def archive(self):
mkdir_p(self.restart_path)
# Need to figure out the end date of the model.
nml_path = os.path.join(self.work_path, 'namelists')
nml = f90nml.read(nml_path)
resubmit_inc = nml['NLSTCALL']['RUN_RESUBMIT_INC']
runtime = um_time_to_time(resubmit_inc)
runtime = datetime.timedelta(seconds=runtime)
basis_time = nml['NLSTCALL']['MODEL_BASIS_TIME']
init_date = um_date_to_date(basis_time)
end_date = date_to_um_dump_date(init_date + runtime)
restart_dump = os.path.join(self.work_path,
'aiihca.da{0}'.format(end_date))
f_dst = os.path.join(self.restart_path, self.restart)
if os.path.exists(restart_dump):
shutil.copy(restart_dump, f_dst)
else:
print('payu: error: Model has not produced a restart dump file'
'{} does not exist. '
'Check DUMPFREQim in namelists'.format(restart_dump))
def setup(self):
super(Oasis, self).setup()
# Copy OASIS data to the other submodels
# TODO: Parse namcouple to determine filelist
# TODO: Let users map files to models
input_files = [
f for f in os.listdir(self.work_path) if f not in self.config_files
]
for model in self.expt.models:
# Skip the oasis self-reference
if model == self:
continue
# Skip models without a work_path (like access)
if not hasattr(model, 'work_path'):
continue
mkdir_p(model.work_path)
for f_name in (self.config_files + input_files):
f_path = os.path.join(self.work_path, f_name)
f_sympath = os.path.join(model.work_path, f_name)
make_symlink(f_path, f_sympath)
if self.expt.runtime:
# TODO: Implement runtime patch to namcouple
pass
def setup(self):
# FMS initialisation
super(Mom, self).setup()
if not self.top_level_model:
# Make log dir
mkdir_p(os.path.join(self.work_path, 'log'))
input_nml_path = os.path.join(self.work_path, 'input.nml')
input_nml = f90nml.read(input_nml_path)
use_core2iaf = self.config.get('core2iaf')
if use_core2iaf:
self.core2iaf_setup()
# Set the runtime
if self.expt.runtime:
ocean_solo_nml = input_nml['ocean_solo_nml']
ocean_solo_nml['years'] = self.expt.runtime['years']
ocean_solo_nml['months'] = self.expt.runtime['months']
ocean_solo_nml['days'] = self.expt.runtime['days']
ocean_solo_nml['seconds'] = self.expt.runtime.get('seconds', 0)
input_nml.write(input_nml_path, force=True)
# Construct the land CPU mask
if self.expt.config.get('mask_table', False):
self.create_mask_table(input_nml)
def setup(self, force_archive=False):
# Confirm that no output path already exists
if os.path.exists(self.output_path):
sys.exit('payu: error: Output path already exists.')
mkdir_p(self.work_path)
if force_archive:
mkdir_p(self.archive_path)
make_symlink(self.archive_path, self.archive_sym_path)
# Archive the payu config
# TODO: This just copies the existing config.yaml file, but we should
# reconstruct a new file including default values
config_src = os.path.join(self.control_path, 'config.yaml')
config_dst = os.path.join(self.work_path)
shutil.copy(config_src, config_dst)
# Stripe directory in Lustre
# TODO: Make this more configurable
do_stripe = self.config.get('stripedio', False)
if do_stripe:
cmd = 'lfs setstripe -c 8 -s 8m {0}'.format(self.work_path)
sp.check_call(shlex.split(cmd))
make_symlink(self.work_path, self.work_sym_path)
# Set up all file manifests
self.manifest.setup()
for model in self.models:
model.setup()
# Call the macro-model setup
if len(self.models) > 1:
self.model.setup()
# Use manifest to populate work directory
self.manifest.make_links()
# Copy manifests to work directory so they archived on completion
self.manifest.copy_manifests(os.path.join(self.work_path,'manifests'))
setup_script = self.userscripts.get('setup')
if setup_script:
self.run_userscript(setup_script)
# Profiler setup
expt_profs = self.config.get('profilers', [])
if not isinstance(expt_profs, list):
expt_profs = [expt_profs]
for prof_name in expt_profs:
ProfType = payu.profilers.index[prof_name]
prof = ProfType(self)
self.profilers.append(prof)
# Testing
prof.setup()
def setup(self):
super(Oasis, self).setup()
# Copy OASIS data to the other submodels
# TODO: Parse namcouple to determine filelist
# TODO: Let users map files to models
input_files = [f for f in os.listdir(self.work_path)
if f not in self.config_files]
for model in self.expt.models:
# Skip the oasis self-reference
if model == self:
continue
# Skip models without a work_path (like access)
if not hasattr(model, 'work_path'):
continue
mkdir_p(model.work_path)
for f_name in (self.config_files + input_files):
f_path = os.path.join(self.work_path, f_name)
f_sympath = os.path.join(model.work_path, f_name)
make_symlink(f_path, f_sympath)
if self.expt.runtime:
# TODO: Implement runtime patch to namcouple
pass
def archive(self):
mkdir_p(self.archive_path)
make_symlink(self.archive_path, self.archive_sym_path)
# Remove work symlink
if os.path.islink(self.work_sym_path):
os.remove(self.work_sym_path)
mkdir_p(self.restart_path)
for model in self.models:
model.archive()
# Postprocess the model suite
if len(self.models) > 1:
self.model.archive()
# Double-check that the run path does not exist
if os.path.exists(self.output_path):
sys.exit('payu: error: Output path already exists.')
cmd = 'mv {} {}'.format(self.work_path, self.output_path)
sp.check_call(shlex.split(cmd))
# Remove old restart files
# TODO: Move to subroutine
restart_freq = self.config.get('restart_freq', default_restart_freq)
restart_history = self.config.get('restart_history',
default_restart_history)
# Remove any outdated restart files
prior_restart_dirs = [
d for d in os.listdir(self.archive_path) if d.startswith('restart')
]
for res_dir in prior_restart_dirs:
res_idx = int(res_dir.lstrip('restart'))
if (self.repeat_run
or (not res_idx % restart_freq == 0 and res_idx <=
(self.counter - restart_history))):
res_path = os.path.join(self.archive_path, res_dir)
# Only delete real directories; ignore symbolic restart links
if os.path.isdir(res_path):
shutil.rmtree(res_path)
if self.config.get('collate', True):
cmd = 'payu collate -i {}'.format(self.counter)
sp.check_call(shlex.split(cmd))
if self.config.get('hpctoolkit', False):
cmd = 'payu profile -i {}'.format(self.counter)
sp.check_call(shlex.split(cmd))
archive_script = self.userscripts.get('archive')
if archive_script:
self.run_userscript(archive_script)
def sweep(self, hard_sweep=False):
# TODO: Fix the IO race conditions!
if hard_sweep:
if os.path.isdir(self.archive_path):
print('Removing archive path {0}'.format(self.archive_path))
cmd = 'rm -rf {0}'.format(self.archive_path)
cmd = shlex.split(cmd)
rc = sp.call(cmd)
assert rc == 0
if os.path.islink(self.archive_sym_path):
print('Removing symlink {0}'.format(self.archive_sym_path))
os.remove(self.archive_sym_path)
if os.path.isdir(self.work_path):
print('Removing work path {0}'.format(self.work_path))
cmd = 'rm -rf {0}'.format(self.work_path)
cmd = shlex.split(cmd)
rc = sp.call(cmd)
assert rc == 0
if os.path.islink(self.work_sym_path):
print('Removing symlink {0}'.format(self.work_sym_path))
os.remove(self.work_sym_path)
# TODO: model outstreams and pbs logs need to be handled separately
default_job_name = os.path.basename(os.getcwd())
short_job_name = str(self.config.get('jobname', default_job_name))[:15]
logs = [
f for f in os.listdir(os.curdir) if os.path.isfile(f) and (
f.startswith(short_job_name + '.o') or
f.startswith(short_job_name + '.e') or
f.startswith(short_job_name[:13] + '_c.o') or
f.startswith(short_job_name[:13] + '_c.e') or
f.startswith(short_job_name[:13] + '_p.o') or
f.startswith(short_job_name[:13] + '_p.e')
)
]
pbs_log_path = os.path.join(self.archive_path, 'pbs_logs')
legacy_pbs_log_path = os.path.join(self.control_path, 'pbs_logs')
if os.path.isdir(legacy_pbs_log_path):
# TODO: New path may still exist!
assert not os.path.isdir(pbs_log_path)
print('payu: Moving pbs_logs to {0}'.format(pbs_log_path))
shutil.move(legacy_pbs_log_path, pbs_log_path)
else:
mkdir_p(pbs_log_path)
for f in logs:
print('Moving log {0}'.format(f))
shutil.move(f, os.path.join(pbs_log_path, f))
# Remove stdout/err
for f in (self.stdout_fname, self.stderr_fname):
if os.path.isfile(f):
os.remove(f)
def sweep(self, hard_sweep=False):
# TODO: Fix the IO race conditions!
# TODO: model outstreams and pbs logs need to be handled separately
default_job_name = os.path.basename(os.getcwd())
short_job_name = str(self.config.get('jobname', default_job_name))[:15]
logs = [
f for f in os.listdir(os.curdir) if os.path.isfile(f) and (
f.startswith(short_job_name + '.o') or
f.startswith(short_job_name + '.e') or
f.startswith(short_job_name[:13] + '_c.o') or
f.startswith(short_job_name[:13] + '_c.e') or
f.startswith(short_job_name[:13] + '_p.o') or
f.startswith(short_job_name[:13] + '_p.e')
)
]
pbs_log_path = os.path.join(self.archive_path, 'pbs_logs')
legacy_pbs_log_path = os.path.join(self.control_path, 'pbs_logs')
if os.path.isdir(legacy_pbs_log_path):
# TODO: New path may still exist!
assert not os.path.isdir(pbs_log_path)
print('payu: Moving pbs_logs to {0}'.format(pbs_log_path))
shutil.move(legacy_pbs_log_path, pbs_log_path)
else:
mkdir_p(pbs_log_path)
for f in logs:
print('Moving log {0}'.format(f))
shutil.move(f, os.path.join(pbs_log_path, f))
if hard_sweep:
if os.path.isdir(self.archive_path):
print('Removing archive path {0}'.format(self.archive_path))
cmd = 'rm -rf {0}'.format(self.archive_path)
cmd = shlex.split(cmd)
rc = sp.call(cmd)
assert rc == 0
if os.path.islink(self.archive_sym_path):
print('Removing symlink {0}'.format(self.archive_sym_path))
os.remove(self.archive_sym_path)
# Remove stdout/err and yaml dumps
for f in self.output_fnames:
if os.path.isfile(f):
os.remove(f)
if os.path.isdir(self.work_path):
print('Removing work path {0}'.format(self.work_path))
cmd = 'rm -rf {0}'.format(self.work_path)
cmd = shlex.split(cmd)
rc = sp.call(cmd)
assert rc == 0
if os.path.islink(self.work_sym_path):
print('Removing symlink {0}'.format(self.work_sym_path))
os.remove(self.work_sym_path)
def setup(self, force_archive=False):
# Confirm that no output path already exists
if os.path.exists(self.output_path):
sys.exit('payu: error: Output path already exists.')
