def test_save_scratch(self):
with patch("moltherm.compute.jobs.os.putenv") as putenv_patch:
with patch("moltherm.compute.jobs.shutil.copy") as copy_patch:
myjob = QCJob(qchem_command="qchem -slurm",
max_cores=32,
scratch_dir=os.getcwd(),
save_scratch=True,
save_name="freq_scratch")
self.assertEqual(myjob.current_command, [
"qchem", "-slurm", "-save", "-nt", "32", "mol.qin",
"mol.qout", "freq_scratch"
])
myjob.setup()
self.assertEqual(copy_patch.call_args_list[0][0][0], "mol.qin")
self.assertEqual(copy_patch.call_args_list[0][0][1],
"mol.qin.orig")
self.assertEqual(putenv_patch.call_args_list[0][0][0],
"QCSCRATCH")
self.assertEqual(putenv_patch.call_args_list[0][0][1],
os.getcwd())
self.assertEqual(putenv_patch.call_args_list[1][0][0],
"QCTHREADS")
self.assertEqual(putenv_patch.call_args_list[1][0][1], "32")
self.assertEqual(putenv_patch.call_args_list[2][0][0],
"OMP_NUM_THREADS")
self.assertEqual(putenv_patch.call_args_list[2][0][1], "32")
def test_not_defaults(self):
with patch("moltherm.compute.jobs.os.putenv") as putenv_patch:
myjob = QCJob(qchem_command="qchem -slurm",
multimode="mpi",
input_file="different.qin",
output_file="not_default.qout",
max_cores=12,
scratch_dir="/not/default/scratch/",
backup=False)
self.assertEqual(myjob.current_command, [
"qchem", "-slurm", "-np", "12", "different.qin",
"not_default.qout"
])
myjob.setup()
self.assertEqual(putenv_patch.call_args_list[0][0][0], "QCSCRATCH")
self.assertEqual(putenv_patch.call_args_list[0][0][1],
"/not/default/scratch/")
def test_defaults(self):
with patch("moltherm.compute.jobs.os.putenv") as putenv_patch:
with patch("moltherm.compute.jobs.shutil.copy") as copy_patch:
myjob = QCJob(qchem_command="qchem", max_cores=32)
self.assertEqual(myjob.current_command,
["qchem", "-nt", "32", "mol.qin", "mol.qout"])
myjob.setup()
self.assertEqual(copy_patch.call_args_list[0][0][0], "mol.qin")
self.assertEqual(copy_patch.call_args_list[0][0][1],
"mol.qin.orig")
self.assertEqual(putenv_patch.call_args_list[0][0][0],
"QCSCRATCH")
self.assertEqual(putenv_patch.call_args_list[0][0][1],
"/dev/shm/qcscratch/")
self.assertEqual(putenv_patch.call_args_list[1][0][0],
"QCTHREADS")
self.assertEqual(putenv_patch.call_args_list[1][0][1], "32")
self.assertEqual(putenv_patch.call_args_list[2][0][0],
"OMP_NUM_THREADS")
self.assertEqual(putenv_patch.call_args_list[2][0][1], "32")
def test_OptFF(self):
self.maxDiff = None
myjob = QCJob.opt_with_frequency_flattener(qchem_command="qchem",
max_cores=32,
input_file="test.qin",
output_file="test.qout",
sp_params=self.sp_params)
expected_next = QCJob(qchem_command="qchem",
max_cores=32,
multimode="openmp",
input_file="test.qin",
output_file="test.qout",
suffix=".opt_0",
backup=True).as_dict()
self.assertEqual(next(myjob).as_dict(), expected_next)
expected_next = QCJob(qchem_command="qchem",
max_cores=32,
multimode="openmp",
input_file="test.qin",
output_file="test.qout",
suffix=".freq_0",
backup=False).as_dict()
self.assertEqual(next(myjob).as_dict(), expected_next)
self.assertEqual(
QCInput.from_file(join(
test_dir, "standard/rct_1_471171.in.freq_0")).as_dict(),
QCInput.from_file(join(scr_dir, "test.qin")).as_dict())
expected_next = QCJob(qchem_command="qchem",
max_cores=32,
multimode="openmp",
input_file="test.qin",
output_file="test.qout",
suffix=".sp",
backup=True).as_dict()
self.assertEqual(next(myjob).as_dict(), expected_next)
self.assertEqual(
QCInput.from_file(join(test_dir,
"standard/rct_1_471171.in.sp")).as_dict(),
QCInput.from_file(join(scr_dir, "test.qin")).as_dict())
self.assertRaises(StopIteration, myjob.__next__)
def test_RunQChemCustodian_using_fw_spec_not_defaults(self):
with patch("moltherm.compute.fireworks.Custodian") as custodian_patch:
firetask = RunQChemCustodian(
qchem_cmd=">>qchem_cmd<<",
multimode=">>multimode<<",
input_file=os.path.join(module_dir, "..", "..", "test_files",
"co_qc.in"),
output_file="this_is_a_test.qout",
max_cores=4,
qclog_file="this_is_a_test.qclog",
suffix="bad_idea",
save_scratch=True,
save_name="no_idea",
max_errors=137,
gzipped_output=False,
handler_group="no_handler",
scratch_dir=">>scratch_dir<<",
)
firetask.run_task(
fw_spec={
"_fw_env": {
"qchem_cmd": "qchem -slurm",
"scratch_dir": "/this/is/a/test",
"max_cores": 32,
"multimode": "mpi"
}
})
custodian_patch.assert_called_once()
self.assertEqual(custodian_patch.call_args[0][0], [])
self.assertEqual(
custodian_patch.call_args[0][1][0].as_dict(),
QCJob(qchem_command="qchem -slurm",
multimode=">>multimode<<",
input_file=os.path.join(module_dir, "..", "..",
