def submit(self, previous_job = None):
from xfel.command_line.cxi_mpi_submit import do_submit
output_path = self.get_global_path()
if not os.path.exists(output_path):
os.makedirs(output_path)
identifier_string = self.get_identifier_string()
target_phil_path = os.path.join(output_path, identifier_string + "_params.phil")
with open(target_phil_path, 'w') as f:
expt_suffix = refl_suffix = None
for job in self.dataset_version.jobs:
input_folder, _expt_suffix, _refl_suffix, _, _ = job.get_output_files()
if expt_suffix is None: expt_suffix = _expt_suffix
else: assert expt_suffix == _expt_suffix
if refl_suffix is None: refl_suffix = _refl_suffix
else: assert refl_suffix == _refl_suffix
f.write("input.path=%s\n"%input_folder)
f.write("input.experiments_suffix=%s\n"%expt_suffix)
f.write("input.reflections_suffix=%s\n"%refl_suffix)
f.write("output.output_dir=%s\n"%output_path)
f.write("output.prefix=%s_v%03d\n"%(self.dataset.name, self.dataset_version.version))
f.write(self.task.parameters)
command = "cctbx.xfel.merge %s"%target_phil_path
submit_path = os.path.join(output_path, identifier_string + "_submit.sh")
params = self.app.params.mp
if params.nnodes_merge:
params = copy.deepcopy(params)
params.nnodes = params.nnodes_merge
return do_submit(command, submit_path, output_path, params, identifier_string)
def submit(self, previous_job = None):
from xfel.command_line.cxi_mpi_submit import do_submit
output_path = self.get_global_path()
if not os.path.exists(output_path):
os.makedirs(output_path)
identifier_string = self.get_identifier_string()
target_phil_path = os.path.join(output_path, identifier_string + "_params.phil")
input_folder, _, _, input_mtz, _ = previous_job.get_output_files()
command = self.task.parameters.split('\n')[0]
phil_params = '\n'.join(self.task.parameters.split('\n')[1:])
phil_params = phil_params.replace('<PREVIOUS_TASK_MTZ>', os.path.join(input_folder, input_mtz))
phil_params = phil_params.replace('<PREVIOUS_TASK_FOLDER>', input_folder)
phil_params = phil_params.replace('<DATASET_NAME>', self.dataset.name)
phil_params = phil_params.replace('<DATASET_VERSION>', str(self.dataset_version.version))
with open(target_phil_path, 'w') as f:
f.write(phil_params)
command = "%s %s"%(command, target_phil_path)
submit_path = os.path.join(output_path, identifier_string + "_submit.sh")
params = copy.deepcopy(self.app.params.mp)
if params.nnodes_merge:
params.nnodes = params.nnodes_merge
params.use_mpi = False
if 'upload' not in command:
params.env_script = params.phenix_script
return do_submit(command, submit_path, output_path, params, identifier_string)
def submit(self, previous_job = None):
from xfel.command_line.cxi_mpi_submit import do_submit
output_path = self.get_global_path()
if not os.path.exists(output_path):
os.makedirs(output_path)
identifier_string = self.get_identifier_string()
target_phil_path = os.path.join(output_path, identifier_string + "_params.phil")
input_folder, _, _, input_mtz, _ = previous_job.get_output_files()
command = self.task.parameters.split('\n')[0]
phil_params = '\n'.join(self.task.parameters.split('\n')[1:])
phil_params = phil_params.replace('<PREVIOUS_TASK_MTZ>', os.path.join(input_folder, input_mtz))
phil_params = phil_params.replace('<PREVIOUS_TASK_FOLDER>', input_folder)
phil_params = phil_params.replace('<DATASET_NAME>', self.dataset.name)
phil_params = phil_params.replace('<DATASET_VERSION>', str(self.dataset_version.version))
with open(target_phil_path, 'w') as f:
f.write(phil_params)
command = "%s %s"%(command, target_phil_path)
submit_path = os.path.join(output_path, identifier_string + "_submit.sh")
params = copy.deepcopy(self.app.params.mp)
if params.nnodes_merge:
params.nnodes = params.nnodes_merge
params.use_mpi = False
params.shifter.staging = None
if 'upload' in command:
params.nnodes = 1
params.nproc_per_node = 1
#params.queue = 'shared'
else:
params.env_script = params.phenix_script
if params.method == 'shifter' and 'upload' not in command:
import libtbx.load_env
params.shifter.sbatch_script_template = os.path.join( \
libtbx.env.find_in_repositories("xfel/ui/db/cfgs"), "phenix_sbatch.sh")
params.shifter.srun_script_template = os.path.join( \
libtbx.env.find_in_repositories("xfel/ui/db/cfgs"), "phenix_srun.sh")
return do_submit(command, submit_path, output_path, params, identifier_string)