mkdir_p(self.work_path)
if force_archive:
mkdir_p(self.archive_path)
make_symlink(self.archive_path, self.archive_sym_path)
# Archive the payu config
# TODO: This just copies the existing config.yaml file, but we should
# reconstruct a new file including default values
config_src = os.path.join(self.control_path, 'config.yaml')
config_dst = os.path.join(self.work_path)
shutil.copy(config_src, config_dst)
# Stripe directory in Lustre
# TODO: Make this more configurable
do_stripe = self.config.get('stripedio', False)
if do_stripe:
cmd = 'lfs setstripe -c 8 -s 8m {0}'.format(self.work_path)
sp.check_call(shlex.split(cmd))
make_symlink(self.work_path, self.work_sym_path)
# Set up all file manifests
self.manifest.setup()
for model in self.models:
model.setup()
# Call the macro-model setup
if len(self.models) > 1:
self.model.setup()
self.manifest.check_manifests()
# Copy manifests to work directory so they archived on completion
manifest_path = os.path.join(self.work_path, 'manifests')
self.manifest.copy_manifests(manifest_path)
setup_script = self.userscripts.get('setup')
if setup_script:
self.run_userscript(setup_script)
# Profiler setup
expt_profs = self.config.get('profilers', [])
if not isinstance(expt_profs, list):
expt_profs = [expt_profs]
for prof_name in expt_profs:
ProfType = payu.profilers.index[prof_name]
prof = ProfType(self)
self.profilers.append(prof)
# Testing
prof.setup()
def copy_manifests(self, path):
mkdir_p(path)
try:
for mf in self.manifests:
self.manifests[mf].copy(path)
except IOError:
pass
def archive(self):
# Need to parse the data namelist file to access the
# endTime
data_path = os.path.join(self.work_path, 'data')
data_nml = self.read_namelist(data_path)
# Save model time to restart next run
with open(os.path.join(self.restart_path, self.restart_calendar_file),
'w') as restart_file:
restart = {'endtime': data_nml['parm03']['endTime']}
restart_file.write(yaml.dump(restart, default_flow_style=False))
# Remove symbolic links to input or pickup files:
for f in os.listdir(self.work_path):
f_path = os.path.join(self.work_path, f)
if os.path.islink(f_path):
os.remove(f_path)
# Move files outside of mnc_* directories
mnc_paths = [
os.path.join(self.work_path, d) for d in os.listdir(self.work_path)
if d.startswith('mnc_')
]
for path in mnc_paths:
for f in os.listdir(path):
f_path = os.path.join(path, f)
sh.move(f_path, self.work_path)
os.rmdir(path)
mkdir_p(self.restart_path)
# Move pickups but don't include intermediate pickupts ('ckpt's)
restart_files = [
f for f in os.listdir(self.work_path) if f.startswith('pickup')
and not f.split('.')[1].startswith('ckpt')
]
# Tar and compress the output files
stdout_files = [
f for f in os.listdir(self.work_path) if f.startswith('STDOUT.')
]
if stdout_files:
cmd = 'tar -C {0} -c -j -f {1}'.format(
self.work_path, os.path.join(self.work_path, 'STDOUT.tar.bz2'))
rc = sp.Popen(shlex.split(cmd) + stdout_files).wait()
assert rc == 0
for f in stdout_files:
os.remove(os.path.join(self.work_path, f))
for f in restart_files:
f_src = os.path.join(self.work_path, f)
sh.move(f_src, self.restart_path)
def archive(self):
mkdir_p(self.archive_path)
make_symlink(self.archive_path, self.archive_sym_path)
# Remove work symlink
if os.path.islink(self.work_sym_path):
os.remove(self.work_sym_path)
mkdir_p(self.restart_path)
for model in self.models:
model.archive()
# Postprocess the model suite
if len(self.models) > 1:
self.model.archive()
# Double-check that the run path does not exist
if os.path.exists(self.output_path):
sys.exit('payu: error: Output path already exists.')
cmd = 'mv {} {}'.format(self.work_path, self.output_path)
sp.check_call(shlex.split(cmd))
# Remove old restart files
# TODO: Move to subroutine
restart_freq = self.config.get('restart_freq', default_restart_freq)
restart_history = self.config.get('restart_history',
default_restart_history)
# Remove any outdated restart files
prior_restart_dirs = [d for d in os.listdir(self.archive_path)
if d.startswith('restart')]
for res_dir in prior_restart_dirs:
res_idx = int(res_dir.lstrip('restart'))
if (not res_idx % restart_freq == 0 and
res_idx <= (self.counter - restart_history)):
res_path = os.path.join(self.archive_path, res_dir)
shutil.rmtree(res_path)
if self.config.get('collate', True):
cmd = 'payu collate -i {} -l {}'.format(self.counter,
self.lab.basepath)
sp.check_call(shlex.split(cmd))
if self.config.get('hpctoolkit', False):
cmd = 'payu profile -i {}'.format(self.counter)
sp.check_call(shlex.split(cmd))
archive_script = self.userscripts.get('archive')
if archive_script:
self.run_userscript(archive_script)
def build_model(self):
if not self.repo_url:
return
# Check to see if executable already exists.
if self.exec_path and os.path.isfile(self.exec_path):
print('payu: warning: {0} will be overwritten.'
''.format(self.exec_path))
# First step is always to go to the codebase.
curdir = os.getcwd()
# Do the build. First check whether there is a build command in the
# config. If not check for the model default, otherwise just run make.
try:
build_path = self.config['build']['path_to_build_command']
except KeyError:
if self.build_path:
build_path = self.build_path
else:
build_path = './'
os.chdir(os.path.join(self.codebase_path, build_path))
try:
cmd = self.config['build']['command']
except KeyError:
if self.build_command:
cmd = self.build_command
else:
cmd = 'make'
print('Running command {0}'.format(cmd))
sp.check_call(shlex.split(cmd))
try:
build_exec_path = os.path.join(self.codebase_path,
self.config['build']['exec_path'])
except KeyError:
if self.build_exec_path:
build_exec_path = self.build_exec_path
else:
build_exec_path = self.codebase_path
# Copy new executable to bin dir
if self.exec_path:
# Create the bin path if it doesn't exist
mkdir_p(self.expt.lab.bin_path)
build_exec_path = os.path.join(build_exec_path, self.exec_name)
shutil.copy(build_exec_path, self.exec_path)
os.chdir(curdir)
def build_model(self):
if not self.repo_url:
return
# Check to see if executable already exists.
if self.exec_path and os.path.isfile(self.exec_path):
print('payu: warning: {} will be overwritten.'
''.format(self.exec_path))
# First step is always to go to the codebase.
curdir = os.getcwd()
# Do the build. First check whether there is a build command in the
# config. If not check for the model default, otherwise just run make.
try:
build_path = self.config['build']['path_to_build_command']
except KeyError:
if self.build_path:
build_path = self.build_path
else:
build_path = './'
os.chdir(os.path.join(self.codebase_path, build_path))
try:
cmd = self.config['build']['command']
except KeyError:
if self.build_command:
cmd = self.build_command
else:
cmd = 'make'
print('Running command {}'.format(cmd))
sp.check_call(shlex.split(cmd))
try:
build_exec_path = os.path.join(self.codebase_path,
self.config['build']['exec_path'])
except KeyError:
if self.build_exec_path:
build_exec_path = self.build_exec_path
else:
build_exec_path = self.codebase_path
# Copy new executable to bin dir
if self.exec_path:
# Create the bin path if it doesn't exist
mkdir_p(self.expt.lab.bin_path)
build_exec_path = os.path.join(build_exec_path, self.exec_name)
shutil.copy(build_exec_path, self.exec_path)
os.chdir(curdir)
def postprocess(self):
gmon_dir = os.path.join(self.expt.work_path, 'gmon')
mkdir_p(gmon_dir)
gmon_fnames = [f for f in os.listdir(self.expt.work_path)
if f.startswith('gmon.out')]
for gmon in gmon_fnames:
f_src = os.path.join(self.expt.work_path, gmon)
f_dst = os.path.join(gmon_dir, gmon)
shutil.move(f_src, f_dst)
def setup(self):
# FMS initialisation
super(Mom, self).setup()
if not self.top_level_model:
# Make log dir
mkdir_p(os.path.join(self.work_path, 'log'))
input_nml_path = os.path.join(self.work_path, 'input.nml')
input_nml = f90nml.read(input_nml_path)
# Set the runtime
if self.expt.runtime:
ocean_solo_nml = input_nml['ocean_solo_nml']
ocean_solo_nml['years'] = self.expt.runtime['years']
ocean_solo_nml['months'] = self.expt.runtime['months']
ocean_solo_nml['days'] = self.expt.runtime['days']
ocean_solo_nml['seconds'] = self.expt.runtime.get('seconds', 0)
input_nml.write(input_nml_path, force=True)
# Construct the land CPU mask
if self.expt.config.get('mask_table', False):
# NOTE: This function actually creates a mask table using the
# `check_mask` command line tool. But it is not very usable
# since you need to know the number of masked CPUs to submit
# the job. It needs a rethink of the submission process.
self.create_mask_table(input_nml)
# NOTE: Don't expect this to be here forever...
# Attempt to set a mask table from the input
if self.config.get('mask', False):
mask_path = os.path.join(self.work_input_path, 'ocean_mask_table')
# Remove any existing mask
# (If no reference mask is available, then we will not use one)
if os.path.isfile(mask_path):
os.remove(mask_path)
# Reference mask table
assert ('layout' in input_nml['ocean_model_nml'])
nx, ny = input_nml['ocean_model_nml'].get('layout')
n_masked_cpus = nx * ny - self.config.get('ncpus')
mask_table_fname = 'mask_table.{nmask}.{nx}x{ny}'.format(
nmask=n_masked_cpus, nx=nx, ny=ny)
ref_mask_path = os.path.join(self.work_input_path,
mask_table_fname)
# Set (or replace) mask table if reference is available
if os.path.isfile(ref_mask_path):
make_symlink(ref_mask_path, mask_path)
def archive(self):
# TODO: Determine the exchange files
restart_files = ['a2i.nc', 'i2a.nc', 'i2o.nc', 'o2i.nc']
mkdir_p(self.restart_path)
for f in restart_files:
f_src = os.path.join(self.work_path, f)
f_dst = os.path.join(self.restart_path, f)
if os.path.exists(f_src):
shutil.copy2(f_src, f_dst)
def archive(self):
# TODO: Determine the exchange files
restart_files = ['a2i.nc', 'i2a.nc', 'i2o.nc', 'o2i.nc']
mkdir_p(self.restart_path)
for f in restart_files:
f_src = os.path.join(self.work_path, f)
f_dst = os.path.join(self.restart_path, f)
if os.path.exists(f_src):
shutil.move(f_src, f_dst)
def postprocess(self):
gmon_dir = os.path.join(self.expt.work_path, 'gmon')
mkdir_p(gmon_dir)
gmon_fnames = [
f for f in os.listdir(self.expt.work_path)
if f.startswith('gmon.out')
]
for gmon in gmon_fnames:
f_src = os.path.join(self.expt.work_path, gmon)
f_dst = os.path.join(gmon_dir, gmon)
shutil.move(f_src, f_dst)
def sweep(self, hard_sweep=False):
# TODO: Fix the IO race conditions!
if hard_sweep:
if os.path.isdir(self.archive_path):
print('Removing archive path {}'.format(self.archive_path))
cmd = 'rm -rf {}'.format(self.archive_path)
cmd = shlex.split(cmd)
rc = sp.call(cmd)
assert rc == 0
if os.path.islink(self.archive_sym_path):
print('Removing symlink {}'.format(self.archive_sym_path))
os.remove(self.archive_sym_path)
if os.path.isdir(self.work_path):
print('Removing work path {}'.format(self.work_path))
cmd = 'rm -rf {}'.format(self.work_path)
cmd = shlex.split(cmd)
rc = sp.call(cmd)
assert rc == 0
if os.path.islink(self.work_sym_path):
print('Removing symlink {}'.format(self.work_sym_path))
os.remove(self.work_sym_path)
# TODO: model outstreams and pbs logs need to be handled separately
default_job_name = os.path.basename(os.getcwd())
short_job_name = self.config.get('jobname', default_job_name)[:15]
logs = [
f for f in os.listdir(os.curdir) if os.path.isfile(f) and (
f == self.stdout_fname or
f == self.stderr_fname or
f.startswith(short_job_name + '.o') or
f.startswith(short_job_name + '.e') or
f.startswith(short_job_name[:13] + '_c.o') or
f.startswith(short_job_name[:13] + '_c.e') or
f.startswith(short_job_name[:13] + '_p.o') or
f.startswith(short_job_name[:13] + '_p.e')
)
]
pbs_log_path = os.path.join(os.curdir, 'pbs_logs')
mkdir_p(pbs_log_path)
for f in logs:
print('Moving log {}'.format(f))
os.rename(f, os.path.join(pbs_log_path, f))
def initialize(self):
"""Create the laboratory directories."""
