=range(2, 4, 1)):
for inp in bse_template.generate(zcut=["0.1 eV", "0.2 eV", "0.3 eV"]):
work.register_bse_task(inp, deps={wfk_file: "WFK"})
flow = abilab.Flow(workdir="flow_bse_ecuteps")
flow.register_work(work)
flow.allocate()
flow.build()
#flow.make_scheduler().start()
import matplotlib.pyplot as plt
import pandas as pd
with abilab.abirobot(flow, "MDF") as robot:
frame = robot.get_dataframe()
#print(frame)
#plotter = robot.get_mdf_plotter()
#plotter.plot()
robot.plot_conv_mdf(hue="broad")
def itest_bandstructure_schedflow(fwp, tvars):
"""
Testing bandstructure flow with the scheduler.
"""
print("tvars:\n %s" % str(tvars))
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs(tvars, pp_paths="Si.GGA_PBE-JTH-paw.xml")
# Build the flow and create the database.
flow = abilab.bandstructure_flow(fwp.workdir, scf_input, nscf_input, manager=fwp.manager)
# Will remove output files (WFK)
flow.set_garbage_collector()
flow.build_and_pickle_dump()
fwp.scheduler.add_flow(flow)
print(fwp.scheduler)
# scheduler cannot handle more than one flow.
with pytest.raises(fwp.scheduler.Error):
fwp.scheduler.add_flow(flow)
assert fwp.scheduler.start() == 0
assert not fwp.scheduler.exceptions
assert fwp.scheduler.nlaunch == 2
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
# The WFK files should have been removed because we called set_garbage_collector
for task in flow[0]:
assert not task.outdir.has_abiext("WFK")
# Test if GSR files are produced and are readable.
for i, task in enumerate(flow[0]):
with task.open_gsr() as gsr:
print(gsr)
assert gsr.nsppol == 1
#assert gsr.structure == structure
ebands = gsr.ebands
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
workdir = options.workdir
if not options.workdir:
workdir = os.path.basename(__file__).replace(".py", "").replace("run_","flow_")
# Instantiate the TaskManager.
manager = abilab.TaskManager.from_user_config() if not options.manager else \
abilab.TaskManager.from_file(options.manager)
pseudos = data.pseudos("12mg.pspnc", "5b.pspnc")
structure = data.structure_from_ucell("MgB2")
nval = structure.num_valence_electrons(pseudos)
#print(nval)
inputs = make_scf_nscf_inputs(structure, pseudos)
scf_input, nscf_input, dos_inputs = inputs[0], inputs[1], inputs[2:]
print(scf_input.pseudos)
return abilab.bandstructure_flow(workdir, manager, scf_input, nscf_input, dos_inputs=dos_inputs)
def make_ebands_flow():
"""Band structure calculation."""
multi = abilab.MultiDataset(structure=abidata.cif_file("si.cif"),
pseudos=abidata.pseudos("14si.pspnc"),
ndtset=2)
# Global variables
multi.set_vars(ecut=10)
# Dataset 1
multi[0].set_vars(tolvrs=1e-9)
multi[0].set_kmesh(ngkpt=[4, 4, 4], shiftk=[0, 0, 0])
# Dataset 2
multi[1].set_vars(tolwfr=1e-15)
multi[1].set_kpath(ndivsm=5)
scf_input, nscf_input = multi.split_datasets()
return abilab.bandstructure_flow(workdir="flow_base3_ebands",
scf_input=scf_input,
nscf_input=nscf_input)
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
workdir = options.workdir
if not options.workdir:
workdir = os.path.basename(__file__).replace(".py", "").replace("run_","flow_")
#pseudos = abidata.pseudos("12mg.pspnc", "5b.pspnc")
structure = abidata.structure_from_ucell("MgB2")
# Get pseudos from a table.
table = abilab.PseudoTable(abidata.pseudos("12mg.pspnc", "5b.pspnc"))
pseudos = table.get_pseudos_for_structure(structure)
nval = structure.num_valence_electrons(pseudos)
#print(nval)
inputs = make_scf_nscf_inputs(structure, pseudos)
scf_input, nscf_input, dos_inputs = inputs[0], inputs[1], inputs[2:]
#print(scf_input.pseudos)
return abilab.bandstructure_flow(workdir, scf_input, nscf_input,
dos_inputs=dos_inputs, manager=options.manager)
def bands_flow():
inp = abilab.AbiInput(pseudos=abidata.pseudos("14si.pspnc"), ndtset=2)
inp.set_structure_from_file(abidata.cif_file("si.cif"))
# Global variables
inp.ecut = 10
# Dataset 1
inp[1].set_variables(tolvrs=1e-9)
inp[1].set_kmesh(ngkpt=[4,4,4], shiftk=[0,0,0])
# Dataset 2
inp[2].set_variables(tolwfr=1e-15)
inp[2].set_kpath(ndivsm=5)
scf_input, nscf_input = inp.split_datasets()
flow = abilab.bandstructure_flow(workdir="flow_bands", scf_input=scf_input, nscf_input=nscf_input)
flow.make_scheduler().start()
nscf_task = flow[0][1]
with nscf_task.open_gsr() as gsr:
gsr.ebands.plot()
def itest_unconverged_scf(fwp, tvars):
"""Testing the treatment of unconverged GS calculations."""
print("tvars:\n %s" % str(tvars))
# Build the SCF and the NSCF input (note nstep to have an unconverged run)
scf_input, nscf_input = make_scf_nscf_inputs(tvars, pp_paths="14si.pspnc", nstep=1)
# Build the flow and create the database.
flow = abilab.bandstructure_flow(fwp.workdir, scf_input, nscf_input, manager=fwp.manager)
flow.allocate()
# Use smart-io
flow.use_smartio()
flow.build_and_pickle_dump()
t0 = flow[0][0]
t1 = flow[0][1]
assert t0.uses_paral_kgb(tvars.paral_kgb)
assert t1.uses_paral_kgb(tvars.paral_kgb)
# This run should not converge.
t0.start_and_wait()
t0.check_status()
assert t0.status == t0.S_UNCONVERGED
# Unconverged with smart-io --> WFK must be there
assert t0.outdir.has_abiext("WFK")
#assert 0
# Remove nstep from the input so that we use the default value.
# Then restart the GS task and test that GS is OK.
assert not t1.can_run
t0.input.pop("nstep")
assert t0.num_restarts == 0
t0.restart()
t0.wait()
assert t0.num_restarts == 1
t0.check_status()
assert t0.status == t1.S_OK
# Converged with smart-io --> WFK is not written
assert not t0.outdir.has_abiext("WFK")
# Now we can start the NSCF step
assert t1.can_run
t1.start_and_wait()
t1.check_status()
assert t1.status == t0.S_UNCONVERGED
assert not flow.all_ok
# Restart (same trick as the one used for the GS run)
t1.input.pop("nstep")
assert t1.num_restarts == 0
assert t1.restart()
t1.wait()
assert t1.num_restarts == 1
assert t1.status == t1.S_DONE
t1.check_status()
assert t1.status == t1.S_OK
flow.show_status()
assert flow.all_ok
# Test inspect methods
if has_matplotlib():
t0.inspect(show=False)
# Test get_results
t0.get_results()
t1.get_results()
# Build tarball file.
tarfile = flow.make_tarfile()
#assert flow.validate_json_schema()
# Test reset_from_scratch
t0.reset_from_scratch()
assert t0.status == t0.S_READY
# Datetime counters shouls be set to None
dt = t0.datetimes
assert (dt.submission, dt.start, dt.end) == (None, None, None)
t0.start_and_wait()
t0.reset_from_scratch()
# Datetime counters shouls be set to None
dt = t0.datetimes
assert (dt.submission, dt.start, dt.end) == (None, None, None)
def itest_bandstructure_flow(fwp, tvars):
"""
Testing band-structure flow with one dependency: SCF -> NSCF.
"""
print("tvars:\n %s" % str(tvars))
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs(tvars, pp_paths="14si.pspnc")
# Build the flow and create the database.
flow = abilab.bandstructure_flow(fwp.workdir, scf_input, nscf_input, manager=fwp.manager)
flow.build_and_pickle_dump(abivalidate=True)
t0 = flow[0][0]
t1 = flow[0][1]
# Test initialization status, task properties and links (t1 requires t0)
assert t0.status == t0.S_INIT
assert t1.status == t1.S_INIT
assert t0.can_run
assert not t1.can_run
assert t1.depends_on(t0)
assert not t1.depends_on(t1)
assert t0.isnc
assert not t0.ispaw
# Flow properties and methods
assert flow.num_tasks == 2
assert not flow.all_ok
assert flow.ncores_reserved == 0
assert flow.ncores_allocated == 0
assert flow.ncores_used == 0
flow.check_dependencies()
flow.show_status()
flow.show_receivers()
# Run t0, and check status
assert t0.returncode == 0
t0.start_and_wait()
assert t0.returncode == 0
assert t0.status == t0.S_DONE
t0.check_status()
