def jobscript_get_exec_command(jg: JobGeneration):
"""
Prefix to executable command
Returns
-------
string
multiline text for scripts
"""
content = """
""" + p_gen_script_info(jg) + """
EXEC=\"""" + jg.get_program_exec() + """\"
echo \"$EXEC\"
$EXEC || exit 1
"""
return content
#SBATCH --clusters=serial #SBATCH --time=96:00:00 # # if a job might take over 2 days to be executed import os import sys import stat import math #Classes containing sweet compile/run basic option from mule_local.JobGeneration import * from mule.SWEETRuntimeParametersScenarios import * #Create main compile/run options jg = JobGeneration() # Request dedicated compile script jg.compilecommand_in_jobscript = False # Wallclock time max_wallclock_seconds = 2 * 24 * 60 * 60 ref_max_wallclock_seconds = 48 * 60 * 60 #Get Earth parameters (if necessary) earth = EarthMKSDimensions() # # Run simulation on plane or sphere # #Basic plane options
def __load_job_raw_data(self, jobdir=None):
"""
Parse all output.out files and extract all kind of job output information
Return a dictionary with content from the job directories
{
#
# Dictionary with data from job generation
# (read from [jobdir]/jobgeneration.pickle)
#
'jobgeneration': # From jobgeneration.pickle
{
'compile': [...],
'runtime': [...],
'parallelization': [...],
'platforms_platform': [...],
'platform_resources': [...],
},
'output': # From output.out with prefix [MULE]
{
'simulation_benchmark_timings.main': [value],
'simulation_benchmark_timings.main_simulationLoop': [value],
[...]
},
'[filename(.pickle)]':
{
[...]
}
},
'[filename(.pickle)]':
{
[...]
}
"""
#
self.__job_raw_data = {}
if self.verbosity > 5:
self.info("")
self.info("Processing '" + jobdir + "'")
"""
* Process 'output.out'
"""
if self.verbosity > 5:
self.info("Loading job output file 'output.out'")
outfile = jobdir + '/output.out'
try:
#if True:
with open(outfile, 'r') as f:
content = f.readlines()
self.__job_raw_data['output'] = self.__parse_job_output(
content)
except Exception as err:
print("*" * 80)
print("* WARNINNG: opening '" + outfile + "' (ignoring)")
print("* " + str(err))
print("*" * 80)
"""
Process 'jobgeneration.pickle'
"""
# Ensure that 'jobgeneration.pickle' exists
jobgenerationfile = jobdir + '/jobgeneration.pickle'
if self.verbosity > 5:
self.info("Loading 'jobgeneration.pickle'")
j = JobGeneration(dummy_init=True)
self.__job_raw_data['jobgeneration'] = j.load_attributes_dict(
jobgenerationfile)
"""
Process other '*.pickle'
"""
pickle_files = glob.glob(jobdir + '/*.pickle')
# Iterate over all found pickle files
for picklefile in pickle_files:
filename = os.path.basename(picklefile)
tag = filename.replace('.pickle', '')
if tag == 'jobgeneration':
continue
if self.verbosity > 5:
self.info("Loading pickle file '" + filename + "'")
import pickle
with open(picklefile, 'rb') as f:
self.__job_raw_data[tag] = pickle.load(f)
from itertools import product
# REXI
from mule_local.rexi.REXICoefficients import *
from mule_local.rexi.trexi.TREXI import *
from mule_local.rexi.cirexi.CIREXI import *
from mule_local.rexi.brexi.BREXI import *
efloat_mode = "float"
#efloat_mode = "mpfloat"
from mule_local.JobGeneration import *
from mule.JobParallelization import *
from mule.JobParallelizationDimOptions import *
jg = JobGeneration()
verbose = False
#verbose = True
##################################################
##################################################
jg.compile.mode = 'release'
if '_gnu' in os.getenv('MULE_PLATFORM_ID'):
jg.compile.compiler = 'gnu'
else:
jg.compile.compiler = 'intel'
jg.compile.sweet_mpi = 'enable'
#! /usr/bin/env python3
import os
import sys
import math
from itertools import product
from mule_local.JobGeneration import *
from mule.JobParallelizationDimOptions import *
from mule.JobParallelization import *
p = JobGeneration()
verbose = False
#verbose = True
##################################################
##################################################
p.compile.mode = 'release'
if '_gnu' in os.getenv('MULE_PLATFORM_ID'):
p.compile.compiler = 'gnu'
else:
p.compile.compiler = 'intel'
p.compile.sweet_mpi = 'enable'
p.compile.sweet_mpi = 'disable'
p.runtime.space_res_spectral = 128
p.runtime.reuse_plans = -1 # enforce using plans (todo, enforcing not yet implemented)!
def jobscript_get_header(jg : JobGeneration):
"""
These headers typically contain the information on e.g. Job exection, number of compute nodes, etc.
