def upload_calculation(node: CalcJobNode,
transport: Transport,
calc_info: CalcInfo,
folder: SandboxFolder,
inputs: Optional[MappingType[str, Any]] = None,
dry_run: bool = False) -> None:
"""Upload a `CalcJob` instance
:param node: the `CalcJobNode`.
:param transport: an already opened transport to use to submit the calculation.
:param calc_info: the calculation info datastructure returned by `CalcJob.presubmit`
:param folder: temporary local file system folder containing the inputs written by `CalcJob.prepare_for_submission`
"""
# pylint: disable=too-many-locals,too-many-branches,too-many-statements
# If the calculation already has a `remote_folder`, simply return. The upload was apparently already completed
# before, which can happen if the daemon is restarted and it shuts down after uploading but before getting the
# chance to perform the state transition. Upon reloading this calculation, it will re-attempt the upload.
link_label = 'remote_folder'
if node.get_outgoing(RemoteData, link_label_filter=link_label).first():
EXEC_LOGGER.warning(
f'CalcJobNode<{node.pk}> already has a `{link_label}` output: skipping upload'
)
return calc_info
computer = node.computer
codes_info = calc_info.codes_info
input_codes = [
load_node(_.code_uuid, sub_classes=(Code, )) for _ in codes_info
]
logger_extra = get_dblogger_extra(node)
transport.set_logger_extra(logger_extra)
logger = LoggerAdapter(logger=EXEC_LOGGER, extra=logger_extra)
if not dry_run and node.has_cached_links():
raise ValueError(
'Cannot submit calculation {} because it has cached input links! If you just want to test the '
'submission, set `metadata.dry_run` to True in the inputs.'.format(
node.pk))
# If we are performing a dry-run, the working directory should actually be a local folder that should already exist
if dry_run:
workdir = transport.getcwd()
else:
remote_user = transport.whoami()
remote_working_directory = computer.get_workdir().format(
username=remote_user)
if not remote_working_directory.strip():
raise exceptions.ConfigurationError(
"[submission of calculation {}] No remote_working_directory configured for computer '{}'"
.format(node.pk, computer.label))
# If it already exists, no exception is raised
try:
transport.chdir(remote_working_directory)
except IOError:
logger.debug(
'[submission of calculation {}] Unable to chdir in {}, trying to create it'
.format(node.pk, remote_working_directory))
try:
transport.makedirs(remote_working_directory)
transport.chdir(remote_working_directory)
except EnvironmentError as exc:
raise exceptions.ConfigurationError(
'[submission of calculation {}] '
'Unable to create the remote directory {} on '
"computer '{}': {}".format(node.pk,
remote_working_directory,
computer.label, exc))
# Store remotely with sharding (here is where we choose
# the folder structure of remote jobs; then I store this
# in the calculation properties using _set_remote_dir
# and I do not have to know the logic, but I just need to
# read the absolute path from the calculation properties.
transport.mkdir(calc_info.uuid[:2], ignore_existing=True)
transport.chdir(calc_info.uuid[:2])
transport.mkdir(calc_info.uuid[2:4], ignore_existing=True)
transport.chdir(calc_info.uuid[2:4])
try:
# The final directory may already exist, most likely because this function was already executed once, but
# failed and as a result was rescheduled by the eninge. In this case it would be fine to delete the folder
# and create it from scratch, except that we cannot be sure that this the actual case. Therefore, to err on
# the safe side, we move the folder to the lost+found directory before recreating the folder from scratch
transport.mkdir(calc_info.uuid[4:])
except OSError:
# Move the existing directory to lost+found, log a warning and create a clean directory anyway
path_existing = os.path.join(transport.getcwd(),
calc_info.uuid[4:])
path_lost_found = os.path.join(remote_working_directory,
REMOTE_WORK_DIRECTORY_LOST_FOUND)
path_target = os.path.join(path_lost_found, calc_info.uuid)
logger.warning(
f'tried to create path {path_existing} but it already exists, moving the entire folder to {path_target}'
)
# Make sure the lost+found directory exists, then copy the existing folder there and delete the original
transport.mkdir(path_lost_found, ignore_existing=True)
transport.copytree(path_existing, path_target)
transport.rmtree(path_existing)
# Now we can create a clean folder for this calculation
transport.mkdir(calc_info.uuid[4:])
finally:
transport.chdir(calc_info.uuid[4:])
# I store the workdir of the calculation for later file retrieval
workdir = transport.getcwd()
node.set_remote_workdir(workdir)
