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.hdf5 files are now forcibly closed (if necessary) upon restarting ARMC procedures #60

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merged 2 commits into from
Dec 19, 2019
Merged

.hdf5 files are now forcibly closed (if necessary) upon restarting ARMC procedures #60

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42bdeed
.hdf5 files are now forcibly closed (if necessary) upon restarting an…
Dec 19, 2019
1d0f0bb
Update hdf5_utils.py
Dec 19, 2019
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14 changes: 13 additions & 1 deletion FOX/classes/armc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,9 @@

from .monte_carlo import MonteCarlo
from ..logger import Plams2Logger, get_logger
from ..io.hdf5_utils import create_hdf5, to_hdf5, create_xyz_hdf5, _get_filename_xyz
from ..io.hdf5_utils import (
create_hdf5, to_hdf5, create_xyz_hdf5, _get_filename_xyz, hdf5_clear_status
)
from ..io.file_container import NullContext
from ..functions.utils import get_template
from ..armc_functions.sanitization import init_armc_sanitization
Expand Down Expand Up @@ -520,6 +522,16 @@ def restart(self) -> None:
if not os.path.isfile(xyz):
create_xyz_hdf5(self.hdf5_file, self.molecule, iter_len=self.sub_iter_len)

# Check that both .hdf5 files can be opened; clear their status if not
closed = hdf5_clear_status(xyz)
if not closed:
self.logger.warning(f"Unable to open ...{os.sep}{os.path.basename(xyz)}, "
"file status was forcibly reset")
closed = hdf5_clear_status(self.hdf5_file)
if not closed:
self.logger.warning(f"Unable to open ...{os.sep}{os.path.basename(self.hdf5_file)}, "
"file status was forcibly reset")

# Finish the current set of sub-iterations
j += 1
for omega in range(j, self.sub_iter_len):
Expand Down
19 changes: 17 additions & 2 deletions FOX/io/hdf5_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,7 @@

"""

import subprocess
from os import remove
from time import sleep
from typing import Dict, Iterable, Optional, Union, Hashable, List, Tuple
Expand Down Expand Up @@ -300,6 +301,17 @@ def _get_kwarg_dict(armc: 'FOX.ARMC') -> Settings:
"""################################### Updating .hdf5 files ####################################"""


@assert_error(H5PY_ERROR)
def hdf5_clear_status(filename: str) -> bool:
"""Run the :code:`h5clear filename` command if **filename** refuses to open."""
try:
with h5py.File(filename, 'r+', libver='latest'):
return True
except OSError:
subprocess.run(['h5clear', '-s', 'repr(filename)'])
return False


@assert_error(H5PY_ERROR)
def hdf5_availability(filename: str, timeout: float = 5.0,
max_attempts: Optional[int] = 10) -> None:
Expand Down Expand Up @@ -329,12 +341,12 @@ def hdf5_availability(filename: str, timeout: float = 5.0,
Raised if **max_attempts** is exceded.

"""
warning = "OSWarning: '{}' is currently unavailable; repeating attempt in {:.0f} seconds"
warning = "WARNING: '{}' is currently unavailable; repeating attempt in {:.0f} seconds"
i = max_attempts or np.inf

while i:
try:
with h5py.File(filename, 'r+', libver='latest') as _:
with h5py.File(filename, 'r+', libver='latest'):
return # the .hdf5 file can safely be opened
except OSError as ex: # the .hdf5 file cannot be safely opened yet
print((warning).format(filename, timeout))
Expand Down Expand Up @@ -405,6 +417,9 @@ def _xyz_to_hdf5(filename: str, omega: int,
All to-be exported :class:`MultiMolecule` instance(s) or float (*e.g.* ``np.nan``).

"""
# Check if the hdf5 file is already opened. If opened: wait for 5 sec and try again.
hdf5_availability(filename)

with h5py.File(filename, 'r+', libver='latest') as f:
if not isinstance(mol_list, abc.Iterable): # Check if mol_list is a scalar (np.nan)
i = 0
Expand Down