def test_base(self):
"base test"
se = ScriptEditor()
se.shebang()
se.declare_var("FOO", "BAR")
se.add_emptyline()
se.add_comment("This is a comment")
se.declare_vars({"FOO1": "BAR1"})
se.load_modules(["module1", "module2"])
print(se.get_script_str())
def test_base(self):
"base test"
se = ScriptEditor()
se.shebang()
se.declare_var("FOO", "BAR")
se.add_emptyline()
se.add_comment("This is a comment")
se.declare_vars({"FOO1": "BAR1"})
se.load_modules(["module1", "module2"])
print(se.get_script_str())
def get_script_str(self, job_name, launch_dir, executable, qout_path, qerr_path, stdin=None, stdout=None, stderr=None):
"""
Returns a (multi-line) String representing the queue script, e.g. PBS script.
Uses the template_file along with internal parameters to create the script.
Args:
launch_dir:
(str) The directory the job will be launched in.
qout_path
Path of the Queue manager output file.
qerr_path:
Path of the Queue manager error file.
"""
# Construct the header for the Queue Manager.
qheader = self._make_qheader(job_name, qout_path, qerr_path)
# Add the bash section.
se = ScriptEditor()
if self.setup:
se.add_comment("Setup section")
se.add_lines(self.setup)
if self.modules:
se.add_comment("Load Modules")
se.add_line("module purge")
se.load_modules(self.modules)
if self.has_omp:
se.add_comment("OpenMp Environment")
se.declare_vars(self.omp_env)
if self.shell_env:
se.add_comment("Shell Environment")
se.declare_vars(self.shell_env)
# Cd to launch_dir
se.add_line("cd " + os.path.abspath(launch_dir))
if self.pre_run:
se.add_comment("Commands before execution")
se.add_lines(self.pre_run)
# Construct the string to run the executable with MPI and mpi_ncpus.
mpi_ncpus = self.mpi_ncpus
line = self.mpi_runner.string_to_run(executable, mpi_ncpus, stdin=stdin, stdout=stdout, stderr=stderr)
se.add_line(line)
if self.post_run:
se.add_comment("Commands after execution")
se.add_lines(self.post_run)
shell_text = se.get_script_str()
return qheader + shell_text
def get_script_str(self,
job_name,
launch_dir,
executable,
qout_path,
qerr_path,
stdin=None,
stdout=None,
stderr=None):
"""
Returns a (multi-line) String representing the queue script, e.g. PBS script.
Uses the template_file along with internal parameters to create the script.
Args:
launch_dir:
(str) The directory the job will be launched in.
qout_path
Path of the Queue manager output file.
qerr_path:
Path of the Queue manager error file.
"""
# Construct the header for the Queue Manager.
qheader = self._make_qheader(job_name, qout_path, qerr_path)
# Add the bash section.
se = ScriptEditor()
if self.setup:
se.add_comment("Setup section")
se.add_lines(self.setup)
if self.modules:
se.add_comment("Load Modules")
se.add_line("module purge")
se.load_modules(self.modules)
if self.has_omp:
se.add_comment("OpenMp Environment")
se.declare_vars(self.omp_env)
if self.shell_env:
se.add_comment("Shell Environment")
se.declare_vars(self.shell_env)
# Cd to launch_dir
se.add_line("cd " + os.path.abspath(launch_dir))
if self.pre_run:
se.add_comment("Commands before execution")
se.add_lines(self.pre_run)
# Construct the string to run the executable with MPI and mpi_ncpus.
mpi_ncpus = self.mpi_ncpus
line = self.mpi_runner.string_to_run(executable,
mpi_ncpus,
stdin=stdin,
stdout=stdout,
stderr=stderr)
se.add_line(line)
if self.post_run:
se.add_comment("Commands after execution")
se.add_lines(self.post_run)
shell_text = se.get_script_str()
return qheader + shell_text