def number_job_user(bj_check_user=None, verbose=True):
"""
Internal function for sleep_job_user
"""
username = getpass.getuser()
if not bj_check_user:
bj_check_user = utils.get_username()
bj_command = "perl /dsk/igs2/soft_wrk/" + username + "/SOFT_EPOS8_BIN_TOOLS/SCRIPTS/e8_bjobs_local.pl"
bj_list = subprocess.check_output(bj_command, shell='/bin/csh')
bj_list = bj_list.decode("utf-8")
bj_list = bj_list.split("\n")
bj_pattern_checked = bj_check_user + ' *' + bj_check_user
bj_list_checked = [bool(re.search(bj_pattern_checked, l)) for l in bj_list]
bj_list_checked_sum = np.sum(bj_list_checked)
if verbose:
print("INFO: ", bj_list_checked_sum, "running jobs found for",
bj_check_user)
return bj_list_checked_sum, bj_list_checked, bj_pattern_checked
def sleep_job_user(bj_check_user=None, maxjob=20, bj_check_wait_time=20):
if not bj_check_user:
bj_check_user = utils.get_username()
n_job = number_job_user(bj_check_user)
if n_job >= maxjob:
print("INFO : sleeping @ " + str(dt.datetime.now()) + " for " +
str(bj_check_wait_time) + "s b.c." + str(n_job) +
" jobs are runing")
time.sleep(bj_check_wait_time)
return None
def sleep_job_user(bj_check_user=None, minjob=20, bj_check_wait_time=20):
"""
Internal function for cluster_GFZ_run
"""
if not bj_check_user:
bj_check_user = utils.get_username()
n_job, bj_list_checked, bj_pattern_checked = number_job_user(bj_check_user)
if n_job >= minjob:
check_tigger = False
print("INFO : sleeping @ " + str(dt.datetime.now()) + " for " +
str(bj_check_wait_time) + "s b.c." + str(n_job) +
" jobs are runing")
time.sleep(bj_check_wait_time)
else:
check_tigger = True
print("INFO : let's continue, no job matchs the pattern " +
bj_pattern_checked)
return check_tigger
def cluster_GFZ_run(commands_list,
bunch_on_off=True,
bunch_job_nbr=10,
bunch_wait_time=600,
bj_check_on_off=True,
bj_check_mini_nbr=2,
bj_check_wait_time=120,
bj_check_user="******",
add_cjob_cmd_prefix=True,
wait_sleeping_before_launch=5):
"""
Parameters
----------
commands_list : list of str
List of commands you want to run (one command per job).
bunch_on_off : bool, optional
If False, send all the jobs to the cluster at once.
If True, just send <bunch_job_nbr> of them.
See the options below.
The default is True.
bunch_job_nbr : int, optional
number of jobs which will be sent to the cluser at once.
The default is 10.
bunch_wait_time : int, optional
Minimal time between two bunch runs in sec.
The default is 600.
bj_check_on_off : bool, optional
Do a check before a new bunch run, if previous jobs are still running.
The default is True.
bj_check_mini_nbr : int, optional
The fuctions will wait <bj_check_wait_time> sec
more if <bj_check_mini_nbr> or more jobs are running.
The default is 2.
bj_check_wait_time : int, optional
wait time between two checks in sec. The default is 120.
bj_check_user : str, optional
username you want to check in the batchjobs.
The default is "auto" i.e. your own username.
add_cjob_cmd_prefix : bool, optional
If, the input commands in command_list do not contain
the cjob prefix command, it will be added automatically
The default is True.
wait_sleeping_before_launch : int, optional
Waiting time between two successive runs.
(To cancel the run if necessary)
The default is 5.
Returns
-------
None.
"""
username = getpass.getuser()
history_file_path = None
i_bunch = 0
if bj_check_user == "auto":
bj_check_user = utils.get_username()
log_path = "/home/" + bj_check_user + "/test_tmp.log"
LOGobj = open(log_path, 'w+')
if not add_cjob_cmd_prefix:
commands_list_opera = commands_list
else:
commands_list_opera = []
for cmd in commands_list:
cmd_ope = "cjob -c '" + cmd + "'"
commands_list_opera.append(cmd_ope)
print("****** JOBS THAT WILL BE LAUNCHED ******")
print('Number of jobs : ' + str(len(commands_list_opera)))
print("****************************************")
for ikommand, kommand in enumerate(commands_list_opera):
########## LOG/PRINT command
print(kommand)
LOGobj.write(kommand + '\n')
########## LOG/PRINT sleep
info_sleep = "INFO : script is sleeping for " + str(
wait_sleeping_before_launch) + "sec (so you can cancel it) "
print(info_sleep)
LOGobj.write(info_sleep + '\n')
time.sleep(wait_sleeping_before_launch)
########## LOG/PRINT start
info_start = "INFO : script starts @ " + str(dt.datetime.now())
print(info_start)
LOGobj.write(info_start + '\n')
########## RUN command here !!
