def test_session_update_and_expiration_2(self):
"""
expire_on_commit=True & committing computer and code objects with
their built-in store function.
"""
from aiida.backends.sqlalchemy.models.user import DbUser
from aiida.orm.computer import Computer
from aiida.orm.code import Code
from aiida.orm.user import User
session = aiida.backends.sqlalchemy.get_scoped_session()
self.set_connection(expire_on_commit=True)
user = User(email=get_configured_user_email())
session.add(user._dbuser)
session.commit()
defaults = dict(name='localhost',
hostname='localhost',
transport_type='local',
scheduler_type='pbspro',
workdir='/tmp/aiida')
computer = Computer(**defaults)
computer.store()
code = Code()
code.set_remote_computer_exec((computer, '/x.x'))
code.store()
self.drop_connection()
def test_remote(self):
import tempfile
from aiida.orm.code import Code
from aiida.orm.computer import Computer
from aiida.common.exceptions import ValidationError
with self.assertRaises(ValueError):
# remote_computer_exec has length 2 but is not a list or tuple
_ = Code(remote_computer_exec='ab')
# invalid code path
with self.assertRaises(ValueError):
_ = Code(remote_computer_exec=(self.computer, ''))
# Relative path is invalid for remote code
with self.assertRaises(ValueError):
_ = Code(remote_computer_exec=(self.computer, 'subdir/run.exe'))
# first argument should be a computer, not a string
with self.assertRaises(TypeError):
_ = Code(remote_computer_exec=('localhost', '/bin/ls'))
code = Code(remote_computer_exec=(self.computer, '/bin/ls'))
with tempfile.NamedTemporaryFile() as f:
f.write("#/bin/bash\n\necho test run\n")
f.flush()
code.add_path(f.name, 'test.sh')
with self.assertRaises(ValidationError):
# There are files inside
code.store()
# If there are no files, I can store
code.remove_path('test.sh')
code.store()
self.assertEquals(code.get_remote_computer().pk, self.computer.pk)
self.assertEquals(code.get_remote_exec_path(), '/bin/ls')
self.assertEquals(code.get_execname(), '/bin/ls')
self.assertTrue(code.can_run_on(self.computer.dbcomputer))
self.assertTrue(code.can_run_on(self.computer))
othercomputer = Computer(name='another_localhost',
hostname='localhost',
transport_type='local',
scheduler_type='pbspro',
workdir='/tmp/aiida').store()
self.assertFalse(code.can_run_on(othercomputer))
def test_code_local(self):
code = Code(local_executable='test.sh')
with self.assertRaises(ValidationError):
# No file with name test.sh
code.store()
with tempfile.NamedTemporaryFile() as f:
f.write("#/bin/bash\n\necho test run\n")
f.flush()
code.add_path(f.name, 'test.sh')
code.store()
self.assertTrue(code.can_run_on(self.computer))
self.assertTrue(code.get_local_executable(), 'test.sh')
self.assertTrue(code.get_execname(), 'stest.sh')
class TestWf(PluginTestCase):
def setUp(self):
"""
"""
from aiida import work
from aiida.orm.code import Code
from aiida.orm.nodes.parameter import Dict
from aiida.orm.nodes.structure import StructureData
from aiida.orm.nodes.remote import RemoteData
from ase.spacegroup import crystal
from aiida_quantumespresso.calculations.pw import PwCalculation
from aiida_yambo.calculations.gw import YamboCalculation
from aiida.common.links import LinkType
from aiida.orm.computer import Computer as AiidaOrmComputer
from aiida.common.datastructures import calc_states
from aiida.plugins.utils import DataFactory
runner = work.Runner(poll_interval=0.,
rmq_config=None,
enable_persistence=None)
work.set_runner(runner)
self.computer = AiidaOrmComputer(name="testcase")
# conf_attrs hostname, description, enabled_state, transport_type, scheduler_type, workdir
# mpirun_command , default_mpiprocs_per_machine,
self.computer._set_hostname_string("localhost")
self.computer._set_enabled_state_string('True')
self.computer._set_transport_type_string("local")
self.computer._set_scheduler_type_string("direct")
self.computer._set_workdir_string("/tmp/testcase/{username}/base")
self.computer.store()
create_authinfo(computer=self.computer).store()
self.code_yambo = Code()
self.code_yambo.label = "yambo"
os_env = os.environ.copy()
yambo_path = subprocess.check_output(['which', 'mock_yambo'],
env=os_env).strip()
self.code_yambo.set_remote_computer_exec((self.computer, yambo_path))
self.code_yambo.set_input_plugin_name('yambo.yambo')
