class Environment():
def __init__(self):
self.shell = Shell()
def get_os(self):
"""
Add a new architecture to this function.
"""
# k: if k_accountj exists
test_k = self.shell.execute("k_accountj", [], [], "")[0]
if type(test_k) is bytes:
test_k = test_k.decode('utf-8')
if test_k != '':
return "k"
test_os = self.shell.execute("uname", [], [], "")[0].lower().rstrip()
if type(test_os) is bytes:
test_os = test_os.decode('utf-8')
if test_os == 'darwin':
return "osx"
if test_os == 'linux':
# centos + ubuntu
test_linux = self.shell.execute("lsb_release", [], ['-a'], "")[0]
if type(test_linux) is bytes:
test_linux = test_linux.decode('utf-8')
exp = re.compile("Distributor ID:\t(?P<os>\w+)\n")
index = test_linux.find("Distributor")
if index == -1:
return "unkown"
m = exp.match(test_linux[index:])
return m.group("os").lower()
return "unknown"
def get_env(self):
os = self.get_os()
if os == "k":
return "k"
elif os != "unknown":
return "cluster"
else:
return "unknown"
class Summarizer:
"""
"
"""
def __init__(self):
self.shell = Shell()
def summary(self, job_id, job_cnt):
core_time = self.obtain_time("job{0}.sh.o{1}".format(job_cnt, job_id))
# self.clean_up(job_type, job_id)
self.clean_up(job_cnt, job_id)
return core_time
def obtain_time(self, filename):
f_check = Path("{0}{1}".format(dir_path, filename))
while not f_check.exists():
time.sleep(5)
f = open("{0}{1}".format(dir_path, filename))
lines = f.readlines()
f.close()
for line in lines:
m = time_exp.match(line)
if m:
calc_time = int(m.group("decimal")) +\
int(m.group("float")) * 10**(-len(m.group("float")))
print(calc_time)
return calc_time
def clean_up(self, job_cnt, job_id):
self.shell.execute(
"cp", ["job{0}.sh.o{1} ../../tmp/".format(job_cnt, job_id)], [],
dir_path)
self.shell.execute(
"cp", ["job{0}.sh.e{1} ../../tmp/".format(job_cnt, job_id)], [],
dir_path)
self.shell.execute("rm", [
"job{0}.sh.o{1}".format(job_cnt, job_id),
"job{0}.sh.e{1}".format(job_cnt, job_id),
], ["-f"], dir_path)
class DeployCommand():
def __init__(self, neuron_path):
self.env = Environment()
self.shell = Shell()
self.neuron_path = neuron_path
job_name = 'job_{0}'.format(self.env.get_env())
self.build_generator = BuildGenerator()
self.job_generator = JobGenerator(job_name)
def build(self, env, bench, params, use_tmp, build_neuron, neuron_use_tmp):
self.build_generator.gen(params, use_tmp, neuron_use_tmp, env)
commands = []
tmp_str = ".tmp" if use_tmp else ""
if env == "cluster":
if build_neuron:
commands.append({
"command":
"make",
"args": ["clean"],
"options": [],
"work_dir":
"{0}/nrn-7.2{1}".format(self.neuron_path, tmp_str)
})
commands.append({
"command":
"../../genie/simulator/tmp/build_config.sh",
"args": [],
"options": [],
"work_dir":
"{0}/nrn-7.2{1}".format(self.neuron_path, tmp_str)
})
commands.append({
"command":
"make",
"args": [],
"options": [],
"work_dir":
"{0}/nrn-7.2{1}".format(self.neuron_path, tmp_str)
})
commands.append({
"command":
"make",
"args": ["install"],
"options": [],
"work_dir":
"{0}/nrn-7.2{1}".format(self.neuron_path, tmp_str)
})
commands.append({
"command":
"./make_special.sh",
"args": ["x86_64", bench, tmp_str],
"options": [],
"work_dir":
"{0}/specials{1}".format(self.neuron_path, tmp_str)
})
if env == "k":
if build_neuron:
commands.append({
"command":
"../config/do_config_k1.sh",
"args": [],
"options": [],
"work_dir":
"{0}/nrn-7.2{1}".format(self.neuron_path, tmp_str)
})
commands.append({
"command":
"make",
"args": [],
"options": [],
"work_dir":
"{0}/nrn-7.2{1}".format(self.neuron_path, tmp_str)
})
commands.append({
"command":
"make",
"args": ["install"],
"options": [],
"work_dir":
"{0}/nrn-7.2{1}".format(self.neuron_path, tmp_str)
})
commands.append({
"command":
"../../genie/simulator/tmp/build_config.sh",
"args": [],
"options": [],
"work_dir":
"{0}/nrn-7.2{1}".format(self.neuron_path, tmp_str)
})
commands.append({
"command":
"export",
"args": ["LANG=C"],
"options": [],
"work_dir":
"{0}/nrn-7.2{1}".format(self.neuron_path, tmp_str)
})
commands.append({
"command":
"export",
"args": ["LC_ALL=C"],
"options": [],
"work_dir":
"{0}/nrn-7.2{1}".format(self.neuron_path, tmp_str)
})
commands.append({
"command":
"make",
"args": [],
"options": [],
"work_dir":
"{0}/nrn-7.2{1}".format(self.neuron_path, tmp_str)
})
commands.append({
"command":
"make",
"args": ["install"],
"options": [],
"work_dir":
"{0}/nrn-7.2{1}".format(self.neuron_path, tmp_str)
})
commands.append({
"command":
"cp",
"args": ["./x86_64/bin/*", "./sparc64/bin/"],
"options": [],
"work_dir":
"{0}/exec{1}".format(self.neuron_path, tmp_str)
})
commands.append({
"command":
"./make_special.sh",
"args": [],
"options": ["sparc64", bench, tmp_str],
"work_dir":
"{0}/specials{1}".format(self.neuron_path, tmp_str)
})
self.shell.run_cmds(commands)
def run(self, env, params, cnt, use_tmp):
self.job_generator.gen(params, cnt, use_tmp)
if env == "cluster":
res = self.shell.execute(
"qsub", ["../../genie/simulator/tmp/job{0}.sh".format(cnt)],
[], "{0}/hoc".format(self.neuron_path))[0]
if type(res) is bytes:
res = res.decode('utf-8')
m = id_cluster_exp.match(res)
return m.group("id")
elif env == "k":
res = self.shell.execute(
"pjsub", ["../../genie/simulator/tmp/job{0}.sh".format(cnt)],
[], "{0}/hoc".format(self.neuron_path))[0]
if type(res) is bytes:
res = res.decode('utf-8')
m = id_k_exp.match(res)
return m.group("id")