# Create laboratory directories
mkdir_p(self.archive_path)
mkdir_p(self.bin_path)
mkdir_p(self.codebase_path)
mkdir_p(self.input_basepath)
def initialize(self):
"""Create the laboratory directories."""
# Create laboratory directories
mkdir_p(self.archive_path)
mkdir_p(self.bin_path)
mkdir_p(self.codebase_path)
mkdir_p(self.input_basepath)
def sweep(self, hard_sweep=False):
# TODO: Fix the IO race conditions!
if hard_sweep:
if os.path.isdir(self.archive_path):
print('Removing archive path {}'.format(self.archive_path))
cmd = 'rm -rf {}'.format(self.archive_path)
cmd = shlex.split(cmd)
rc = sp.call(cmd)
assert rc == 0
if os.path.islink(self.archive_sym_path):
print('Removing symlink {}'.format(self.archive_sym_path))
os.remove(self.archive_sym_path)
if os.path.isdir(self.work_path):
print('Removing work path {}'.format(self.work_path))
cmd = 'rm -rf {}'.format(self.work_path)
cmd = shlex.split(cmd)
rc = sp.call(cmd)
assert rc == 0
if os.path.islink(self.work_sym_path):
print('Removing symlink {}'.format(self.work_sym_path))
os.remove(self.work_sym_path)
# TODO: model outstreams and pbs logs need to be handled separately
default_job_name = os.path.basename(os.getcwd())
short_job_name = self.config.get('jobname', default_job_name)[:15]
logs = [
f for f in os.listdir(os.curdir) if os.path.isfile(f) and
(f == self.stdout_fname or f == self.stderr_fname
or f.startswith('slurm-')
#f.startswith(short_job_name + '.o') or
#f.startswith(short_job_name + '.e') or
#f.startswith(short_job_name[:13] + '_c.o') or
#f.startswith(short_job_name[:13] + '_c.e')
)
]
pbs_log_path = os.path.join(os.curdir, 'slurm_logs')
mkdir_p(pbs_log_path)
for f in logs:
print('Moving log {}'.format(f))
os.rename(f, os.path.join(pbs_log_path, f))
def archive(self):
super(UnifiedModel, self).archive()
# Delete all the stdout log files except the root PE
# Sorts to ensure root PE is first entry
files = sorted(glob.glob(
os.path.join(self.work_path, 'atm.fort6.pe*')),
key=lambda name: int(name.rpartition('.')[-1][2:]))
if len(files) > 1:
for f_path in files[1:]:
os.remove(f_path)
mkdir_p(self.restart_path)
# Need to figure out the end date of the model.
nml_path = os.path.join(self.work_path, 'namelists')
nml = f90nml.read(nml_path)
resubmit_inc = nml['NLSTCALL']['RUN_RESUBMIT_INC']
runtime = um_time_to_time(resubmit_inc)
# runtime = datetime.timedelta(seconds=runtime)
basis_time = nml['NLSTCALL']['MODEL_BASIS_TIME']
init_date = um_date_to_date(basis_time)
end_date = cal.date_plus_seconds(init_date,
runtime,
cal.GREGORIAN)
# Save model time to restart next run
with open(os.path.join(self.restart_path,
self.restart_calendar_file), 'w') as restart_file:
restart_file.write(yaml.dump({'end_date': end_date},
default_flow_style=False))
end_date = date_to_um_dump_date(end_date)
restart_dump = os.path.join(self.work_path,
'aiihca.da{0}'.format(end_date))
f_dst = os.path.join(self.restart_path, self.restart)
if os.path.exists(restart_dump):
shutil.copy(restart_dump, f_dst)
else:
print('payu: error: Model has not produced a restart dump file:\n'
'{} does not exist.\n'
'Check DUMPFREQim in namelists'.format(restart_dump))
def archive(self, **kwargs):
# Remove symbolic links
for f in os.listdir(self.work_input_path):
f_path = os.path.join(self.work_input_path, f)
if os.path.islink(f_path):
os.remove(f_path)
# Archive the restart files
mkdir_p(self.restart_path)
restart_files = [f for f in os.listdir(self.work_path)
if f.endswith('lastday.nc')]
for f in restart_files:
f_src = os.path.join(self.work_path, f)
shutil.move(f_src, self.restart_path)
def archive(self):
# Remove symbolic links to input or pickup files:
for f in os.listdir(self.work_path):
f_path = os.path.join(self.work_path, f)
if os.path.islink(f_path):
os.remove(f_path)
# Move files outside of mnc_* directories
mnc_paths = [
os.path.join(self.work_path, d) for d in os.listdir(self.work_path)
if d.startswith('mnc_')
]
for path in mnc_paths:
for f in os.listdir(path):
f_path = os.path.join(path, f)
sh.move(f_path, self.work_path)
os.rmdir(path)
mkdir_p(self.restart_path)
# Move pickups but don't include intermediate pickupts ('ckpt's)
restart_files = [
f for f in os.listdir(self.work_path) if f.startswith('pickup')
and not f.split('.')[1].startswith('ckpt')
]
# Tar and compress the output files
stdout_files = [
f for f in os.listdir(self.work_path) if f.startswith('STDOUT.')
]
if stdout_files:
cmd = 'tar -C {0} -c -j -f {1}'.format(
self.work_path, os.path.join(self.work_path, 'STDOUT.tar.bz2'))
rc = sp.Popen(shlex.split(cmd) + stdout_files).wait()
assert rc == 0
for f in stdout_files:
os.remove(os.path.join(self.work_path, f))
for f in restart_files:
f_src = os.path.join(self.work_path, f)
sh.move(f_src, self.restart_path)
def archive(self, **kwargs):
# Remove symbolic links
for f in os.listdir(self.work_input_path):
f_path = os.path.join(self.work_input_path, f)
if os.path.islink(f_path):
os.remove(f_path)
# Archive the restart files
mkdir_p(self.restart_path)
restart_files = [
f for f in os.listdir(self.work_path) if f.endswith('lastday.nc')
]
for f in restart_files:
f_src = os.path.join(self.work_path, f)
shutil.move(f_src, self.restart_path)
def archive(self):
super(UnifiedModel, self).archive()
# Delete all the stdout log files except the root PE
# Sorts to ensure root PE is first entry
files = sorted(glob.glob(os.path.join(self.work_path,
'atm.fort6.pe*')),
key=lambda name: int(name.rpartition('.')[-1][2:]))
if len(files) > 1:
for f_path in files[1:]:
os.remove(f_path)
mkdir_p(self.restart_path)
# Need to figure out the end date of the model.
nml_path = os.path.join(self.work_path, 'namelists')
nml = f90nml.read(nml_path)
resubmit_inc = nml['NLSTCALL']['RUN_RESUBMIT_INC']
runtime = um_time_to_time(resubmit_inc)
# runtime = datetime.timedelta(seconds=runtime)
basis_time = nml['NLSTCALL']['MODEL_BASIS_TIME']
init_date = um_date_to_date(basis_time)
end_date = cal.date_plus_seconds(init_date, runtime, cal.GREGORIAN)
# Save model time to restart next run
with open(os.path.join(self.restart_path, self.restart_calendar_file),
'w') as restart_file:
restart_file.write(
yaml.dump({'end_date': end_date}, default_flow_style=False))
end_date = date_to_um_dump_date(end_date)
restart_dump = os.path.join(self.work_path,
'aiihca.da{0}'.format(end_date))
f_dst = os.path.join(self.restart_path, self.restart)
if os.path.exists(restart_dump):
shutil.copy(restart_dump, f_dst)
else:
print('payu: error: Model has not produced a restart dump file:\n'
'{} does not exist.\n'
'Check DUMPFREQim in namelists'.format(restart_dump))
def archive(self):
# Remove symbolic links to input or pickup files:
for f in os.listdir(self.work_path):
f_path = os.path.join(self.work_path, f)
if os.path.islink(f_path):
os.remove(f_path)
# Move files outside of mnc_* directories
mnc_paths = [os.path.join(self.work_path, d)
for d in os.listdir(self.work_path)
if d.startswith('mnc_')]
for path in mnc_paths:
for f in os.listdir(path):
f_path = os.path.join(path, f)
sh.move(f_path, self.work_path)
os.rmdir(path)
mkdir_p(self.restart_path)
# Move pickups but don't include intermediate pickupts ('ckpt's)
restart_files = [f for f in os.listdir(self.work_path)
if f.startswith('pickup') and
not f.split('.')[1].startswith('ckpt')]
# Tar and compress the output files
stdout_files = [f for f in os.listdir(self.work_path)
if f.startswith('STDOUT.')]