assert t0.status == t0.S_OK
assert t1.can_run
# Cannot start t0 twice...
with pytest.raises(t0.Error):
t0.start()
# But we can restart it.
fired = t0.restart()
assert fired
t0.wait()
assert t0.num_restarts == 1
assert t0.status == t0.S_DONE
t0.check_status()
assert t0.status == t0.S_OK
assert not t0.can_run
# Now we can run t1.
t1.start_and_wait()
assert t1.status == t0.S_DONE
t1.check_status()
assert t1.status == t1.S_OK
assert not t1.can_run
# This one does not work yet
#fired = t1.restart()
#atrue(fired)
#t1.wait()
#aequal(t1.num_restarts, 1)
#aequal(t1.status, t1.S_DONE)
#t1.check_status()
#aequal(t1.status, t1.S_OK)
#afalse(t1.can_run)
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
for task in flow.iflat_tasks():
assert len(task.outdir.list_filepaths(wildcard="*GSR.nc")) == 1
# Test GSR robot
with abilab.abirobot(flow, "GSR") as robot:
table = robot.get_dataframe()
assert table is not None
print(table)
# Test AbinitTimer.
timer = t0.parse_timing()
print(timer)
if has_matplotlib:
timer.plot_pie(show=False)
timer.plot_stacked_hist(show=False)
timer.plot_efficiency(show=False)
def itest_unconverged_scf(fwp, tvars):
"""Testing the treatment of unconverged GS calculations."""
print("tvars:\n %s" % str(tvars))
# Build the SCF and the NSCF input (note nstep to have an unconverged run)
scf_input, nscf_input = make_scf_nscf_inputs(tvars,
pp_paths="14si.pspnc",
nstep=1)
# Build the flow and create the database.
flow = abilab.bandstructure_flow(fwp.workdir,
scf_input,
nscf_input,
manager=fwp.manager)
flow.allocate()
# Use smart-io
flow.use_smartio()
flow.build_and_pickle_dump(abivalidate=True)
t0 = flow[0][0]
t1 = flow[0][1]
assert t0.uses_paral_kgb(tvars.paral_kgb)
assert t1.uses_paral_kgb(tvars.paral_kgb)
# This run should not converge.
t0.start_and_wait()
t0.check_status()
assert t0.status == t0.S_UNCONVERGED
# Unconverged with smart-io --> WFK must be there
assert t0.outdir.has_abiext("WFK")
#assert 0
# Remove nstep from the input so that we use the default value.
# Then restart the GS task and test that GS is OK.
assert not t1.can_run
t0.input.pop("nstep")
assert t0.num_restarts == 0
t0.restart()
t0.wait()
assert t0.num_restarts == 1
t0.check_status()
assert t0.status == t1.S_OK
# Converged with smart-io --> WFK is not written
assert not t0.outdir.has_abiext("WFK")
# Now we can start the NSCF step
assert t1.can_run
t1.start_and_wait()
t1.check_status()
assert t1.status == t0.S_UNCONVERGED
assert not flow.all_ok
# Restart (same trick as the one used for the GS run)
t1.input.pop("nstep")
assert t1.num_restarts == 0
assert t1.restart()
t1.wait()
assert t1.num_restarts == 1
assert t1.status == t1.S_DONE
t1.check_status()
assert t1.status == t1.S_OK
flow.show_status()
assert flow.all_ok
# Test inspect methods
if has_matplotlib():
t0.inspect(show=False)
# Test get_results
t0.get_results()
t1.get_results()
# Build tarball file.
tarfile = flow.make_tarfile()
#assert flow.validate_json_schema()
# Test reset_from_scratch
t0.reset_from_scratch()
assert t0.status == t0.S_READY
# Datetime counters shouls be set to None
dt = t0.datetimes
assert (dt.submission, dt.start, dt.end) == (None, None, None)
t0.start_and_wait()
t0.reset_from_scratch()
# Datetime counters shouls be set to None
dt = t0.datetimes
assert (dt.submission, dt.start, dt.end) == (None, None, None)
def itest_bandstructure_flow(fwp, tvars):
"""
Testing band-structure flow with one dependency: SCF -> NSCF.