Returns
-------
string
multiline text for scripts
"""
job_id = jg.getUniqueID()
p = jg.parallelization
time_str = p.get_max_wallclock_seconds_hh_mm_ss()
# Available queues:
# premium (only use this in extreme cases)
# regular
# economy
queue = 'economy'
# Use regular queue if we need more than 32 nodes
# Otherwise, the job doesn't seem to be scheduled
if p.num_nodes >= 32:
queue = 'premium'
elif p.num_nodes >= 16:
queue = 'regular'
#
# See https://www.lrz.de/services/compute/linux-cluster/batch_parallel/example_jobs/
#
content = """#! /bin/bash
#
## project code
#PBS -A NCIS0002
#PBS -q """+queue+"""
## wall-clock time (hrs:mins:secs)
#PBS -l walltime="""+time_str+"""
## select: number of nodes
## ncpus: number of CPUs per node
## mpiprocs: number of ranks per node
#PBS -l select="""+str(p.num_nodes)+""":ncpus="""+str(p.num_cores_per_node)+""":mpiprocs="""+str(p.num_ranks_per_node)+""":ompthreads="""+str(p.num_threads_per_rank)+"\n"
#"default": 2301000
#"turbo": 2301000
#"rated": 2300000
#"slow": 1200000
if p.force_turbo_off:
content += "#PBS -l select=cpufreq=2300000\n"
content += """#
#PBS -N """+job_id[0:100]+"""
#PBS -o """+jg.p_job_stdout_filepath+"""
#PBS -e """+jg.p_job_stderr_filepath+"""
#source /etc/profile.d/modules.sh
#module load openmpi
"""+("module load mkl" if jg.compile.mkl==True or jg.compile.mkl=='enable' else "")+"""
"""+p_gen_script_info(jg)+"""
echo
echo "hostname"
hostname
echo
echo
echo "lscpu -e"
lscpu -e
echo
echo
echo "CPU Frequencies (uniquely reduced):"
cat /sys/devices/system/cpu/cpu*/cpufreq/scaling_cur_freq | sort -u
echo
"""
if jg.compile.threading != 'off':
content += """
export OMP_NUM_THREADS="""+str(p.num_threads_per_rank)+"""
export OMP_DISPLAY_ENV=VERBOSE
"""
if p.core_oversubscription:
raise Exception("Not supported with this script!")
else:
if p.core_affinity != None:
content += "\necho \"Affnity: "+str(p.core_affinity)+"\"\n"
if p.core_affinity == 'compact':
content += "source $MULE_ROOT/platforms/bin/setup_omp_places.sh nooversubscription close\n"
#content += "\nexport OMP_PROC_BIND=close\n"
elif p.core_affinity == 'scatter':
raise Exception("Affinity '"+str(p.core_affinity)+"' not supported")
content += "\nexport OMP_PROC_BIND=spread\n"
else:
raise Exception("Affinity '"+str(p.core_affinity)+"' not supported")
content += "\n"
return content
#! /usr/bin/env python3 import os import sys import stat import math from mule_local.JobGeneration import * jg = JobGeneration() # # Run simulation on plane or sphere # jg.compile.program = 'swe_plane' jg.compile.plane_spectral_space = 'enable' jg.compile.plane_spectral_dealiasing = 'enable' jg.compile.sphere_spectral_space = 'disable' jg.compile.sphere_spectral_dealiasing = 'disable' jg.compile.numa_block_allocator = 0 # Verbosity mode jg.runtime.verbosity = 3 # # Mode and Physical resolution # jg.runtime.space_res_spectral = -1 jg.runtime.space_res_physical = 512
def p_gen_script_info(jg : JobGeneration):
return """#
# Generating function: """+_whoami(2)+"""
# Platform: """+get_platform_id()+"""
# Job id: """+jg.getUniqueID()+"""
#! /usr/bin/env python3 import os import sys import math import numpy as np from itertools import product from mule_local.JobGeneration import * from mule.JobParallelization import * from mule.JobParallelizationDimOptions import * p = JobGeneration() verbose = False #verbose = True ################################################## ################################################## p.compile.mode = 'release' #p.compile.sweet_mpi = 'disable' p.runtime.space_res_spectral = 128 p.parallelization.core_oversubscription = False p.parallelization.core_affinity = 'compact' p.compile.threading = 'omp'
#! /usr/bin/env python3
import os
import sys
import math
efloat_mode = "float"
#efloat_mode = "mpfloat"
from mule_local.JobGeneration import *
from mule.JobParallelization import *
from mule.JobParallelizationDimOptions import *
jg = JobGeneration()
verbose = False
#verbose = True
##################################################
# Software enviroment stuff
##################################################
jg.compile.mode = 'release'
if '_gnu' in os.getenv('MULE_PLATFORM_ID'):
jg.compile.compiler = 'gnu'
else:
jg.compile.compiler = 'intel'
jg.compile.sweet_mpi = 'disable'
jg.parallelization.core_oversubscription = False
jg.parallelization.core_affinity = 'compact'
#! /usr/bin/env python3 import os import sys import stat import math from mule_local.JobGeneration import * #Create main compile/run options jg = JobGeneration() jg.compile.program = "swe_plane" jg.runtime.verbosity = 2 jg.runtime.space_res_spectral = 128 jg.runtime.benchmark_name = 'benchmark_id_1' jg.runtime.gravitation= 1 jg.runtime.sphere_rotating_coriolis_omega = 1 jg.runtime.h0 = 1 jg.runtime.plane_domain_size = 1 jg.runtime.rexi_method = 'direct' jg.runtime.viscosity = 0.0 jg.runtime.max_simulation_time = 0.1 jg.runtime.output_timestep_size = jg.runtime.max_simulation_time
import os
import sys
import stat
import math
from mule.SWEETRuntimeParametersScenarios import *
from mule_local.JobGeneration import *
from mule.JobParallelization import *
from mule.JobParallelizationDimOptions import *
#Classes containing sweet compile/run basic option
#from mule_local.JobGeneration import *
#Create main compile/run options
jg = JobGeneration()
# Request dedicated compile script
jg.compilecommand_in_jobscript = True
# Wallclock time
max_wallclock_seconds = 2 * 24 * 60 * 60
ref_max_wallclock_seconds = 48 * 60 * 60
jg.parallelization.max_wallclock_seconds = ref_max_wallclock_seconds
# HPC stuff
pspace = JobParallelizationDimOptions('space')
pspace.num_cores_per_rank = jg.platform_resources.num_cores_per_node / 2
pspace.num_threads_per_rank = 8
pspace.num_ranks = 1
jg.setup_parallelization([pspace])
