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cosolver/python_scripts/kperp_scan.py
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kperp_scan.py
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#!/usr/bin/env python
# generates GK collision matrices for different kperp
import os
import sys
import f90nml
import numpy as np
# To create directory, if doesn't exist
def mkdir_p(dir):
'''make a directory (dir) if it doesn't exist'''
if not os.path.exists(dir):
print('Create ', dir)
os.mkdir(dir)
# directories
cwd_directory = os.getcwd()
scandir_name = 'gk.sugama'
scandir_path = os.path.join( cwd_directory, scandir_name)
# Where to find the exec
exec_path= "/marconi/home/userexternal/bfrei000/cosolver/bin/CO"
exec_name ='CO'
# Read input namelist
input_file = os.path.join(cwd_directory, "fort.90")
with open( input_file) as fh:
inputs = f90nml.read(fh)
# Define kperp scan
coordkperp = np.linspace(0.1,10,4)
# Define job name
job_name = 'gk.sugama'
# Define jobfile name
job_file_name = 'job.submit.cmd'
if len(sys.argv) == 2 :
scan_mode= sys.argv[1]
else :
print('You need to specified the thing to do (e.g. python scanscritpt (create/run)')
if scan_mode == 'create':
print('Create scan:')
# Make top level directories
mkdir_p(scandir_path)
# Flush out paramscan
with open( os.path.join( scandir_path, 'kperp.log') ,'w') as fh:
for kperp in coordkperp:
fh.write( "%s \n" % kperp)
for ikperp, kperp in enumerate( coordkperp):
job_directory= os.path.join(scandir_path, "scanfiles_"+"{0:05d}".format(ikperp))
mkdir_p(job_directory)
# Create symbolic link to exec
os.system("ln -s " + exec_path + " " + os.path.join(job_directory,exec_name))
# Update kperp
inputs['model_par']['kperp'] = kperp
# Flush out the input parameters in job_directory
inputs.write(os.path.join(job_directory,"fort.90"),'w')
# copy T4.in file
os.system("cp T4.in " + os.path.join(job_directory, "T4.in") )
# Create submit slurm script in job_directory
job_file_path= os.path.join(job_directory, job_file_name)
with open(job_file_path, 'w') as fh:
fh.writelines("#!/bin/bash\n")
fh.writelines("#SBATCH -J " + job_name + "\n")
fh.writelines("#SBATCH --nodes=1 \n")
fh.writelines("#SBATCH --ntasks-per-node=6 \n")
fh.writelines("#SBATCH --time=01:00:00 \n")
fh.writelines("#SBATCH --error=%x.%j.err\n")
fh.writelines("#SBATCH --output=%x.%j.out\n")
fh.writelines("#SBATCH --account=FUA35_TSVVT421 \n")
fh.writelines("#SBATCH --partition=skl_fua_dbg\n")
fh.writelines("#SBATCH --mail-type=ALL\n")
fh.writelines("#SBATCH --mail-user=baptiste.frei@epfl.ch\n")
# sum of <nprocs_ei> <nprocs_ie> <nprocs_self> must be equal to <ntasks-per-node x nodes>
fh.writelines("srun ./CO 2 2 2 \n")
elif scan_mode == 'run':
print('Run scan:')
for ikperp, kperp in enumerate(coordkperp):
job_directory= os.path.join(scandir_path, "scanfiles_"+"{0:05d}".format(ikperp))
job_file_path= os.path.join(job_directory, job_file_name)
print('Submit job ' + job_file_path)
os.system('cd ' + job_directory + '; sbatch ' + job_file_name)
else:
print('Cannot recognize scanmode')
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