def test_execute_with_called_process_error(
capsys, docker_container, return_code, tmp_path
):
tmp_file = os.path.join(tmp_path, "CalledProcessError.sh")
# "This is stdout" to stdout, "This is stderr" to stderr
script = f"""#!/bin/bash
echo "This is stdout"
>&2 echo "This is stderr"
{"exit 1" if return_code else ""}
"""
write_file(tmp_file, script)
if return_code:
with pytest.raises(CalledProcessError):
for line in Client.execute(
docker_container[1], f"/bin/sh {tmp_file}", stream=True
):
print(line, "")
else:
for line in Client.execute(
docker_container[1], f"/bin/sh {tmp_file}", stream=True
):
print(line, "")
captured = capsys.readouterr()
assert "stdout" in captured.out
if return_code:
assert "stderr" in captured.err
else:
assert "stderr" not in captured.err
def test_instance_cmds(self, docker_container):
image = docker_container[1]
myinstance = Client.instance(image)
assert myinstance.get_uri().startswith("instance://")
print("...Case 2: List instances")
instances = Client.instances()
assert len(instances) == 1
instances = Client.instances(return_json=True)
assert len(instances) == 1
assert isinstance(instances[0], dict)
print("...Case 3: Commands to instances")
result = Client.execute(myinstance, ["echo", "hello"])
assert result == "hello\n"
print("...Case 4: Return value from instance")
result = Client.execute(myinstance, "ls /", return_result=True)
print(result)
assert "tmp\nusr\nvar" in result["message"]
assert result["return_code"] == 0
print("...Case 5: Stop instances")
myinstance.stop()
instances = Client.instances()
assert instances == []
myinstance1 = Client.instance(image)
myinstance2 = Client.instance(image)
assert myinstance1 is not None
assert myinstance2 is not None
instances = Client.instances()
assert len(instances) == 2
Client.instance_stopall()
instances = Client.instances()
assert instances == []
def test_instance_cmds(self, docker_container):
image = docker_container[1]
myinstance = Client.instance(image)
assert myinstance.get_uri().startswith('instance://')
print("...Case 2: List instances")
instances = Client.instances()
assert len(instances) == 1
instances = Client.instances(return_json=True)
assert len(instances) == 1
assert isinstance(instances[0], dict)
print("...Case 3: Commands to instances")
result = Client.execute(myinstance, ['echo', 'hello'])
assert result == 'hello\n'
print('...Case 4: Return value from instance')
result = Client.execute(myinstance, 'ls /', return_result=True)
print(result)
assert 'tmp\nusr\nvar' in result['message']
assert result['return_code'] == 0
print("...Case 5: Stop instances")
myinstance.stop()
instances = Client.instances()
assert instances == []
myinstance1 = Client.instance(image)
myinstance2 = Client.instance(image)
assert myinstance1 is not None
assert myinstance2 is not None
instances = Client.instances()
assert len(instances) == 2
Client.instance_stopall()
instances = Client.instances()
assert instances == []
def make_separate_directory(file_all, protein, source):
#shutil.rmtree('trajectories')
isdir = os.path.isdir('trajectories')
if isdir == False:
print('Trajectories do not exist')
os.mkdir('trajectories')
else:
print('exist')
for count, file in enumerate(file_all, start=0):
ismod = os.path.isdir(f'./trajectories/model_{count}')
if ismod == False:
os.mkdir(f'./trajectories/model_{count}')
with open(f'./trajectories/model_{count}/position_ligand_{count}.pdbqt', 'w') as file_traj:
file_traj.write(file)
shutil.copy(protein, f'./trajectories/model_{count}/')
# nakopiruje navic potrebna data
shutil.copy(f'{source}/_Xqmin_tmp.in', f'./trajectories/model_{count}/')
shutil.copy(f'{source}/_11_run_tleap.sh', f'./trajectories/model_{count}/')
shutil.copy(f'{source}/_21_run-mm_meta.sh', f'./trajectories/model_{count}/')
shutil.copy(f'{source}/{protein}', f'./trajectories/model_{count}/')
shutil.copy(f'{source}/ligand.prepi', f'./trajectories/model_{count}/')
try:
subprocess.run(f'rm ./trajectories/model_{count}/emin2*', shell = True)
except:
pass
try:
subprocess.run(f'rm ./trajectories/model_{count}/complex.inpcrd', shell = True)
except:
pass
try:
subprocess.run(f'rm ./trajectories/model_{count}/complex.prmtop', shell = True)
except:
pass
# convert traj_position_ligand_{count}.pdbqt to pdb -> singularity
Client.load('/home/petrahrozkova/Stažené/caverdock_1.1.sif')
Client.execute(['/opt/mgltools-1.5.6/bin/pythonsh',
'/opt/mgltools-1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/pdbqt_to_pdb.py',
'-f',os.getcwd()+'/trajectories/model_'+str(count)+'/position_ligand_*.pdbqt',
'-o', os.getcwd()+'/trajectories/model_'+str(count)+'/ligand.pdb'])
subprocess.call(f'sed -i \'s/<0> d/TIP d/g\' ./trajectories/model_{count}/ligand.pdb', shell = True) #ligand_for_complex.pdb
subprocess.call(f'tail -n +2 \"./trajectories/model_{count}/ligand.pdb\" > '
f'\"./trajectories/model_{count}/ligand_for_complex.pdb\"', shell = True)
# spojit 'hloupe" ligand, protein do complex.pdb
subprocess.call( #remove last line in file with END. IMPORTANT!
f'head -n -1 ./trajectories/model_{count}/{protein} > ./trajectories/model_{count}/complex.pdb | '
f'echo TER >> ./trajectories/model_{count}/complex.pdb',
shell=True)
subprocess.call(f'cat ./trajectories/model_{count}/ligand_for_complex.pdb'
f' >> ./trajectories/model_{count}/complex.pdb ',
#f'| echo TER >> ./trajectories/model_{count}/complex.pdb',
shell=True)
subprocess.call(f'echo END >> ./trajectories/model_{count}/complex.pdb',
shell=True)
def call(container, command, cwd='', paths={}, remove=True):
###load container
Client.load(container)
###setup mount point paths
#{"/path/outside":"/path/incontainer"}
volumes = []
if paths:
for key in paths.keys():
volumes.append(key + ':' + paths[key])
###setup command as a list
command_list = shlex.split(command)
###run the container
output = Client.execute(command_list,
bind=volumes,
options=['--pwd', cwd, '--cleanenv'],
stream=True)
try:
###stream the output
for line in output:
yield line.strip()
#catch singularity errors from non-zero exit
#TODO figure out how to read them
except subprocess.CalledProcessError:
pass
def extract_content(image_path, member_name, return_hash=False):
'''extract_content will extract content from an image using cat.
If hash=True, a hash sum is returned instead
'''
if member_name.startswith('./'):
member_name = member_name.replace('.','',1)
if return_hash:
hashy = hashlib.md5()
try:
content = Client.execute(image_path,'cat %s' %(member_name))
except:
return None
if not isinstance(content,bytes):
content = content.encode('utf-8')
content = bytes(content)
# If permissions don't allow read, return None
if len(content) == 0:
return None
if return_hash:
hashy.update(content)
return hashy.hexdigest()
return content
def exec(self, process: ProcessContainer, args):
"""Execute a process
Parameters
----------
process
Metadata of the process
args
list of arguments
"""
# print('container type = ', process.container()['type'])
if (process.container()['type'] != 'singularity'
and process.container()['type'] != 'docker'):
raise RunnerExecError("The process " + process.name +
" is not compatible with Singularity")
image_uri = replace_env_variables(process, process.container()['uri'])
if process.container()['type'] == 'docker':
image_uri = 'docker://' + image_uri
self.notify_message('run singularity container: ' + image_uri)
self.notify_message('args:' + ' '.join(args))
# print("run singularity container:", image_uri)
# print('args:', args)
puller = Client.execute(image_uri, args)
for line in puller:
self.notify_message(line)
print(line)
def get_nvidia_devices(use_docker=True):
"""
Returns a Dict[index, UUID] of all NVIDIA devices available to docker
Arguments:
use_docker: whether or not to use a docker container to run nvidia-smi. if not, use singularity
Raises docker.errors.ContainerError if GPUs are unreachable,
docker.errors.ImageNotFound if the CUDA image cannot be pulled
docker.errors.APIError if another server error occurs
"""
cuda_image = 'nvidia/cuda:9.0-cudnn7-devel-ubuntu16.04'
nvidia_command = 'nvidia-smi --query-gpu=index,uuid --format=csv,noheader'
if use_docker:
client.images.pull(cuda_image)
output = client.containers.run(
cuda_image,
nvidia_command,
runtime=NVIDIA_RUNTIME,
detach=False,
stdout=True,
remove=True,
)
gpus = output.decode()
else:
# use the singularity runtime to run nvidia-smi
img = Client.pull('docker://' + cuda_image, pull_folder='/tmp')
output = Client.execute(img, nvidia_command, options=['--nv'])
if output['return_code'] != 0:
raise SingularityError
gpus = output['message']
# Get newline delimited gpu-index, gpu-uuid list
logger.info("GPUs: " + str(gpus.split('\n')[:-1]))
return {gpu.split(',')[0].strip(): gpu.split(',')[1].strip() for gpu in gpus.split('\n')[:-1]}
def run_singularity_container_executable(uuid, container_image,
executable_path, logs_path,
args_dict):
"""Launch an executable within a Singularity container.
Args:
uuid: A string containing the uuid of the job being run.
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.
logs_path: A string (or None) containing the path of the
directory containing the relevant logs 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(
image=container_image,
pull_folder=os.environ['WORKER_SINGULARITY_IMAGES_DIRECTORY'],
)
# Run the executable with the arguments
if logs_path is None:
bind_option = None
else:
# Create the host path. This is required by the Singularity
# library (though not the Docker library)
host_path = os.path.join(os.environ['WORKER_LOGS_DIRECTORY'], uuid)
os.makedirs(host_path, exist_ok=True)
# Build the bind option to pass on to Singularity
bind_option = host_path.rstrip('/') + ":" + logs_path.rstrip('/')
client.execute(
image=singularity_image,
command=[executable_path, json.dumps(args_dict)],
bind=bind_option,
)
# TODO give a real return value
return "FINISHED"
def run(self, cmd, bind_dir):
self._make_dir()
self._pull_image()
client.load(os.path.join(self.img_dir, self.img_name))
output = client.execute(cmd,
bind=bind_dir + ":/data",
options=['--pwd', '/data', '--cleanenv'],
stream=True)
return output
def run_case(image_dir, image_name, testcase_dir):
client.load(os.path.join(image_dir, image_name))
output = client.execute(
['mpirun', '-np', '6', '/SU2/bin/SU2_CFD', 'Jones.cfg'],
bind=testcase_dir + ":/data:",
options=['--pwd', '/data'],
stream=True)
for val in output:
print(val.strip('\n'))
def run_command(self, command):
if self.mode == 'docker':
res = self.docker_container.exec_run(command)
return str(res.output)
elif self.mode == 'singularity':
from spython.main import Client
res = Client.execute(self.client_instance, command)
if isinstance(res, dict):
res = res['message']
return res
def run(self, cmd, cores, cfg, log):
self._pull_image()
client.load(os.path.join(self.image_dir, self.image_name))
totalcmd = ['mpirun', '-np', str(cores), '/SU2/bin/' + cmd, cfg.fname]
output = client.execute(
totalcmd,
bind=','.join([self.case_dir + ":/data",
self.mesh_dir + ":/mesh"]),
options=['--pwd', '/data', '--cleanenv'],
stream=True)
with open(log.fname, 'w', buffering=10) as lfile:
for line in output:
lfile.write(line)
def remove_ligand_from_emin(protein, verbose, configfile):
# ted defaultne vypocitany emin5.pdb
with open(protein) as oldfile, open('protein.pdb', 'w+') as newfile:
for line in oldfile:
if not configfile["LIGAND"]["name"] in line:
newfile.write(line)
# convert pdb to pdbqt
prepare_receptor = ''
if int(configfile["SINGULARITY"]["value"]) == 1:
Client.load(configfile["SINGULARITY"]["singularity"])
prepare_receptor = Client.execute([
configfile["PREPARE_RECEPTOR"]["path_prepare_receptor"], '-r',
'protein.pdb'
])
if verbose:
print(
f'{configfile["PREPARE_RECEPTOR"]["path_prepare_receptor"]} -r protein.pdb'
)
if not os.path.isfile('protein.pdbqt'):
logging.error(
f'Cannot run prepare_receptor. Try: \n {configfile["PREPARE_RECEPTOR"]["path_prepare_receptor"]} -r protein.pdb \n Message: \n {prepare_receptor}'
)
if verbose:
print(
f'Cannot run prepare_receptor. Try: \n {configfile["PREPARE_RECEPTOR"]["path_prepare_receptor"]} -r protein.pdb \n {prepare_receptor}'
)
sys.exit(1)
else:
subprocess.call(
f'{configfile["PREPARE_RECEPTOR"]["path_prepare_receptor"]} -r protein.pdb',
shell=True)
logging.info(
f'Run prepare_receptor. Message: \n {configfile["PREPARE_RECEPTOR"]["path_prepare_receptor"]} -r protein.pdb '
)
if verbose:
print(
f'{configfile["PREPARE_RECEPTOR"]["path_prepare_receptor"]} -r protein.pdb'
)
print(f'Message{prepare_receptor}')
if not os.path.isfile('protein.pdbqt'):
logging.error(
f'Cannot run prepare_receptor. Try: \n {configfile["PREPARE_RECEPTOR"]["path_prepare_receptor"]} -r protein.pdb \n'
)
if verbose:
print(
f'Cannot run prepare_receptor. Try: \n {configfile["PREPARE_RECEPTOR"]["path_prepare_receptor"]} -r protein.pdb'
)
sys.exit(1)
check_exist_file('protein.pdbqt')
def test_AFNI_libraries():
SINGULARITY_IMAGE_PATH = '/home/circleci/project/C-PAC-CI.simg'
if not os.path.exists(SINGULARITY_IMAGE_PATH):
try:
SINGULARITY_IMAGE_PATH = [
d for d in os.listdir(str(Path(__file__).parent.parent.parent))
if (d.endswith('.simg') or d.endswith('.sif'))
][0]
except:
raise Exception("Singularity image not in expected location.")
if os.path.exists(SINGULARITY_IMAGE_PATH):
afni_libraries = Client.execute(
Client.instance(SINGULARITY_IMAGE_PATH),
['./dev/circleci_data/AFNI_libraries.sh'])
assert "not found" not in afni_libraries, '\n'.join([
line.strip() for line in afni_libraries.split('\n')
if "not found" in line
])
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 call(container, command, cwd='', paths={}, remove=True):
###load container
container = 'docker://' + container
Client.load(container)
###setup mount point paths
#{"/path/outside":"/path/incontainer"}
volumes = []
if paths:
for key in paths.keys():
volumes.append(key + ':' + paths[key])
###setup command as a list
command_list = command.split()
###run the container
output = Client.execute(command_list,
bind=volumes,
writable=True,
options=['--pwd', cwd])
#once container is finished return output as a string
return output
def run_cd_energy_profile(tunnel, traj, configfile, verbose):
file = ''
try:
if int(configfile["SINGULARITY"]["value"]) == 1:
Client.load(str(configfile['SINGULARITY']['singularity']))
if verbose:
print(
f'{configfile["CD-ENERGYPROFILE"]["path_cd-energyprofile"]} -d {os.getcwd()}/{str(tunnel)} -t {str(traj)} -s {str(configfile["CPU"]["cpu"])}'
)
if int(configfile["SINGULARITY"]["value"]) == 1:
file = Client.execute([
'cd-energyprofile', '-d',
os.getcwd() + '/' + str(tunnel), '-t',
str(traj), '-s',
str(configfile['CPU']['cpu'])
])
with open(f'{os.getcwd()}/energy.dat', 'w') as file_energy_dat:
file_energy_dat.write(str(file))
else:
subprocess.call(
f'{configfile["CD-ENERGYPROFILE"]["path_cd-energyprofile"]} -d {os.getcwd()}/{str(tunnel)} -t {str(traj)} -s {str(configfile["CPU"]["cpu"])} > energy.dat',
shell=True)
if verbose:
print(f'Message from cd-energyprofile: \n {file}')
logging.info(f'Message from cd-energyprofieL: \n {file}')
except:
if verbose:
print('cd-energyprofile returncode is not 0. Check logfile.')