if stdout_files:
cmd = 'tar -C {0} -c -j -f {1}'.format(
self.work_path,
os.path.join(self.work_path, 'STDOUT.tar.bz2'))
rc = sp.Popen(shlex.split(cmd) + stdout_files).wait()
assert rc == 0
for f in stdout_files:
os.remove(os.path.join(self.work_path, f))
for f in restart_files:
f_src = os.path.join(self.work_path, f)
sh.move(f_src, self.restart_path)
def archive(self):
mkdir_p(self.restart_path)
# Need to figure out the end date of the model.
nml_path = os.path.join(self.work_path, "namelists")
nml = f90nml.read(nml_path)
resubmit_inc = nml["NLSTCALL"]["RUN_RESUBMIT_INC"]
runtime = um_time_to_time(resubmit_inc)
runtime = datetime.timedelta(seconds=runtime)
basis_time = nml["NLSTCALL"]["MODEL_BASIS_TIME"]
init_date = um_date_to_date(basis_time)
end_date = date_to_um_dump_date(init_date + runtime)
restart_dump = os.path.join(self.work_path, "aiihca.da{}".format(end_date))
f_dst = os.path.join(self.restart_path, self.restart)
shutil.copy(restart_dump, f_dst)
def archive(self):
mkdir_p(self.restart_path)
# Need to figure out the end date of the model.
nml_path = os.path.join(self.work_path, 'namelists')
nml = f90nml.read(nml_path)
resubmit_inc = nml['NLSTCALL']['RUN_RESUBMIT_INC']
runtime = um_time_to_time(resubmit_inc)
runtime = datetime.timedelta(seconds=runtime)
basis_time = nml['NLSTCALL']['MODEL_BASIS_TIME']
init_date = um_date_to_date(basis_time)
end_date = date_to_um_dump_date(init_date + runtime)
restart_dump = os.path.join(self.work_path,
'aiihca.da{}'.format(end_date))
f_dst = os.path.join(self.restart_path, self.restart)
shutil.copy(restart_dump, f_dst)
def __init__(self, config, reproduce):
# Manifest control configuration
self.manifest_config = config
# Not currently supporting specifying hash functions
self.fast_hashes = self.manifest_config.get('fasthash', fast_hashes)
self.full_hashes = self.manifest_config.get('fullhash', full_hashes)
if type(self.fast_hashes) is str:
self.fast_hashes = [
self.fast_hashes,
]
if type(self.full_hashes) is str:
self.full_hashes = [
self.full_hashes,
]
self.ignore = self.manifest_config.get('ignore', ['.*'])
if isinstance(self.ignore, str):
self.ignore = [self.ignore]
# Initialise manifests and reproduce flags
self.manifests = {}
self.have_manifest = {}
reproduce_config = self.manifest_config.get('reproduce', {})
self.reproduce = {}
for mf in ['input', 'restart', 'exe']:
self.init_mf(mf)
self.reproduce[mf] = reproduce_config.get(mf, reproduce)
# Make sure the manifests directory exists
mkdir_p(os.path.dirname(self.manifests['exe'].path))
# Set flag to auto-scan input directories
self.scaninputs = self.manifest_config.get('scaninputs', True)
if self.reproduce['input'] and self.scaninputs:
print("scaninputs set to False when reproduce input is True")
self.scaninputs = False
def __init__(self, expt, reproduce):
# Inherit experiment configuration
self.expt = expt
# Manifest control configuration
self.manifest_config = self.expt.config.get('manifest', {})
# Not currently supporting specifying hash functions
# self.hash_functions = manifest_config.get(
# 'hashfns',
# ['nchash','binhash','md5']
# )
self.ignore = self.manifest_config.get('ignore', ['.*'])
if isinstance(self.ignore, str):
self.ignore = [self.ignore]
# Initialise manifests
self.manifests = {}
for mf in ['input', 'restart', 'exe']:
self.manifests[mf] = PayuManifest(os.path.join(
'manifests', '{}.yaml'.format(mf)),
ignore=self.ignore)
self.have_manifest = {}
for mf in self.manifests:
self.have_manifest[mf] = False
# Set reproduce flags
self.reproduce_config = self.manifest_config.get('reproduce', {})
self.reproduce = {}
for mf in self.manifests.keys():
self.reproduce[mf] = self.reproduce_config.get(mf, reproduce)
# Make sure the manifests directory exists
mkdir_p(os.path.dirname(self.manifests['exe'].path))
self.scaninputs = self.manifest_config.get('scaninputs', True)
def setup(self):
# Create experiment directory structure
mkdir_p(self.work_input_path)
mkdir_p(self.work_restart_path)
mkdir_p(self.work_output_path)
# Copy configuration files from control path
for f_name in self.config_files:
f_path = os.path.join(self.control_path, f_name)
shutil.copy(f_path, self.work_path)
for f_name in self.optional_config_files:
f_path = os.path.join(self.control_path, f_name)
try:
shutil.copy(f_path, self.work_path)
except IOError as exc:
if exc.errno == errno.ENOENT:
pass
else:
raise
# Add restart files from prior run to restart manifest
if not self.expt.manifest.have_manifest[
'restart'] and self.prior_restart_path:
restart_files = self.get_prior_restart_files()
for f_name in restart_files:
f_orig = os.path.join(self.prior_restart_path, f_name)
f_link = os.path.join(self.work_init_path_local, f_name)
self.expt.manifest.add_filepath('restart', f_link, f_orig,
self.copy_inputs)
# Add input files to manifest if we don't already have a populated
# input manifest, or we specify scan_inputs is True (default)
if not self.expt.manifest.have_manifest[
'input'] or self.expt.manifest.scaninputs:
# Add files to manifest
for input_path in self.input_paths:
input_files = os.listdir(input_path)
for f_name in input_files:
f_orig = os.path.join(input_path, f_name)
f_link = os.path.join(self.work_input_path_local, f_name)
# Do not use input file if it is in RESTART
if not os.path.exists(f_link):
self.expt.manifest.add_filepath(
'input', f_link, f_orig, self.copy_inputs)
# Make symlink to executable in work directory
if self.exec_path:
# Add to exe manifest (this is always done so any change in exe path will be picked up)
self.expt.manifest.add_filepath('exe', self.exec_path_local,
self.exec_path)
timestep = self.config.get('timestep')
if timestep:
self.set_timestep(timestep)
def setup(self):
# Create experiment directory structure
mkdir_p(self.work_input_path)
mkdir_p(self.work_restart_path)
mkdir_p(self.work_output_path)
# Copy configuration files from control path
for f_name in self.config_files:
f_path = os.path.join(self.control_path, f_name)
shutil.copy(f_path, self.work_path)
for f_name in self.optional_config_files:
f_path = os.path.join(self.control_path, f_name)
try:
shutil.copy(f_path, self.work_path)
except IOError as exc:
if exc.errno == errno.ENOENT:
pass
else:
raise
# Link restart files from prior run
if self.prior_restart_path and not self.expt.repeat_run:
restart_files = self.get_prior_restart_files()
for f_name in restart_files:
f_restart = os.path.join(self.prior_restart_path, f_name)
f_input = os.path.join(self.work_init_path, f_name)
if self.copy_restarts:
shutil.copy(f_restart, f_input)
else:
make_symlink(f_restart, f_input)
# Link input data
for input_path in self.input_paths:
input_files = os.listdir(input_path)
for f_name in input_files:
f_input = os.path.join(input_path, f_name)
f_work_input = os.path.join(self.work_input_path, f_name)
# Do not use input file if it is in RESTART
if not os.path.exists(f_work_input):
if self.copy_inputs:
shutil.copy(f_input, f_work_input)
else:
make_symlink(f_input, f_work_input)
# Some models overwrite their own input for restarts
# (e.g. OASIS)
if self.make_inputs_writeable:
os.chmod(f_work_input,
stat.S_IWUSR | stat.S_IRUSR | stat.S_IRGRP)
t_step = self.config.get('timestep')
if t_step:
self.set_timestep(t_step)
def setup(self):
# Create experiment directory structure
mkdir_p(self.work_input_path)
mkdir_p(self.work_restart_path)
mkdir_p(self.work_output_path)
# Copy configuration files from control path
for f_name in self.config_files:
f_path = os.path.join(self.control_path, f_name)
shutil.copy(f_path, self.work_path)
for f_name in self.optional_config_files:
f_path = os.path.join(self.control_path, f_name)
try:
shutil.copy(f_path, self.work_path)
except IOError as exc:
if exc.errno == errno.ENOENT:
pass
else:
raise
# Add restart files from prior run to restart manifest
if not self.expt.manifest.have_manifest['restart'] and self.prior_restart_path:
restart_files = self.get_prior_restart_files()
for f_name in restart_files:
f_orig = os.path.join(self.prior_restart_path, f_name)
f_link = os.path.join(self.work_init_path_local, f_name)
self.expt.manifest.add_filepath('restart',f_link,f_orig,self.copy_inputs)
# Add input files to manifest if we don't already have a populated
# input manifest, or we specify scan_inputs is True (default)
if not self.expt.manifest.have_manifest['input'] or self.expt.manifest.scaninputs:
# Add files to manifest
for input_path in self.input_paths:
input_files = os.listdir(input_path)
for f_name in input_files:
f_orig = os.path.join(input_path, f_name)
f_link = os.path.join(self.work_input_path_local,f_name)
# Do not use input file if it is in RESTART
if not os.path.exists(f_link):
self.expt.manifest.add_filepath('input',f_link,f_orig,self.copy_inputs)
# Make symlink to executable in work directory
if self.exec_path:
# Add to exe manifest (this is always done so any change in exe path will be picked up)
self.expt.manifest.add_filepath('exe',self.exec_path_local,self.exec_path)
timestep = self.config.get('timestep')
if timestep:
self.set_timestep(timestep)
def setup(self):
# Create experiment directory structure
mkdir_p(self.work_input_path)
mkdir_p(self.work_restart_path)
mkdir_p(self.work_output_path)
# Copy configuration files from control path
for f_name in self.config_files:
f_path = os.path.join(self.control_path, f_name)
shutil.copy(f_path, self.work_path)
for f_name in self.optional_config_files:
f_path = os.path.join(self.control_path, f_name)
try:
shutil.copy(f_path, self.work_path)
except IOError as exc:
if exc.errno == errno.ENOENT:
pass
else:
raise
# Link restart files from prior run
if self.prior_restart_path and not self.expt.repeat_run:
restart_files = self.get_prior_restart_files()
for f_name in restart_files:
f_restart = os.path.join(self.prior_restart_path, f_name)
f_input = os.path.join(self.work_init_path, f_name)
if self.copy_restarts:
shutil.copy(f_restart, f_input)
else:
make_symlink(f_restart, f_input)
# Link input data
for input_path in self.input_paths:
input_files = os.listdir(input_path)
for f_name in input_files:
f_input = os.path.join(input_path, f_name)
f_work_input = os.path.join(self.work_input_path, f_name)
# Do not use input file if it is in RESTART
if not os.path.exists(f_work_input):
if self.copy_inputs:
shutil.copy(f_input, f_work_input)
else:
make_symlink(f_input, f_work_input)
timestep = self.config.get('timestep')
if timestep:
self.set_timestep(timestep)
def archive(self):
# Create an empty restart directory
mkdir_p(self.restart_path)
shutil.rmtree(self.work_input_path)
def setup(self):
print("Setting up {model}".format(model=self.name))
# Create experiment directory structure
mkdir_p(self.work_init_path)
