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job_on_hpc.py
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import os
import sys
dir_check=sys.argv[1]
root_dir = os.path.expandvars('$HOME')
#code_dir="%s/bin/QE-batch"%root_dir
code_dir=sys.path[0]
############job_script_settings##########
flat_info=open("%s/flat.save/FLAT_INFO"%code_dir).readlines()
for lines in flat_info:
if lines.find("flat_number=")!=-1:
flat_number=int(lines.split("flat_number=")[-1].split("#")[0])
if lines.find("node_num=")!=-1:
node_num=int(lines.split("node_num=")[-1].split("#")[0])
if lines.find("ppn_num")!=-1:
ppn_num_man=int(lines.split("ppn_num=")[-1].split("#")[0])
if ppn_num_man==0:
ppn_set=0
elif ppn_num_man!=0:
ppn_set=1
if lines.find("wall_time=")!=-1:
wall_time=lines.split("wall_time=")[-1].split("#")[0].strip("\n")
#flat_number=2 # 1 for"zf_normal",2 for "spst_pub",3 for "dm_pub_cpu"
#node_num=2
#wall_time="116:00:00"
#ppn_set=1
#ppn_num_man=16
####################"zf_normal" has 52ppn,"spst_pub" has 32 ppn ,"dm_pub_cpu" has 32 ppn
def JOB_func(flat_number):
type_hpc=""
if (flat_number==1)|(flat_number==2):
type_hpc="pbs"
elif (flat_number==3):
type_hpc="sbatch"
return type_hpc
dir_file=(os.popen("pwd").read())
dir=max(dir_file.split('\n'))
def split_lines(infiles):
f1=infiles
read_data=[]
for lines in f1:
read_data_row=[]
if "JOBID" in lines:
continue
if "Job ID" in lines:
continue
if "----" in lines:
continue
if len(lines) <= 1:
continue
if "\t" in lines:
a_bf=(lines.split("\n")[0]).split("\t")
else:
a_bf=(lines.split("\n")[0]).split(" ")
for i in a_bf:
if len(i)>0:
read_data_row.append(i)
read_data.append(read_data_row)
# print(len(read_data),len(read_data[0]))
return read_data
if JOB_func(flat_number)=="pbs":
job_on_hpc=split_lines(os.popen("qstat").readlines())
wait_node_list=[]
run_node_list=[]
for i in job_on_hpc:
if i[4]=="Q":
wait_node_list.append(i[0].split(".node1")[0])
if i[4]=="R":
run_node_list.append(i[0].split(".node1")[0])
wait_file_list=[]
run_file_list=[]
working_file=[]
running_file=[]
for i in wait_node_list:
all_data=os.popen("qstat -f %s"%i).readlines()
read_start=0
working_file_raw=""
for j in range(len(all_data)):
if all_data[j].find("PBS_O_WORKDIR")!=-1:
read_start=1
if all_data[j].find("PBS_O_HOST")!=-1:
read_start=2
if read_start==1:
#print(all_data[j])
working_file_raw+=all_data[j].split("\n")[0].strip("\t").strip(",")
if read_start==2:
read_start=0
if all_data[j].split("\n")[0].strip("\t").strip()[:len("PBS_O_HOST")]=="PBS_O_HOST":
donothing=1
else:
working_file_raw+=all_data[j].split(",PBS_O_HOST")[0].strip("\t")
working_file.append(working_file_raw)
for i in range(len(working_file)):
working_file[i]=working_file[i].split("PBS_O_WORKDIR=")[-1]
for i in run_node_list:
all_data=os.popen("qstat -f %s"%i).readlines()
read_start=0
running_file_raw=""
for j in range(len(all_data)):
if all_data[j].find("PBS_O_WORKDIR")!=-1:
read_start=1
if all_data[j].find("PBS_O_HOST")!=-1:
read_start=2
if read_start==1:
#print(all_data[j])
running_file_raw+=all_data[j].split("\n")[0].strip("\t").strip(",")
if read_start==2:
read_start=0
if all_data[j].split("\n")[0].strip("\t").strip()[:len("PBS_O_HOST")]=="PBS_O_HOST":
donothing=1
else:
running_file_raw+=all_data[j].split(",PBS_O_HOST")[0].strip("\t")
running_file.append(running_file_raw)
for i in range(len(running_file)):
running_file[i]=running_file[i].split("PBS_O_WORKDIR=")[-1]
elif JOB_func(flat_number)=="sbatch":
job_on_hpc=split_lines(os.popen("squeue").readlines())
wait_node_list=[]
run_node_list=[]
for i in job_on_hpc:
if i[4]=="PD":
wait_node_list.append(i[0])
if i[4]=="R":
run_node_list.append(i[0])
wait_file_list=[]
working_file=[]
run_file_list=[]
running_file=[]
for i in wait_node_list:
all_data=os.popen("scontrol show job %s"%i).readlines()
read_start=0
working_file_raw=""
for j in range(len(all_data)):
if all_data[j].find("WorkDir")!=-1:
read_start=1
if all_data[j].find("StdErr")!=-1:
read_start=0
if read_start==1:
#print(all_data[j])
working_file_raw+=all_data[j].split("\n")[0].strip("\t").strip("./")
working_file.append(working_file_raw)
for i in range(len(working_file)):
working_file[i]=working_file[i].split("WorkDir=")[-1]
for i in run_node_list:
all_data=os.popen("scontrol show job %s"%i).readlines()
read_start=0
running_file_raw=""
for j in range(len(all_data)):
if all_data[j].find("WorkDir")!=-1:
read_start=1
if all_data[j].find("StdErr")!=-1:
read_start=0
if read_start==1:
#print(all_data[j])
running_file_raw+=all_data[j].split("\n")[0].strip("\t").strip("./")
running_file.append(running_file_raw)
for i in range(len(running_file)):
running_file[i]=running_file[i].split("WorkDir=")[-1]
#print(working_file)
os.chdir(dir_check)
read_dir=max(os.popen("pwd").read().split("\n"))
#print(read_dir)
if read_dir in working_file:
print("waiting on line")
elif read_dir in running_file:
print("running")
else:
print("Not here")
os.chdir(dir)