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submit.py
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submit.py
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#!/usr/bin/env python
# coding: utf-8
"""
Submit an AxiSEM job to create an Instaseis database
locally or into a HPC queue.
Currently only supports CSCS.
Runs the Mesher, the Solver and the DB Repacker
Author: Simon Stähler, ETH Zürich
"""
import os
import subprocess as sp
import shutil
import stat
import argparse
import glob
int_models = ['prem_iso', 'prem_iso_solid', 'prem_iso_onecrust',
'prem_iso_light', 'prem_iso_solid_light',
'prem_ani', 'prem_ani_onecrust', 'prem_ani_light',
'ak135', 'ak135f', 'iasp91']
def create_inparam_mesh(mesh_file, mesh_period, nrad, ncl, ntheta=0,
max_depth=None, max_colat=None):
with open('inparam_mesh', 'w') as fid:
if mesh_file in int_models:
fid.write('BACKGROUND_MODEL %s\n' % mesh_file)
fid.write('EXT_MODEL none \n')
else:
fid.write('BACKGROUND_MODEL external \n')
fid.write('EXT_MODEL "%s" \n' % os.path.abspath(mesh_file))
fid.write('DOMINANT_PERIOD %f \n' % mesh_period)
fid.write('NRADIAL_SLICES %d \n' % nrad)
if max_depth:
fid.write('MAX_DEPTH %f \n' % max_depth)
if ncl:
fid.write('COARSENING_LAYERS %d \n' % ncl)
if max_colat:
fid.write('LOCAL_MAX_COLAT %f \n' % max_colat)
if ntheta == 0:
fid.write('NTHETA_SLICES %d \n' % 1)
fid.write('ONLY_SUGGEST_NTHETA TRUE \n')
else:
fid.write('NTHETA_SLICES %d \n' % ntheta)
def progress(directory):
pct = 0
print('[---------------------------------------------------]')
while True:
ts = glob.glob(os.path.join(directory, 'timestamp*.txt'))
for i in range(pct, len(ts)):
print('=', end='')
pct = len(ts)
if pct == 100:
return
def get_ntheta(mesh_file, mesh_period, ncl,
max_depth=None, max_colat=None):
create_inparam_mesh(mesh_file, mesh_period, ntheta=0, nrad=1,
max_depth=max_depth, max_colat=max_colat, ncl=ncl)
output = sp.check_output('./xmesh')
output_lines = output.split(sep=b'\n')
for iline in range(0, len(output_lines)):
line = output_lines[iline]
if line[0:8] == b' sugg':
return int(output_lines[iline + 1])
def hour2hms(hours):
hour = int(hours)
hours -= hour
hours *= 60.
minute = int(hours)
hours -= minute
hours *= 60.
sec = int(hours)
return '%02d:%02d:%02d' % (hour, minute, sec)
def define_arguments():
helptext = 'Create AxiSEM run and submit job.'
