def run_singularity_container_executable(container_image, executable_path,
args_dict):
"""Launch an executable within a Singularity container.
Args:
container_image: A string containing the name of the container
to pull.
executable_path: A string containing the path of the executable
to execute within the container.
args_dict: A dictionary containing arguments and corresponding
values.
"""
# Import Singularity library
from spython.main import Client as client
# Pull the specified container. This pull in the latest version of
# the container (with the specified tag if provided).
singularity_image = client.pull(container_image)
# Run the executable with the arguments
# TODO how do we get logs?
client.run(
singularity_image,
[executable_path, json.dumps(args_dict)],
)
# TODO give a real return value
return "FINISHED"
def singularity_run(image_path,
path_bind,
args_list,
container_dir='/tmp',
return_results=True,
use_ephemeral_space=False,
dry_run=False):
'''
A wrapper module for running singularity based containers
:param image_path: Singularrity image path
:param path_bind: Path to bind to singularity /tmp dir
:param args_list: List of args for singulatiy run
:param return_results: Return singulatiy run results, default True
:param use_ephemeral_space: Toggle for using ephemeral space for temp dir, default False
:param dry_run: Return the singularity command without run, default False
:returns: A response from container run and a string containing singularity command line
'''
try:
check_file_path(image_path)
check_file_path(path_bind)
temp_dir = get_temp_dir(use_ephemeral_space=use_ephemeral_space)
res = None
temp_image_path = \
os.path.join(
temp_dir,
os.path.basename(image_path))
copy_local_file(image_path, temp_image_path) # copy image to tmp dir
if not isinstance(args_list,list) and \
len(args_list) > 0:
raise ValueError(
'No args provided for singularity run') # safemode
args = ' '.join(args_list) # flatten args
singularity_run_cmd = \
'singularity run {0} --bind {1}:{2} {3}'.\
format(
temp_image_path,
path_bind,
container_dir,
args)
if dry_run:
return res, singularity_run_cmd
else:
res = \
Client.run(
image=temp_image_path,
bind='{0}:{1}'.format(path_bind,container_dir),
args=args,
return_result=return_results)
remove_dir(temp_dir) # remove copied image after run
return res, singularity_run_cmd
except Exception as e:
raise ValueError(
'Failed to run image {0}, error: {1}'.\
format(image_path,e))
def test_pull_and_run(tmp_path):
image = Client.pull("shub://vsoch/singularity-images",
pull_folder=str(tmp_path))
print(image)
assert os.path.exists(image)
ext = 'sif' if Client.version_info().major >= 3 else 'simg'
assert image == str(tmp_path / ('singularity-images.' + ext))
result = Client.run(image)
print(result)
assert 'You say please, but all I see is pizza..' in result
def _try_to_stream(self, args, stream_command='run'):
self._bindings_as_option()
try:
if stream_command == 'run':
for line in Client.run(Client.instance(self.image),
args=args,
options=self.options,
stream=True,
return_result=True):
yield line
elif stream_command == 'execute':
for line in Client.execute(self.image,
command=args['command'].split(' '),
options=self.options,
stream=True,
quiet=False):
yield line
except CalledProcessError: # pragma: no cover
return
def _run(self, *args, **kwargs):
# This function should run in a background thread
kwargs = kwargs.copy()
kwargs['image'] = self.image
# Always stream
kwargs['stream'] = True
# spython will error if we don't return the result...
kwargs['return_result'] = True
self._stream_command = client.run(**kwargs)
# Write logs as they come in
for output in self._stream_command:
with self._logs_lock:
self._logs.append(output)
self._stream_command = None
def singularity_start(self, image):
"""Starts a singularity instance based on the image.
"""
env_vars = self.action.get('env', {})
for s in self.action.get('secrets', []):
env_vars.update({s: os.environ[s]})
for e, v in self.env.items():
env_vars.update({e: v})
env_vars.update({'HOME': os.environ['HOME']})
# sets the env variables
for k, v in env_vars.items():
Client.setenv(k, v)
e = Client.run(image=self.generate_image_name(image),
args=' '.join(self.action.get('args', '')),
return_result=True)
return e['return_code']