From 42bdeed93c38d534589823100f39373fa538de62 Mon Sep 17 00:00:00 2001
From: Bas van Beek <b.f.van.beek@vu.nl>
Date: Thu, 19 Dec 2019 15:45:06 +0100
Subject: [PATCH 1/2] .hdf5 files are now forcibly closed (if necessary) upon
 restarting an ARMC procedure

---
 FOX/classes/armc.py  | 14 +++++++++++++-
 FOX/io/hdf5_utils.py | 17 ++++++++++++++++-
 2 files changed, 29 insertions(+), 2 deletions(-)

diff --git a/FOX/classes/armc.py b/FOX/classes/armc.py
index 54cc900b..84ceee27 100644
--- a/FOX/classes/armc.py
+++ b/FOX/classes/armc.py
@@ -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
@@ -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):
diff --git a/FOX/io/hdf5_utils.py b/FOX/io/hdf5_utils.py
index 078655b1..5afd79ab 100644
--- a/FOX/io/hdf5_utils.py
+++ b/FOX/io/hdf5_utils.py
@@ -42,6 +42,7 @@
 
 """
 
+import subprocess
 from os import remove
 from time import sleep
 from typing import Dict, Iterable, Optional, Union, Hashable, List, Tuple
@@ -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:
@@ -334,7 +346,7 @@ def hdf5_availability(filename: str, timeout: float = 5.0,
 
     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))
@@ -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

From 1d0f0bb1f11022eadd937bfdeaae972e71eada99 Mon Sep 17 00:00:00 2001
From: Bas van Beek <b.f.van.beek@vu.nl>
Date: Thu, 19 Dec 2019 15:46:16 +0100
Subject: [PATCH 2/2] Update hdf5_utils.py

---
 FOX/io/hdf5_utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/FOX/io/hdf5_utils.py b/FOX/io/hdf5_utils.py
index 5afd79ab..b6621281 100644
--- a/FOX/io/hdf5_utils.py
+++ b/FOX/io/hdf5_utils.py
@@ -341,7 +341,7 @@ 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: