def test_unicode(self):
"""Check that there are no exceptions raised when using unicode folders."""
tmpsource = tempfile.mkdtemp()
tmpdest = tempfile.mkdtemp()
with open(os.path.join(tmpsource, 'sąžininga'), 'w',
encoding='utf8') as fhandle:
fhandle.write('test')
with open(os.path.join(tmpsource, 'žąsis'), 'w',
encoding='utf8') as fhandle:
fhandle.write('test')
folder = Folder(tmpdest)
folder.insert_path(tmpsource, 'destination')
folder.insert_path(tmpsource, 'šaltinis')
self.assertEqual(sorted(folder.get_content_list()),
sorted(['destination', 'šaltinis']))
self.assertEqual(
sorted(folder.get_subfolder('destination').get_content_list()),
sorted(['sąžininga', 'žąsis']))
self.assertEqual(
sorted(folder.get_subfolder('šaltinis').get_content_list()),
sorted(['sąžininga', 'žąsis']))
folder = Folder(os.path.join(tmpsource, 'šaltinis'))
folder.insert_path(tmpdest, 'destination')
folder.insert_path(tmpdest, 'kitas-šaltinis')
self.assertEqual(sorted(folder.get_content_list()),
sorted(['destination', 'kitas-šaltinis']))
def _collect_files(base, path=''):
"""
Recursively collects files from the tree, starting at a given path.
"""
from aiida.common.folders import Folder
from aiida.common.utils import md5_file,sha1_file
import os
if os.path.isdir(os.path.join(base,path)):
folder = Folder(os.path.join(base,path))
files_now = []
if path != '':
if not path.endswith(os.sep):
path = "{}{}".format(path,os.sep)
if path != '':
files_now.append({
'name': path,
'type': 'folder',
})
for f in sorted(folder.get_content_list()):
files = _collect_files(base,path=os.path.join(path,f))
files_now.extend(files)
return files_now
else:
with open(os.path.join(base,path)) as f:
return [{
'name': path,
'contents': f.read(),
'md5': md5_file(os.path.join(base,path)),
'sha1': sha1_file(os.path.join(base,path)),
'type': 'file',
}]
def _collect_files(base, path=''):
"""
Recursively collects files from the tree, starting at a given path.
"""
from aiida.common.folders import Folder
from aiida.common.utils import md5_file, sha1_file
import os
def get_filename(file_dict):
return file_dict['name']
if os.path.isdir(os.path.join(base, path)):
folder = Folder(os.path.join(base, path))
files_now = []
if path != '':
if not path.endswith(os.sep):
path = "{}{}".format(path, os.sep)
if path != '':
files_now.append({
'name': path,
'type': 'folder',
})
for f in folder.get_content_list():
files = _collect_files(base, path=os.path.join(path, f))
files_now.extend(files)
return sorted(files_now, key=get_filename)
elif path == '.aiida/calcinfo.json':
files = []
with open(os.path.join(base, path)) as f:
files.append({
'name': path,
'contents': f.read(),
'md5': md5_file(os.path.join(base, path)),
'sha1': sha1_file(os.path.join(base, path)),
'type': 'file',
})
import json
with open(os.path.join(base, path)) as f:
calcinfo = json.load(f)
if 'local_copy_list' in calcinfo:
for local_copy in calcinfo['local_copy_list']:
with open(local_copy[0]) as f:
files.append({
'name': os.path.normpath(local_copy[1]),
'contents': f.read(),
'md5': md5_file(local_copy[0]),
'sha1': sha1_file(local_copy[0]),
'type': 'file',
})
return files
else:
with open(os.path.join(base, path)) as f:
return [{
'name': path,
'contents': f.read(),
'md5': md5_file(os.path.join(base, path)),
'sha1': sha1_file(os.path.join(base, path)),
'type': 'file',
}]
def test_prepare(vasp_calc, vasp_chgcar, vasp_wavecar, vasp_inputs,
localhost_dir):
"""Check that preparing creates all necessary files."""