mkdir_p(self.work_input_path)
mkdir_p(self.work_restart_path)
mkdir_p(self.work_output_path)
# Copy configuration files from control path
for f_name in self.config_files:
f_path = os.path.join(self.control_path, f_name)
shutil.copy(f_path, self.work_path)
for f_name in self.optional_config_files:
f_path = os.path.join(self.control_path, f_name)
try:
shutil.copy(f_path, self.work_path)
except IOError as exc:
if exc.errno == errno.ENOENT:
pass
else:
raise
# Add restart files from prior run to restart manifest
if (not self.expt.manifest.have_manifest['restart']
and self.prior_restart_path):
restart_files = self.get_prior_restart_files()
for f_name in restart_files:
f_orig = os.path.join(self.prior_restart_path, f_name)
f_link = os.path.join(self.work_init_path_local, f_name)
self.expt.manifest.add_filepath('restart', f_link, f_orig,
self.copy_restarts)
# Add input files to manifest if we don't already have a populated
# input manifest, or we specify scaninputs is True (default)
if (not self.expt.manifest.have_manifest['input']
or self.expt.manifest.scaninputs):
for input_path in self.input_paths:
if os.path.isfile(input_path):
# Build a mock walk iterator for a single file
fwalk = iter([(os.path.dirname(input_path), [],
[os.path.basename(input_path)])])
# Overwrite the input_path as a directory
input_path = os.path.dirname(input_path)
else:
fwalk = os.walk(input_path)
for path, dirs, files in fwalk:
workrelpath = os.path.relpath(path, input_path)
subdir = os.path.normpath(
os.path.join(self.work_input_path_local, workrelpath))
if not os.path.exists(subdir):
os.mkdir(subdir)
for f_name in files:
f_orig = os.path.join(path, f_name)
f_link = os.path.join(self.work_input_path_local,
workrelpath, f_name)
# Do not use input file if it is in RESTART
if not os.path.exists(f_link):
self.expt.manifest.add_filepath(
'input', f_link, f_orig, self.copy_inputs)
# Make symlink to executable in work directory
if self.exec_path:
# Add to exe manifest (this is always done so any change in exe
# path will be picked up)
self.expt.manifest.add_filepath('exe', self.exec_path_local,
self.exec_path)
timestep = self.config.get('timestep')
if timestep:
self.set_timestep(timestep)
def setup(self):
super(Yatm, self).setup()
# Make log dir
mkdir_p(os.path.join(self.work_path, 'log'))
def archive(self):
# Create an empty restart directory
mkdir_p(self.restart_path)
def setup(self):
print("Setting up {model}".format(model=self.name))
# Create experiment directory structure
mkdir_p(self.work_init_path)
mkdir_p(self.work_input_path)
mkdir_p(self.work_restart_path)
mkdir_p(self.work_output_path)
# Copy configuration files from control path
for f_name in self.config_files:
f_path = os.path.join(self.control_path, f_name)
shutil.copy(f_path, self.work_path)
for f_name in self.optional_config_files:
f_path = os.path.join(self.control_path, f_name)
try:
shutil.copy(f_path, self.work_path)
except IOError as exc:
if exc.errno == errno.ENOENT:
pass
else:
raise
# Add restart files from prior run to restart manifest
if (not self.expt.manifest.have_manifest['restart'] and
self.prior_restart_path):
restart_files = self.get_prior_restart_files()
for f_name in restart_files:
f_orig = os.path.join(self.prior_restart_path, f_name)
f_link = os.path.join(self.work_init_path_local, f_name)
self.expt.manifest.add_filepath(
'restart',
f_link,
f_orig,
self.copy_restarts
)
# Add input files to manifest if we don't already have a populated
# input manifest, or we specify scan_inputs is True (default)
if (not self.expt.manifest.have_manifest['input'] or
self.expt.manifest.scaninputs):
for input_path in self.input_paths:
if os.path.isfile(input_path):
# Build a mock walk iterator for a single file
fwalk = iter([(
os.path.dirname(input_path),
[],
[os.path.basename(input_path)]
)])
# Overwrite the input_path as a directory
input_path = os.path.dirname(input_path)
else:
fwalk = os.walk(input_path)
for path, dirs, files in fwalk:
workrelpath = os.path.relpath(path, input_path)
subdir = os.path.normpath(
os.path.join(self.work_input_path_local,
workrelpath)
)
if not os.path.exists(subdir):
os.mkdir(subdir)
for f_name in files:
f_orig = os.path.join(path, f_name)
f_link = os.path.join(
self.work_input_path_local,
workrelpath,
f_name
)
# Do not use input file if it is in RESTART
if not os.path.exists(f_link):
self.expt.manifest.add_filepath(
'input',
f_link,
f_orig,
self.copy_inputs
)
# Make symlink to executable in work directory
if self.exec_path:
# Add to exe manifest (this is always done so any change in exe
# path will be picked up)
self.expt.manifest.add_filepath(
'exe',
self.exec_path_local,
self.exec_path
)
timestep = self.config.get('timestep')
if timestep:
self.set_timestep(timestep)
def archive(self):
# Create an empty restart directory
mkdir_p(self.restart_path)
shutil.rmtree(self.work_input_path)
def run(self, *user_flags):
# XXX: This was previously done in reversion
envmod.setup()
self.load_modules()
f_out = open(self.stdout_fname, 'w')
f_err = open(self.stderr_fname, 'w')
# Set MPI environment variables
env = self.config.get('env')
# Explicitly check for `None`, in case of an empty `env:` entry
if env is None:
env = {}
for var in env:
if env[var] is None:
env_value = ''
else:
env_value = str(env[var])
os.environ[var] = env_value
mpi_config = self.config.get('mpi', {})
mpi_runcmd = mpi_config.get('runcmd', 'mpirun')
if self.config.get('scalasca', False):
mpi_runcmd = ' '.join(['scalasca -analyze', mpi_runcmd])
# MPI runtime flags
mpi_flags = mpi_config.get('flags', [])
if not mpi_flags:
mpi_flags = self.config.get('mpirun', [])
# TODO: Legacy config removal warning
if type(mpi_flags) != list:
mpi_flags = [mpi_flags]
# TODO: More uniform support needed here
if self.config.get('scalasca', False):
mpi_flags = ['\"{0}\"'.format(f) for f in mpi_flags]
# XXX: I think this may be broken
if user_flags:
mpi_flags.extend(list(user_flags))
if self.debug:
mpi_flags.append('--debug')
mpi_progs = []
for model in self.models:
# Skip models without executables (e.g. couplers)
if not model.exec_path_local:
continue
mpi_config = self.config.get('mpi', {})
mpi_module = mpi_config.get('module', None)
# Update MPI library module (if not explicitly set)
# TODO: Check for MPI library mismatch across multiple binaries
if mpi_module is None:
mpi_module = envmod.lib_update(
model.exec_path_local,
'libmpi.so'
)
model_prog = []
# Our MPICH wrapper does not support a working directory flag
if not mpi_module.startswith('mvapich'):
model_prog.append('-wdir {0}'.format(model.work_path))
# Append any model-specific MPI flags
model_flags = model.config.get('mpiflags', [])
if not isinstance(model_flags, list):
model_prog.append(model_flags)
else:
model_prog.extend(model_flags)
model_ncpus = model.config.get('ncpus')
if model_ncpus:
model_prog.append('-np {0}'.format(model_ncpus))
model_npernode = model.config.get('npernode')
# TODO: New Open MPI format?
if model_npernode:
if model_npernode % 2 == 0:
npernode_flag = ('-map-by ppr:{0}:socket'
''.format(model_npernode / 2))
else:
npernode_flag = ('-map-by ppr:{0}:node'
''.format(model_npernode))
if self.config.get('scalasca', False):
npernode_flag = '\"{0}\"'.format(npernode_flag)
model_prog.append(npernode_flag)
if self.config.get('hpctoolkit', False):
os.environ['HPCRUN_EVENT_LIST'] = 'WALLCLOCK@5000'
model_prog.append('hpcrun')
for prof in self.profilers:
if prof.runscript:
model_prog = model_prog.append(prof.runscript)
model_prog.append(model.exec_prefix)
# Use the full path to symlinked exec_name in work as some
# older MPI libraries complained executable was not in PATH
model_prog.append(os.path.join(model.work_path, model.exec_name))
mpi_progs.append(' '.join(model_prog))
cmd = '{runcmd} {flags} {exes}'.format(
runcmd=mpi_runcmd,
flags=' '.join(mpi_flags),
exes=' : '.join(mpi_progs)
)
for prof in self.profilers:
cmd = prof.wrapper(cmd)
# Expand shell variables inside flags
if self.expand_shell_vars:
cmd = os.path.expandvars(cmd)
# TODO: Consider making this default
if self.config.get('coredump', False):
enable_core_dump()
# Our MVAPICH wrapper does not support working directories
if mpi_module.startswith('mvapich'):
curdir = os.getcwd()
os.chdir(self.work_path)
else:
curdir = None
# Dump out environment
with open(self.env_fname, 'w') as file:
file.write(yaml.dump(dict(os.environ), default_flow_style=False))
self.runlog.create_manifest()
if self.runlog.enabled:
self.runlog.commit()
# NOTE: This may not be necessary, since env seems to be getting
# correctly updated. Need to look into this.
print(cmd)
if env:
# TODO: Replace with mpirun -x flag inputs
proc = sp.Popen(shlex.split(cmd), stdout=f_out, stderr=f_err,
env=os.environ.copy())
proc.wait()
rc = proc.returncode
else:
rc = sp.call(shlex.split(cmd), stdout=f_out, stderr=f_err)
# Return to control directory
if curdir:
os.chdir(curdir)
f_out.close()
f_err.close()
self.finish_time = datetime.datetime.now()
info = get_job_info()
if info is None:
# Not being run under PBS, reverse engineer environment
info = {
'PAYU_PATH': os.path.dirname(self.payu_path)
}
# Add extra information to save to jobinfo
info.update(
{
'PAYU_CONTROL_DIR': self.control_path,
'PAYU_RUN_ID': self.run_id,
'PAYU_CURRENT_RUN': self.counter,
'PAYU_N_RUNS': self.n_runs,
'PAYU_JOB_STATUS': rc,
'PAYU_START_TIME': self.start_time.isoformat(),
'PAYU_FINISH_TIME': self.finish_time.isoformat(),
'PAYU_WALLTIME': "{0} s".format(
(self.finish_time - self.start_time).total_seconds()
),
}
)
# Dump job info
with open(self.job_fname, 'w') as file:
file.write(yaml.dump(info, default_flow_style=False))
# Remove any empty output files (e.g. logs)
for fname in os.listdir(self.work_path):
fpath = os.path.join(self.work_path, fname)
if os.path.getsize(fpath) == 0:
os.remove(fpath)
# Clean up any profiling output
# TODO: Move after `rc` code check?
for prof in self.profilers:
prof.postprocess()
# TODO: Need a model-specific cleanup method call here
# NOTE: This does not appear to catch hanging jobs killed by PBS
if rc != 0:
# Backup logs for failed runs
error_log_dir = os.path.join(self.archive_path, 'error_logs')
mkdir_p(error_log_dir)
# NOTE: This is PBS-specific
job_id = get_job_id(short=False)
if job_id == '':
job_id = self.run_id[:6]
for fname in self.output_fnames:
src = os.path.join(self.control_path, fname)
stem, suffix = os.path.splitext(fname)
dest = os.path.join(error_log_dir,
".".join((stem, job_id)) + suffix)
print(src, dest)
shutil.copyfile(src, dest)
# Create the symlink to the logs if it does not exist
make_symlink(self.archive_path, self.archive_sym_path)
# Terminate payu
sys.exit('payu: Model exited with error code {0}; aborting.'