"""
print("tvars:\n %s" % str(tvars))
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs(tvars, pp_paths="14si.pspnc")
# Build the flow and create the database.
flow = abilab.bandstructure_flow(fwp.workdir,
scf_input,
nscf_input,
manager=fwp.manager)
flow.build_and_pickle_dump(abivalidate=True)
t0 = flow[0][0]
t1 = flow[0][1]
# Test initialization status, task properties and links (t1 requires t0)
assert t0.status == t0.S_INIT
assert t1.status == t1.S_INIT
assert t0.can_run
assert not t1.can_run
assert t1.depends_on(t0)
assert not t1.depends_on(t1)
assert t0.isnc
assert not t0.ispaw
# Flow properties and methods
assert flow.num_tasks == 2
assert not flow.all_ok
assert flow.ncores_reserved == 0
assert flow.ncores_allocated == 0
assert flow.ncores_used == 0
flow.check_dependencies()
flow.show_status()
flow.show_receivers()
# Run t0, and check status
assert t0.returncode == 0
t0.start_and_wait()
assert t0.returncode == 0
assert t0.status == t0.S_DONE
t0.check_status()
assert t0.status == t0.S_OK
assert t1.can_run
# Cannot start t0 twice...
with pytest.raises(t0.Error):
t0.start()
# But we can restart it.
fired = t0.restart()
assert fired
t0.wait()
assert t0.num_restarts == 1
assert t0.status == t0.S_DONE
t0.check_status()
assert t0.status == t0.S_OK
assert not t0.can_run
# Now we can run t1.
t1.start_and_wait()
assert t1.status == t0.S_DONE
t1.check_status()
assert t1.status == t1.S_OK
assert not t1.can_run
# This one does not work yet
#fired = t1.restart()
#atrue(fired)
#t1.wait()
#aequal(t1.num_restarts, 1)
#aequal(t1.status, t1.S_DONE)
#t1.check_status()
#aequal(t1.status, t1.S_OK)
#afalse(t1.can_run)
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
for task in flow.iflat_tasks():
assert len(task.outdir.list_filepaths(wildcard="*GSR.nc")) == 1
# Test GSR robot
with abilab.abirobot(flow, "GSR") as robot:
table = robot.get_dataframe()
assert table is not None
print(table)
# Test AbinitTimer.
timer = t0.parse_timing()
print(timer)
if has_matplotlib:
timer.plot_pie(show=False)
timer.plot_stacked_hist(show=False)
timer.plot_efficiency(show=False)
def itest_bandstructure_flow(fwp, tvars):
"""
Test band-structure flow with one dependency: SCF -> NSCF.
"""
print("tvars:\n %s" % str(tvars))
# Get the SCF and the NSCF input.
scf_input, nscf_input = make_scf_nscf_inputs(tvars, pp_paths="14si.pspnc")
# Build the flow and create the database.
flow = abilab.bandstructure_flow(fwp.workdir, fwp.manager, scf_input, nscf_input)
flow.build_and_pickle_dump()
t0 = flow[0][0]
t1 = flow[0][1]
# Test initialization status, task properties and links (t1 requires t0)
assert t0.status == t0.S_INIT
assert t1.status == t1.S_INIT
assert t0.can_run
assert not t1.can_run
assert t1.depends_on(t0)
assert not t1.depends_on(t1)
assert t0.isnc
assert not t0.ispaw
# Flow properties and methods
assert flow.num_tasks == 2
assert not flow.all_ok
assert flow.ncpus_reserved == 0
assert flow.ncpus_allocated == 0
assert flow.ncpus_inuse == 0
flow.check_dependencies()
flow.show_status()
flow.show_receivers()
# Run t0, and check status
assert t0.returncode == 0
t0.start_and_wait()
assert t0.returncode == 0
assert t0.status == t0.S_DONE
t0.check_status()
assert t0.status == t0.S_OK
assert t1.can_run
# Cannot start t0 twice...
with pytest.raises(t0.Error):
t0.start()
# But we can restart it.
fired = t0.restart()
assert fired
t0.wait()
assert t0.num_restarts == 1
assert t0.status == t0.S_DONE
t0.check_status()
assert t0.status == t0.S_OK
assert not t0.can_run
# Now we can run t1.
t1.start_and_wait()
assert t1.status == t0.S_DONE
t1.check_status()
assert t1.status == t1.S_OK
assert not t1.can_run
# This one does not work yet
#fired = t1.restart()
#atrue(fired)
#t1.wait()
#aequal(t1.num_restarts, 1)
#aequal(t1.status, t1.S_DONE)
#t1.check_status()
#aequal(t1.status, t1.S_OK)
#afalse(t1.can_run)
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
for task in flow.iflat_tasks():
assert len(task.outdir.list_filepaths(wildcard="*GSR.nc")) == 1
