def test_missing_template_dir():
'''test that we raise an exception if the specified template location
does not exist'''
template_dir = os.path.join(SCRIPT_DIR, "invalid")
with pytest.raises(RuntimeError) as excinfo:
_ = create_input(OPTION, TEMPLATE_NAME, template_location=template_dir)
assert "template '" + TEMPLATE_NAME + "' not found" in str(excinfo.value)
def test_non_existant_template():
'''test that we raise an exception if the specified template does not
exist'''
template_name = "invalid.txt"
with pytest.raises(RuntimeError) as excinfo:
_ = create_input(OPTION, template_name, template_location=TEMPLATE_DIR)
assert "template '" + template_name + "' not found" in str(excinfo.value)
def test_option_wrong_format():
'''check that we raise an exception if the input option is not in the
expected format (a dictionary within a list).'''
option = ["fred"]
with pytest.raises(RuntimeError) as excinfo:
_ = create_input(option, TEMPLATE_NAME, template_location=TEMPLATE_DIR)
assert "Expecting a dictionary" in str(excinfo.value)
def launch(option):
'''Set the gromacs input data using the supplied input options, run
gromacs and extract and return the required outputs.'''
from melody.inputs import create_input
_ = create_input(option, template_name="input.mdp")
# save the input file in the appropriate place and launch gromacs using
# longbow ...
# determine if the run was successful
success = True
results = None
if success:
# extract the required outputs
results = {
"rate": {
"value": 35,
"units": "ns/day"
},
}
return success, results
def execute(option):
'''A script that melody calls with each valid set of options. This
script runs the required code and returns the results.'''
namelist_option = []
makefile_option = []
flags = ""
for entry in option:
key = entry.keys()[0]
if key == "Problem Size":
namelist_option.append({"SIZE": entry[key]})
elif key == "F90":
makefile_option.append(entry)
else:
flags += entry[key] + " "
makefile_option.append({"F90FLAGS": flags})
namelist = create_input(namelist_option,
"namelist",
template_location="templates")
makefile_include = create_input(makefile_option,
"Makefile.include",
template_location="templates")
benchmark_base = "shallow"
# save the input files in the appropriate place
location = benchmark_base + "/original/namelist"
my_file = open(location, 'w')
my_file.write(namelist)
my_file.flush()
location = benchmark_base + "/common/Makefile.include"
my_file = open(location, 'w')
my_file.write(makefile_include)
my_file.flush()
# compile shallow if required
base_path = benchmark_base + "/original"
import subprocess
make_process = subprocess.Popen(["make", "clean"],
cwd=base_path,
stderr=subprocess.PIPE,
stdout=subprocess.PIPE)
if make_process.wait() != 0:
return False, []
make_process = subprocess.Popen(["make"],
cwd=base_path,
stderr=subprocess.PIPE,
stdout=subprocess.PIPE)
if make_process.wait() != 0:
return False, []
# run shallow
make_process = subprocess.Popen(["./shallow_base"],
cwd=base_path,
stderr=subprocess.PIPE,
stdout=subprocess.PIPE)
if make_process.wait() != 0:
return False, []
# _ = make_process.stderr.read()
stdout = make_process.stdout.read()
# determine if the results are correct. We will need to look at
# the results from stdout but for the moment we assume they are
# correct
# extract the required outputs
for line in stdout.split("\n"):
if "Time-stepping" in line:
total_time = line.split()[2]
return True, total_time
def test_create_input():
''' test that we can modify a template file correctly '''
result = create_input(OPTION,
TEMPLATE_NAME,
template_location=TEMPLATE_DIR)
assert EXPECTED in result