From ebc16a360f8ef11578d42588d871195c16aa0997 Mon Sep 17 00:00:00 2001
From: "Mads M. Pedersen" <mmpe@dtu.dk>
Date: Wed, 19 Oct 2016 10:08:44 +0200
Subject: [PATCH] bug fix in hawc2.simulation
---
wetb/hawc2/simulation.py | 21 +++++++++++++--------
1 file changed, 13 insertions(+), 8 deletions(-)
diff --git a/wetb/hawc2/simulation.py b/wetb/hawc2/simulation.py
index c25b0807..b53acd1a 100755
--- a/wetb/hawc2/simulation.py
+++ b/wetb/hawc2/simulation.py
@@ -86,7 +86,7 @@ class Simulation(object):
if not os.path.isabs(htcfilename):
htcfilename = os.path.join(modelpath, htcfilename)
self.filename = os.path.basename(htcfilename)
- self.htcFile = HTCFile(htcfilename)
+ self.htcFile = HTCFile(htcfilename, os.path.relpath(self.modelpath,os.path.dirname(htcfilename)))
self.time_stop = self.htcFile.simulation.time_stop[0]
self.hawc2exe = hawc2exe
self.copy_turbulence = copy_turbulence
@@ -127,7 +127,7 @@ class Simulation(object):
def abort(self, update_status=True):
if self.status != QUEUED:
self.host.stop()
- for _ in range(100):
+ for _ in range(50):
if self.is_simulating is False:
break
time.sleep(0.1)
@@ -175,7 +175,7 @@ class Simulation(object):
src = os.path.relpath (src)
assert not src.startswith(".."), "%s referes to a file outside the model path\nAll input files be inside model path" % src
return src
- input_patterns = [fmt(src) for src in self.htcFile.input_files() + self.htcFile.turbulence_files() + self.additional_files().get('input', [])]
+ input_patterns = [fmt(src) for src in self.htcFile.input_files() + ([], self.htcFile.turbulence_files())[self.copy_turbulence] + self.additional_files().get('input', [])]
input_files = set([f for pattern in input_patterns for f in glob.glob(os.path.join(self.modelpath, pattern)) if os.path.isfile(f)])
if not os.path.isdir(os.path.dirname(self.modelpath + self.stdout_filename)):
os.makedirs(os.path.dirname(self.modelpath + self.stdout_filename))
@@ -435,7 +435,6 @@ class LocalSimulationHost(SimulationResource):
self.logFile.update_status()
def stop(self):
- if self.simulationThread.is_alive():
self.simulationThread.stop()
self.simulationThread.join()
@@ -466,7 +465,8 @@ class SimulationThread(Thread):
with open (os.path.join(self.modelpath, stdout), 'wb') as stdout:
if isinstance(hawc2exe, tuple):
- self.process = subprocess.Popen(list(hawc2exe + (htcfile, stdout)), stdout=stdout, stderr=STDOUT, shell=False, cwd=modelpath)
+ wine, hawc2exe = hawc2exe
+ self.process = subprocess.Popen([wine, hawc2exe, htcfile], stdout=stdout, stderr=STDOUT, shell=True, cwd=modelpath) #shell must be True to inwoke wine
else:
self.process = subprocess.Popen([hawc2exe, htcfile], stdout=stdout, stderr=STDOUT, shell=False, cwd=modelpath) #, creationflags=CREATE_NO_WINDOW)
self.process.communicate()
@@ -506,7 +506,7 @@ class SimulationThread(Thread):
def stop(self):
if hasattr(self, 'process'):
subprocess.Popen("TASKKILL /F /PID {pid} /T".format(pid=self.process.pid))
-
+
class PBSClusterSimulationHost(SimulationResource, SSHClient):
def __init__(self, simulation, resource, host, username, password, port=22):
@@ -649,7 +649,7 @@ class PBSClusterSimulationHost(SimulationResource, SSHClient):
#PBS -j oe
#PBS -o %s
### Maximum wallclock time format HOURS:MINUTES:SECONDS
-#PBS -l walltime=01:00:00
+#PBS -l walltime=04:00:00
###PBS -a 201547.53
#PBS -lnodes=1:ppn=1
### Queue name
@@ -661,6 +661,11 @@ cp -R . /scratch/$USER/$PBS_JOBID
### Execute commands on scratch nodes
cd /scratch/$USER/$PBS_JOBID
pwd
+export PATH=/home/python/miniconda3/bin:$PATH
+source activate wetb_py3
+WINEARCH=win32 WINEPREFIX=~/.wine32 winefix
+### modelpath: %s
+### htc: %s
echo "---------------------"
%s -c "from wetb.hawc2.cluster_simulation import ClusterSimulation;ClusterSimulation('.','%s', ('%s','%s'))"
echo "---------------------"
@@ -672,7 +677,7 @@ cd /scratch/$USER/$PBS_JOBID
echo $PBS_JOBID
cd /scratch/
### rm -r $PBS_JOBID
-exit""" % (self.simulation_id, self.stdout_filename, self.resource.python_cmd, rel_htcfilename, self.resource.wine_cmd, self.hawc2exe, cp_back)
+exit""" % (self.simulation_id, self.stdout_filename, self.modelpath, self.htcFile.filename, self.resource.python_cmd, rel_htcfilename, self.resource.wine_cmd, self.hawc2exe, cp_back)
--
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