''.format(rc))
# Decrement run counter on successful run
stop_file_path = os.path.join(self.control_path, 'stop_run')
if os.path.isfile(stop_file_path):
assert os.stat(stop_file_path).st_size == 0
os.remove(stop_file_path)
print('payu: Stop file detected; terminating resubmission.')
self.n_runs = 0
else:
self.n_runs -= 1
# Move logs to archive (or delete if empty)
for f in self.output_fnames:
f_path = os.path.join(self.control_path, f)
if os.path.getsize(f_path) == 0:
os.remove(f_path)
else:
shutil.move(f_path, self.work_path)
run_script = self.userscripts.get('run')
if run_script:
self.run_userscript(run_script)
def setup(self):
# FMS initialisation
super(Mom, self).setup()
if not self.top_level_model:
# Make log dir
mkdir_p(os.path.join(self.work_path, 'log'))
input_nml_path = os.path.join(self.work_path, 'input.nml')
input_nml = f90nml.read(input_nml_path)
use_core2iaf = self.config.get('core2iaf')
if use_core2iaf:
self.core2iaf_setup()
# Set the runtime
if self.expt.runtime:
ocean_solo_nml = input_nml['ocean_solo_nml']
ocean_solo_nml['years'] = self.expt.runtime['years']
ocean_solo_nml['months'] = self.expt.runtime['months']
ocean_solo_nml['days'] = self.expt.runtime['days']
ocean_solo_nml['seconds'] = self.expt.runtime.get('seconds', 0)
input_nml.write(input_nml_path, force=True)
# Construct the land CPU mask
if self.expt.config.get('mask_table', False):
# NOTE: This function actually creates a mask table using the
# `check_mask` command line tool. But it is not very usable
# since you need to know the number of masked CPUs to submit
# the job. It needs a rethink of the submission process.
self.create_mask_table(input_nml)
# NOTE: Don't expect this to be here forever...
# Attempt to set a mask table from the input
if self.config.get('mask', False):
mask_path = os.path.join(self.work_input_path, 'ocean_mask_table')
# Remove any existing mask
# (If no reference mask is available, then we will not use one)
if os.path.isfile(mask_path):
os.remove(mask_path)
# Reference mask table
assert('layout' in input_nml['ocean_model_nml'])
nx, ny = input_nml['ocean_model_nml'].get('layout')
n_masked_cpus = nx * ny - self.config.get('ncpus')
mask_table_fname = 'mask_table.{nmask}.{nx}x{ny}'.format(
nmask=n_masked_cpus,
nx=nx,
ny=ny
)
ref_mask_path = os.path.join(self.work_input_path,
mask_table_fname)
# Set (or replace) mask table if reference is available
if os.path.isfile(ref_mask_path):
make_symlink(ref_mask_path, mask_path)
def run(self, *user_flags):
self.load_modules()
f_out = open(self.stdout_fname, 'w')
f_err = open(self.stderr_fname, 'w')
# Set MPI environment variables
env = self.config.get('env')
# Explicitly check for `None`, in case of an empty `env:` entry
if env is None:
env = {}
for var in env:
if env[var] is None:
env_value = ''
else:
env_value = str(env[var])
os.environ[var] = env_value
mpi_config = self.config.get('mpi', {})
mpi_runcmd = mpi_config.get('runcmd', 'mpirun')
if self.config.get('scalasca', False):
mpi_runcmd = ' '.join(['scalasca -analyze', mpi_runcmd])
# MPI runtime flags
mpi_flags = mpi_config.get('flags', [])
if not mpi_flags:
mpi_flags = self.config.get('mpirun', [])
# TODO: Legacy config removal warning
if type(mpi_flags) != list:
mpi_flags = [mpi_flags]
# TODO: More uniform support needed here
if self.config.get('scalasca', False):
mpi_flags = ['\"{}\"'.format(f) for f in mpi_flags]
# XXX: I think this may be broken
if user_flags:
mpi_flags.extend(list(user_flags))
if self.debug:
mpi_flags.append('--debug')
mpi_progs = []
for model in self.models:
# Skip models without executables (e.g. couplers)
if not model.exec_path:
continue
mpi_config = self.config.get('mpi', {})
mpi_module = mpi_config.get('module', None)
# Update MPI library module (if not explicitly set)
# TODO: Check for MPI library mismatch across multiple binaries
if mpi_module is None:
mpi_module = envmod.lib_update(model.exec_path, 'libmpi.so')
model_prog = []
# Our MPICH wrapper does not support a working directory flag
if not mpi_module.startswith('mvapich'):
model_prog.append('-wdir {}'.format(model.work_path))
# Append any model-specific MPI flags
model_flags = model.config.get('mpiflags', [])
if not isinstance(model_flags, list):
model_prog.append(model_flags)
else:
model_prog.extend(model_flags)
model_ncpus = model.config.get('ncpus')
if model_ncpus:
model_prog.append('-np {}'.format(model_ncpus))
model_npernode = model.config.get('npernode')
# TODO: New Open MPI format?
if model_npernode:
if model_npernode % 2 == 0:
npernode_flag = ('-map-by ppr:{}:socket'
''.format(model_npernode / 2))
else:
npernode_flag = ('-map-by ppr:{}:node'
''.format(model_npernode))
if self.config.get('scalasca', False):
npernode_flag = '\"{}\"'.format(npernode_flag)
model_prog.append(npernode_flag)
if self.config.get('hpctoolkit', False):
os.environ['HPCRUN_EVENT_LIST'] = 'WALLCLOCK@5000'
model_prog.append('hpcrun')
for prof in self.profilers:
if prof.runscript:
model_prog = model_prog.append(prof.runscript)
model_prog.append(model.exec_prefix)
model_prog.append(model.exec_path)
mpi_progs.append(' '.join(model_prog))
cmd = '{} {} {}'.format(mpi_runcmd, ' '.join(mpi_flags),
' : '.join(mpi_progs))
for prof in self.profilers:
cmd = prof.wrapper(cmd)
# Expand shell variables inside flags
if self.expand_shell_vars:
cmd = os.path.expandvars(cmd)
print(cmd)
# Our MVAPICH wrapper does not support working directories
if mpi_module.startswith('mvapich'):
curdir = os.getcwd()
os.chdir(self.work_path)
else:
curdir = None
# NOTE: This may not be necessary, since env seems to be getting
# correctly updated. Need to look into this.
if env:
# TODO: Replace with mpirun -x flag inputs
proc = sp.Popen(shlex.split(cmd),
stdout=f_out,
stderr=f_err,
env=os.environ.copy())
proc.wait()
rc = proc.returncode
else:
rc = sp.call(shlex.split(cmd), stdout=f_out, stderr=f_err)
# Return to control directory
if curdir:
os.chdir(curdir)
if self.runlog:
self.runlog.commit()
f_out.close()
f_err.close()
# Remove any empty output files (e.g. logs)
for fname in os.listdir(self.work_path):
fpath = os.path.join(self.work_path, fname)
if os.path.getsize(fpath) == 0:
os.remove(fpath)
# Clean up any profiling output
# TODO: Move after `rc` code check?
for prof in self.profilers:
prof.postprocess()
# TODO: Need a model-specific cleanup method call here
# NOTE: This does not appear to catch hanging jobs killed by PBS
if rc != 0:
# Backup logs for failed runs
error_log_dir = os.path.join(self.archive_path, 'error_logs')
mkdir_p(error_log_dir)
# NOTE: This is PBS-specific
job_id = os.environ.get('PBS_JOBID', '')
for fname in (self.stdout_fname, self.stderr_fname):
src = os.path.join(self.control_path, fname)
# NOTE: This assumes standard .out/.err extensions
dest = os.path.join(error_log_dir,
fname[:-4] + '.' + job_id + fname[-4:])
print(src, dest)
shutil.copyfile(src, dest)
# Create the symlink to the logs if it does not exist
make_symlink(self.archive_path, self.archive_sym_path)
# Terminate payu
sys.exit('payu: Model exited with error code {}; aborting.'
''.format(rc))
# Decrement run counter on successful run
stop_file_path = os.path.join(self.control_path, 'stop_run')
if os.path.isfile(stop_file_path):
assert os.stat(stop_file_path).st_size == 0
os.remove(stop_file_path)
print('payu: Stop file detected; terminating resubmission.')
self.n_runs = 0
else:
self.n_runs -= 1
# Move logs to archive (or delete if empty)
for f in (self.stdout_fname, self.stderr_fname):
f_path = os.path.join(self.control_path, f)
if os.path.getsize(f_path) == 0:
os.remove(f_path)
else:
shutil.move(f_path, self.work_path)
run_script = self.userscripts.get('run')
if run_script:
self.run_userscript(run_script)
def archive(self):
if not self.config.get('archive', True):
print('payu: not archiving due to config.yaml setting.')
return
# Check there is a work directory, otherwise bail
if not os.path.exists(self.work_sym_path):
sys.exit('payu: error: No work directory to archive.')
mkdir_p(self.archive_path)
make_symlink(self.archive_path, self.archive_sym_path)
# Remove work symlink
if os.path.islink(self.work_sym_path):
os.remove(self.work_sym_path)
mkdir_p(self.restart_path)
for model in self.models:
model.archive()
# Postprocess the model suite
if len(self.models) > 1:
self.model.archive()
# Double-check that the run path does not exist
if os.path.exists(self.output_path):
sys.exit('payu: error: Output path already exists.')
cmd = 'mv {work} {output}'.format(
work=self.work_path,
output=self.output_path
)
sp.check_call(shlex.split(cmd))
# Remove old restart files
# TODO: Move to subroutine
restart_freq = self.config.get('restart_freq', default_restart_freq)
restart_history = self.config.get('restart_history',
default_restart_history)
# Remove any outdated restart files
prior_restart_dirs = [d for d in os.listdir(self.archive_path)
if d.startswith('restart')]
for res_dir in prior_restart_dirs:
res_idx = int(res_dir.lstrip('restart'))
if (self.repeat_run or
(not res_idx % restart_freq == 0 and
res_idx <= (self.counter - restart_history))):
res_path = os.path.join(self.archive_path, res_dir)
# Only delete real directories; ignore symbolic restart links
if os.path.isdir(res_path):
shutil.rmtree(res_path)
collate_config = self.config.get('collate', {})
if collate_config.get('enable', True):
cmd = '{python} {payu} collate -i {expt}'.format(
python=sys.executable,
payu=self.payu_path,
expt=self.counter
)
sp.check_call(shlex.split(cmd))
if self.config.get('hpctoolkit', False):
cmd = '{python} {payu} profile -i {expt}'.format(
python=sys.executable,
payu=self.payu_path,
expt=self.counter
)
sp.check_call(shlex.split(cmd))
archive_script = self.userscripts.get('archive')
if archive_script:
self.run_userscript(archive_script)
def github_setup(self):
"""Set up authentication keys and API tokens."""
github_auth = self.authenticate()
github_username = github_auth[0]
expt_name = self.config.get('name', self.expt.name)
expt_description = self.expt.config.get('description')
if not expt_description:
expt_description = input('Briefly describe the experiment: ')
assert isinstance(expt_description, str)
expt_private = self.config.get('private', False)
# 1. Create the organisation if needed
github_api_url = 'https://api.github.com'
org_name = self.config.get('organization')
if org_name:
repo_target = org_name
# Check if org exists
org_query_url = os.path.join(github_api_url, 'orgs', org_name)
org_req = requests.get(org_query_url)
if org_req.status_code == 404:
# NOTE: Orgs cannot be created via the API
print('payu: github organization {org} does not exist.'