formatter_class = argparse.RawTextHelpFormatter
parser = argparse.ArgumentParser(description=helptext,
formatter_class=formatter_class)
helptext = "Job directory name. \n"
parser.add_argument('job_name', help=helptext)
helptext = 'Mesh file. Choose path to external mesh file or one\n' \
+ 'of the following AxiSEM internal models:\n' \
+ "'prem_iso', 'prem_iso_solid', 'prem_iso_onecrust',\n" \
+ "'prem_iso_light', 'prem_iso_solid_light',\n" \
+ "'prem_ani', 'prem_ani_onecrust', 'prem_ani_light',\n" \
+ "'ak135', 'ak135f', 'iasp91'\n"
parser.add_argument('mesh_file', help=helptext)
helptext = 'Mesh period \n'
parser.add_argument('mesh_period', type=float, help=helptext)
helptext = 'Number of radial slices (default: 1)\n'
parser.add_argument('--nrad', type=int, help=helptext,
default=1)
helptext = 'Number of theta slices (default: 2)\n' \
+ 'Set to 0 to use the maximum number possible for this\n' \
+ 'model and frequency'
parser.add_argument('--ntheta', type=int, help=helptext,
default=2)
helptext = 'Job type (local, CSCS Daint)\n'
parser.add_argument('-j', '--job_type', type=str,
default='local',
help=helptext)
helptext = 'Run type (Forward, Backward)\n'
parser.add_argument('-r', '--run_type', type=str,
default='bwd',
help=helptext)
helptext = 'Maximum colatitude of mesh (default: 180 degree)\n'
parser.add_argument('--max_colat', type=float,
help=helptext)
helptext = 'Maximum depth in kilometer (default: radius)\n'
parser.add_argument('--max_depth', type=float,
help=helptext)
helptext = 'Source depth in kilometer\n'
parser.add_argument('--src_depth', type=float, default=0.0,
help=helptext)
helptext = 'Number of coarsening layers (default: 1)\n'
parser.add_argument('--ncl', type=int, help=helptext,
default=1)
helptext = 'Wall time for the solver in hours\n'
parser.add_argument('-w', '--wall_time', type=float, default=1.0,
help=helptext)
helptext = 'Mail adress for notifications\n'
parser.add_argument('-m', '--mail_address', type=str,
default='[email protected]',
help=helptext)
helptext = 'Daint project account\n'
parser.add_argument('-a', '--account', type=str,
default='ACCOUNT',
help=helptext)
return parser
def main():
parser = define_arguments()
args = parser.parse_args()
run_axisem(**vars(args))
def run_axisem(job_name: str,
mesh_file: str,
mesh_period: float,
job_type='local',
run_type='bwd',
src_depth=0.,
wall_time=24.,
mesher_only=False,
nrad=1,
ncl=3,
max_colat=None,
max_depth=None,
account=None,
mail_address: str = None,
ntheta: int = None):
base_dir = os.getcwd()
os.chdir(base_dir)
# Create rundir
rundir = os.path.abspath(os.path.join('runs', job_name))
os.mkdir(rundir)
# Create directory for the mesh
print('[MESHER]')
os.chdir(base_dir)
print(' Creating mesh directory')
meshdir = os.path.abspath(os.path.join(rundir, 'Mesh'))
os.mkdir(meshdir)
os.mkdir(os.path.join(meshdir, 'Diags'))
mesh_exe_path = os.path.join(meshdir, 'xmesh')
shutil.copyfile(src=os.path.join('MESHER', 'xmesh'),
dst=mesh_exe_path)
