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read_relax_E_for_UI.py
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import numpy
import os
import time
import sys
error_waiting_recal=0 #set this on to recal for error files
wavefc_rm=1 #!!!!!!DON‘T set to 1 if you want further calculation like BANDS!!!!
#set this to 1 to remove wavefunction when job is done
prefix="BTO" #the prefix same in your input file
qe_dir="/hpc/data/home/spst/zhengfan/open/replace"
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
if flat_number==1:
type_flat="zf_normal"
if flat_number==2:
type_flat="spst_pub"
if flat_number==3:
type_flat="dm_pub_cpu"
###################
def JOB_func(type_flat,node_num):
type_hpc=""
if type_flat=="spst_pub":
ppn_num=32
type_hpc="pbs"
elif type_flat=="zf_normal":
ppn_num=52
type_hpc="pbs"
elif type_flat=="dm_pub_cpu":
ppn_num=32
type_hpc="sbatch"
if ppn_set==1:
ppn_num=ppn_num_man
ppn_tot=node_num*ppn_num
if type_hpc=="pbs":
jobscript_file_in=['#!/bin/bash\n',
'#PBS -N coolxty\n',
'#PBS -l nodes=%d:ppn=%d\n'%(node_num,ppn_num),
'#PBS -l walltime=%s\n'%wall_time,
'#PBS -S /bin/bash\n',
'#PBS -j oe\n',
'#PBS -q %s\n'%(type_flat),
'\n',
'cd $PBS_O_WORKDIR\n',
'\n',
'NPROC=`wc -l < $PBS_NODEFILE`\n',
'JOBID=$( echo $PBS_JOBID | awk -F \".\" \'{print $1}\')\n',
"echo \'JOB-ID = \' $JOBID >> JOB-${JOBID}\n",
"echo This job has allocated $NPROC procs >> JOB-${JOBID}\n",
"TW=$( qstat -f \"$JOBID\" | grep -e \'Resource_List.walltime\' | awk -F \"=\" \'{print $(NF)}\' )\n",
"echo \'requested walltime = \' $TW >> JOB-${JOBID}\n",
"Q=$( qstat -f \"$JOBID\" | grep -e \'queue\' | awk \'{print $3}\' )\n",
"echo \'requested queue = \' $Q >> JOB-${JOBID}\n",
"TC=$( qstat -f \"$JOBID\" | grep -e \'etime\' | awk -F \"=\" \'{print $(NF)}\' )\n",
"TC_s=$( date -d \"$TC\" +%s )\n",
"echo \'time submit = \' $TC $TC_s >> JOB-${JOBID}\n",
"TS=$( qstat -f \"$JOBID\" | grep -e \'start_time\' | awk -F \"=\" \'{print $(NF)}\' )\n",
"TS_s=$( date -d \"$TS\" +%s )\n",
"echo \'time start = \' $TS $TS_s >> JOB-${JOBID}\n",
"TimeDu=`expr $TS_s - $TC_s`\n",
"echo \'Waiting time(s) = \' $TimeDu >> JOB-${JOBID}\n",
"\n",
"echo This job has allocated $NPROC proc > log\n",
"\n",
"module load compiler/intel/2021.3.0\n",
"module load mpi/intelmpi/2021.3.0\n",
"\n",
]
if type_hpc=="sbatch":
jobscript_file_in=[
"#!/bin/bash\n",
"#SBATCH --job-name=xty\n",
"#SBATCH -D ./\n",
"#SBATCH --nodes=%d\n"%node_num,
"#SBATCH --ntasks-per-node=%d\n"%ppn_num,
"#SBATCH -o output.%j\n",
"##SBATCH -e error.%j\n",
"#SBATCH --time=%s\n"%wall_time,
"#SBATCH --partition=dm_pub_cpu\n",
"\n",
"##SBATCH --gres=gpu:4 #if use gpu, uncomment this\n",
"#export I_MPI_PMI_LIBRARY=/opt/gridview/slurm/lib/libpmi.so\n",
"ulimit -s unlimited\n",
"ulimit -l unlimited\n",
"\n",
"#setup intel oneapi environment \n",
"source /dm_data/apps/intel/oneapi/setvars.sh\n",
"#source /etc/profile\n",
"module load compiler/latest\n",
"module load mpi/latest\n",