if True:
p = subprocess.Popen('',
executable='/bin/csh',
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
stdout, stderr = p.communicate(kommand.encode())
else:
os.system(kommand)
if history_file_path:
with open(history_file_path, "a") as myfile:
myfile.write(kommand + '\n')
i_bunch += 1
########## Bunch On/Off : check if a bunch of job has been launched
if bunch_on_off and np.mod(i_bunch, bunch_job_nbr) == 0:
info_bunch = "INFO : sleeping @ " + str(dt.datetime.now(
)) + " for " + str(bunch_wait_time) + "s b.c. a bunch of " + str(
bunch_job_nbr) + " jobs has been launched"
print(info_bunch)
time.sleep(bunch_wait_time)
LOGobj.write(info_bunch + '\n')
########## Bunch On/Off Check : check if the bunch is finished (experimental but on is better)
###### THIS PART MUST BE MERGE WITH THE SMALLER FCT BELLOW
if bj_check_on_off:
print(
"INFO : BJ Check : All jobs should be finished now, let's see if there is some latecomers"
)
bj_check_tigger = False
while not bj_check_tigger:
bj_check_tigger = sleep_job_user(
minjob=bj_check_mini_nbr,
bj_check_wait_time=bj_check_wait_time)
return None
def cluster_GFZ_run(commands_list,
bunch_on_off=True,
bunch_job_nbr=10,
bunch_wait_time=600,
bj_check_on_off=True,
bj_check_mini_nbr=2,
bj_check_wait_time=120,
bj_check_user="******"):
history_file_path = None
wait_sleeping_before_launch = 5
i_bunch = 0
if bj_check_user == "auto":
bj_check_user = utils.get_username()
log_path = "/home/" + bj_check_user + "/test_tmp.log"
LOGobj = open(log_path, 'w+')
print("****** JOBS THAT WILL BE LAUNCHED ******")
print('Number of jobs : ' + str(len(commands_list)))
print("****************************************")
for kommand in commands_list:
########## LOG/PRINT command
print(kommand)
LOGobj.write(kommand + '\n')
########## LOG/PRINT sleep
info_sleep = "INFO : script is sleeping for " + str(
wait_sleeping_before_launch) + "sec (so you can cancel it) "
print(info_sleep)
LOGobj.write(info_sleep + '\n')
time.sleep(wait_sleeping_before_launch)
########## LOG/PRINT start
info_start = "INFO : script starts @ " + str(dt.datetime.now())
print(info_start)
LOGobj.write(info_start + '\n')
########## RUN command here !!
p = subprocess.Popen('',
executable='/bin/csh',
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
stdout, stderr = p.communicate(kommand.encode())
if history_file_path:
with open(history_file_path, "a") as myfile:
myfile.write(kommand + '\n')
i_bunch += 1
########## Bunch On/Off : check if a bunch of job has been launched
if bunch_on_off and np.mod(i_bunch, bunch_job_nbr) == 0:
info_bunch = "INFO : sleeping @ " + str(dt.datetime.now(
)) + " for " + str(bunch_wait_time) + "s b.c. a bunch of " + str(
bunch_job_nbr) + " jobs has been launched"
print(info_bunch)
time.sleep(bunch_wait_time)
LOGobj.write(info_bunch + '\n')
########## Bunch On/Off Check : check if the bunch is finished (experimental but on is better)
###### THIS PART MUST BE MERGE WITH THE SMALLER FCT BELLOW
if bj_check_on_off:
print(
"INFO : BJ Check : All jobs should be finished now, let's see if there is some latecomers"
)
bj_check_tigger = False
bj_command = "perl /dsk/igs2/soft_wrk/psakicki/SOFT_EPOS8_BIN_TOOLS/SCRIPTS/e8_bjobs_local.pl"
while not bj_check_tigger:
bj_list = subprocess.check_output(bj_command, shell='/bin/csh')
bj_pattern_checked = bj_check_user + ' *' + bj_check_user
bj_list_checked = [
re.search(bj_pattern_checked, l) for l in bj_list
]
bj_list_checked_sum = np.sum(bj_list_checked)
if bj_list_checked_sum > bj_check_mini_nbr:
print("INFO : sleeping @ " + str(dt.datetime.now()) +
" for " + str(bj_check_wait_time) + "s b.c." +
str(bj_list_checked_sum) + "job(s) match pattern " +
bj_pattern_checked)
print(bj_list)
time.sleep(bj_check_wait_time)
else:
bj_check_tigger = True
print("INFO : let's continue, no job matchs the pattern " +
bj_pattern_checked)