Merge pull request #91 from OpenBioSim/fix_90

Fix issue #90

Author: lohedges

src/somd2/runner/_runner.py

@@ -631,6 +631,9 @@ def generate_lam_vals(lambda_base, increment=0.001):
         # Store the checkpoint time in nanoseconds.
         checkpoint_interval = self._config.checkpoint_frequency.to("ns")
 
+        # Store the start time.
+        start = _timer()
+
         # Run the simulation, checkpointing in blocks.
         if self._config.checkpoint_frequency.value() > 0.0:
 
@@ -645,9 +648,6 @@ def generate_lam_vals(lambda_base, increment=0.001):
             num_blocks = int(frac)
             rem = round(frac - num_blocks, 12)
 
-            # Store the star time.
-            start = _timer()
-
             # Run the dynamics in blocks.
             for block in range(int(num_blocks)):
                 # Add the start block number.
@@ -938,6 +938,9 @@ def generate_lam_vals(lambda_base, increment=0.001):
             # Calculate the speed in nanoseconds per day.
             speed = time.to("ns") / days
 
+            # Create the lock.
+            lock = _FileLock(self._lock_file)
+
             # Acquire the file lock to ensure that the checkpoint files are
             # in a consistent state if read by another process.
             with lock.acquire(timeout=self._config.timeout.to("seconds")):