"module load mkl/latest\n",
]
return jobscript_file_in,type_hpc,ppn_tot
def JOB_modify(JOB,mode,molecule_i,type_hpc_out,ppn_tot_out):
vaspfile=molecule_i
fj=open(JOB,"w+")
jobscript_file_1=[]
for i in range(len(jobscript_file)):
j_rename=""
#print(jobscript_file[i],type(jobscript_file[i]),i)
if type_hpc_out=="pbs":
if jobscript_file[i].find('#PBS -N')!=-1:
job_name_split=vaspfile.split("_")
for j_names in job_name_split:
j_rename+=j_names[:2].zfill(2)
jobscript_file[i]='#PBS -N %s\n'%(j_rename)
jobscript_file_1.append(jobscript_file[i])
if type_hpc_out=="sbatch":
if jobscript_file[i].find('#SBATCH --job-name')!=-1:
job_name_split=vaspfile.split("_")
for j_names in job_name_split:
j_rename+=j_names[:2].zfill(2)
jobscript_file[i]='#SBATCH --job-name=%s\n'%(j_rename)
jobscript_file_1.append(jobscript_file[i])
if (type_hpc_out=="pbs") & (mode!="pdos") & (mode!="BaderCharge"):
if solvation_model==0:
jobscript_file_1.append("mpirun --bind-to core -np $NPROC -hostfile $PBS_NODEFILE %s/pw-6.8.x -npool 4 -ndiag 4 < in_%s_%s >& out_%s_%s"%(qe_dir,mode,molecule_i,mode,molecule_i))
elif solvation_model==1:
jobscript_file_1.append("mpirun --bind-to core -np $NPROC -hostfile $PBS_NODEFILE %s/pw-7.2-environ.x -npool 4 -ndiag 4 --environ < in_%s_%s >& out_%s_%s"%(qe_dir,mode,molecule_i,mode,molecule_i))
elif (type_hpc_out=="sbatch") & (mode!="pdos") & (mode!="BaderCharge"):
if solvation_model==0:
jobscript_file_1.append("mpirun --bind-to core -np %s %s/pw-6.8.x -npool 4 -ndiag 4 < in_%s_%s >& out_%s_%s"%(ppn_tot_out,qe_dir,mode,molecule_i,mode,molecule_i))
elif solvation_model==1:
jobscript_file_1.append("mpirun --bind-to core -np %s -hostfile $PBS_NODEFILE %s/pw-7.2-environ.x -npool 4 -ndiag 4 --environ < in_%s_%s >& out_%s_%s"%(ppn_tot_out,qe_dir,mode,molecule_i,mode,molecule_i))
elif mode=="pdos":
jobscript_file_1.append("mpirun --bind-to core -np %s %s/projwfc.x -npool 4 -ndiag 4 < in_%s_%s >& out_%s_%s"%(ppn_tot_out,qe_dir,mode,molecule_i,mode,molecule_i))
elif mode=="BaderCharge":
jobscript_file_1.append("mpirun --bind-to core -np %s %s/pp.x -npool 4 -ndiag 4 < in_%s_%s >& out_%s_%s"%(ppn_tot_out,qe_dir,mode,molecule_i,mode,molecule_i))
fj.writelines(jobscript_file_1)
jobscript_file_1=[]
fj.close()
jobscript_file,type_hpc_out,ppn_tot_out=JOB_func(type_flat,node_num)
##default value of mode is relax
if len(sys.argv)==1:
mode="relax"
else:
mode=sys.argv[1]
print(mode)
dir_file=(os.popen("pwd").read())
dir=max(dir_file.split('\n'))
JOB_name=""
error=0
if os.path.isfile("%s/replace.py"%code_dir)==1:
replace_line=open("%s/replace.py"%code_dir).readlines()
#get the job_script name:
for i in replace_line:
if i.find("JOB=")!=-1:
JOB_name=i.split("JOB=")[-1].split("#")[0].split("\"")[1]
#print("JOB_name**************",JOB_name)
if i.find("#solvation")!=-1:
solvation_model=int(i.split("#")[0].split("solvation_model=")[-1].strip())
if (JOB_name==""):
print("ERROR: replace.py not set correctly!")
