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Changes for remote systems with shared file system #92

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Changes for remote systems with shared file system
jan-janssen Aug 11, 2021
ca0cb43
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pyiron-runner Oct 13, 2022
34415fb
Merge branch 'main' into same_storage
jan-janssen Nov 29, 2022
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76 changes: 39 additions & 37 deletions pysqa/utils/remote.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@ def submit_job(
raise NotImplementedError(
"Submitting jobs with dependencies to a remote cluster is not yet supported."
)
self._transfer_data_to_remote(working_directory=working_directory)
# self._transfer_data_to_remote(working_directory=working_directory)
output = self._execute_remote_command(command=command)
return int(output.split()[-1])

Expand Down Expand Up @@ -108,44 +108,46 @@ def get_job_from_remote(self, working_directory, delete_remote=False):
"""
Get the results of the calculation - this is necessary when the calculation was executed on a remote host.
"""
working_directory = os.path.abspath(os.path.expanduser(working_directory))
remote_working_directory = self._get_remote_working_dir(
working_directory=working_directory
)
remote_dict = json.loads(
self._execute_remote_command(
command="python -m pysqa.cmd --list --working_directory "
+ remote_working_directory
)
)
for d in remote_dict["dirs"]:
local_dir = self._get_file_transfer(
file=d, local_dir=remote_working_directory, remote_dir=working_directory
)
os.makedirs(local_dir, exist_ok=True)
file_dict = {}
for f in remote_dict["files"]:
local_file = self._get_file_transfer(
file=f, local_dir=remote_working_directory, remote_dir=working_directory
)
file_dict[local_file] = f
self._transfer_files(file_dict=file_dict, sftp=None, transfer_back=True)
if delete_remote:
self._execute_remote_command(command="rm -r " + remote_working_directory)
pass
# working_directory = os.path.abspath(os.path.expanduser(working_directory))
# remote_working_directory = self._get_remote_working_dir(
# working_directory=working_directory
# )
# remote_dict = json.loads(
# self._execute_remote_command(
# command="python -m pysqa.cmd --list --working_directory "
# + remote_working_directory
# )
# )
# for d in remote_dict["dirs"]:
# local_dir = self._get_file_transfer(
# file=d, local_dir=remote_working_directory, remote_dir=working_directory
# )
# os.makedirs(local_dir, exist_ok=True)
# file_dict = {}
# for f in remote_dict["files"]:
# local_file = self._get_file_transfer(
# file=f, local_dir=remote_working_directory, remote_dir=working_directory
# )
# file_dict[local_file] = f
# self._transfer_files(file_dict=file_dict, sftp=None, transfer_back=True)
# if delete_remote:
# self._execute_remote_command(command="rm -r " + remote_working_directory)

def transfer_file(self, file, transfer_back=False, delete_remote=False):
working_directory = os.path.abspath(os.path.expanduser(file))
remote_working_directory = self._get_remote_working_dir(
working_directory=working_directory
)
self._create_remote_dir(directory=os.path.dirname(remote_working_directory))
self._transfer_files(
file_dict={working_directory: remote_working_directory},
sftp=None,
transfer_back=transfer_back,
)
if delete_remote and transfer_back:
self._execute_remote_command(command="rm " + remote_working_directory)
pass
# working_directory = os.path.abspath(os.path.expanduser(file))
# remote_working_directory = self._get_remote_working_dir(
# working_directory=working_directory
# )
# self._create_remote_dir(directory=os.path.dirname(remote_working_directory))
# self._transfer_files(
# file_dict={working_directory: remote_working_directory},
# sftp=None,
# transfer_back=transfer_back,
# )
# if delete_remote and transfer_back:
# self._execute_remote_command(command="rm " + remote_working_directory)

def __del__(self):
if self._ssh_connection is not None:
Expand Down