logging.error(f'cd-energyprofile returncode is not 0.')
sys.exit(1)
if not os.path.exists('energy.dat'):
logging.error(f'Cannot make energy.dat')
if verbose:
print('Energy.dat not exists')
sys.exit(1)
def make_separate_directory(file_all, protein, source, configfile):
try:
shutil.rmtree('trajectories')
isdir = False
except:
isdir = os.path.isdir('trajectories')
if isdir == False:
print('Trajectories do not exist')
os.mkdir('trajectories')
else:
print('exist')
for count, file in enumerate(file_all, start=0):
ismod = os.path.isdir(f'./trajectories/model_{count}')
if ismod == False:
os.mkdir(f'./trajectories/model_{count}')
with open(
f'./trajectories/model_{count}/position_ligand_{count}.pdbqt',
'w') as file_traj:
file_traj.write(file)
shutil.copy(protein, f'./trajectories/model_{count}/')
# nakopiruje navic potrebna data
#shutil.copy(f'{source}/_11_run_tleap', f'./trajectories/model_{count}/')
#shutil.copy(f'{source}/_21_run_prepare_sander', f'./trajectories/model_{count}/')
shutil.copy(f'{source}/{protein}', f'./trajectories/model_{count}/')
try:
subprocess.run(f'rm ./trajectories/model_{count}/emin*',
shell=True)
except:
pass
try:
subprocess.run(f'rm ./trajectories/model_{count}/complex.inpcrd',
shell=True)
except:
pass
try:
subprocess.run(f'rm ./trajectories/model_{count}/complex.prmtop',
shell=True)
except:
pass
try:
subprocess.run(f'rm ./trajectories/model_{count}/ligand.prepi',
shell=True)
except:
pass
# convert traj_position_ligand_{count}.pdbqt to pdb -> singularity
if int(configfile["SINGULARITY"]["value"]) == 1:
Client.load('/home/petrahrozkova/Stažené/caverdock_1.1.sif')
Client.execute([
'/opt/mgltools-1.5.6/bin/pythonsh',
'/opt/mgltools-1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/pdbqt_to_pdb.py',
'-f',
os.getcwd() + '/trajectories/model_' + str(count) +
'/position_ligand_*.pdbqt', '-o',
os.getcwd() + '/trajectories/model_' + str(count) +
'/ligand_H.pdb'
])
else:
subprocess.call(
f'{configfile["PDBQT_TO_PDB"]["path_pdbqt_to_pdb"]} -f {os.getcwd()}/trajectories/model_{str(count)}/position_ligand_{str(count)}.pdbqt '
f'-o {os.getcwd()}/trajectories/model_{str(count)}/ligand_H.pdb',
shell=True)
check_exist_file(
f'{os.getcwd()}/trajectories/model_{str(count)}/ligand_H.pdb')
subprocess.call(
f'sed -i \'s/<0> d/{configfile["LIGAND"]["name"]} d/g\' ./trajectories/model_{count}/ligand_H.pdb',
shell=True) #ligand_for_complex.pdb
#subprocess.call(f'pdb4amber -i ./trajectories/model_{count}/ligand_H.pdb -o ./trajectories/model_{count}/ligand.pdb --nohyd', shell = True)
check_exist_file(
f'{os.getcwd()}/trajectories/model_{str(count)}/ligand_H.pdb')
#subprocess.call(f'antechamber -i {ligand} -fi pdbqt -o ligand.pdb -if pdb', shell = True)
subprocess.call(
f'antechamber -i ./trajectories/model_{count}/ligand_H.pdb -fi pdb -o ./trajectories/model_{count}/ligand.prepi -fo prepi',
shell=True)
check_exist_file(
f'{os.getcwd()}/trajectories/model_{str(count)}/ligand.prepi')
subprocess.call(
f'cat \"./trajectories/model_{count}/ligand_H.pdb\" > '
f'\"./trajectories/model_{count}/ligand_for_complex.pdb\"',
shell=True)
# split (ugly) ligand and protein into complex.pdb
subprocess.call(
f'pdb4amber -i ./trajectories/model_{count}/{protein} -o ./trajectories/model_{count}/protein_w_H.pdb --nohyd',
shell=True)
subprocess.call( #remove last line in file with END. IMPORTANT!
f'head -n -1 ./trajectories/model_{count}/protein_w_H.pdb > ./trajectories/model_{count}/complex.pdb | '
f'echo TER >> ./trajectories/model_{count}/complex.pdb',
shell=True)
subprocess.call(
f'cat ./trajectories/model_{count}/ligand_for_complex.pdb'
f' >> ./trajectories/model_{count}/complex.pdb ',
#f'| echo TER >> ./trajectories/model_{count}/complex.pdb',
shell=True)
subprocess.call(
f'echo END >> ./trajectories/model_{count}/complex.pdb',
shell=True)
check_exist_file(
f'{os.getcwd()}/trajectories/model_{str(count)}/complex.pdb')
print(f'{os.getcwd()}')
#subprocess.call(f'pdb4amber -i ./trajectories/model_{count}/complex_H.pdb -o ./trajectories/model_{count}/complex.pdb --nohyd', shell = True)
check_exist_file(
f'{os.getcwd()}/trajectories/model_{str(count)}/complex.pdb')
def test_execute_with_return_code(docker_container):
result = Client.execute(docker_container[1], "ls /", return_result=True)
print(result)
assert "tmp\nusr\nvar" in result["message"]
assert result["return_code"] == 0
def test_execute(docker_container):
result = Client.execute(docker_container[1], "ls /")
print(result)
assert "tmp\nusr\nvar" in result
def run_singularity_container_command(
uuid,
container_image,
command_to_run,
logs_path,
results_path,
env_vars_list,
args_dict,
):
"""Launch an executable within a Singularity container.
Args:
uuid: A string containing the uuid of the job being run.
container_image: A string containing the name of the container
to pull.
command_to_run: A string containing the command to run.
logs_path: A string (or None) containing the path of the
directory containing the relevant logs within the container.
results_path: A string (or None) containing the path of the
directory containing any output files from the container.
env_vars_list: A list of strings containing the environment
variable names for the worker to consume from its
environment.
args_dict: A dictionary containing arguments and corresponding
values.
Raises:
KeyError: An environment variable specified was not available in
the worker's environment.
SingularityPullFailure: The Singularity pull could not complete
with the specified timeout and number of retries.
"""
# 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).
timeout = int(os.environ["SINGULARITY_PULL_TIMEOUT"])
num_retries = int(os.environ["SINGULARITY_PULL_RETRIES"])
# Put a timeout on the client pull method
client.pull = timeout_decorator.timeout(timeout,
timeout_exception=StopIteration)(
client.pull)
for retry in range(num_retries):
try:
singularity_image = client.pull(
image=container_image,
pull_folder=os.environ["WORKER_SINGULARITY_IMAGES_DIRECTORY"],
name_by_commit=True,
)
break
except StopIteration:
# If this is the last retry, raise an exception to indicate
# a failed job
if retry == num_retries - 1:
raise SingularityPullFailure(
("Could not pull {image_url} within "
"{timeout} seconds after {num_retries} retries.").format(
image_url=container_image,
timeout=timeout,
num_retries=num_retries,
))
# Find out where to put the logs
if logs_path is None:
bind_option = []
else:
# Create the host logs path. This is required by the Singularity
# library (though not the Docker library)
host_logs_path = os.path.join(os.environ["WORKER_LOGS_DIRECTORY"],
uuid)
create_local_directory(host_logs_path)
# Build the bind option to pass on to Singularity
bind_option = [
host_logs_path.rstrip("/") + ":" + logs_path.rstrip("/")
]
# Find out where to put the results
if results_path is not None:
# Create the host results path
host_results_path = os.path.join(
os.environ["WORKER_RESULTS_DIRECTORY"], uuid)
create_local_directory(host_results_path)
# Build the bind option to pass on to Singularity
bind_option += [
host_results_path.rstrip("/") + ":" + results_path.rstrip("/")
]
# Check for required environment variables. Note that by default
# Singularity containers have access to their outside environment
# variables, so we don't need to pass them along explicitly like we
# need to for a Docker container.
try:
# Test to see that all keys are defined
{key: os.environ[key] for key in env_vars_list}
except KeyError as e:
raise KeyError(
"Environment variable %s not present in the worker's environment!"
