test for numpy (dup via fcntl) not logging writes

Author: roblatham00

darshan-test/python_mpi_scripts/runtime_prog_issue_1072.py

@@ -0,0 +1,15 @@
+#!/usr/bin/env python3
+
+from mpi4py import MPI
+import numpy as np
+import os
+
+def main():
+    comm = MPI.COMM_WORLD
+    arr1 = np.arange(50)
+    np.save('single_array.npy', arr1)
+    os.remove('single_array.npy')
+
+
+if __name__ == "__main__":
+    main()

darshan-test/python_runtime_tests.py

@@ -231,3 +231,44 @@ def test_forked_process_mpi(tmpdir):
     # regression test for gh-786, mpi version
     darshan_install_path = os.environ.get("DARSHAN_INSTALL_PATH")
     do_forked_process_test(tmpdir, darshan_install_path)
+
+def test_os_dup(tmpdir):
+    # numpy calls Python's os.dup() which in turn was duplicating a file
+    # descriptor via fcntl
+    n_ranks = 1
+    root_path = os.environ.get("DARSHAN_ROOT_PATH")
+    darshan_install_path = os.environ.get("DARSHAN_INSTALL_PATH")
+    test_script_path = os.path.join(root_path,
+                                    "darshan-test",
+                                    "python_mpi_scripts",
+                                    "runtime_prog_issue_690.py")
+    darshan_lib_path = os.path.join(darshan_install_path,
+                                    "lib",
+                                    "libdarshan.so")
+    hdf5_lib_path = os.environ.get("HDF5_LIB")
+
+    with tmpdir.as_cwd():
+        cwd = os.getcwd()
+        subprocess.check_output(["mpirun",
+                     "--allow-run-as-root",
+                     "-n",
+                     f"{n_ranks}",
+                     "-x",
+                     f"LD_PRELOAD={darshan_lib_path}:{hdf5_lib_path}",
+                     "-x",
+                     f"DARSHAN_LOGPATH={cwd}",
+                     "python",
+                     f"{test_script_path}"])
+
+        log_file_list = glob.glob("*.darshan")
+        # only a single log file should be generated
+        # by darshan
+        assert len(log_file_list) == 1
+        path_to_log = os.path.join(cwd, log_file_list[0])
+        # numpy will read a bunch of python files but we only care about the
+        # numpy file
+        report = darshan.DarshanReport(path_to_log, filter_patterns=[".npy"], filter_mode='include')
+        # common stuff done.  Real check for the "dup via fcntl" issue
+
+        posix_counters = report.records['POSIX'].to_dict()["counters"]
+        assert posix_counters['POSIX_BYTES_WRITTEN'] == 928