def submit(self,
script_name,
immediate=False,
depends_on=None,
depends_on_always_run=False):
job_id = None
output = subprocess.run(
f"qsub -V -terse {script_name}",
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True,
)
if output.returncode == 0:
job_id = 0
out = output.stdout.decode("utf-8")
try:
job_id = int(out.readline().strip())
return job_id
except:
raise SchedulerException("Error submitting job to SGE")
else:
raise SchedulerException(
f"Error submitting job to SGE: {output.stderr.decode('utf-8')}"
)
def submit(
self, script_name, immediate=False, depends_on=None, depends_on_always_run=False
):
job_id = None
if immediate:
raise NotYetImplementedException("Immediate not yet implemented for LSF")
if depends_on and depends_on_always_run:
cmd = 'bsub -w "ended(%s)" < %s ' % (depends_on, script_name)
with os.popen(cmd) as f:
output = f.readline()
try:
job_id = int(output.split(" ")[1].replace("<", "").replace(">", ""))
except:
raise SchedulerException("Job submission failed: " + output)
elif depends_on is not None:
cmd = 'bsub -w "done(%s)" < %s ' % (depends_on, script_name)
with os.popen(cmd) as f:
output = f.readline()
try:
job_id = int(output.split(" ")[1].replace("<", "").replace(">", ""))
except:
raise SchedulerException("Job submission failed: " + output)
else:
with os.popen("bsub <" + script_name) as f:
output = f.readline()
try:
job_id = int(output.split(" ")[1].replace("<", "").replace(">", ""))
except:
raise SchedulerException("Job submission failed: " + output)
return job_id
def submit(self,
script_name,
immediate=False,
depends_on=None,
depends_on_always_run=False):
additional_cmd = ""
if "MYCLUSTER_SUBMIT_OPT" in os.environ:
additional_cmd = os.environ["MYCLUSTER_SUBMIT_OPT"]
if not immediate:
if depends_on and depends_on_always_run:
command = f"sbatch {additional_cmd} --kill-on-invalid-dep=yes --dependency=afterany:{depends_on} {script_name}"
elif depends_on is not None:
command = f"sbatch {additional_cmd} --kill-on-invalid-dep=yes --dependency=afterok:{depends_on} {script_name}"
else:
command = f"sbatch {additional_cmd} {script_name}"
print(f"running {command}")
with os.popen(command) as f:
output = f.readline()
try:
job_id = int(output.split(" ")[-1].strip())
except:
raise SchedulerException("Job submission failed: " +
output)
else:
with os.popen('grep -- "SBATCH -p" ' + script_name +
" | sed 's/#SBATCH//'") as f:
partition = f.readline().rstrip()
with os.popen('grep -- "SBATCH --nodes" ' + script_name +
" | sed 's/#SBATCH//'") as f:
nnodes = f.readline().rstrip()
with os.popen('grep -- "SBATCH --ntasks" ' + script_name +
" | sed 's/#SBATCH//'") as f:
ntasks = f.readline().rstrip()
with os.popen('grep -- "SBATCH -A" ' + script_name +
" | sed 's/#SBATCH//'") as f:
project = f.readline().rstrip()
with os.popen('grep -- "SBATCH -J" ' + script_name +
" | sed 's/#SBATCH//'") as f:
job = f.readline().rstrip()
cmd_line = ("salloc --exclusive " + nnodes + " " + partition +
" " + ntasks + " " + project + " " + job + " bash ./" +
script_name)
try:
output = subprocess.check_output(cmd_line, shell=True)
try:
job_id = int(output.split(" ")[-1].strip())
except:
raise SchedulerException("Job submission failed: " +
output)
except:
raise SchedulerException("Job submission failed: " + cmd_line)
return job_id
def node_config(self, queue_id):
max_threads = 1
max_memory = 1
try:
tpn = tasks_per_node(queue_id)
vnode_type = vnode_type = vnode_type = self._get_vnode_name(
queue_id)
if vnode_type is not None:
output = self._check_output(
"pbsnodes -a -F dsv | grep {}".format(vnode_type),
shell=True)
for line in output.splitlines():
for item in line.split("|"):
[key, value] = item.strip().split("=")
if key.strip() == "resources_available.vps_per_ppu":
if int(value) > max_threads:
max_threads = int(value) * tpn
if key.strip() == "resources_available.mem":
# strip kb and convert to mb
mem = float(value[:-2]) / 1024
if mem > max_memory:
max_memory = mem
except Exception as e:
raise SchedulerException("Error fetching node config")
return {"max thread": max_threads, "max memory": max_memory}
def delete(self, job_id):
cmd = f"bkill {job_id}"
output = subprocess.run(
cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True
)
if output.returncode != 0:
raise SchedulerException(f"Error cancelling job {job_id}")