from aiida.common.folders import Folder
from aiida_vasp.calcs.vasp import VaspCalculation
wavecar, _ = vasp_wavecar
chgcar, _ = vasp_chgcar
inputs_dict = {
'gga': 'PE',
'gga_compat': False,
'lorbit': 11,
'sigma': 0.5,
'magmom': '30 * 2*0.',
'icharg': 11
}
inputs = vasp_inputs(parameters=inputs_dict)
inputs.charge_density = chgcar
inputs.wavefunctions = wavecar
calc = vasp_calc(inputs=inputs)
temp_folder = Folder(str(localhost_dir.parent))
calcinfo = calc.prepare_for_submission(temp_folder)
input_files = temp_folder.get_content_list()
for file_name in ['INCAR', 'KPOINTS', 'POSCAR', 'POTCAR']:
assert file_name in input_files
assert 'EIGENVAL' in calcinfo.retrieve_list
assert 'DOSCAR' in calcinfo.retrieve_list
assert 'wannier90*' in calcinfo.retrieve_list
assert calcinfo.codes_info[0].stdout_name == VaspCalculation._VASP_OUTPUT
assert calcinfo.codes_info[0].join_files is True
inputs_dict.update({'icharg': 2})
inputs = vasp_inputs(parameters=inputs_dict)
inputs.charge_density = chgcar
inputs.wavefunctions = wavecar
calc = vasp_calc(inputs=inputs)
temp_folder = Folder(str(localhost_dir.parent))
calcinfo = calc.prepare_for_submission(temp_folder)
assert 'WAVECAR' in [item[1] for item in calcinfo.local_copy_list]
def presubmit(self, folder: Folder) -> CalcInfo:
"""Prepares the calculation folder with all inputs, ready to be copied to the cluster.
:param folder: a SandboxFolder that can be used to write calculation input files and the scheduling script.
:return calcinfo: the CalcInfo object containing the information needed by the daemon to handle operations.
"""
# pylint: disable=too-many-locals,too-many-statements,too-many-branches
from aiida.common.exceptions import PluginInternalError, ValidationError, InvalidOperation, InputValidationError
from aiida.common import json
from aiida.common.utils import validate_list_of_string_tuples
from aiida.common.datastructures import CodeInfo, CodeRunMode
from aiida.orm import load_node, Code, Computer
from aiida.plugins import DataFactory
from aiida.schedulers.datastructures import JobTemplate
computer = self.node.computer
inputs = self.node.get_incoming(link_type=LinkType.INPUT_CALC)
if not self.inputs.metadata.dry_run and self.node.has_cached_links(
): # type: ignore[union-attr]
raise InvalidOperation(
'calculation node has unstored links in cache')
codes = [_ for _ in inputs.all_nodes() if isinstance(_, Code)]
for code in codes:
if not code.can_run_on(computer):
raise InputValidationError(
'The selected code {} for calculation {} cannot run on computer {}'
.format(code.pk, self.node.pk, computer.label))
if code.is_local() and code.get_local_executable(
) in folder.get_content_list():
raise PluginInternalError(
f'The plugin created a file {code.get_local_executable()} that is also the executable name!'
)
calc_info = self.prepare_for_submission(folder)
calc_info.uuid = str(self.node.uuid)
scheduler = computer.get_scheduler()
# I create the job template to pass to the scheduler
job_tmpl = JobTemplate()
job_tmpl.shebang = computer.get_shebang()
job_tmpl.submit_as_hold = False
job_tmpl.rerunnable = False
job_tmpl.job_environment = {}
# 'email', 'email_on_started', 'email_on_terminated',
job_tmpl.job_name = f'aiida-{self.node.pk}'
job_tmpl.sched_output_path = self.options.scheduler_stdout
if self.options.scheduler_stderr == self.options.scheduler_stdout:
job_tmpl.sched_join_files = True
else:
job_tmpl.sched_error_path = self.options.scheduler_stderr
job_tmpl.sched_join_files = False
# Set retrieve path, add also scheduler STDOUT and STDERR
retrieve_list = calc_info.retrieve_list or []
if (job_tmpl.sched_output_path is not None
and job_tmpl.sched_output_path not in retrieve_list):
retrieve_list.append(job_tmpl.sched_output_path)
if not job_tmpl.sched_join_files:
if (job_tmpl.sched_error_path is not None
and job_tmpl.sched_error_path not in retrieve_list):
