From ca0cda9b9973dd51cc4b2a2da0247bfa43d0f098 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Wed, 10 Jun 2020 13:32:41 -0500
Subject: [PATCH] Removed os.sync() lines prior to running arbd/oxDNA
simulations because they can hang indefinitely; needs testing
---
mrdna/arbdmodel/__init__.py | 9 ++++++---
mrdna/segmentmodel.py | 3 ++-
2 files changed, 8 insertions(+), 4 deletions(-)
diff --git a/mrdna/arbdmodel/__init__.py b/mrdna/arbdmodel/__init__.py
index b5d894b..63d0397 100644
--- a/mrdna/arbdmodel/__init__.py
+++ b/mrdna/arbdmodel/__init__.py
@@ -815,7 +815,7 @@ class ArbdModel(PdbModel):
self.writePdb( output_name + ".pdb" )
self.writePsf( output_name + ".psf" )
self.writeArbdFiles( output_name, numSteps=num_steps, outputPeriod=output_period, restart_file=restart_file )
- os.sync()
+ # os.sync()
## http://stackoverflow.com/questions/18421757/live-output-from-subprocess-command
@@ -833,7 +833,10 @@ class ArbdModel(PdbModel):
fd = sys.stdout if log_file is None else log_file
process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
for line in process.stdout:
- fd.write(line)
+ try:
+ fd.write(line)
+ except:
+ print("WARNING: could not encode line; your locale might not be set correctly")
fd.flush()
else:
with open(log_file,'w') as fd:
@@ -1339,7 +1342,7 @@ run {num_steps:d}
self.writePdb( output_name + ".fixed.pdb", beta_from_fixed=True )
self.writePsf( output_name + ".psf" )
self.write_namd_configuration( output_name, output_directory = output_directory )
- os.sync()
+ # os.sync()
if not dry_run:
if namd2 is None:
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index 54a0b82..7a56362 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -1,4 +1,5 @@
import pdb
+import subprocess
from pathlib import Path
import numpy as np
import random
@@ -3803,7 +3804,7 @@ external_forces = 0
last_conf_file = last_conf_file,
log_file="{}/{}.log".format(output_directory,output_name),
**oxdna_args)
- os.sync()
+ # os.sync()
## TODO: call oxdna
cmd = [oxDNA, input_file]
--
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