def tasks_per_node(self, queue_id):
parallel_env = queue_id.split(":")[0]
queue_name = queue_id.split(":")[1]
tasks = 0
with os.popen("qconf -sq " + queue_name) as f:
for line in f:
if line.split(" ")[0] == "slots":
tasks = int(re.split("\W+", line)[1])
pe_tasks = tasks
with os.popen("qconf -sp " + parallel_env) as f:
try:
for line in f:
if line.split(" ")[0] == "allocation_rule":
try:
# This may throw exception as allocation rule
# may not always be an integer
pe_tasks = int(re.split("\W+", line)[1])
except ValueError as e:
raise SchedulerException(
"Error parsing SGE output")
except:
pass
return min(tasks, pe_tasks)
def _get_vnode_name(self, queue_id):
try:
output = self._check_output(["qstat", "-Qf", queue_id])
for line in output.splitlines():
if line.strip().startswith("default_chunk.vntype"):
return line.split("=")[-1].strip()
except Exception as e:
raise SchedulerException("Error fetching node config")
def queues(self):
queue_list = []
try:
output = self._check_output(["qstat", "-Q"])
lines = output.splitlines()[2:]
for queue in lines:
queue_list.append(queue.split(" ")[0])
except Exception as e:
raise SchedulerException("Error fetching queues")
return queue_list
def submit(self,
script_name,
immediate=False,
depends_on=None,
depends_on_always_run=False):
job_id = None
if not immediate:
if depends_on and depends_on_always_run:
with os.popen("qsub -W depend=afterany:%s %s" %
(depends_on, script_name)) as f:
output = f.readline()
try:
job_id = output.strip().split(".")[0]
except:
raise SchedulerException("Job submission failed: " +
output)
elif depends_on is not None:
with os.popen("qsub -W depend=afterok:%s %s" %
(depends_on, script_name)) as f:
output = f.readline()
try:
job_id = output.strip().split(".")[0]
except:
raise SchedulerException("Job submission failed: " +
output)
else:
with os.popen("qsub " + script_name) as f:
output = f.readline()
try:
job_id = output.strip().split(".")[0]
except:
raise SchedulerException("Job submission failed: " +
output)
else:
raise NotYetImplementedException(
"Immediate not yet implemented for PBS")
return job_id
def tasks_per_node(self, queue_id):
tpn = 1
try:
vnode_type = vnode_type = self._get_vnode_name(queue_id)
if vnode_type is not None:
output = self._check_output(
"pbsnodes -a -F dsv | grep {}".format(vnode_type),
shell=True)
for line in output.splitlines():
for item in line.split("|"):
[key, value] = item.strip().split("=")
if key.strip() == "resources_available.ncpus":
if int(value) > tpn:
tpn = int(value)
except Exception as e:
raise SchedulerException("Error fetching node config")
return tpn
def node_config(self, queue_id):
# Find first node with queue and record node config
queue_name = queue_id
tasks = 0
config = {}
with os.popen("sinfo -Nelh -p " + queue_name) as f:
line = f.readline()
if len(line):
new_line = re.sub(" +", " ", line.strip())
tasks = int(new_line.split(" ")[4])
memory = int(new_line.split(" ")[6])
config["max task"] = tasks
config["max thread"] = tasks
config["max memory"] = memory
else:
raise SchedulerException(
"Requested partition %s has no nodes" % queue_name)
return config
def get_job_details(self, job_id):
"""
Get full job and step stats for job_id
"""
stats_dict = {}
with os.popen(
"bjobs -o \"jobid run_time cpu_used queue slots stat exit_code start_time estimated_start_time finish_time delimiter='|'\" -noheader "
+ str(job_id)
) as f:
try:
line = f.readline()
cols = line.split("|")
stats_dict["job_id"] = cols[0]
if cols[1] != "-":
stats_dict["wallclock"] = datetime.timedelta(
seconds=float(cols[1].split(" ")[0])
)
if cols[2] != "-":
stats_dict["cpu"] = datetime.timedelta(seconds=float(cols[2].split(" ")[0]))
stats_dict["queue"] = cols[3]
stats_dict["status"] = cols[5]
stats_dict["exit_code"] = cols[6]
stats_dict["start"] = cols[7]
stats_dict["start_time"] = cols[8]
if stats_dict["status"] in ["DONE", "EXIT"]:
stats_dict["end"] = cols[9]
except:
with os.popen("bhist -l " + str(job_id)) as f:
try:
output = f.readlines()
for line in output:
if "Done successfully" in line:
stats_dict["status"] = "DONE"
return stats_dict
elif "Completed <exit>" in line:
stats_dict["status"] = "EXIT"
return stats_dict
else:
stats_dict["status"] = "UNKNOWN"
except Exception as e:
raise SchedulerException(
"Error fetching job details from bjobs, check job id."