st = os.stat(mesh_exe_path)
os.chmod(mesh_exe_path, st.st_mode | stat.S_IEXEC)
os.chdir(meshdir)
if mesh_file in int_models:
print(' Using internal model %s' % mesh_file)
int_model = True
else:
int_model = False
fnam_mesh_file = os.path.split(mesh_file)[-1]
shutil.copyfile(src=mesh_file,
dst=os.path.join(meshdir, fnam_mesh_file))
print(' Using external model %s' % fnam_mesh_file)
if ntheta:
ntheta = ntheta
else:
ntheta = get_ntheta(fnam_mesh_file, mesh_period,
ncl=ncl,
max_depth=max_depth,
max_colat=max_colat)
print(' Optimal number of theta slices used: %d' % ntheta)
create_inparam_mesh(mesh_file,
mesh_period,
ntheta=ntheta,
nrad=nrad,
ncl=ncl,
max_depth=max_depth,
max_colat=max_colat)
ncpu = ntheta * nrad
print(' Number of cores used: %4d' % ncpu)
if job_type == 'local': # local run, consecutive
os.chdir(os.path.abspath(meshdir))
print(' Starting Mesher')
output = sp.check_output('./xmesh > OUTPUT_MESH', shell=True)
elif job_type == 'Euler':
os.chdir(os.path.abspath(meshdir))
print(' Starting Mesher')
output = sp.check_output('bsub' +
' -J m_%s' % job_name +
' -B' + # Send mail at beginning
' -R "rusage[mem=8192]"' +
' "./xmesh > OUTPUT_MESH"',
shell=True)
elif job_type == 'Daint':
batch_mesher_fmt = \
'#!/bin/bash -l \n' + \
'#SBATCH --ntasks=1 \n' + \
'#SBATCH --ntasks-per-node=1 \n' + \
'#SBATCH --ntasks-per-core=1 \n' + \
'#SBATCH --cpus-per-task=1 \n' + \
'#SBATCH --time=00:30:00 \n' + \
'#SBATCH --account=%s \n' % account + \
'#SBATCH --mail-type=BEGIN,FAIL \n' + \
'#SBATCH --mail-user=%s \n' % mail_address + \
'#SBATCH --partition=prepost \n' + \
'#SBATCH --constraint=mc \n' + \
'#SBATCH --workdir=%s \n' % meshdir + \
'export OMP_NUM_THREADS=8 \n' + \
'module load slurm \n' + \
'echo "The current job ID is $SLURM_JOB_ID" \n' + \
'echo "Running on $SLURM_JOB_NUM_NODES nodes" \n' + \
'echo "Using $SLURM_NTASKS_PER_NODE tasks per node" \n' + \
'echo "A total of $SLURM_NTASKS tasks is used" \n' + \
'echo "using $SLURM_CPUS_PER_TASK omp threads" \n' + \
'./xmesh > OUTPUT_MESHER'
path_sbatch_mesher = os.path.join(rundir,
'job_%s_mesh.sh' % job_name)
with open(path_sbatch_mesher, 'w') as fid:
fid.write(batch_mesher_fmt)
if not mesher_only:
# SOLVER
print('[SOLVER]')
if run_type == 'fwd':
runs = ['MXZ_MYZ', 'MZZ', 'MXX_P_MYY',
'MXY_MXX_M_MYY']
inparam_source = {
'MZZ':
'SOURCE_TYPE mrr \n' +
'SOURCE_DEPTH %f \n' +
'SOURCE_LAT 90.0 \n' +
'SOURCE_LON 0.0 \n' +
'SOURCE_AMPLITUDE 1.E20',
'MXX_P_MYY':
'SOURCE_TYPE mtt_p_mpp \n' +
'SOURCE_DEPTH %f \n' +
'SOURCE_LAT 90.0 \n' +
'SOURCE_LON 0.0 \n' +
'SOURCE_AMPLITUDE 1.E20',
'MXZ_MYZ':
'SOURCE_TYPE mtr \n' +
'SOURCE_DEPTH %f \n' +
'SOURCE_LAT 90.0 \n' +
'SOURCE_LON 0.0 \n' +
'SOURCE_AMPLITUDE 1.E20',
'MXY_MXX_M_MYY':
'SOURCE_TYPE mtp \n' +
'SOURCE_DEPTH %f \n' +
'SOURCE_LAT 90.0 \n' +
'SOURCE_LON 0.0 \n' +
'SOURCE_AMPLITUDE 1.E20'}
desc = {'MZZ': 'Mzz',
'MXZ_MYZ': 'Mxz/Myz',
'MXX_P_MYY': 'Mxx + Myy',
'MXY_MXX_M_MYY': 'Mxy / Mxx - Myy'}
else:
runs = ['PX', 'PZ']