error=1
elif os.path.isfile("%s/replace.py"%code_dir)==0:
print("plz copy /hpc/data/home/spst/zhengfan/open/replace/replace.py here, otherwise some func does not work! ")
error=1
sub_method=""
if (flat_number==1)|(flat_number==2):
sub_method="qsub"
elif (flat_number==3):
sub_method="sbatch"
#print("**************************%s %s"%(sub_method,JOB_name))
find_bcon=0
root_dir = os.path.expandvars('$HOME')
#print("%s/bin/bcon.sh"%root_dir)
if os.path.isfile("%s/bin/bcon.sh"%root_dir)==1:
print("bcon.sh found")
find_bcon=1
if find_bcon==0:
print("bcon.sh not found,copy from /hpc/data/home/spst/zhengfan/open/ to ~/bin")
os.system("cp /hpc/data/home/spst/zhengfan/open/bcon.sh ~/bin/.")
if error==0:
str_in_dir=[]
str_in_dir0=[]
depth=1
stuff = os.path.abspath(os.path.expanduser(os.path.expandvars(".")))
for root,dirnames,filenames in os.walk(stuff):
if root[len(stuff):].count(os.sep) < depth:
for filename in filenames:
if ".vasp" in filename:
str_in_dir0.append(filename.split(".vasp")[0])
for dirname in dirnames:
if dirname in str_in_dir0:
str_in_dir.append(dirname)
str_in_dir=list(set(str_in_dir))
str_in_dir=sorted(str_in_dir,key=len,reverse=True)
print("*******************",str_in_dir)
if len(str_in_dir)==0:
print("!!!!!!! No .vasp file found in this directory !!!")
len_max=len(str_in_dir[0])
#print(str_name0)
fileout=[]
yes_to_all_continue=""
yes_to_all_error=""
yes_to_all_error1=""
for i in range(len(str_in_dir)):
job_on_hpc=os.popen("python %s/job_on_hpc.py %s"%(code_dir,str_in_dir[i])).readlines()[0].strip("\n")
if (os.path.isfile("%s/%s/out_%s_%s"%(dir,(str_in_dir[i]),mode,(str_in_dir[i])))==1):
etot1=(os.popen("grep JOB %s/%s/out_%s_%s"%(dir,(str_in_dir[i]),mode,(str_in_dir[i]))).readlines())
if len(etot1)!=1:
etot0=(os.popen("grep \"! \" %s/%s/out_%s_%s"%(dir,(str_in_dir[i]),mode,(str_in_dir[i])))).readlines()
read_error=0
etot11=open("%s/%s/out_%s_%s"%(dir,(str_in_dir[i]),mode,(str_in_dir[i]))).readlines()
for error_line in etot11:
#if error_line.find("BAD TERMINATION")!=-1:
# read_error=2
if error_line.find("ERROR")!=-1:
read_error=2
if error_line.find("stopping ...")!=-1:
read_error=2
if error_line.find("DUE TO TIME LIMIT")!=-1:
read_error=1
if error_line.find("error waiting for event")!=-1:
read_error=2
if error_line.find("longjmp causes")!=-1:
read_error=1
if error_line.find("process killed")!=-1:
read_error=1
if error_line.find("CANCELLED AT")!=-1:
read_error=2
if error_line.find("error parsing")!=-1:
read_error=2
if (read_error==1):
if len(etot0) > 0:
if etot0[0].find("failed")==-1:
energy0=etot0[-1].split(" =")[-1].split("Ry")[0].strip()
#print("energy0",energy0,"11",etot0[-1])
energy_eV0=float(energy0)*27.211396/2
print("%*s"%(len_max,str_in_dir[i]),energy0,"Ry","%.11f"%energy_eV0,"eV"," out of timing")
fileout.append(["%*s"%(len_max,str_in_dir[i]),energy0,"Ry","%.11f"%energy_eV0,"eV"," out of timing"])
elif etot0[0].find("failed")!=-1:
print("%*s"%(len_max,str_in_dir[i]),"unknown error")
fileout.append(["%*s"%(len_max,str_in_dir[i]),"unknown error"])
elif len(etot0)==0:
print("%*s"%(len_max,str_in_dir[i]),"out of timing")
fileout.append(["%*s"%(len_max,str_in_dir[i]),"out of timing"])