''.format(org=org_name))
print(' You must first create this on the website.')
elif org_req.status_code == 200:
# TODO: Confirm that the user can interact with the repo
pass
else:
# TODO: Exit with grace
print('payu: abort!')
sys.exit(-1)
repo_query_url = os.path.join(github_api_url, 'orgs', org_name,
'repos')
repo_api_url = os.path.join(github_api_url, 'repos', org_name,
expt_name)
else:
repo_target = github_username
# Create repo in user account
repo_query_url = os.path.join(github_api_url, 'user', 'repos')
repo_api_url = os.path.join(github_api_url, 'repos',
github_username, expt_name)
# 2. Create the remote repository
user_repos = []
page = 1
while True:
repo_params = {'page': page, 'per_page': 100}
repo_query = requests.get(repo_query_url, auth=github_auth,
params=repo_params)
assert repo_query.status_code == 200
if repo_query.json():
user_repos.extend(list(r['name'] for r in repo_query.json()))
page += 1
else:
break
if expt_name not in user_repos:
repo_config = {
'name': expt_name,
'description': expt_description,
'private': expt_private,
'has_issues': True,
'has_downloads': True,
'has_wiki': False
}
repo_gen = requests.post(repo_query_url, json.dumps(repo_config),
auth=github_auth)
assert repo_gen.status_code == 201
# 3. Check if remote is set
git_remote_out = sp.check_output(shlex.split('git remote -v'),
cwd=self.expt.control_path)
git_remotes = dict([(r.split()[0], r.split()[1])
for r in git_remote_out.split('\n') if r])
remote_name = self.config.get('remote', 'payu')
remote_url = os.path.join('ssh://[email protected]', repo_target,
self.expt.name + '.git')
if remote_name not in git_remotes:
cmd = ('git remote add {name} {url}'
''.format(name=remote_name, url=remote_url))
sp.check_call(shlex.split(cmd), cwd=self.expt.control_path)
elif git_remotes[remote_name] != remote_url:
print('payu: error: Existing remote URL does not match '
'the proposed URL.')
print('payu: error: To delete the old remote, type '
'`git remote rm {name}`.'.format(name=remote_name))
sys.exit(-1)
# 4. Generate a payu-specific SSH key
default_ssh_key = 'id_rsa_payu_' + expt_name
ssh_key = self.config.get('sshid', default_ssh_key)
ssh_dir = os.path.join(os.path.expanduser('~'), '.ssh', 'payu')
mkdir_p(ssh_dir)
ssh_keypath = os.path.join(ssh_dir, ssh_key)
if not os.path.isfile(ssh_keypath):
cmd = 'ssh-keygen -t rsa -f {key} -q -P ""'.format(key=ssh_key)
sp.check_call(shlex.split(cmd), cwd=ssh_dir)
# 5. Deploy key to repo
with open(ssh_keypath + '.pub') as keyfile:
pubkey = ' '.join(keyfile.read().split()[:-1])
# TODO: Get this from github?
repo_keys_url = os.path.join(repo_api_url, 'keys')
keys_req = requests.get(repo_keys_url, auth=github_auth)
assert keys_req.status_code == 200
if not any(k['key'] == pubkey for k in keys_req.json()):
add_key_param = {'title': 'payu', 'key': pubkey}
add_key_req = requests.post(repo_keys_url, auth=github_auth,
json=add_key_param)
assert add_key_req.status_code == 201
def run(self, *user_flags):
# XXX: This was previously done in reversion
envmod.setup()
self.load_modules()
f_out = open(self.stdout_fname, 'w')
f_err = open(self.stderr_fname, 'w')
# Set MPI environment variables
env = self.config.get('env')
# Explicitly check for `None`, in case of an empty `env:` entry
if env is None:
env = {}
for var in env:
if env[var] is None:
env_value = ''
else:
env_value = str(env[var])
os.environ[var] = env_value
mpi_config = self.config.get('mpi', {})
mpi_runcmd = mpi_config.get('runcmd', 'mpirun')
if self.config.get('scalasca', False):
mpi_runcmd = ' '.join(['scalasca -analyze', mpi_runcmd])
# MPI runtime flags
mpi_flags = mpi_config.get('flags', [])
if not mpi_flags:
mpi_flags = self.config.get('mpirun', [])
# TODO: Legacy config removal warning
if type(mpi_flags) != list:
mpi_flags = [mpi_flags]
# TODO: More uniform support needed here
if self.config.get('scalasca', False):
mpi_flags = ['\"{0}\"'.format(f) for f in mpi_flags]
# XXX: I think this may be broken
if user_flags:
mpi_flags.extend(list(user_flags))
if self.debug:
mpi_flags.append('--debug')
mpi_progs = []
for model in self.models:
# Skip models without executables (e.g. couplers)
if not model.exec_path:
continue
mpi_config = self.config.get('mpi', {})
mpi_module = mpi_config.get('module', None)
# Update MPI library module (if not explicitly set)
# TODO: Check for MPI library mismatch across multiple binaries
if mpi_module is None:
mpi_module = envmod.lib_update(model.exec_path, 'libmpi.so')
model_prog = []
# Our MPICH wrapper does not support a working directory flag
if not mpi_module.startswith('mvapich'):
model_prog.append('-wdir {0}'.format(model.work_path))
# Append any model-specific MPI flags
model_flags = model.config.get('mpiflags', [])
if not isinstance(model_flags, list):
model_prog.append(model_flags)
else:
model_prog.extend(model_flags)
model_ncpus = model.config.get('ncpus')
if model_ncpus:
model_prog.append('-np {0}'.format(model_ncpus))
model_npernode = model.config.get('npernode')
# TODO: New Open MPI format?
if model_npernode:
if model_npernode % 2 == 0:
npernode_flag = ('-map-by ppr:{0}:socket'
''.format(model_npernode / 2))
else:
npernode_flag = ('-map-by ppr:{0}:node'
''.format(model_npernode))
if self.config.get('scalasca', False):
npernode_flag = '\"{0}\"'.format(npernode_flag)
model_prog.append(npernode_flag)
if self.config.get('hpctoolkit', False):
os.environ['HPCRUN_EVENT_LIST'] = 'WALLCLOCK@5000'
model_prog.append('hpcrun')
for prof in self.profilers:
if prof.runscript:
model_prog = model_prog.append(prof.runscript)
model_prog.append(model.exec_prefix)
model_prog.append(model.exec_path)
mpi_progs.append(' '.join(model_prog))
cmd = '{runcmd} {flags} {exes}'.format(
runcmd=mpi_runcmd,
flags=' '.join(mpi_flags),
exes=' : '.join(mpi_progs)
)
for prof in self.profilers:
cmd = prof.wrapper(cmd)
# Expand shell variables inside flags
if self.expand_shell_vars:
cmd = os.path.expandvars(cmd)
print(cmd)
# Our MVAPICH wrapper does not support working directories
if mpi_module.startswith('mvapich'):
curdir = os.getcwd()
os.chdir(self.work_path)
else:
curdir = None
# NOTE: This may not be necessary, since env seems to be getting
# correctly updated. Need to look into this.
if env:
# TODO: Replace with mpirun -x flag inputs
proc = sp.Popen(shlex.split(cmd), stdout=f_out, stderr=f_err,
env=os.environ.copy())
proc.wait()
rc = proc.returncode
else:
rc = sp.call(shlex.split(cmd), stdout=f_out, stderr=f_err)
# Return to control directory
if curdir:
os.chdir(curdir)
if self.runlog:
self.runlog.commit()
f_out.close()
f_err.close()
# Remove any empty output files (e.g. logs)
for fname in os.listdir(self.work_path):
fpath = os.path.join(self.work_path, fname)
if os.path.getsize(fpath) == 0:
os.remove(fpath)
# Clean up any profiling output
# TODO: Move after `rc` code check?
for prof in self.profilers:
prof.postprocess()
# TODO: Need a model-specific cleanup method call here
# NOTE: This does not appear to catch hanging jobs killed by PBS
if rc != 0:
# Backup logs for failed runs
error_log_dir = os.path.join(self.archive_path, 'error_logs')
mkdir_p(error_log_dir)
# NOTE: This is PBS-specific
job_id = os.environ.get('PBS_JOBID', '')
for fname in (self.stdout_fname, self.stderr_fname):
src = os.path.join(self.control_path, fname)
# NOTE: This assumes standard .out/.err extensions
dest = os.path.join(error_log_dir,
fname[:-4] + '.' + job_id + fname[-4:])
print(src, dest)
shutil.copyfile(src, dest)
# Create the symlink to the logs if it does not exist
make_symlink(self.archive_path, self.archive_sym_path)
# Terminate payu
sys.exit('payu: Model exited with error code {0}; aborting.'
''.format(rc))
# Decrement run counter on successful run
stop_file_path = os.path.join(self.control_path, 'stop_run')
if os.path.isfile(stop_file_path):
assert os.stat(stop_file_path).st_size == 0
os.remove(stop_file_path)
print('payu: Stop file detected; terminating resubmission.')
self.n_runs = 0
else:
self.n_runs -= 1
# Move logs to archive (or delete if empty)
for f in (self.stdout_fname, self.stderr_fname):
f_path = os.path.join(self.control_path, f)
if os.path.getsize(f_path) == 0:
os.remove(f_path)
else:
shutil.move(f_path, self.work_path)
run_script = self.userscripts.get('run')
if run_script:
self.run_userscript(run_script)
def github_setup(self):
"""Set up authentication keys and API tokens."""
github_auth = self.authenticate()
github_username = github_auth[0]
expt_name = self.config.get('name', self.expt.name)
expt_description = self.expt.config.get('description')
if not expt_description:
expt_description = input('Briefly describe the experiment: ')
assert isinstance(expt_description, str)
expt_private = self.config.get('private', False)
# 1. Create the organisation if needed
github_api_url = 'https://api.github.com'
org_name = self.config.get('organization')
if org_name:
repo_target = org_name
# Check if org exists
org_query_url = os.path.join(github_api_url, 'orgs', org_name)
org_req = requests.get(org_query_url)
if org_req.status_code == 404:
# NOTE: Orgs cannot be created via the API
print('payu: github organization {org} does not exist.'
''.format(org=org_name))
print(' You must first create this on the website.')
elif org_req.status_code == 200:
# TODO: Confirm that the user can interact with the repo
pass
else:
# TODO: Exit with grace
print('payu: abort!')
sys.exit(-1)
repo_query_url = os.path.join(github_api_url, 'orgs', org_name,
'repos')
repo_api_url = os.path.join(github_api_url, 'repos', org_name,
expt_name)
else:
repo_target = github_username
# Create repo in user account
repo_query_url = os.path.join(github_api_url, 'user', 'repos')
repo_api_url = os.path.join(github_api_url, 'repos',
github_username, expt_name)
# 2. Create the remote repository
user_repos = []
page = 1
while True:
repo_params = {'page': page, 'per_page': 100}
repo_query = requests.get(repo_query_url,
auth=github_auth,
params=repo_params)
assert repo_query.status_code == 200
if repo_query.json():
user_repos.extend(list(r['name'] for r in repo_query.json()))
page += 1
else:
break
if expt_name not in user_repos:
repo_config = {
'name': expt_name,
'description': expt_description,
'private': expt_private,
'has_issues': True,
'has_downloads': True,
'has_wiki': False
}
repo_gen = requests.post(repo_query_url,
json.dumps(repo_config),
auth=github_auth)
assert repo_gen.status_code == 201
# 3. Check if remote is set
git_remote_out = sp.check_output(shlex.split('git remote -v'),
cwd=self.expt.control_path)
git_remotes = dict([(r.split()[0], r.split()[1])
for r in git_remote_out.split('\n') if r])
remote_name = self.config.get('remote', 'payu')
remote_url = os.path.join('ssh://[email protected]', repo_target,
self.expt.name + '.git')
if remote_name not in git_remotes:
cmd = ('git remote add {name} {url}'
''.format(name=remote_name, url=remote_url))
sp.check_call(shlex.split(cmd), cwd=self.expt.control_path)
elif git_remotes[remote_name] != remote_url:
print('payu: error: Existing remote URL does not match '
'the proposed URL.')