"test_files", "co_qc.in"),
output_file="this_is_a_test.qout",
max_cores=4,
qclog_file="this_is_a_test.qclog",
suffix="bad_idea",
save_scratch=True,
save_name="no_idea",
scratch_dir="/this/is/a/test").as_dict())
self.assertEqual(custodian_patch.call_args[1], {
"max_errors": 137,
"gzipped_output": False
})
def test_RunQChemCustodian_using_fw_spec_defaults(self):
with patch("moltherm.compute.fireworks.Custodian") as custodian_patch:
firetask = RunQChemCustodian(qchem_cmd=">>qchem_cmd<<",
scratch_dir=">>scratch_dir<<",
input_file=os.path.join(
module_dir, "..", "..",
"test_files", "co_qc.in"),
max_cores=">>max_cores<<",
multimode=">>multimode<<")
firetask.run_task(
fw_spec={
"_fw_env": {
"qchem_cmd": "qchem -slurm",
"scratch_dir": "/this/is/a/test",
"max_cores": 32,
"multimode": "openmp"
}
})
custodian_patch.assert_called_once()
self.assertEqual(
custodian_patch.call_args[0][0][0].as_dict(),
QChemErrorHandler(input_file=os.path.join(
module_dir, "..", "..", "test_files", "co_qc.in"),
output_file="mol.qout").as_dict())
self.assertEqual(
custodian_patch.call_args[0][1][0].as_dict(),
QCJob(qchem_command="qchem -slurm",
max_cores=">>max_cores<<",
multimode=">>multimode<<",
input_file=os.path.join(module_dir, "..", "..",
"test_files", "co_qc.in"),
output_file="mol.qout",
scratch_dir="/this/is/a/test").as_dict())
self.assertEqual(custodian_patch.call_args[1], {
"max_errors": 5,
"gzipped_output": True
})
def test_RunQChemCustodian_basic_defaults(self):
with patch("moltherm.compute.fireworks.Custodian") as custodian_patch:
firetask = RunQChemCustodian(qchem_cmd="qchem",
input_file=os.path.join(
files_dir, "qchem", "co_qc.in"),
max_cores=32)
firetask.run_task(fw_spec={})
custodian_patch.assert_called_once()
self.assertEqual(
custodian_patch.call_args[0][0][0].as_dict(),
QChemErrorHandler(input_file=os.path.join(
files_dir, "qchem", "co_qc.in"),
output_file="mol.qout").as_dict())
self.assertEqual(
custodian_patch.call_args[0][1][0].as_dict(),
QCJob(qchem_command="qchem",
max_cores=32,
multimode="openmp",
input_file=os.path.join(files_dir, "qchem", "co_qc.in"),
output_file="mol.qout").as_dict())
self.assertEqual(custodian_patch.call_args[1], {
"max_errors": 5,
"gzipped_output": True
})
def run_task(self, fw_spec):
# initialize variables
qchem_cmd = env_chk(self["qchem_cmd"], fw_spec)
multimode = self.get("multimode", "openmp")
input_file = self.get("input_file", "mol.qin")
output_file = self.get("output_file", "mol.qout")
max_cores = self.get("max_cores", 32)
qclog_file = self.get("qclog_file", "mol.qclog")
suffix = self.get("suffix", "")
scratch_dir = env_chk(self.get("scratch_dir"), fw_spec)
if scratch_dir == None:
scratch_dir = "/dev/shm/qcscratch/"
save_scratch = self.get("save_scratch", False)
save_name = self.get("save_name", "default_save_name")
max_errors = self.get("max_errors", 5)
max_iterations = self.get("max_iterations", 10)
max_molecule_perturb_scale = self.get("max_molecule_perturb_scale",
0.3)
job_type = self.get("job_type", "normal")
gzipped_output = self.get("gzipped_output", True)
sp_params = self.get("sp_params", None)
handler_groups = {
"default": [
QChemErrorHandler(input_file=input_file,
output_file=output_file)
],
"no_handler": []
}
# construct jobs
if job_type == "normal":
jobs = [
QCJob(qchem_command=qchem_cmd,
multimode=multimode,
input_file=input_file,
output_file=output_file,
max_cores=max_cores,
qclog_file=qclog_file,
suffix=suffix,
scratch_dir=scratch_dir,
save_scratch=save_scratch,
save_name=save_name)
]
elif job_type == "opt_with_frequency_flattener":
jobs = QCJob.opt_with_frequency_flattener(
qchem_command=qchem_cmd,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
sp_params=sp_params,
max_iterations=max_iterations,
max_molecule_perturb_scale=max_molecule_perturb_scale,
scratch_dir=scratch_dir,
save_scratch=save_scratch,
save_name=save_name,
max_cores=max_cores)
elif job_type == "ts_with_frequency_flattener":
jobs = QCJob.ts_with_frequency_flattener(
qchem_command=qchem_cmd,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
ts_guess_method="fsm",
max_iterations=max_iterations,
max_molecule_perturb_scale=max_molecule_perturb_scale,
scratch_dir=scratch_dir,
save_scratch=save_scratch,
save_name=save_name,
max_cores=max_cores)
else:
raise ValueError("Unsupported job type: {}".format(job_type))
# construct handlers
handlers = handler_groups[self.get("handler_group", "default")]
c = Custodian(handlers,
jobs,
max_errors=max_errors,
gzipped_output=gzipped_output)
c.run()