self.code_p2y = Code()
self.code_p2y.label = "p2y"
p2y_path = subprocess.check_output(['which', 'mock_p2y'],
env=os_env).strip()
self.code_p2y.set_remote_computer_exec((self.computer, p2y_path))
self.code_p2y.set_input_plugin_name('yambo.yambo')
self.code_yambo.store()
self.code_p2y.store()
self.calc_pw = PwCalculation()
self.calc_pw.set_computer(self.computer)
self.calc_pw.set_resources({
"num_machines": 1,
"num_mpiprocs_per_machine": 16,
'default_mpiprocs_per_machine': 16
})
StructureData = DataFactory('structure')
cell = [[15.8753100000, 0.0000000000, 0.0000000000],
[0.0000000000, 15.8753100000, 0.0000000000],
[0.0000000000, 0.0000000000, 2.4696584760]]
s = StructureData(cell=cell)
self.calc_pw.use_structure(s)
print((self.calc_pw.store_all(), " pw calc"))
pw_remote_folder = RemoteData(computer=self.computer,
remote_path="/tmp/testcase/work/calcPW")
print((pw_remote_folder.store(), "pw remote data"))
self.calc_pw._set_state(calc_states.PARSING)
pw_remote_folder.add_link_from(self.calc_pw,
label='remote_folder',
link_type=LinkType.CREATE)
outputs = Dict(
dict={
"lsda": False,
"number_of_bands": 80,
"number_of_electrons": 8.0,
"number_of_k_points": 147,
"non_colinear_calculation": False
})
outputs.store()
outputs.add_link_from(self.calc_pw,
label='output_parameters',
link_type=LinkType.CREATE)
self.calc = YamboCalculation()
self.calc.set_computer(self.computer)
self.calc.use_code(self.code_p2y)
p2y_settings = {
u'ADDITIONAL_RETRIEVE_LIST':
[u'r-*', u'o-*', u'l-*', u'l_*', u'LOG/l-*_CPU_1'],
u'INITIALISE':
True
}
yambo_settings = {
u'ADDITIONAL_RETRIEVE_LIST':
[u'r-*', u'o-*', u'l-*', u'l_*', u'LOG/l-*_CPU_1']
}
self.calc.use_settings(Dict(dict=p2y_settings))
self.calc.set_resources({
"num_machines": 1,
"num_mpiprocs_per_machine": 16,
'default_mpiprocs_per_machine': 16
})
self.calc.use_parent_calculation(self.calc_pw)
print((self.calc.store_all(), " yambo calc"))
self.calc._set_state(calc_states.PARSING)
a = 5.388
cell = crystal('Si', [(0, 0, 0)],
spacegroup=227,
cellpar=[a, a, a, 90, 90, 90],
primitive_cell=True)
self.struc = StructureData(ase=cell)
self.struc.store()
self.parameters = Dict(
dict={
"BndsRnXp": [1.0, 48.0],
"Chimod": "Hartree",
"DysSolver": "n",
"FFTGvecs": 25,
"FFTGvecs_units": "Ry",
"GbndRnge": [1.0, 48.0],
"HF_and_locXC": True,
"LongDrXp": [1.0, 0.0, 0.0],
"NGsBlkXp": 2,
"NGsBlkXp_units": "Ry",
"QPkrange": [[1, 145, 3, 5]],
"SE_CPU": "1 2 4",
"SE_ROLEs": "q qp b",
"X_all_q_CPU": "1 1 4 2",
"X_all_q_ROLEs": "q k c v",
"em1d": True,
"gw0": True,
"ppa": True,
"rim_cut": True
})
self.yambo_settings = Dict(
dict={
"ADDITIONAL_RETRIEVE_LIST": [
"r-*", "o-*", "l-*", "l_*", "LOG/l-*_CPU_1",
"aiida/ndb.QP", "aiida/ndb.HF_and_locXC"
]
})
self.p2y_settings = Dict(
dict={
"ADDITIONAL_RETRIEVE_LIST": [
'r-*', 'o-*', 'l-*', 'l_*', 'LOG/l-*_CPU_1',
'aiida/ndb.QP', 'aiida/ndb.HF_and_locXC'
],
'INITIALISE':
True
})
self.yambo_calc_set = Dict(
dict={
'resources': {
"num_machines": 1,
"num_mpiprocs_per_machine": 16
},
'max_wallclock_seconds': 60 * 29,
'max_memory_kb': 1 * 88 * 1000000,
"queue_name":
"s3parvc3", #'custom_scheduler_commands': u"#PBS -A Pra14_3622" ,
'environment_variables': {
"OMP_NUM_THREADS": "1"
}
})
self.p2y_calc_set = Dict(
dict={
'resources': {
"num_machines": 1,
"num_mpiprocs_per_machine": 2
},
'max_wallclock_seconds': 60 * 2,
'max_memory_kb': 1 * 10 * 1000000,
"queue_name":
"s3parvc3", # 'custom_scheduler_commands': u"#PBS -A Pra14_3622" ,
'environment_variables': {
"OMP_NUM_THREADS": "2"
}
})
self.remote_folder = RemoteData(computer=self.computer,
remote_path="/tmp/testcase/work/calcX")
self.remote_folder.store()
self.remote_folder.add_link_from(self.calc,
label='remote_folder',
link_type=LinkType.CREATE)
self.calc._set_state(calc_states.FINISHED)
#self.calc.store_all()
def tearDown(self):
"""
"""
pass
def test_simple_log(self):
from aiida.engine.launch import run
from aiida.orm.nodes import Float, Str, NumericType, List, Bool
from aiida_yambo.workflows.yamborestart import YamboRestartWf
p2y_result = run(YamboRestartWf,
precode=Str('p2y'),
yambocode=Str('yambo'),
parameters=self.parameters,
calculation_set=self.yambo_calc_set,
parent_folder=self.remote_folder,
settings=self.yambo_settings)
assert 'retrieved' in p2y_result
