def test_computer_delete(self):
"""
Test if 'verdi computer delete' command works
"""
from aiida.orm.computer import Computer as AiidaOrmComputer
from aiida.common.exceptions import NotExistent
# Setup a computer to delete during the test
comp = AiidaOrmComputer(name='computer_for_test_delete',
hostname='localhost',
transport_type='local',
scheduler_type='direct',
workdir='/tmp/aiida')
comp.store()
# See if the command complains about not getting an invalid computer
options = ['non_existent_computer_name']
result = self.runner.invoke(computer_delete, options)
# Exception should be raised
self.assertIsNotNone(result.exception)
# Delete a computer name successully.
options = ['computer_for_test_delete']
result = self.runner.invoke(computer_delete, options)
# Exception should be not be raised
self.assertIsNone(result.exception)
# Check that the computer really was deleted
with self.assertRaises(NotExistent):
AiidaOrmComputer.get('computer_for_test_delete')
def get_computer(self, name):
"""
Get a Computer object with given name, or raise NotExistent
"""
from aiida.orm.computer import Computer as AiidaOrmComputer
return AiidaOrmComputer.get(name)
def setUpClass(cls):
from aiida.orm.user import User
from aiida.orm.computer import Computer
from aiida.common.utils import get_configured_user_email
# I create the user only once:
# We create the user only once:
# Otherwise, get_automatic_user() will fail when the
# user is recreated because it caches the user!
# In any case, store it in cls.user though
# Other possibility: flush the user cache on delete
users = User.search_for_users(email=get_configured_user_email())
assert (len(users) <= 1)
if users:
cls.user = users[0]
else:
cls.user = User(get_configured_user_email())
cls.user.password = '******'
cls.user.save()
try:
cls.computer = Computer.get('test_comp')
except NotExistent:
cls.computer = Computer(name='test_comp',
hostname='localhost',
transport_type='local',
scheduler_type='pbspro',
workdir='/tmp/aiida')
cls.computer.store()
def test_computer_rename(self):
"""
Test if 'verdi computer rename' command works
"""
from aiida.orm.computer import Computer as AiidaOrmComputer
from aiida.common.exceptions import NotExistent
# See if the command complains about not getting an invalid computer
options = ['not_existent_computer_name']
result = self.runner.invoke(computer_rename, options)
# Exception should be raised
self.assertIsNotNone(result.exception)
# See if the command complains about not getting both names
options = ['comp_cli_test_computer']
result = self.runner.invoke(computer_rename, options)
# Exception should be raised
self.assertIsNotNone(result.exception)
# The new name must be different to the old one
options = ['comp_cli_test_computer', 'comp_cli_test_computer']
result = self.runner.invoke(computer_rename, options)
# Exception should be raised
self.assertIsNotNone(result.exception)
# Change a computer name successully.
options = ['comp_cli_test_computer', 'renamed_test_computer']
result = self.runner.invoke(computer_rename, options)
# Exception should be not be raised
self.assertIsNone(result.exception)
# Check that the name really was changed
# The old name should not be available
with self.assertRaises(NotExistent):
AiidaOrmComputer.get('comp_cli_test_computer')
# The new name should be avilable
try:
AiidaOrmComputer.get('renamed_test_computer')
except NotExistent:
assertTrue(False)
# Now change the name back
options = ['renamed_test_computer', 'comp_cli_test_computer']
result = self.runner.invoke(computer_rename, options)
# Exception should be not be raised
self.assertIsNone(result.exception)
# Check that the name really was changed
# The old name should not be available
with self.assertRaises(NotExistent):
AiidaOrmComputer.get('renamed_test_computer')
# The new name should be avilable
try:
AiidaOrmComputer.get('comp_cli_test_computer')
except NotExistent:
assertTrue(False)
def generate_ApeCalculation(codename, element, s, p, d, f):
inp = ApeCalculation.process().get_inputs_template()
inp.code = Code.get_from_string(codename)
inp._options.computer = Computer.get('localhost')
inp._options.resources = {"num_machines": 1}
check = False
for ele in ELEMENTS:
if element == ele.symbol:
nc = int(ele.number)
check = True
print check, nc
if not check:
sys.exit("element is not valid")
corpar = 1
if nc <= 2:
corpar = 0
parameters = ParameterData(
dict={
'Title': '{}'.format(element),
'CalculationMode': 'ae + pp',
'Verbose': '40',
'WaveEquation': 'schrodinger',
'XCFunctional': 'lda_x + lda_c_pz',
'NuclearCharge': '{}'.format(nc),
'PPCalculationTolerance': '1.e-6',
'PPOutputFileFormat': 'upf + siesta',
'CoreCorrection': '{}'.format(corpar),
'EigenSolverTolerance': '1.e-8',
'ODEIntTolerance': '1.e-12'
})
orbitals, PPComponents = get_orb_and_PPcomp(nc, s, p, d, f)
inp.parameters = parameters
inp.orbitals = orbitals
inp.PPComponents = PPComponents
inp._label = "{0} {1} {2} {3}".format(s, p, d, f)
inp._description = "{} pseudo generation with cut of radii in label".format(
element)
return inp
def get_computers_work_dir(calculations, user):
"""
Get a list of computers and their remotes working directory.