% e)
# Pass along the job's UUID
os.environ["JOB_UUID"] = uuid
# Compose the command to run
command = shlex.split(command_to_run)
if args_dict:
command += [json.dumps(args_dict)]
# Run the executable
iter_ = client.execute(image=singularity_image,
command=command,
bind=bind_option,
stream=True)
# Okay, here's some magic. The issue is that without stream=True in
# the above call, there's no way of determining the return code of
# the above operation, and so no way of knowing whether it failed.
# However, with stream=True, it'll raise a
# subprocess.CalledProcessError exception for any non-zero return
# code. Great! But before we can get that exception triggered we
# need to iterate through all of the command's stdout, which is what
# the below (seemingly useless) loop does.
for _ in iter_:
pass
def run_command(self, model: Model, command_str,
mounts=None, environment=None,
stdin=None, stdout=sys.stdout, stderr=sys.stderr,
raise_errors=True):
model = cast(SingularityModel, model)
if mounts is None:
mounts = []
if environment is None:
environment = {}
# Support custom checkpoint loading
if model.checkpoint is not None:
host_checkpoint_path = Path(model.checkpoint).absolute()
# Mount given checkpoint read-only within the guest
guest_checkpoint_path = "/opt/lmzoo_checkpoint"
mounts.append((host_checkpoint_path, guest_checkpoint_path, "ro"))
# Update relevant environment variable
environment["LMZOO_CHECKPOINT_PATH"] = guest_checkpoint_path
binds = ["%s:%s:%s" % (host, guest, mode)
for host, guest, mode in mounts]
nv = False # TODO
command = command_str.split(" ")
if stdin is not None:
stdin_f = NamedTemporaryFile("w")
stdin_f.write(stdin.read())
stdin_f.flush()
binds.append("%s:/host_stdin:ro" % stdin_f.name)
command = ["sh", "-c", 'cat /host_stdin | %s' % " ".join(command)]
# TODO no separate stderr support :( manually reroute stderr for now
command.append("2>/dev/null")
# Prepare environment variables for export
environment = {"SINGULARITYENV_%s" % key: value
for key, value in environment.items()}
try:
with modified_environ(**environment):
result = Client.execute(image=model.reference, command=command,
bind=binds, stream=True)
for line in result:
stdout.write(line)
except CalledProcessError as e:
if raise_errors:
if e.returncode == STATUS_CODES["unsupported_feature"]:
feature = command_str.split(" ")[0]
raise errors.UnsupportedFeatureError(feature=feature,
model=str(model))
else:
raise
if stdin is not None:
stdin_f.close()
return result
def test_execute(docker_container):
result = Client.execute(docker_container[1], 'ls /')
print(result)
assert 'tmp\nusr\nvar' in result
def test_execute_with_return_code(docker_container):
result = Client.execute(docker_container[1], 'ls /', return_result=True)
print(result)
assert 'tmp\nusr\nvar' in result['message']
assert result['return_code'] == 0
def run_caverdock(ligand, tunnel, configfile, verbose):
# IN: protein, ligand, tunel
# OUT: pdbqt file with lb and ub
prepare_conf = ''
if int(configfile["SINGULARITY"]["value"]) == 1:
singularity = Client.load(str(
configfile["SINGULARITY"]["singularity"]))
logging.info(
f'Singularity for caverdock: {configfile["SINGULARITY"]["singularity"]} \n'
)
