Exception handling (#343)

* Handle Lammps crashing

* Add test case

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* bug fixes

* break after error

* clean up after test

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: jan-janssen

pylammpsmpi/mpi/lmpmpi.py

@@ -482,11 +482,16 @@ def _run_lammps_mpi(argument_lst):
                 interface_send(socket=socket, result_dict={"result": True})
                 interface_shutdown(socket=socket, context=context)
             break
-        output = select_cmd(input_dict["command"])(
-            job=job, funct_args=input_dict["args"]
-        )
-        if MPI.COMM_WORLD.rank == 0 and output is not None:
-            interface_send(socket=socket, result_dict={"result": output})
+        try:
+            output = select_cmd(input_dict["command"])(
+                job=job, funct_args=input_dict["args"]
+            )
+        except Exception as error:
+            if MPI.COMM_WORLD.rank == 0:
+                interface_send(socket=socket, result_dict={"error": error})
+        else:
+            if MPI.COMM_WORLD.rank == 0 and output is not None:
+                interface_send(socket=socket, result_dict={"result": output})
 
 
 if __name__ == "__main__":

pylammpsmpi/wrapper/concurrent.py

@@ -68,7 +68,11 @@ def execute_async(
         elif "command" in task_dict and "future" in task_dict:
             f = task_dict.pop("future")
             if f.set_running_or_notify_cancel():
-                f.set_result(interface.send_and_receive_dict(input_dict=task_dict))
+                try:
+                    f.set_result(interface.send_and_receive_dict(input_dict=task_dict))
+                except Exception as error:
+                    f.set_exception(error)
+                    break
 
 
 class LammpsConcurrent:

tests/test_exception.py

@@ -0,0 +1,56 @@
+import os.path
+from unittest import TestCase
+from pylammpsmpi import LammpsLibrary
+
+
+lmp_str = """\
+# 3d Lennard-Jones melt
+
+units		lj
+atom_style	atomic
+atom_modify	map array
+
+lattice		fcc 0.8442
+region		box block 0 4 0 4 0 4
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 100.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+compute         1 all temp
+compute         2 all pressure 1
+compute         ke all ke/atom
+compute         msd all msd
+compute         v all property/atom vx vy vz 
+
+variable        fx atom fx
+variable        tt equal temp
+variable        test string "25"
+fix		           1 all nve
+fix              2 all ave/time 10 1 10 c_1 c_2
+
+
+
+run		1000
+"""
+
+
+class TestException(TestCase):
+    def test_overlapping_atoms(self):
+        with open("in.error", "w") as f:
+            f.writelines(lmp_str)
+        with self.assertRaises(Exception):
+            lmp = LammpsLibrary(cores=2, mode="local")
+            lmp.file("in.error")
+
+    def tearDown(self):
+        for f in ["in.error", "log.lammps"]:
+            if os.path.exists(f):
+                os.remove(f)