Modified test_mpi_func.py and .circleci/config.yml

.circleci/config.yml

@@ -56,10 +56,10 @@ jobs:
             pip3 install pytest
             pip3 install pytest-mpi
             pip3 install pytest-cov
-            pytest -vv --disable-pytest-warnings --cov=ensemble_md --cov-report=xml --color=yes ensemble_md/tests/
-            # COVERAGE_FILE=.coverage_1 pytest -vv --disable-pytest-warnings --cov=ensemble_md --cov-report=xml --color=yes ensemble_md/tests/
-            # COVERAGE_FILE=.coverage_2 mpirun -np 4 pytest -vv --disable-pytest-warnings --cov=ensemble_md --cov-report=xml --color=yes ensemble_md/tests/test_mpi_func.py --with-mpi
-            # coverage combine .coverage_*
+            # pytest -vv --disable-pytest-warnings --cov=ensemble_md --cov-report=xml --color=yes ensemble_md/tests/
+            COVERAGE_FILE=.coverage_1 pytest -vv --disable-pytest-warnings --cov=ensemble_md --cov-report=xml --color=yes ensemble_md/tests/
+            COVERAGE_FILE=.coverage_2 mpirun -np 4 pytest -vv --disable-pytest-warnings --cov=ensemble_md --cov-report=xml --color=yes ensemble_md/tests/test_mpi_func.py --with-mpi
+            coverage combine .coverage_*
 
       - run:
           name: CodeCov

ensemble_md/tests/test_mpi_func.py

@@ -12,8 +12,10 @@
 """
 import os
 import yaml
+import glob
 import shutil
 import pytest
+from mpi4py import MPI
 from ensemble_md.replica_exchange_EE import ReplicaExchangeEE
 
 
@@ -22,11 +24,14 @@ def params_dict():
     """
     Generates a dictionary containing the required REXEE parameters.
     """
+    comm = MPI.COMM_WORLD
+    rank = comm.Get_rank()
+
     REXEE_dict = {
         'gmx_executable': 'gmx',
         'gro': 'ensemble_md/tests/data/sys.gro',
         'top': 'ensemble_md/tests/data/sys.top',
-        'mdp': 'ensemble_md/tests/data/mdp/expanded.mdp',
+        'mdp': 'ensemble_md/tests/data/expanded.mdp',
         'n_sim': 4,
         'n_iter': 10,
         's': 1,
@@ -35,14 +40,21 @@ def params_dict():
     yield REXEE_dict
 
     # Remove the file after the unit test is done.
-    if os.path.isfile('params.yaml') is True:
-        os.remove('params.yaml')
+    yml_file = f'params_{rank}.yaml'
+    if os.path.isfile(yml_file):
+        os.remove(yml_file)
 
 
-def get_REXEE_instance(input_dict, yml_file='params.yaml'):
+def get_REXEE_instance(input_dict, rank, yml_file=None):
     """
     Saves a dictionary as a yaml file and use it to instantiate the ReplicaExchangeEE class.
+    This version of the function creates a unique YAML file for each MPI process. This could
+    avoid race conditions between MPI processes where one process reads the file before another
+    finished writing it, or even worse, tries to read it while it's being written, leading to
+    inconsistent or incomplete data being read.
     """
+    if yml_file is None:
+        yml_file = f'params_{rank}.yaml'
     with open(yml_file, 'w') as f:
         yaml.dump(input_dict, f)
     REXEE = ReplicaExchangeEE(yml_file)
@@ -94,7 +106,6 @@ def get_gmx_cmd_from_output(output):
 
 @pytest.mark.mpi
 def test_run_grompp(params_dict):
-    from mpi4py import MPI
     comm = MPI.COMM_WORLD
     rank = comm.Get_rank()
 
@@ -103,7 +114,7 @@ def test_run_grompp(params_dict):
     # Case 1: The first iteration, i.e., n = 0
     n = 0
     swap_pattern = [1, 0, 2, 3]
-    REXEE = get_REXEE_instance(params_dict)
+    REXEE = get_REXEE_instance(params_dict, rank)
 
     if rank == 0:
         for i in range(params_dict['n_sim']):
@@ -133,7 +144,7 @@ def test_run_grompp(params_dict):
 
     # Case 2: Other iterations, i.e., n != 0
     n = 1  # For swap_pattern, we stick with [1, 0, 2, 3]
-    REXEE = get_REXEE_instance(params_dict)
+    REXEE = get_REXEE_instance(params_dict, rank)
     if rank == 0:
         for i in range(params_dict['n_sim']):
             os.makedirs(f'{REXEE.working_dir}/sim_{i}/iteration_{n}')