`calculations` should be a list of JobCalculation object.
"""
from aiida.orm.computer import Computer
from aiida.backends.utils import get_authinfo
computers = [Computer.get(c.dbcomputer) for c in calculations]
remotes = {}
for computer in computers:
remotes[computer.name] = {
'transport':
get_authinfo(computer=computer, aiidauser=user).get_transport(),
'computer':
computer,
}
return remotes
def computer_update(self, *args):
"""
Update an existing computer
"""
import argparse
from aiida.common.exceptions import NotExistent
if not is_dbenv_loaded():
load_dbenv()
# from aiida.backends.djsite.db.models import DbNode
from aiida.orm.computer import Computer
parser = argparse.ArgumentParser(prog=self.get_full_command_name(),
description='Update a computer')
# The default states are those that are shown if no option is given
parser.add_argument('computer_name', help="The name of the computer")
parsed_args = parser.parse_args(args)
computer_name = parsed_args.computer_name
try:
computer = Computer.get(computer_name)
except NotExistent:
print "No computer {} was found".format(computer_name)
sys.exit(1)
calculation_on_computer = computer.get_calculations_on_computer()
if calculation_on_computer:
# Note: this is an artificial comment.
# If you comment the following lines, you will be able to overwrite
# the old computer anyway, at your own risk.
print "You cannot modify a computer, after you run some calculations on it."
print "Disable this computer and set up a new one."
sys.exit(1)
print "*" * 75
print "WARNING! Modifying existing computer with name '{}'".format(
computer_name)
print "Are you sure you want to continue? The UUID will remain the same!"
print "Continue only if you know what you are doing."
print "If you just want to rename a computer, use the 'verdi computer rename'"
print "command. In most cases, it is better to create a new computer."
print "Moreover, if you change the transport, you must also reconfigure"
print "each computer for each user!"
print "*" * 75
print "Press [Enter] to continue, or [Ctrl]+C to exit."
raw_input()
prompt_for_computer_configuration(computer)
try:
computer.store()
except ValidationError as e:
print "Unable to store the computer: {}. Exiting...".format(
e.message)
sys.exit(1)
print "Computer '{}' successfully updated.".format(computer_name)
print "pk: {}, uuid: {}".format(computer.pk, computer.uuid)
print "(Note: machine_dependent transport parameters cannot be set via "
print "the command-line interface at the moment)"
print "OK"
pass
def computer_list(self, *args):
"""
List available computers
"""
import argparse
if not is_dbenv_loaded():
load_dbenv()
from aiida.orm.computer import Computer as AiiDAOrmComputer
from aiida.backends.utils import get_automatic_user
parser = argparse.ArgumentParser(
prog=self.get_full_command_name(),
description='List the computers in the database.')
# The default states are those that are shown if no option is given
parser.add_argument(
'-C',
'--color',
action='store_true',
help="Use colors to help visualizing the different categories",
)
parser.add_argument(
'-o',
'--only-usable',
action='store_true',
help="Show only computers that are usable (i.e., "
"configured for the given user and enabled)",
)
parser.add_argument(
'-p',
'--parsable',
action='store_true',
help="Show only the computer names, one per line, "
"without any other information or string.",
)
parser.add_argument(
'-a',
'--all',
action='store_true',
help="Show also disabled or unconfigured computers",
)
parser.set_defaults(also_disabled=False)
parsed_args = parser.parse_args(args)
use_colors = parsed_args.color
only_usable = parsed_args.only_usable
parsable = parsed_args.parsable
all_comps = parsed_args.all
computer_names = self.get_computer_names()
if use_colors:
color_id = 90 # Dark gray
color_id = None # Default color
if color_id is not None:
start_color = "\x1b[{}m".format(color_id)
end_color = "\x1b[0m"
else:
start_color = ""
end_color = ""
else:
start_color = ""
end_color = ""
if not parsable:
print "{}# List of configured computers:{}".format(
start_color, end_color)
print(
"{}# (use 'verdi computer show COMPUTERNAME' "
"to see the details){}".format(start_color, end_color))
if computer_names:
for name in sorted(computer_names):
computer = AiiDAOrmComputer.get(name)
# color_id = 90 # Dark gray
# color_id = 34 # Blue
is_configured = computer.is_user_configured(
get_automatic_user())
is_user_enabled = computer.is_user_enabled(
get_automatic_user())
is_usable = False # True if both enabled and configured
if not all_comps:
if not is_configured or not is_user_enabled or not computer.is_enabled(
):
continue
if computer.is_enabled():
if is_configured:
configured_str = ""
if is_user_enabled:
symbol = "*"
color_id = None
enabled_str = ""
is_usable = True
else:
symbol = "x"
color_id = 31 # Red
enabled_str = "[DISABLED for this user]"
else:
symbol = "x"
color_id = 90 # Dark gray
enabled_str = ""
configured_str = " [unconfigured]"
else: # GLOBALLY DISABLED
symbol = "x"
color_id = 31 # Red
if is_configured and not is_user_enabled:
enabled_str = " [DISABLED globally AND for this user]"
else:
enabled_str = " [DISABLED globally]"
if is_configured:
configured_str = ""
else:
configured_str = " [unconfigured]"
if use_colors:
if color_id is not None:
start_color = "\x1b[{}m".format(color_id)
bold_sequence = "\x1b[1;{}m".format(color_id)
nobold_sequence = "\x1b[0;{}m".format(color_id)
else:
start_color = "\x1b[0m"
bold_sequence = "\x1b[1m"
nobold_sequence = "\x1b[0m"
end_color = "\x1b[0m"
else:
start_color = ""
end_color = ""
bold_sequence = ""
nobold_sequence = ""
if parsable:
print "{}{}{}".format(start_color, name, end_color)
else:
if (not only_usable) or is_usable:
print "{}{} {}{}{} {}{}{}".format(
start_color, symbol, bold_sequence, name,
nobold_sequence, enabled_str, configured_str,
end_color)
else:
print "# No computers configured yet. Use 'verdi computer setup'"
def deposit(what,
type,
author_name=None,
author_email=None,
url=None,
title=None,
username=None,
password=False,
user_email=None,
code_label=default_options['code'],
computer_name=None,
replace=None,
message=None,
**kwargs):
"""
Launches a
:py:class:`aiida.orm.implementation.general.calculation.job.AbstractJobCalculation`
to deposit data node to \*COD-type database.
:return: launched :py:class:`aiida.orm.implementation.general.calculation.job.AbstractJobCalculation`
instance.
:raises ValueError: if any of the required parameters are not given.
"""
from aiida.common.setup import get_property
parameters = {}
if not what:
raise ValueError("Node to be deposited is not supplied")
if not type:
raise ValueError("Deposition type is not supplied. Should be "
"one of the following: 'published', "
"'prepublication' or 'personal'")
if not username:
username = get_property('tcod.depositor_username')
if not username:
raise ValueError("Depositor username is not supplied")
if not password:
parameters['password'] = get_property('tcod.depositor_password')
if not parameters['password']:
raise ValueError("Depositor password is not supplied")
if not user_email:
user_email = get_property('tcod.depositor_email')
if not user_email:
raise ValueError("Depositor email is not supplied")
parameters['deposition-type'] = type
parameters['username'] = username
parameters['user_email'] = user_email
if type == 'published':
pass
elif type in ['prepublication', 'personal']:
if not author_name:
author_name = get_property('tcod.depositor_author_name')
if not author_name:
raise ValueError("Author name is not supplied")
if not author_email:
author_email = get_property('tcod.depositor_author_email')
if not author_email:
raise ValueError("Author email is not supplied")
if not title:
raise ValueError("Publication title is not supplied")
else:
raise ValueError("Unknown deposition type '{}' -- should be "
"one of the following: 'published', "
"'prepublication' or 'personal'".format(type))
if replace:
if str(int(replace)) != replace or int(replace) < 10000000 \
or int(replace) > 99999999:
raise ValueError("ID of the replaced structure ({}) does not "
"seem to be valid TCOD ID: must be in "
"range [10000000,99999999]".format(replace))
elif message:
raise ValueError("Message is given while the structure is not "
"redeposited -- log message is relevant to "
"redeposition only")
kwargs['additional_tags'] = {}
if title:
kwargs['additional_tags']['_publ_section_title'] = title
if author_name:
kwargs['additional_tags']['_publ_author_name'] = author_name
if replace:
kwargs['additional_tags']['_tcod_database_code'] = replace
kwargs['datablock_names'] = [replace]
cif = export_cifnode(what, store=True, **kwargs)
from aiida.orm.code import Code
from aiida.orm.computer import Computer
from aiida.orm.data.parameter import ParameterData
from aiida.common.exceptions import NotExistent
code = Code.get_from_string(code_label)
computer = None
if computer_name:
computer = Computer.get(computer_name)
calc = code.new_calc(computer=computer)
calc.set_resources({'num_machines': 1, 'num_mpiprocs_per_machine': 1})
if password:
import getpass
parameters['password'] = getpass.getpass("Password: ")
if author_name:
parameters['author_name'] = author_name
if author_email:
parameters['author_email'] = author_email
if url:
parameters['url'] = url
if replace:
parameters['replace'] = True
if message:
parameters['log-message'] = str(message)
pd = ParameterData(dict=parameters)
calc.use_cif(cif)
calc.use_parameters(pd)
calc.store_all()
calc.submit()
return calc
def computer_list(only_usable, parsable, all_comps):
"""
List available computers
"""
from aiida.orm.computer import Computer as AiiDAOrmComputer
from aiida.orm.backend import construct_backend
backend = construct_backend()
computer_names = get_computer_names()
if not parsable:
echo.echo("# List of configured computers:")
echo.echo("# (use 'verdi computer show COMPUTERNAME' "
"to see the details)")
if computer_names:
for name in sorted(computer_names):
computer = AiiDAOrmComputer.get(name)
is_configured = computer.is_user_configured(
backend.users.get_automatic_user())
is_user_enabled = computer.is_user_enabled(
backend.users.get_automatic_user())
is_usable = False # True if both enabled and configured
if not all_comps:
if not is_configured or not is_user_enabled or not computer.is_enabled(
):
continue
if computer.is_enabled():
if is_configured:
configured_str = ""
if is_user_enabled:
symbol = "*"
color = 'green'
enabled_str = ""
is_usable = True
else:
symbol = "x"
color = 'red'
enabled_str = "[DISABLED for this user]"
else:
symbol = "x"
color = 'reset'
enabled_str = ""
configured_str = " [unconfigured]"
else: # GLOBALLY DISABLED
symbol = "x"
color = 'red'
if is_configured and not is_user_enabled:
enabled_str = " [DISABLED globally AND for this user]"
else:
enabled_str = " [DISABLED globally]"
if is_configured:
configured_str = ""
else:
configured_str = " [unconfigured]"
if parsable:
echo.echo(click.style("{}".format(name), fg=color))
else:
if (not only_usable) or is_usable:
echo.echo(click.style("{} ".format(symbol), fg=color),
nl=False)
echo.echo(click.style("{} ".format(name),
bold=True,
fg=color),
nl=False)
echo.echo(
click.style("{}{}".format(enabled_str, configured_str),
fg=color))
else:
echo.echo("# No computers configured yet. Use 'verdi computer setup'")