if (read_error==2):
if len(etot0) > 0:
if etot0[0].find("failed")==-1:
energy0=etot0[-1].split(" =")[-1].split("Ry")[0].strip()
#print("energy0",energy0,"11",etot0[-1])
energy_eV0=float(energy0)*27.211396/2
print("%*s"%(len_max,str_in_dir[i]),energy0,"Ry","%.11f"%energy_eV0,"eV"," ERROR")
fileout.append(["%*s"%(len_max,str_in_dir[i]),energy0,"Ry","%.11f"%energy_eV0,"eV"," ERROR"])
elif etot0[0].find("failed")!=-1:
print("%*s"%(len_max,str_in_dir[i]),"unknown error")
fileout.append(["%*s"%(len_max,str_in_dir[i]),"unknown error"])
elif len(etot0)==0:
print("%*s"%(len_max,str_in_dir[i]),"ERROR")
fileout.append(["%*s"%(len_max,str_in_dir[i]),"ERROR"])
#recalculate if out of timing
'''
if (yes_to_all_error==""):
print("would you like me to continue cal for you?")
print("plz input Y/y for yes, N/n for no, A/a for yes to all, Q/q for no to all")
continue_error=input(">>>>>>")
if continue_error.lower()=="y":
os.chdir("%s/%s/"%(dir,(str_in_dir[i])))
#a=os.popen("pwd").readlines()
#print(a)
if mode=="relax":
os.system("bcon.sh out_relax_%s in_relax_%s"%((str_in_dir[i]),(str_in_dir[i])))
print("bcon.sh out_relax_%s in_relax_%s"%((str_in_dir[i]),(str_in_dir[i])))
JOB_modify(JOB_name,mode,str_in_dir[i],type_hpc_out,ppn_tot_out)
os.system("%s %s"%(sub_method,JOB_name))
os.system("mv out_%s_%s out_buffer_%s"%(mode,str_in_dir[i],mode))
os.chdir(dir)
print("%s subed!"%str_in_dir[i])
elif continue_error.lower()=="q":
yes_to_all_error="q"
elif continue_error.lower()=="a":
yes_to_all_error="a"
os.chdir("%s/%s/"%(dir,(str_in_dir[i])))
if mode=="relax":
os.system("bcon.sh out_relax_%s in_relax_%s"%((str_in_dir[i]),(str_in_dir[i])))
JOB_modify(JOB_name,mode,str_in_dir[i],type_hpc_out,ppn_tot_out)
os.system("%s %s"%(sub_method,JOB_name))
os.system("mv out_%s_%s out_buffer_%s"%(mode,str_in_dir[i],mode))
os.chdir(dir)
print("%s subed!"%str_in_dir[i])
elif continue_error.lower()=="n":
print("skip this file")
else:
print("unknow input,skip this loop")
elif (yes_to_all_error=="a"):
os.chdir("%s/%s/"%(dir,(str_in_dir[i])))
if mode=="relax":
os.system("bcon.sh out_relax_%s in_relax_%s"%((str_in_dir[i]),(str_in_dir[i])))
JOB_modify(JOB_name,mode,str_in_dir[i],type_hpc_out,ppn_tot_out)
os.system("%s %s"%(sub_method,JOB_name))
os.system("mv out_%s_%s out_buffer_%s"%(mode,str_in_dir[i],mode))
os.chdir(dir)
print("%s subed!"%str_in_dir[i])
'''
#output some data if there is no error
elif read_error==0:
if len(etot0) > 0:
energy0=etot0[-1].split(" =")[-1].split("Ry")[0].strip()
energy_eV0=float(energy0)*27.211396/2
if job_on_hpc!="Not here":
print("%*s"%(len_max,str_in_dir[i]),energy0,"Ry","%.11f"%energy_eV0,"eV"," running",end='')
elif job_on_hpc=="Not here":
print("%*s"%(len_max,str_in_dir[i]),energy0,"Ry","%.11f"%energy_eV0,"eV"," disc quota exceeded",end='')
if len(os.popen("grep \"Gradient error\" %s/%s/out_%s_%s"%(dir,(str_in_dir[i]),mode,(str_in_dir[i]))).readlines())>0:
force_now=(os.popen("grep \"Gradient error\" %s/%s/out_%s_%s"%(dir,(str_in_dir[i]),mode,(str_in_dir[i]))).readlines()[-1]).split("Gradient error")[-1].strip().split("=")[-1].strip()
print(" ",force_now)
else:
print("force not generated!")