retrieve_list.append(job_tmpl.sched_error_path)
retrieve_list.extend(
self.node.get_option('additional_retrieve_list') or [])
self.node.set_retrieve_list(retrieve_list)
retrieve_singlefile_list = calc_info.retrieve_singlefile_list or []
# a validation on the subclasses of retrieve_singlefile_list
for _, subclassname, _ in retrieve_singlefile_list:
file_sub_class = DataFactory(subclassname)
if not issubclass(file_sub_class, orm.SinglefileData):
raise PluginInternalError(
'[presubmission of calc {}] retrieve_singlefile_list subclass problem: {} is '
'not subclass of SinglefileData'.format(
self.node.pk, file_sub_class.__name__))
if retrieve_singlefile_list:
self.node.set_retrieve_singlefile_list(retrieve_singlefile_list)
# Handle the retrieve_temporary_list
retrieve_temporary_list = calc_info.retrieve_temporary_list or []
self.node.set_retrieve_temporary_list(retrieve_temporary_list)
# the if is done so that if the method returns None, this is
# not added. This has two advantages:
# - it does not add too many \n\n if most of the prepend_text are empty
# - most importantly, skips the cases in which one of the methods
# would return None, in which case the join method would raise
# an exception
prepend_texts = [computer.get_prepend_text()] + \
[code.get_prepend_text() for code in codes] + \
[calc_info.prepend_text, self.node.get_option('prepend_text')]
job_tmpl.prepend_text = '\n\n'.join(prepend_text
for prepend_text in prepend_texts
if prepend_text)
append_texts = [self.node.get_option('append_text'), calc_info.append_text] + \
[code.get_append_text() for code in codes] + \
[computer.get_append_text()]
job_tmpl.append_text = '\n\n'.join(append_text
for append_text in append_texts
if append_text)
# Set resources, also with get_default_mpiprocs_per_machine
resources = self.node.get_option('resources')
scheduler.preprocess_resources(
resources, computer.get_default_mpiprocs_per_machine())
job_tmpl.job_resource = scheduler.create_job_resource(**resources)
subst_dict = {
'tot_num_mpiprocs': job_tmpl.job_resource.get_tot_num_mpiprocs()
}
for key, value in job_tmpl.job_resource.items():
subst_dict[key] = value
mpi_args = [
arg.format(**subst_dict) for arg in computer.get_mpirun_command()
]
extra_mpirun_params = self.node.get_option(
'mpirun_extra_params') # same for all codes in the same calc
# set the codes_info
if not isinstance(calc_info.codes_info, (list, tuple)):
raise PluginInternalError(
'codes_info passed to CalcInfo must be a list of CalcInfo objects'
)
codes_info = []
for code_info in calc_info.codes_info:
if not isinstance(code_info, CodeInfo):
raise PluginInternalError(
'Invalid codes_info, must be a list of CodeInfo objects')
if code_info.code_uuid is None:
raise PluginInternalError(
'CalcInfo should have the information of the code to be launched'
)
this_code = load_node(code_info.code_uuid, sub_classes=(Code, ))
this_withmpi = code_info.withmpi # to decide better how to set the default
if this_withmpi is None:
if len(calc_info.codes_info) > 1:
raise PluginInternalError(
'For more than one code, it is necessary to set withmpi in codes_info'
)
else:
this_withmpi = self.node.get_option('withmpi')
if this_withmpi:
this_argv = (mpi_args + extra_mpirun_params +
[this_code.get_execname()] +
(code_info.cmdline_params
if code_info.cmdline_params is not None else []))
else:
this_argv = [this_code.get_execname()
] + (code_info.cmdline_params if
code_info.cmdline_params is not None else [])
# overwrite the old cmdline_params and add codename and mpirun stuff
code_info.cmdline_params = this_argv
codes_info.append(code_info)
job_tmpl.codes_info = codes_info
# set the codes execution mode
if len(codes) > 1:
try:
job_tmpl.codes_run_mode = calc_info.codes_run_mode
except KeyError as exc:
raise PluginInternalError(
'Need to set the order of the code execution (parallel or serial?)'
