def prepare_for_submission(self, folder):
# create calculation info
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.codes_info = []
calcinfo.retrieve_list = []
for key, params in self.inputs.parameters.get_dict().items():
cube_name = key+".cube"
kind_str = params["kind"]
npts = params["npts"]
# create code info
codeinfo = CodeInfo()
codeinfo.cmdline_params = []
codeinfo.cmdline_params.append(str(self.inputs.metadata.options.resources['tot_num_mpiprocs']))
codeinfo.cmdline_params.append(kind_str)
codeinfo.cmdline_params.append(self._PARENT_FOLDER_NAME + "/" + self._DEFAULT_INPUT_FILE)
codeinfo.cmdline_params.append(cube_name)
codeinfo.cmdline_params.append(str(npts))
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.withmpi = self.inputs.metadata.options.withmpi
calcinfo.codes_info.append(codeinfo)
if self.inputs.retrieve_cubes.value:
calcinfo.retrieve_list.append(cube_name)
extra_prepend = "\nexport GAUSS_MEMDEF=%dMB\n" % self.inputs.gauss_memdef
if not hasattr(calcinfo, 'prepend_text') or not calcinfo.prepend_text:
calcinfo.prepend_text = extra_prepend
else:
calcinfo.prepend_text += extra_prepend
# symlink or copy to parent calculation
calcinfo.remote_symlink_list = []
calcinfo.remote_copy_list = []
comp_uuid = self.inputs.parent_calc_folder.computer.uuid
remote_path = self.inputs.parent_calc_folder.get_remote_path()
copy_info = (comp_uuid, remote_path, self._PARENT_FOLDER_NAME)
if self.inputs.code.computer.uuid == comp_uuid: # if running on the same computer - make a symlink
# if not - copy the folder
calcinfo.remote_symlink_list.append(copy_info)
else:
calcinfo.remote_copy_list.append(copy_info)
return calcinfo
def prepare_for_submission(self, tempfolder):
# Setup template
with open(self.inputs.template, 'r') as tempfile:
temp_contents = tempfile.read()
lmp_template = Template(temp_contents)
# # check variables
# for variable in self.inputs.variables.values():
# if not isinstance(variable, list):
# raise TypeError('Values in variables must be list')
# check kinds
if 'kinds' in self.inputs:
kind_var = {
kind: kind_index + 1
for kind_index, kind in enumerate(self.inputs.kinds)
}
lmp_template = Template(lmp_template.safe_substitute(**kind_var))
for i, case in enumerate(self.inputs.cases):
structure = case.pop('structure')
if isinstance(structure, StructureData):
structure_txt, struct_transform = generate_lammps_structure(
structure, kinds=self.inputs.kinds)
elif isinstance(structure, SinglefileData):
structure_txt = structure.get_content()
else:
raise TypeError(
'Input structure must be StructureData or SinglefileData')
input_txt = lmp_template.safe_substitute(**case)
# ========================= dump to file ===========================
tempfolder.get_subfolder(i, create=True)
input_filename = tempfolder.get_abs_path(
f'{i}/{self._INPUT_FILE_NAME}')
with open(input_filename, 'w') as infile:
infile.write(input_txt)
structure_filename = tempfolder.get_abs_path(
f'{i}/{self._INPUT_STRUCTURE}')
with open(structure_filename, 'w') as infile:
infile.write(structure_txt)
case_filename = tempfolder.get_abs_path(f'{i}/case.json')
case.update({'structure pk': structure.pk})
with open(case_filename, 'w') as infile:
json.dump(case, infile, sort_keys=True, indent=2)
# ============================ calcinfo ================================
settings = self.inputs.settings.get_dict() \
if 'settings' in self.inputs else {}
codeinfo = CodeInfo()
codeinfo.cmdline_params = self._cmdline_params
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.stdout_name = self._stdout_name
codeinfo.join_files = True
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.prepend_text = (f'for i in $(seq 0 {i})\n'
'do\n'
'cd "${i}" || exit')
calcinfo.append_text = ('cd ..\n' 'done')
calcinfo.cmdline_params = codeinfo.cmdline_params
calcinfo.stdin_name = self._INPUT_FILE_NAME
calcinfo.stdout_name = self._stdout_name
calcinfo.retrieve_list = self._retrieve_list + [
self.options.output_filename
]
calcinfo.retrieve_list += settings.pop('additional_retrieve_list', [])
calcinfo.retrieve_temporary_list = self._retrieve_temporary_list
calcinfo.codes_info = [codeinfo]
# =========================== local_copy_list ==========================
if 'file' in self.inputs:
calcinfo.local_copy_list = []
for name, obj in self.inputs.file.items():
calcinfo.local_copy_list.append(
(obj.uuid, obj.filename, f'{name}.pb'))
return calcinfo
def prepare_for_submission(self, folder):
# create calculation info
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
calcinfo.codes_info = []
calcinfo.retrieve_list = []
calcinfo.retrieve_temporary_list = []
calcinfo.prepend_text = "export GAUSS_MEMDEF=%dMB\n" % self.inputs.gauss_memdef
calcinfo.local_copy_list = []
if "stencil" in self.inputs:
calcinfo.local_copy_list.append(
(self.inputs.stencil.uuid, self.inputs.stencil.filename,
'stencil.txt'))
for key, params in self.inputs.parameters.get_dict().items():
cube_name = key + ".cube"
kind_str = params["kind"]
npts = params["npts"]
# create code info
codeinfo = CodeInfo()
codeinfo.cmdline_params = []
codeinfo.cmdline_params.append(
str(self.inputs.metadata.options.resources['tot_num_mpiprocs'])
)
codeinfo.cmdline_params.append(kind_str)
codeinfo.cmdline_params.append(self.PARENT_FOLDER_NAME + "/" +
self.DEFAULT_INPUT_FILE)
codeinfo.cmdline_params.append(cube_name)
if npts == -1:
if 'stencil' not in self.inputs:
self.report(
"Warning: npts: -1 set but no stencil provided, using -2"
)
codeinfo.cmdline_params.append("-2")
else:
codeinfo.cmdline_params.append(str(npts))
codeinfo.stdin_name = "stencil.txt"
else:
codeinfo.cmdline_params.append(str(npts))
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.withmpi = self.inputs.metadata.options.withmpi
calcinfo.codes_info.append(codeinfo)
if self.inputs.retrieve_cubes.value:
calcinfo.retrieve_list.append(cube_name)
else:
calcinfo.retrieve_temporary_list.append(cube_name)
# symlink or copy to parent calculation
calcinfo.remote_symlink_list = []
calcinfo.remote_copy_list = []
comp_uuid = self.inputs.parent_calc_folder.computer.uuid
remote_path = self.inputs.parent_calc_folder.get_remote_path()
copy_info = (comp_uuid, remote_path, self.PARENT_FOLDER_NAME)
if self.inputs.code.computer.uuid == comp_uuid:
# if running on the same computer - make a symlink
# if not - copy the folder
calcinfo.remote_symlink_list.append(copy_info)
else:
calcinfo.remote_copy_list.append(copy_info)
return calcinfo