if job_on_hpc!="Not here":
fileout.append(["%*s"%(len_max,str_in_dir[i]),energy0,"Ry","%.11f"%energy_eV0,"eV"," running"])
elif job_on_hpc=="Not here":
fileout.append(["%*s"%(len_max,str_in_dir[i]),energy0,"Ry","%.11f"%energy_eV0,"eV"," ERROR"])
elif len(etot0)==0:
if job_on_hpc!="Not here":
print("%*s"%(len_max,str_in_dir[i]),"running")
fileout.append(["%*s"%(len_max,str_in_dir[i]),"running"])
elif job_on_hpc=="Not here":
print("%*s"%(len_max,str_in_dir[i]),"ERROR")
fileout.append(["%*s"%(len_max,str_in_dir[i]),"ERROR"])
#if there is JOB DONE output:
else:
if mode=="relax":
etot_relax_0=os.popen("grep ! %s/%s/out_%s_%s"%(dir,(str_in_dir[i]),mode,(str_in_dir[i]))).readlines()
if len(etot_relax_0)==0:#if no energy data output
print("!!!!!!!!!!",str_in_dir[i],"scf_not_converge")
etot="a = 0 Ry"
else:
etot=etot_relax_0[-1]
elif mode=="pdos":
print("%*s"%(len_max,str_in_dir[i]),"PDOS"," !!DONE!!!")
if wavefc_rm==1:
if os.path.exists("%s/%s.save"%(str_in_dir[i],prefix))==1:
os.system("rm -r %s/%s.save"%(str_in_dir[i],prefix))
print("!!rm -r %s/%s.save"%(str_in_dir[i],prefix))
os.system("rm %s/%s.mix*"%(str_in_dir[i],prefix))
os.system("rm %s/%s.wfc*"%(str_in_dir[i],prefix))
print("!!rm %s/%s.wfc*"%(str_in_dir[i],prefix))
print("!!rm %s/%s.mix*"%(str_in_dir[i],prefix))
fileout.append(["%*s"%(len_max,str_in_dir[i]),"PDOS"," !!DONE!!!"])
continue
elif mode=="BaderCharge":
print("%*s"%(len_max,str_in_dir[i]),"BaderCharge"," !!DONE!!!")
if wavefc_rm==1:
if os.path.exists("%s/%s.save"%(str_in_dir[i],prefix))==1:
os.system("rm -r %s/%s.save"%(str_in_dir[i],prefix))
print("!!rm -r %s/%s.save"%(str_in_dir[i],prefix))
os.system("rm %s/%s.mix*"%(str_in_dir[i],prefix))
os.system("rm %s/%s.wfc*"%(str_in_dir[i],prefix))
print("!!rm %s/%s.wfc*"%(str_in_dir[i],prefix))
print("!!rm %s/%s.mix*"%(str_in_dir[i],prefix))
fileout.append(["%*s"%(len_max,str_in_dir[i]),"BaderCharge"," !!DONE!!!"])
continue
elif mode=="bands":
print("%*s"%(len_max,str_in_dir[i]),"BANDS"," !!DONE!!!")
