Integrating a generic, non-python tool in pyiron (Level B, recommended approach)¶
To integrate a new tool into pyiron, one needs to create a pyiron job class, which is inherited from pyiron generic job class: GenericJob
from os.path import join
from pyiron_base import GenericJob, GenericParameters
Definition of the job class¶
Here, as a simple and generic process, we would like to use the bash command cat to print some values in an output file.
class ToyBashJob(GenericJob):
def __init__(self, project, job_name):
super().__init__(project, job_name)
self.input = GenericParameters(table_name="input")
self.input['input_energy'] = 100
self.executable = "cat input > output"
def write_input(self):
self.input.write_file(
file_name="input",
cwd=self.working_directory
)
def collect_output(self):
file = join(self.working_directory, "output")
with open(file) as f:
line = f.readlines()[0]
energy = float(line.split()[1])
with self.project_hdf5.open("output/generic") as h5out:
h5out["energy_tot"] = energy
def to_hdf(self, hdf=None, group_name=None):
super().to_hdf(
hdf=hdf,
group_name=group_name
)
with self.project_hdf5.open("input") as h5in:
self.input.to_hdf(h5in)
def from_hdf(self, hdf=None, group_name=None):
super().from_hdf(
hdf=hdf,
group_name=group_name
)
with self.project_hdf5.open("input") as h5in:
self.input.from_hdf(h5in)
Exercise 1:¶
using the above job class, create a project and run a job of type ToyBashJob
from pyiron_base import Project
pr = Project('test')
pr.remove_jobs_silently(recursive=True)
job = pr.create_job(job_type=ToyBashJob, job_name="toy")
print(job.input)
job.run()
job['output/generic/energy_tot']
Parameter Value Comment
0 input_energy 100
The job toy was saved and received the ID: 64
/home/muhammad/miniconda3/envs/workshop_test/lib/python3.8/site-packages/pyiron_base/generic/hdfio.py:361: UserWarning: swmr=True only affects read ('r') mode. For swmr write mode, set f.swmr_mode = True after opening the file.
with h5py.File(self.file_name, mode="a", libver="latest", swmr=True) as h:
100.0