def get_meta(recipe, config):
"""
Given a package name, find the current meta.yaml file, parse it, and return
the dict.
Parameters
----------
recipe : str
Path to recipe (directory containing the meta.yaml file)
config : str or dict
Config YAML or dict
"""
cfg = utils.load_config(config)
# TODO: Currently just uses the first env. Should turn this into
# a generator.
env = dict(next(iter(utils.EnvMatrix(cfg['env_matrix']))))
pth = os.path.join(recipe, 'meta.yaml')
jinja_env = jinja2.Environment()
content = jinja_env.from_string(open(pth, 'r',
encoding='utf-8').read()).render(env)
meta = yaml.round_trip_load(content, preserve_quotes=True)
return meta
def dynamic_jinja_to_static_ruamel_yaml(filename):
tmp_file = 'tmp.ruamel_yaml'
converted_file_string, compilers_in_build = convert_jinja_syntax(filename)
data = ruamel_yaml.round_trip_load(converted_file_string)
with open(tmp_file, 'w') as fp:
ruamel_yaml.round_trip_dump(data, fp)
environment = jinja2.Environment(
loader=jinja2.FileSystemLoader(searchpath='.'),
trim_blocks=True,
block_start_string='#%',
block_end_string='%#',
variable_start_string='<{',
variable_end_string='}>')
try:
recipe_dict = environment.get_template(tmp_file).render()
os.remove("tmp.ruamel_yaml")
return recipe_dict, compilers_in_build
except:
print("ERROR in dynamic_jinja_to_static_ruamel_yaml")
return ""
def yaml_round_trip_load(string):
return yaml.round_trip_load(string, version="1.2")
def write_template(method, image, command, workdir, parallel, **kwargs):
with open(
f"{os.path.dirname(os.path.realpath(__file__))}/kubernetes-template.yaml"
) as ifile:
doc = ruamel_yaml.round_trip_load(ifile, preserve_quotes=True)
double = kwargs.get('double', 'OFF')
rdtscp = kwargs.get('rdtscp', 'OFF')
orca_method_file = kwargs.get('orca_method_file', '')
arch = kwargs.get('arch', '')
# Set default values
default_image = GMX_IMAGE
default_name = "gromacs"
if method == "orca":
default_image = ORCA_IMAGE
default_name = "orca"
# Always replace "" with "-" because "" is not kubernetes accepted char in the name
method = method.replace("_", "-")
# Set names
timestamp = str(time.time()).replace(".", "")
identificator = "{}-{}-rdtscp-{}".format(default_name, method,
timestamp)
doc['metadata']['name'] = identificator
doc['spec']['template']['spec']['containers'][0][
'name'] = "{}-{}-deployment-{}".format(default_name, method,
timestamp)
doc['spec']['template']['metadata']['labels']['app'] = identificator
# Set gromacs args
doc['spec']['template']['spec']['containers'][0]['args'] = [
"/bin/bash", "-c",
DoubleQuotedScalarString(command)
]
# If not orca, set options for gmx container
if method != "orca":
double_env = {
'name': "GMX_DOUBLE",
'value': DoubleQuotedScalarString("ON" if double else "OFF")
}
rdtscp_env = {
'name': "GMX_RDTSCP",
'value': DoubleQuotedScalarString("ON" if rdtscp else "OFF")
}
arch_env = {
'name': "GMX_ARCH",
'value': DoubleQuotedScalarString(arch)
}
doc['spec']['template']['spec']['containers'][0]['env'] = [
double_env, rdtscp_env, arch_env
]
# If parallel is enabled set label so kubectl logs can print logs according to label
if parallel:
with open(f"{PICKLE_PATH}/lock.pkl", "rb") as fp:
lock_object = pickle.load(fp)
if len(lock_object['Parallel_label']) == 0:
label = {"Parallel_label": identificator, "Count": 0}
with open(f"{PICKLE_PATH}/lock.pkl", "wb") as fp:
pickle.dump(label, fp)
else:
doc['spec']['template']['metadata']['labels'][
'app'] = lock_object['Parallel_label']
# Set image
doc['spec']['template']['spec']['containers'][0][
'image'] = default_image if not image else image
# Set working directory
doc['spec']['template']['spec']['containers'][0][
'workingDir'] = "/tmp/"
if workdir:
doc['spec']['template']['spec']['containers'][0][
'workingDir'] += workdir
# set PVC
pvc_name = os.environ['PVC_NAME']
if len(pvc_name) == 0:
raise Exception(
"Error setting pvc_name, probably problem in setting env variable of actual container"
)
doc['spec']['template']['spec']['volumes'][0]['persistentVolumeClaim'][
'claimName'] = pvc_name
# Set orca required cpus
if method == "orca":
no_of_procs = get_no_of_procs(orca_method_file)
if no_of_procs != -1:
doc['spec']['template']['spec']['containers'][0]['resources'][
'requests']['cpu'] = no_of_procs
# Write to file
ofile_name = "{}-{}-rdtscp.yaml".format(default_name, method)
with open(ofile_name, "w") as ofile:
ruamel_yaml.round_trip_dump(doc, ofile, explicit_start=True)
return ofile_name, identificator