) from exc
else:
job_tmpl.codes_run_mode = CodeRunMode.SERIAL
########################################################################
custom_sched_commands = self.node.get_option(
'custom_scheduler_commands')
if custom_sched_commands:
job_tmpl.custom_scheduler_commands = custom_sched_commands
job_tmpl.import_sys_environment = self.node.get_option(
'import_sys_environment')
job_tmpl.job_environment = self.node.get_option(
'environment_variables')
queue_name = self.node.get_option('queue_name')
account = self.node.get_option('account')
qos = self.node.get_option('qos')
if queue_name is not None:
job_tmpl.queue_name = queue_name
if account is not None:
job_tmpl.account = account
if qos is not None:
job_tmpl.qos = qos
priority = self.node.get_option('priority')
if priority is not None:
job_tmpl.priority = priority
max_memory_kb = self.node.get_option('max_memory_kb')
if max_memory_kb is not None:
job_tmpl.max_memory_kb = max_memory_kb
max_wallclock_seconds = self.node.get_option('max_wallclock_seconds')
if max_wallclock_seconds is not None:
job_tmpl.max_wallclock_seconds = max_wallclock_seconds
max_memory_kb = self.node.get_option('max_memory_kb')
if max_memory_kb is not None:
job_tmpl.max_memory_kb = max_memory_kb
submit_script_filename = self.node.get_option('submit_script_filename')
script_content = scheduler.get_submit_script(job_tmpl)
folder.create_file_from_filelike(io.StringIO(script_content),
submit_script_filename,
'w',
encoding='utf8')
subfolder = folder.get_subfolder('.aiida', create=True)
subfolder.create_file_from_filelike(io.StringIO(json.dumps(job_tmpl)),
'job_tmpl.json',
'w',
encoding='utf8')
subfolder.create_file_from_filelike(io.StringIO(json.dumps(calc_info)),
'calcinfo.json',
'w',
encoding='utf8')
if calc_info.local_copy_list is None:
calc_info.local_copy_list = []
if calc_info.remote_copy_list is None:
calc_info.remote_copy_list = []
# Some validation
this_pk = self.node.pk if self.node.pk is not None else '[UNSTORED]'
local_copy_list = calc_info.local_copy_list
try:
validate_list_of_string_tuples(local_copy_list, tuple_length=3)
except ValidationError as exception:
raise PluginInternalError(
f'[presubmission of calc {this_pk}] local_copy_list format problem: {exception}'
) from exception
remote_copy_list = calc_info.remote_copy_list
try:
validate_list_of_string_tuples(remote_copy_list, tuple_length=3)
except ValidationError as exception:
raise PluginInternalError(
f'[presubmission of calc {this_pk}] remote_copy_list format problem: {exception}'
) from exception
for (remote_computer_uuid, _, dest_rel_path) in remote_copy_list:
try:
Computer.objects.get(uuid=remote_computer_uuid) # pylint: disable=unused-variable
except exceptions.NotExistent as exception:
raise PluginInternalError(
'[presubmission of calc {}] '
'The remote copy requires a computer with UUID={}'
'but no such computer was found in the '
'database'.format(this_pk,
remote_computer_uuid)) from exception
if os.path.isabs(dest_rel_path):
raise PluginInternalError(
'[presubmission of calc {}] '
'The destination path of the remote copy '
'is absolute! ({})'.format(this_pk, dest_rel_path))
return calc_info
def dryrun_test(cls, inputs, castep_exe='castep.serial', verbose=True):
"""
Do a dryrun test in a folder with prepared builder or inputs
"""
if isinstance(inputs, ProcessBuilder):
res = cls.submit_test(inputs)
else:
res = cls.submit_test(cls, **inputs)
folder = Folder(res[1])
dry_run_node = res[0]
seedname = dry_run_node.get_option('seedname')
def _print(inp):
if verbose:
print(inp)
# Do a dryrun
try:
output = check_output([castep_exe, "-v"], universal_newlines=True)
except OSError:
_print("CASTEP executable '{}' is not found".format(castep_exe))
return None
# Now start dryrun
_print("Running with {}".format(
check_output(["which", castep_exe], universal_newlines=True)))
_print(output)
_print("Starting dryrun...")
call([castep_exe, "--dryrun", seedname], cwd=folder.abspath)
# Check if any *err files
contents = folder.get_content_list()
for fname in contents:
if fnmatch(fname, "*.err"):
with folder.open(fname) as fhandle:
_print("Error found in {}:\fname".format(fname))
_print(fhandle.read())
raise InputValidationError("Error found during dryrun")
# Gather information from the dryrun file
dryrun_results = {}
out_file = seedname + '.castep'
with folder.open(out_file) as fhandle:
for line in fhandle:
mth = re.match(r"\s*k-Points For SCF Sampling:\s+(\d+)\s*",
line)
if mth:
dryrun_results["num_kpoints"] = int(mth.group(1))
_print("Number of k-points: {}".format(mth.group(1)))
mth = None
continue
mth = re.match(
r"\| Approx\. total storage required"
r" per process\s+([0-9.]+)\sMB\s+([0-9.]+)", line)
if mth:
dryrun_results["memory_MB"] = (float(mth.group(1)))
dryrun_results["disk_MB"] = (float(mth.group(2)))
_print("RAM: {} MB, DISK: {} MB".format(
mth.group(1), mth.group(2)))
mth = None
continue
return folder, dryrun_results