def __init__(self, hawc2_path, hawc2_cmd, htc_file, exe_dir, input_files, output_files, queue='workq', walltime='00:10:00'):
self.hawc2_path = hawc2_path
self.hawc2_cmd = hawc2_cmd
self.htc_file = htc_file
self.exe_dir = exe_dir
self.queue = queue
self.walltime = walltime
if not os.path.isabs(htc_file):
htc_file = pjoin(exe_dir, htc_file)
else:
htc_file = htc_file.replace("\\", "/")
if htc_file not in input_files:
input_files.append(htc_file)
self.input_files = [abspath((pjoin(exe_dir, f), abspath(f))[os.path.isabs(f)])
for f in input_files]
self.htc_file = relpath(htc_file, exe_dir)
self.output_files = [abspath((pjoin(exe_dir, f), abspath(f))[os.path.isabs(f)])
for f in output_files]
self.model_path = abspath(pjoin(exe_dir, relpath(os.path.commonprefix(
self.input_files + self.output_files).rpartition("/")[0], exe_dir)))
self.model_name = os.path.basename(abspath(self.model_path))
self.jobname = os.path.splitext(os.path.basename(htc_file))[0]
PBSFile.__init__(self, self.model_path, self.jobname, self.commands, queue, walltime=walltime)
def copy_input(self):
rel_input_files = [relpath(f, self.model_path) for f in self.input_files]
copy_input = "\n".join(["mkdir -p [TARGET]/%s && cp -u -r %s [TARGET]/%s" % (os.path.dirname(f), f, os.path.dirname(f))
for f in rel_input_files])
return (copy_input.replace("[TARGET]", "/scratch/$USER/$PBS_JOBID/[model_name]"),
copy_input.replace("[TARGET]", "/scratch/$USER/$PBS_JOBID/[model_name]/run_[jobname]"))
def copy_output(self):
rel_output_files = [
relpath(f, self.modelpath) for f in self.output_files
]
return "\n".join([
'mkdir -p "[modelpath]/%s" && cp -u -r "%s" "[modelpath]/%s"' %
(os.path.dirname(f), f, os.path.dirname(f))
for f in rel_output_files
])
def copy_output(self):
rel_output_files = [
relpath(f, self.model_path) for f in self.output_files
]
return "\n".join([
"mkdir -p [model_path]/%s && cp -u -r %s [model_path]/%s" %
(os.path.dirname(f), f, os.path.dirname(f))
for f in rel_output_files
])
def commands(self):
rel_exe_dir = relpath(abspath(self.exe_dir), abspath(self.modelpath))
copy_input_to_scratch, copy_input_to_exe_dir = self.copy_input()
return template(copy_hawc2=self.copy_hawc2(),
exe_dir=cluster_path(self.exe_dir),
copy_input_to_scratch=copy_input_to_scratch,
copy_input_to_exe_dir=copy_input_to_exe_dir,
rel_exe_dir=rel_exe_dir,
hawc2_cmd=self.hawc2_cmd,
htc_file=self.htc_file,
jobname=self.jobname,
copy_output=self.copy_output(),
modelpath=cluster_path(self.modelpath),
modelname=self.modelname)