def _create_runscript(self):
"""Utility method to create runscript"""
runscript = Script(
directory=self.directory,
prefix="sge_",
suffix=".script",
stem=str(uuid.uuid1().int),
)
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " -V")
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " -w e")
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " -j yes")
runscript.append(self.__class__.SCRIPT_DIRECTIVE + f" -N {self.name}")
if self.dependency:
cmd = f'-hold_jid {",".join(map(str, self.dependency))}'
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.priority:
cmd = f"-p {self.priority}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.queue:
cmd = f"-q {self.queue}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.runtime:
cmd = f"-l h_rt={self.get_time(self.runtime)}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.shell:
cmd = f"-S {self.shell}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.nprocesses and self.environment:
cmd = f"-pe {self.environment} {self.nprocesses}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.directory:
cmd = f"-wd {self.directory}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.extra:
cmd = " ".join(map(str, self.extra))
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if len(self.script) > 1:
logf = runscript.path.replace(".script", ".log")
jobsf = runscript.path.replace(".script", ".jobs")
with open(jobsf, "w") as f_out:
f_out.write("\n".join(self.script))
cmd = f"-t 1-{len(self.script)} -tc {self.max_array_size}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
runscript.append(self.__class__.SCRIPT_DIRECTIVE + f" -o {logf}")
runscript.extend(self.get_array_bash_extension(jobsf, 0))
else:
runscript.append(self.__class__.SCRIPT_DIRECTIVE +
f" -o {self.log[0]}")
runscript.append(self.script[0])
return runscript
def _create_runscript(self):
"""Utility method to create runscript"""
runscript = Script(
directory=self.directory,
prefix="lsf_",
suffix=".script",
stem=str(uuid.uuid1().int),
)
if self.dependency:
cmd = "-w {}".format(" && ".join(
[f"deps({d})" for d in self.dependency]))
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.directory:
cmd = f"-cwd {self.directory}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.priority:
cmd = f"-sp {self.priority}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.queue:
cmd = f"-q {self.queue}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.runtime:
cmd = f"-W {self.runtime}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.shell:
cmd = f"-L {self.shell}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.nprocesses:
cmd = f'-R "span[ptile={self.nprocesses}]"'
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.extra:
cmd = " ".join(map(str, self.extra))
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if len(self.script) > 1:
logf = runscript.path.replace(".script", ".log")
jobsf = runscript.path.replace(".script", ".jobs")
with open(jobsf, "w") as f_out:
f_out.write("\n".join(self.script))
cmd = f"-J {self.name}[1-{len(self.script)}]%{self.max_array_size}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
runscript.append(self.__class__.SCRIPT_DIRECTIVE + f" -o {logf}")
runscript.extend(self.get_array_bash_extension(jobsf, 1))
else:
runscript.append(self.__class__.SCRIPT_DIRECTIVE +
f" -J {self.name}")
runscript.append(self.__class__.SCRIPT_DIRECTIVE +
f" -o {self.log[0]}")
runscript.append(self.script[0])
return runscript
def get_py_script(i, target):
script = Script(
shebang="#!{}".format(sys.executable),
prefix="pyjob",
stem="test{}".format(i),
suffix=".py",
)
script.extend(inspect.getsource(fibonacci).splitlines())
script.pop(0) # remove decorator
script.extend([
"if __name__ == '__main__':",
"\ttarget = {}".format(target),
"\tprint('{}th fib is: {}'.format(target, fibonacci(target)))",
])
return script
def _create_runscript(self):
"""Utility method to create runscript"""
runscript = Script(
directory=self.directory,
prefix="slurm_",
suffix=".script",
stem=str(uuid.uuid1().int),
)
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " --export=ALL")
runscript.append(self.__class__.SCRIPT_DIRECTIVE +
f" --job-name={self.name}")
if self.dependency:
cmd = f'--depend=afterok:{":".join(map(str, self.dependency))}'
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.queue:
cmd = f"-p {self.queue}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.nprocesses:
cmd = f"-n {self.nprocesses}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.directory:
cmd = f"--workdir={self.directory}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.runtime:
cmd = f"-t {self.runtime}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.extra:
cmd = " ".join(map(str, self.extra))
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if len(self.script) > 1:
logf = runscript.path.replace(".script", ".log")
jobsf = runscript.path.replace(".script", ".jobs")
with open(jobsf, "w") as f_out:
f_out.write("\n".join(self.script))
cmd = f"--array=1-{len(self.script)}%{self.max_array_size}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
runscript.append(self.__class__.SCRIPT_DIRECTIVE + f" -o {logf}")
runscript.extend(self.get_array_bash_extension(jobsf, 0))
else:
runscript.append(self.__class__.SCRIPT_DIRECTIVE +
f" -o {self.log[0]}")
runscript.append(self.script[0])
return runscript