inparam_source = {'PX':
'SOURCE_TYPE thetaforce \n' +
'SOURCE_DEPTH %f \n' +
'SOURCE_LAT 90.0 \n' +
'SOURCE_LON 0.0 \n' +
'SOURCE_AMPLITUDE 1.E20',
'PZ':
'SOURCE_TYPE vertforce \n' +
'SOURCE_DEPTH %f \n' +
'SOURCE_LAT 90.0 \n' +
'SOURCE_LON 0.0 \n' +
'SOURCE_AMPLITUDE 1.E20'}
desc = {'PX': 'horizontal', 'PZ': 'vertical'}
path_sbatch_solver = dict()
for part_run in runs:
print(' Creating solver dir for %s force source' % desc[part_run])
os.chdir(base_dir)
# Create directory for the solver (PZ)
solverdir = os.path.abspath(os.path.join(rundir, part_run))
os.mkdir(solverdir)
# Copy Solver executable and make it executable
solver_exe_path = os.path.join(solverdir, 'axisem')
shutil.copyfile(src=os.path.join('SOLVER', 'axisem'),
dst=solver_exe_path)
st = os.stat(solver_exe_path)
os.chmod(solver_exe_path, st.st_mode | stat.S_IEXEC)
# Copy inparam files
for file in ['inparam_basic', 'inparam_advanced']:
shutil.copyfile(src=file,
dst=os.path.join(solverdir, file))
if not int_model:
shutil.copyfile(src=mesh_file,
dst=os.path.join(solverdir,
'external_model.bm'))
with open(os.path.join(solverdir, 'inparam_source'), 'w') as fid:
fid.write(inparam_source[part_run] % src_depth)
# Create output directories
os.mkdir(os.path.join(solverdir, 'Data'))
os.mkdir(os.path.join(solverdir, 'Info'))
# Create symlink to mesh directory
os.symlink(os.path.abspath(meshdir),
os.path.join(solverdir, 'Mesh'))
if job_type == 'local': # local run, consecutive
os.chdir(os.path.abspath(solverdir))
print(' Starting %s AxiSEM simulation' % desc[part_run])
try:
command = 'mpirun -n %d ./axisem -quiet > OUTPUT' % ncpu
output = sp.check_output(command,
stderr=sp.STDOUT,
shell=True)
except sp.CalledProcessError as e:
print(e)
print(output)
print('\nLast lines of OUTPUT\n')
_ = sp.run('tail OUTPUT -n 40', shell=True)
raise
elif job_type == 'Euler':
os.chdir(os.path.abspath(solverdir))
output = sp.check_output('bsub' +
' -J s_%s_%s' % (job_name, part_run) +
' -n %d' % ncpu +
' -R "rusage[mem=1024]"' +
' -B' + # Send mail at beginning
' -W %03d' % (int(wall_time * 60)) +
' -w "done(m_%s)"' % (job_name) +
' "mpirun -n %d ./axisem > OUTPUT_%s"' % (ncpu, part_run),
shell=True)
elif job_type == 'Daint':
batch_solver_fmt = \
'#!/bin/bash -l \n' + \
'#SBATCH --ntasks=%d \n' % ncpu + \
'#SBATCH --ntasks-per-node=12 \n' + \
'#SBATCH --ntasks-per-core=1 \n' + \
'#SBATCH --cpus-per-task=1 \n' + \
'#SBATCH --time=%s \n' % hour2hms(wall_time) + \
'#SBATCH --account=%s \n' % account + \
'#SBATCH --mail-type=FAIL \n' + \
'#SBATCH --mail-user=%s \n' % mail_address + \
'#SBATCH --partition=normal \n' + \
'#SBATCH --constraint=gpu \n' + \
'#SBATCH --workdir=%s \n' % os.path.abspath(solverdir) + \
'export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK \n' + \
'module load slurm \n' + \
'echo "The current job ID is $SLURM_JOB_ID" \n' + \
'echo "Running on $SLURM_JOB_NUM_NODES nodes" \n' + \
'echo "Using $SLURM_NTASKS_PER_NODE tasks per node" \n' + \