if wavefc_rm==1:
if os.path.exists("%s/%s.save"%(str_in_dir[i],prefix))==1:
os.system("rm -r %s/%s.save"%(str_in_dir[i],prefix))
print("!!rm -r %s/%s.save"%(str_in_dir[i],prefix))
os.system("rm %s/%s.mix*"%(str_in_dir[i],prefix))
os.system("rm %s/%s.wfc*"%(str_in_dir[i],prefix))
print("!!rm %s/%s.wfc*"%(str_in_dir[i],prefix))
print("!!rm %s/%s.mix*"%(str_in_dir[i],prefix))
fileout.append(["%*s"%(len_max,str_in_dir[i]),"BANDS"," !!DONE!!!"])
continue
elif mode=="scf":
etot=(os.popen("grep ! %s/%s/out_%s_%s"%(dir,(str_in_dir[i]),mode,(str_in_dir[i]))).readlines()[0])
energy=etot.split(" =")[-1].split("Ry")[0].strip()
energy_eV=float(energy)*27.211396/2
lines=open("%s/%s/out_%s_%s"%(dir,(str_in_dir[i]),mode,(str_in_dir[i]))).readlines()
if "JOB" in lines[-2]:#relax/scf converged
if wavefc_rm==1:
if os.path.exists("%s/%s.save"%(str_in_dir[i],prefix))==1:
os.system("rm -r %s/%s.save"%(str_in_dir[i],prefix))
print("!!rm -r %s/%s.save"%(str_in_dir[i],prefix))
os.system("rm %s/%s.mix*"%(str_in_dir[i],prefix))
os.system("rm %s/%s.wfc*"%(str_in_dir[i],prefix))
print("!!rm %s/%s.wfc*"%(str_in_dir[i],prefix))
print("!!rm %s/%s.mix*"%(str_in_dir[i],prefix))
print("%*s"%(len_max,str_in_dir[i]),energy,"Ry","%.11f"%energy_eV,"eV"," !!DONE!!!")
fileout.append(["%*s"%(len_max,str_in_dir[i]),energy,"Ry","%.11f"%energy_eV,"eV"," !!DONE!!!"])
if "JOB" not in lines[-2]:#relax/scf not converged
print("%*s"%(len_max,str_in_dir[i]),energy,"Ry","%.11f"%energy_eV,"eV"," not converged")
fileout.append(["%*s"%(len_max,str_in_dir[i]),energy,"Ry","%.11f"%energy_eV,"eV"," not converged"])
'''
if (yes_to_all_continue==""):
print("would you like me to continue cal for you?")
print("plz input Y/y for yes, N/n for no, A/a for yes to all, Q/q for no to all")
continue_cal=input(">>>>>>")
if continue_cal.lower()=="y":
os.chdir("%s/%s/"%(dir,(str_in_dir[i])))
#a=os.popen("pwd").readlines()
#print(a)
if mode=="relax":
os.system("bcon.sh out_relax_%s in_relax_%s"%((str_in_dir[i]),(str_in_dir[i])))
print("bcon.sh out_relax_%s in_relax_%s"%((str_in_dir[i]),(str_in_dir[i])))
JOB_modify(JOB_name,mode,str_in_dir[i],type_hpc_out,ppn_tot_out)
os.system("%s %s"%(sub_method,JOB_name))
os.system("mv out_%s_%s out_buffer_%s"%(mode,str_in_dir[i],mode))
os.chdir(dir)
print("%s subed!"%str_in_dir[i])
elif continue_cal.lower()=="q":
yes_to_all_continue="q"
elif continue_cal.lower()=="a":
yes_to_all_continue="a"
os.chdir("%s/%s/"%(dir,(str_in_dir[i])))
if mode=="relax":
os.system("bcon.sh out_relax_%s in_relax_%s"%((str_in_dir[i]),(str_in_dir[i])))
JOB_modify(JOB_name,mode,str_in_dir[i],type_hpc_out,ppn_tot_out)
os.system("%s %s"%(sub_method,JOB_name))
os.system("mv out_%s_%s out_buffer_%s"%(mode,str_in_dir[i],mode))
os.chdir(dir)
print("%s subed!"%str_in_dir[i])
elif continue_cal.lower()=="n":
print("skip this file")
else:
print("unknow input,skip this loop")