logging.info(f'Message from singularity: \n {singularity}')
if verbose:
print(
f'Singularity for caverdock: {configfile["SINGULARITY"]["singularity"]} \n'
)
print(f'Message from singularity: \n {singularity} \n')
prepare_conf = Client.execute([
configfile["CD-PREPARECONF"]["path_cd-prepareconf"], '-r',
'protein.pdbqt', '-l',
str(ligand), '-t',
str(tunnel)
])
with open('caverdock.conf', 'w+') as file_conf:
file_conf.write(prepare_conf)
if not os.path.isfile('caverdock.conf'):
logging.error(
f'cd-prepareconf -r protein.pdbqt -l {ligand} -t {tunnel} > caverdock.conf'
)
logging.error(f'Message from cd-prepareconf: \n {prepare_conf}')
if verbose:
print(
f'ERROR: {configfile["CD-PREPARECONF"]["path_cd-prepareconf"]} -r protein.pdbqt -l {ligand} -t {tunnel} > caverdock.conf'
)
print(f'ERROR: Message from cd-prepareconf: \n {prepare_conf}')
sys.exit(1)
else:
subprocess.call(
f'{configfile["CD-PREPARECONF"]["path_cd-prepareconf"]} -r protein.pdbqt -l {ligand} -t {tunnel} > caverdock.conf',
shell=True)
logging.info(
f'cd-prepareconf -r protein.pdbqt -l {ligand} -t {tunnel} > caverdock.conf'
)
#logging.info(f'Message from cd-prepareconf: \n {prepare_conf}')
if verbose:
print(
f'{configfile["CD-PREPARECONF"]["path_cd-prepareconf"]} -r protein.pdbqt -l {ligand} -t {tunnel} > caverdock.conf'
)
#print(f'Message from cd-prepareconf: \n {prepare_conf}')
if not os.path.isfile('caverdock.conf'):
logging.error(
f'cd-prepareconf -r protein.pdbqt -l {ligand} -t {tunnel} > caverdock.conf'
)
#logging.error(f'Message from cd-prepareconf: \n {prepare_conf}')
if verbose:
print(
f'ERROR: {configfile["CD-PREPARECONF"]["path_cd-prepareconf"]} -r protein.pdbqt -l {ligand} -t {tunnel} > caverdock.conf'
)
#print(f'ERROR: Message from cd-prepareconf: \n {prepare_conf}')
sys.exit(1)
mpirun = ''
if int(configfile["SINGULARITY"]["value"]) == 1:
mpirun = Client.execute([
'mpirun', '-np', configfile["CPU"]["cpu"], 'caverdock', '--config',
'caverdock.conf', '--out',
str(configfile["RESULT_CD"]["name"])
])
else:
subprocess.call(
f'/usr/bin/mpirun.mpich -np {str(configfile["CPU"]["cpu"])} {configfile["CAVERDOCK"]["path_caverdock"]} --config caverdock.conf --out {str(configfile["RESULT_CD"]["name"])}',
shell=True)
logging.info(
f'mpirun -np {str(configfile["CPU"]["cpu"])} caverdock --config caverdock.conf --out {str(configfile["RESULT_CD"]["name"])}'
)
logging.info(f'Message from mpirun: \n {mpirun}')
if verbose:
print(
f'mpirun -np {str(configfile["CPU"]["cpu"])} caverdock --config caverdock.conf --out {str(configfile["RESULT_CD"]["name"])}'
)
print(f'Message from mpirun: \n {mpirun}')
if not (os.path.isfile(f'{configfile["RESULT_CD"]["name"]}-lb.pdbqt')
or os.path.isfile(f'{configfile["RESULT_CD"]["name"]}-ub.pdbqt')):
print(f'{configfile["RESULT_CD"]["name"]}-lb.pdbqt')
logging.error(
f'mpirun -np {str(configfile["CPU"]["cpu"])} caverdock --config caverdock.conf --out {str(configfile["RESULT_CD"]["name"])}'
)
logging.error(f'Message from mpirun: \n {mpirun}')
if verbose:
print(
f'ERROR: mpirun -np {str(configfile["CPU"]["cpu"])} caverdock --config caverdock.conf --out {str(configfile["RESULT_CD"]["name"])}'
)
print(f'ERROR: Message from mpirun: \n {mpirun}')
sys.exit(1)