print('payu: error: To delete the old remote, type '
'`git remote rm {name}`.'.format(name=remote_name))
sys.exit(-1)
# 4. Generate a payu-specific SSH key
default_ssh_key = 'id_rsa_payu_' + expt_name
ssh_key = self.config.get('sshid', default_ssh_key)
ssh_dir = os.path.join(os.path.expanduser('~'), '.ssh', 'payu')
mkdir_p(ssh_dir)
ssh_keypath = os.path.join(ssh_dir, ssh_key)
if not os.path.isfile(ssh_keypath):
cmd = 'ssh-keygen -t rsa -f {key} -q -P ""'.format(key=ssh_key)
sp.check_call(shlex.split(cmd), cwd=ssh_dir)
# 5. Deploy key to repo
with open(ssh_keypath + '.pub') as keyfile:
pubkey = ' '.join(keyfile.read().split()[:-1])
# TODO: Get this from github?
repo_keys_url = os.path.join(repo_api_url, 'keys')
keys_req = requests.get(repo_keys_url, auth=github_auth)
assert keys_req.status_code == 200
if not any(k['key'] == pubkey for k in keys_req.json()):
add_key_param = {'title': 'payu', 'key': pubkey}
add_key_req = requests.post(repo_keys_url,
auth=github_auth,
json=add_key_param)
assert add_key_req.status_code == 201
def archive(self):
if not self.config.get('archive', True):
print('payu: not archiving due to config.yaml setting.')
return
# Check there is a work directory, otherwise bail
if not os.path.exists(self.work_sym_path):
sys.exit('payu: error: No work directory to archive.')
mkdir_p(self.archive_path)
make_symlink(self.archive_path, self.archive_sym_path)
# Remove work symlink
if os.path.islink(self.work_sym_path):
os.remove(self.work_sym_path)
mkdir_p(self.restart_path)
for model in self.models:
model.archive()
# Postprocess the model suite
if len(self.models) > 1:
self.model.archive()
# Double-check that the run path does not exist
if os.path.exists(self.output_path):
sys.exit('payu: error: Output path already exists.')
movetree(self.work_path, self.output_path)
# Remove old restart files
# TODO: Move to subroutine
restart_freq = self.config.get('restart_freq', default_restart_freq)
restart_history = self.config.get('restart_history',
default_restart_history)
# Remove any outdated restart files
prior_restart_dirs = [d for d in os.listdir(self.archive_path)
if d.startswith('restart')]
for res_dir in prior_restart_dirs:
res_idx = int(res_dir.lstrip('restart'))
if (self.repeat_run or
(not res_idx % restart_freq == 0 and
res_idx <= (self.counter - restart_history))):
res_path = os.path.join(self.archive_path, res_dir)
# Only delete real directories; ignore symbolic restart links
if (os.path.isdir(res_path) and not os.path.islink(res_path)):
shutil.rmtree(res_path)
# Ensure dynamic library support for subsequent python calls
ld_libpaths = os.environ['LD_LIBRARY_PATH']
py_libpath = sysconfig.get_config_var('LIBDIR')
if py_libpath not in ld_libpaths.split(':'):
os.environ['LD_LIBRARY_PATH'] = ':'.join([py_libpath, ld_libpaths])
collate_config = self.config.get('collate', {})
if collate_config.get('enable', True):
cmd = '{python} {payu} collate -i {expt}'.format(
python=sys.executable,
payu=self.payu_path,
expt=self.counter
)
sp.check_call(shlex.split(cmd))
if self.config.get('hpctoolkit', False):
cmd = '{python} {payu} profile -i {expt}'.format(
python=sys.executable,
payu=self.payu_path,
expt=self.counter
)
sp.check_call(shlex.split(cmd))
archive_script = self.userscripts.get('archive')
if archive_script:
self.run_userscript(archive_script)
def run(self, *user_flags):
# XXX: This was previously done in reversion
envmod.setup()
self.load_modules()
f_out = open(self.stdout_fname, 'w')
f_err = open(self.stderr_fname, 'w')
# Set MPI environment variables
env = self.config.get('env')
# Explicitly check for `None`, in case of an empty `env:` entry
if env is None:
env = {}
for var in env:
if env[var] is None:
env_value = ''
else:
env_value = str(env[var])
os.environ[var] = env_value
mpi_config = self.config.get('mpi', {})
mpi_runcmd = mpi_config.get('runcmd', 'mpirun')
if self.config.get('scalasca', False):
mpi_runcmd = ' '.join(['scalasca -analyze', mpi_runcmd])
# MPI runtime flags
mpi_flags = mpi_config.get('flags', [])
if not mpi_flags:
mpi_flags = self.config.get('mpirun', [])
# TODO: Legacy config removal warning
if type(mpi_flags) != list:
mpi_flags = [mpi_flags]
# TODO: More uniform support needed here
if self.config.get('scalasca', False):
mpi_flags = ['\"{0}\"'.format(f) for f in mpi_flags]
# XXX: I think this may be broken
if user_flags:
mpi_flags.extend(list(user_flags))
if self.debug:
mpi_flags.append('--debug')
mpi_progs = []
for model in self.models:
# Skip models without executables (e.g. couplers)
if not model.exec_path_local:
continue
mpi_config = self.config.get('mpi', {})
mpi_module = mpi_config.get('module', None)
# Update MPI library module (if not explicitly set)
# TODO: Check for MPI library mismatch across multiple binaries
if mpi_module is None:
mpi_module = envmod.lib_update(
model.exec_path_local,
'libmpi.so'
)
model_prog = []
# Our MPICH wrapper does not support a working directory flag
if not mpi_module.startswith('mvapich'):
model_prog.append('-wdir {0}'.format(model.work_path))
# Append any model-specific MPI flags
model_flags = model.config.get('mpiflags', [])
if not isinstance(model_flags, list):
model_prog.append(model_flags)
else:
model_prog.extend(model_flags)
model_ncpus = model.config.get('ncpus')
if model_ncpus:
model_prog.append('-np {0}'.format(model_ncpus))
model_npernode = model.config.get('npernode')
# TODO: New Open MPI format?
if model_npernode:
if model_npernode % 2 == 0:
npernode_flag = ('-map-by ppr:{0}:socket'
''.format(model_npernode / 2))
else:
npernode_flag = ('-map-by ppr:{0}:node'
''.format(model_npernode))
if self.config.get('scalasca', False):
npernode_flag = '\"{0}\"'.format(npernode_flag)
model_prog.append(npernode_flag)
if self.config.get('hpctoolkit', False):
os.environ['HPCRUN_EVENT_LIST'] = 'WALLCLOCK@5000'
model_prog.append('hpcrun')
for prof in self.profilers:
if prof.runscript:
model_prog = model_prog.append(prof.runscript)
model_prog.append(model.exec_prefix)
# Use the full path to symlinked exec_name in work as some
# older MPI libraries complained executable was not in PATH
model_prog.append(os.path.join(model.work_path, model.exec_name))
mpi_progs.append(' '.join(model_prog))
cmd = '{runcmd} {flags} {exes}'.format(
runcmd=mpi_runcmd,
flags=' '.join(mpi_flags),
exes=' : '.join(mpi_progs)
)
for prof in self.profilers:
cmd = prof.wrapper(cmd)
# Expand shell variables inside flags
if self.expand_shell_vars:
cmd = os.path.expandvars(cmd)
# TODO: Consider making this default
if self.config.get('coredump', False):
enable_core_dump()
# Our MVAPICH wrapper does not support working directories
if mpi_module.startswith('mvapich'):
curdir = os.getcwd()
os.chdir(self.work_path)
else:
curdir = None
# Dump out environment
with open(self.env_fname, 'w') as file:
file.write(yaml.dump(dict(os.environ), default_flow_style=False))
self.runlog.create_manifest()
if self.runlog.enabled:
self.runlog.commit()
# NOTE: This may not be necessary, since env seems to be getting
# correctly updated. Need to look into this.
print(cmd)
if env:
# TODO: Replace with mpirun -x flag inputs
proc = sp.Popen(shlex.split(cmd), stdout=f_out, stderr=f_err,
env=os.environ.copy())
proc.wait()
rc = proc.returncode
else:
rc = sp.call(shlex.split(cmd), stdout=f_out, stderr=f_err)
# Return to control directory
if curdir:
os.chdir(curdir)
f_out.close()
f_err.close()
self.finish_time = datetime.datetime.now()
info = get_job_info()
if info is None:
# Not being run under PBS, reverse engineer environment
info = {
'PAYU_PATH': os.path.dirname(self.payu_path)
}
# Add extra information to save to jobinfo
info.update(
{
'PAYU_CONTROL_DIR': self.control_path,
'PAYU_RUN_ID': self.run_id,
'PAYU_CURRENT_RUN': self.counter,
'PAYU_N_RUNS': self.n_runs,
'PAYU_JOB_STATUS': rc,
'PAYU_START_TIME': self.start_time.isoformat(),
'PAYU_FINISH_TIME': self.finish_time.isoformat(),
'PAYU_WALLTIME': "{0} s".format(
(self.finish_time - self.start_time).total_seconds()
),
}
)
# Dump job info
with open(self.job_fname, 'w') as file:
file.write(yaml.dump(info, default_flow_style=False))
# Remove any empty output files (e.g. logs)
for fname in os.listdir(self.work_path):
fpath = os.path.join(self.work_path, fname)
if os.path.getsize(fpath) == 0:
os.remove(fpath)
# Clean up any profiling output
# TODO: Move after `rc` code check?
for prof in self.profilers:
prof.postprocess()
# TODO: Need a model-specific cleanup method call here
# NOTE: This does not appear to catch hanging jobs killed by PBS
if rc != 0:
# Backup logs for failed runs
error_log_dir = os.path.join(self.archive_path, 'error_logs')
mkdir_p(error_log_dir)
# NOTE: This is PBS-specific
job_id = get_job_id(short=False)
if job_id == '':
job_id = str(self.run_id)[:6]
for fname in self.output_fnames:
src = os.path.join(self.control_path, fname)
stem, suffix = os.path.splitext(fname)
dest = os.path.join(error_log_dir,
".".join((stem, job_id)) + suffix)
print(src, dest)
shutil.copyfile(src, dest)
# Create the symlink to the logs if it does not exist
make_symlink(self.archive_path, self.archive_sym_path)
error_script = self.userscripts.get('error')
if error_script:
self.run_userscript(error_script)
# Terminate payu
sys.exit('payu: Model exited with error code {0}; aborting.'
''.format(rc))
# Decrement run counter on successful run
stop_file_path = os.path.join(self.control_path, 'stop_run')
if os.path.isfile(stop_file_path):
assert os.stat(stop_file_path).st_size == 0
os.remove(stop_file_path)
print('payu: Stop file detected; terminating resubmission.')
self.n_runs = 0
else:
self.n_runs -= 1
# Move logs to archive (or delete if empty)
for f in self.output_fnames:
f_path = os.path.join(self.control_path, f)
if os.path.getsize(f_path) == 0:
os.remove(f_path)
else:
shutil.move(f_path, self.work_path)
run_script = self.userscripts.get('run')
if run_script:
self.run_userscript(run_script)
def setup(self):
super(Cice5, self).setup()
# Make log dir
mkdir_p(os.path.join(self.work_path, 'log'))