elif (yes_to_all_continue=="a"):
os.chdir("%s/%s/"%(dir,(str_in_dir[i])))
if mode=="relax":
os.system("bcon.sh out_relax_%s in_relax_%s"%((str_in_dir[i]),(str_in_dir[i])))
JOB_modify(JOB_name,mode,str_in_dir[i],type_hpc_out,ppn_tot_out)
os.system("%s %s"%(sub_method,JOB_name))
os.system("mv out_%s_%s out_buffer_%s"%(mode,str_in_dir[i],mode))
os.chdir(dir)
print("%s subed!"%str_in_dir[i])
'''
else:
#print("I am here~")
#error exists recalculate
job_on_hpc=os.popen("python %s/job_on_hpc.py %s"%(code_dir,str_in_dir[i])).readlines()[0].strip("\n")
if job_on_hpc=="waiting on line":
print("%*s"%(len_max,str_in_dir[i]),"waiting")
fileout.append(["%*s"%(len_max,str_in_dir[i]),"waiting"])
elif job_on_hpc=="Not here":
print("%*s"%(len_max,str_in_dir[i]),"No Calculation")
fileout.append(["%*s"%(len_max,str_in_dir[i]),"No Calculation"])
elif job_on_hpc=="running":
print("%*s"%(len_max,str_in_dir[i]),"running")
fileout.append(["%*s"%(len_max,str_in_dir[i]),"running"])
'''
if (yes_to_all_error1=="")&(error_waiting_recal==1):
print("would you like me to restart cal for you?")
print("plz input Y/y for yes, N/n for no, A/a for yes to all, Q/q for no to all")
continue_error1=input(">>>>>>")
if continue_error1.lower()=="y":
os.chdir("%s/%s/"%(dir,(str_in_dir[i])))
#a=os.popen("pwd").readlines()
#print(a)
if mode=="relax":
os.system("bcon.sh out_relax_%s in_relax_%s"%((str_in_dir[i]),(str_in_dir[i])))
print("bcon.sh out_relax_%s in_relax_%s"%((str_in_dir[i]),(str_in_dir[i])))
JOB_modify(JOB_name,mode,str_in_dir[i],type_hpc_out,ppn_tot_out)
os.system("%s %s"%(sub_method,JOB_name))
os.system("mv out_%s_%s out_buffer_%s"%(mode,str_in_dir[i],mode))
os.chdir(dir)
print("%s subed!"%str_in_dir[i])
elif continue_error1.lower()=="q":
yes_to_all_error1="q"
elif continue_error1.lower()=="a":
yes_to_all_error1="a"
os.chdir("%s/%s/"%(dir,(str_in_dir[i])))
if mode=="relax":
os.system("bcon.sh out_relax_%s in_relax_%s"%((str_in_dir[i]),(str_in_dir[i])))
JOB_modify(JOB_name,mode,str_in_dir[i],type_hpc_out,ppn_tot_out)
os.system("%s %s"%(sub_method,JOB_name))
os.system("mv out_%s_%s out_buffer_%s"%(mode,str_in_dir[i],mode))
os.chdir(dir)
print("%s subed!"%str_in_dir[i])
elif continue_error1.lower()=="n":
print("skip this file")
else:
print("unknow input,skip this loop")
elif (yes_to_all_error1=="a"):
os.chdir("%s/%s/"%(dir,(str_in_dir[i])))
if mode=="relax":
os.system("bcon.sh out_relax_%s in_relax_%s"%((str_in_dir[i]),(str_in_dir[i])))
JOB_modify(JOB_name,mode,str_in_dir[i],type_hpc_out,ppn_tot_out)
os.system("%s %s"%(sub_method,JOB_name))
os.system("mv out_%s_%s out_buffer_%s"%(mode,str_in_dir[i],mode))
os.chdir(dir)
print("%s subed!"%str_in_dir[i])
'''
f_ou=open("pv_result_out","w+")
for i in range(len(fileout)):
for j in range(len(fileout[i])):
f_ou.write(str(fileout[i][j])+"\t")
f_ou.write("\n")
print("pv_result_out generated!")