# I first create the code files, so that the code can put
# default files to be overwritten by the plugin itself.
# Still, beware! The code file itself could be overwritten...
# But I checked for this earlier.
for code in input_codes:
if code.is_local():
# Note: this will possibly overwrite files
for filename in code.list_object_names():
# Note, once #2579 is implemented, use the `node.open` method instead of the named temporary file in
# combination with the new `Transport.put_object_from_filelike`
# Since the content of the node could potentially be binary, we read the raw bytes and pass them on
with NamedTemporaryFile(mode='wb+') as handle:
handle.write(code.get_object_content(filename, mode='rb'))
handle.flush()
transport.put(handle.name, filename)
transport.chmod(code.get_local_executable(), 0o755) # rwxr-xr-x
# local_copy_list is a list of tuples, each with (uuid, dest_rel_path)
# NOTE: validation of these lists are done inside calculation.presubmit()
local_copy_list = calc_info.local_copy_list or []
remote_copy_list = calc_info.remote_copy_list or []
remote_symlink_list = calc_info.remote_symlink_list or []
provenance_exclude_list = calc_info.provenance_exclude_list or []
for uuid, filename, target in local_copy_list:
logger.debug(
f'[submission of calculation {node.uuid}] copying local file/folder to {target}'
)
try:
data_node = load_node(uuid=uuid)
except exceptions.NotExistent:
data_node = _find_data_node(inputs, uuid) if inputs else None
if data_node is None:
logger.warning(
f'failed to load Node<{uuid}> specified in the `local_copy_list`'
)
else:
dirname = os.path.dirname(target)
if dirname:
os.makedirs(os.path.join(folder.abspath, dirname),
exist_ok=True)
with folder.open(target, 'wb') as handle:
with data_node.open(filename, 'rb') as source:
shutil.copyfileobj(source, handle)
provenance_exclude_list.append(target)
# In a dry_run, the working directory is the raw input folder, which will already contain these resources
if not dry_run:
for filename in folder.get_content_list():
logger.debug(
f'[submission of calculation {node.pk}] copying file/folder {filename}...'
)
transport.put(folder.get_abs_path(filename), filename)
for (remote_computer_uuid, remote_abs_path,
dest_rel_path) in remote_copy_list:
if remote_computer_uuid == computer.uuid:
logger.debug(
'[submission of calculation {}] copying {} remotely, directly on the machine {}'
.format(node.pk, dest_rel_path, computer.label))
try:
transport.copy(remote_abs_path, dest_rel_path)
except (IOError, OSError):
logger.warning(
'[submission of calculation {}] Unable to copy remote resource from {} to {}! '
'Stopping.'.format(node.pk, remote_abs_path,
dest_rel_path))
raise
else:
raise NotImplementedError(
'[submission of calculation {}] Remote copy between two different machines is '
'not implemented yet'.format(node.pk))
for (remote_computer_uuid, remote_abs_path,
dest_rel_path) in remote_symlink_list:
if remote_computer_uuid == computer.uuid:
logger.debug(
'[submission of calculation {}] copying {} remotely, directly on the machine {}'
.format(node.pk, dest_rel_path, computer.label))
try:
transport.symlink(remote_abs_path, dest_rel_path)
except (IOError, OSError):
logger.warning(
'[submission of calculation {}] Unable to create remote symlink from {} to {}! '
'Stopping.'.format(node.pk, remote_abs_path,
dest_rel_path))
raise
else:
raise IOError(
f'It is not possible to create a symlink between two different machines for calculation {node.pk}'
)
else:
if remote_copy_list:
with open(os.path.join(workdir, '_aiida_remote_copy_list.txt'),
'w') as handle:
for remote_computer_uuid, remote_abs_path, dest_rel_path in remote_copy_list:
handle.write(
'would have copied {} to {} in working directory on remote {}'
.format(remote_abs_path, dest_rel_path,
computer.label))
if remote_symlink_list:
with open(os.path.join(workdir, '_aiida_remote_symlink_list.txt'),
'w') as handle:
for remote_computer_uuid, remote_abs_path, dest_rel_path in remote_symlink_list:
handle.write(
'would have created symlinks from {} to {} in working directory on remote {}'
.format(remote_abs_path, dest_rel_path,
computer.label))
# Loop recursively over content of the sandbox folder copying all that are not in `provenance_exclude_list`. Note
# that directories are not created explicitly. The `node.put_object_from_filelike` call will create intermediate
# directories for nested files automatically when needed. This means though that empty folders in the sandbox or
# folders that would be empty when considering the `provenance_exclude_list` will *not* be copied to the repo. The
# advantage of this explicit copying instead of deleting the files from `provenance_exclude_list` from the sandbox
# first before moving the entire remaining content to the node's repository, is that in this way we are guaranteed
# not to accidentally move files to the repository that should not go there at all cost. Note that all entries in
# the provenance exclude list are normalized first, just as the paths that are in the sandbox folder, otherwise the
# direct equality test may fail, e.g.: './path/file.txt' != 'path/file.txt' even though they reference the same file
provenance_exclude_list = [
os.path.normpath(entry) for entry in provenance_exclude_list
]
for root, _, filenames in os.walk(folder.abspath):
for filename in filenames:
filepath = os.path.join(root, filename)
relpath = os.path.normpath(
os.path.relpath(filepath, folder.abspath))
if relpath not in provenance_exclude_list:
with open(filepath, 'rb') as handle:
node._repository.put_object_from_filelike(handle,
relpath,
'wb',
force=True) # pylint: disable=protected-access
if not dry_run:
# Make sure that attaching the `remote_folder` with a link is the last thing we do. This gives the biggest
# chance of making this method idempotent. That is to say, if a runner gets interrupted during this action, it
# will simply retry the upload, unless we got here and managed to link it up, in which case we move to the next
# task. Because in that case, the check for the existence of this link at the top of this function will exit
# early from this command.
remotedata = RemoteData(computer=computer, remote_path=workdir)
remotedata.add_incoming(node,
link_type=LinkType.CREATE,
link_label='remote_folder')
remotedata.store()
def retrieve_calculation(calculation: CalcJobNode, transport: Transport,
retrieved_temporary_folder: str) -> None:
"""Retrieve all the files of a completed job calculation using the given transport.
If the job defined anything in the `retrieve_temporary_list`, those entries will be stored in the
`retrieved_temporary_folder`. The caller is responsible for creating and destroying this folder.
:param calculation: the instance of CalcJobNode to update.
:param transport: an already opened transport to use for the retrieval.
:param retrieved_temporary_folder: the absolute path to a directory in which to store the files
listed, if any, in the `retrieved_temporary_folder` of the jobs CalcInfo
"""
logger_extra = get_dblogger_extra(calculation)
workdir = calculation.get_remote_workdir()
EXEC_LOGGER.debug(f'Retrieving calc {calculation.pk}', extra=logger_extra)
EXEC_LOGGER.debug(f'[retrieval of calc {calculation.pk}] chdir {workdir}',
extra=logger_extra)
# If the calculation already has a `retrieved` folder, simply return. The retrieval was apparently already completed
# before, which can happen if the daemon is restarted and it shuts down after retrieving but before getting the
# chance to perform the state transition. Upon reloading this calculation, it will re-attempt the retrieval.
link_label = calculation.link_label_retrieved
if calculation.get_outgoing(FolderData,
link_label_filter=link_label).first():
EXEC_LOGGER.warning(
f'CalcJobNode<{calculation.pk}> already has a `{link_label}` output folder: skipping retrieval'
)
return
# Create the FolderData node into which to store the files that are to be retrieved
retrieved_files = FolderData()
with transport:
transport.chdir(workdir)
# First, retrieve the files of folderdata
retrieve_list = calculation.get_retrieve_list()
retrieve_temporary_list = calculation.get_retrieve_temporary_list()
retrieve_singlefile_list = calculation.get_retrieve_singlefile_list()
with SandboxFolder() as folder:
retrieve_files_from_list(calculation, transport, folder.abspath,
retrieve_list)
# Here I retrieved everything; now I store them inside the calculation
retrieved_files.put_object_from_tree(folder.abspath)
# Second, retrieve the singlefiles, if any files were specified in the 'retrieve_temporary_list' key
if retrieve_singlefile_list:
with SandboxFolder() as folder:
_retrieve_singlefiles(calculation, transport, folder,
retrieve_singlefile_list, logger_extra)
# Retrieve the temporary files in the retrieved_temporary_folder if any files were
# specified in the 'retrieve_temporary_list' key
if retrieve_temporary_list:
retrieve_files_from_list(calculation, transport,
retrieved_temporary_folder,
retrieve_temporary_list)
# Log the files that were retrieved in the temporary folder
for filename in os.listdir(retrieved_temporary_folder):
EXEC_LOGGER.debug(
f"[retrieval of calc {calculation.pk}] Retrieved temporary file or folder '{filename}'",
extra=logger_extra)
# Store everything
EXEC_LOGGER.debug(
f'[retrieval of calc {calculation.pk}] Storing retrieved_files={retrieved_files.pk}',
extra=logger_extra)
retrieved_files.store()
# Make sure that attaching the `retrieved` folder with a link is the last thing we do. This gives the biggest chance
# of making this method idempotent. That is to say, if a runner gets interrupted during this action, it will simply
# retry the retrieval, unless we got here and managed to link it up, in which case we move to the next task.
retrieved_files.add_incoming(calculation,
link_type=LinkType.CREATE,
link_label=calculation.link_label_retrieved)