'echo "A total of $SLURM_NTASKS tasks is used" \n' + \
'echo "using $SLURM_CPUS_PER_TASK omp threads" \n' + \
'srun --ntasks-per-node $SLURM_NTASKS_PER_NODE ' + \
'-n $SLURM_NTASKS ./axisem >& OUTPUT_%s' % part_run
path_sbatch_solver[part_run] = \
os.path.join(rundir, 'job_%s_%s.sh' % (job_name, part_run))
with open(path_sbatch_solver[part_run], 'w') as fid:
fid.write(batch_solver_fmt)
# Run field_transform (the Instaseis version)
repack_path = os.path.join(base_dir, 'SOLVER', 'UTILS', 'repack_db.py')
repack_call = repack_path + ' --method repack ' + '. ' \
+ job_name + '_database ' + '> OUTPUT_FT'
print('[REPACK]')
if job_type == 'local': # local run, consecutive
os.chdir(os.path.abspath(rundir))
print(' Starting database repack for Instaseis')
try:
output = sp.check_output(repack_call, shell=True)
except sp.CalledProcessError as e:
print(e)
print(output)
_ = sp.run('tail OUTPUT_FT -n 20', shell=True)
raise
elif job_type == 'Euler':
os.chdir(os.path.abspath(rundir))
repack_call = 'bsub' + \
' -w "done(s_%s_%s)" ' % (job_name, runs[0]) + \
' -J r_%s' % job_name + \
' -n 4' + \
' -R "rusage[mem=4000]" -B -N' + \
' -W 24:00 ' + \
repack_call
_ = sp.run(repack_call,
shell=True)
elif job_type == 'Daint':
batch_FT_fmt = \
'#!/bin/bash -l \n' + \
'#SBATCH --ntasks=1 \n' + \
'#SBATCH --ntasks-per-node=1 \n' + \
'#SBATCH --ntasks-per-core=1 \n' + \
'#SBATCH --cpus-per-task=1 \n' + \
'#SBATCH --time=24:00:00 \n' + \
'#SBATCH --account=%s \n' % account + \
'#SBATCH --mail-type=END,FAIL \n' + \
'#SBATCH --mail-user=%s \n' % mail_address + \
'#SBATCH --partition=normal \n' + \
'#SBATCH --constraint=gpu \n' + \
'#SBATCH --workdir=%s \n' % rundir + \
'export OMP_NUM_THREADS=1 \n' + \
'module load slurm \n' + \
'echo "The current job ID is $SLURM_JOB_ID" \n' + \
'echo "Running on $SLURM_JOB_NUM_NODES nodes" \n' + \
'echo "Using $SLURM_NTASKS_PER_NODE tasks per node" \n' + \
'echo "A total of $SLURM_NTASKS tasks is used" \n' + \
'echo "using $SLURM_CPUS_PER_TASK omp threads" \n' + \
repack_call
# Submit the jobs
# Only necessary, if the job is not run locally
if job_type == 'Daint': # Daint (CSCS), Slurm-based
path_sbatch_FT = os.path.join(rundir, 'job_%s_FT.sh' % job_name)
with open(path_sbatch_FT, 'w') as fid:
fid.write(batch_FT_fmt)
res_submit_mesh = sp.check_output('sbatch ' + path_sbatch_mesher,
shell=True)
jobid_mesher = int(res_submit_mesh.split()[3])
print('Mesher JOBID: ', jobid_mesher)
jobid_solver = []
for part_run in ['PX', 'PZ']:
res_submit_solver = sp.check_output(
'sbatch --dependency=afterok:%d ' % jobid_mesher +
path_sbatch_solver[part_run],
shell=True)
jobid_solver.append(int(res_submit_solver.split()[3]))
print('Solver %s JOBID: ' % part_run, jobid_solver[-1])
res_submit_FT = sp.check_output(
'sbatch --dependency=afterok:%d:%d %s' %
(jobid_solver[0], jobid_solver[1], path_sbatch_FT),
shell=True)
jobid_FT = int(res_submit_FT.split()[3])
print('FT JOBID: ', jobid_FT)
os.chdir(base_dir)
if __name__ == "__main__":
main()