)
return stats_dict
def list_current_jobs(self):
jobs = []
output = subprocess.run(
"squeue -h -u `whoami`",
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True,
)
if output.returncode == 0:
for line in output.stdout.decode("utf-8").splitlines():
job_info = re.sub(" +", " ", line.strip()).split(" ")
jobs.append({
"id": int(job_info[0]),
"queue": job_info[1],
"name": job_info[2],
"state": job_info[4],
})
else:
raise SchedulerException("Error fetching job queue listing")
return jobs
def available_tasks(self, queue_id):
free_tasks = 0
max_tasks = 0
assigned_tasks = 0
try:
vnode_type = self._get_vnode_name(queue_id)
if vnode_type is not None:
output = self._check_output(
"pbsnodes -a -F dsv | grep {}".format(vnode_type),
shell=True)
for line in output.splitlines():
for item in line.split("|"):
[key, value] = item.strip().split("=")
if key.strip() == "resources_available.ncpus":
max_tasks += int(value)
elif key.strip() == "resources_assigned.ncpus":
assigned_tasks += int(value)
free_tasks = max_tasks - assigned_tasks
except Exception as e:
raise SchedulerException("Error fetching node config")
return {"available": free_tasks, "max tasks": max_tasks}
def list_current_jobs(self):
jobs = []
output = subprocess.run(
'bjobs -noheader -u `whoami` -o "jobid queue job_name stat"',
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True,
)
if output.returncode == 0:
for line in output.stdout.decode("utf-8").splitlines():
if line == "No unfinished job found":
return jobs
job_info = re.sub(" +", " ", line.strip()).split(" ")
jobs.append(
{
"id": int(job_info[0]),
"queue": job_info[1],
"name": job_info[2],
"state": job_info[3],
}
)
else:
raise SchedulerException("Error fetching job queue listing")
return jobs
def get_job_details(self, job_id):
"""
Get full job and step stats for job_id
First check using sacct, then fallback to squeue
"""
stats_dict = {}
sacct_cmd = f"sacct --noheader --format JobId,Elapsed,TotalCPU,Partition,NTasks,AveRSS,State,ExitCode,start,end -P -j {job_id}"
squeue_cmd = f'squeue --format "%.18i %.9P %.8j %.8u %.2t %.10M %.6D %R %S" -h -j {job_id}'
output = subprocess.run(sacct_cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True)
if output.returncode != 0:
raise SchedulerException("Error fetching job details from sacct")
lines = output.stdout.decode("utf-8").splitlines()
if len(lines) != 0:
if lines[0] not in [
"SLURM accounting storage is disabled",
"slurm_load_jobs error: Invalid job id specified",
]:
cols = lines[0].split("|")
stats_dict["job_id"] = cols[0]
stats_dict["wallclock"] = self._get_timedelta(cols[1])
stats_dict["cpu"] = self._get_timedelta(cols[2])
stats_dict["queue"] = cols[3]
stats_dict["status"] = cols[6]
stats_dict["exit_code"] = cols[7].split(":")[0]
stats_dict["start"] = cols[8]
stats_dict["end"] = cols[9]
steps = []
for line in lines[1:]:
step = {}
cols = line.split("|")
step_val = cols[0].split(".")[1]
step["step"] = step_val
step["wallclock"] = self._get_timedelta(cols[1])
step["cpu"] = self._get_timedelta(cols[2])
step["ntasks"] = cols[4]
step["status"] = cols[6]
step["exit_code"] = cols[7].split(":")[0]
step["start"] = cols[8]
step["end"] = cols[9]
steps.append(step)
stats_dict["steps"] = steps
else:
output = subprocess.run(squeue_cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True)
if output.returncode != 0:
raise SchedulerException(
"Error fetching job details from squeue, check job id.")
lines = output.stdout.decode("utf-8").splitlines()
for line in lines:
if line == "slurm_load_jobs error: Invalid job id specified":
raise SchedulerException("Invalid job id specified")
new_line = re.sub(" +", " ", line.strip())
job_id = int(new_line.split(" ")[0])
state = new_line.split(" ")[4]
stats_dict["job_id"] = str(job_id)
stats_dict["status"] = state
stats_dict["start_time"] = new_line.split(" ")[8]
return stats_dict