README.md

@@ -35,15 +35,21 @@ cd ${sources_dir}/scientific-computing-use-cases
 with `${path_to_output_dir}` pointing to the file system that should be tested.
 
 
-## Modifying the timeout
+## Modifying the timeout (removed)
 
-We can use an env var `${PYTEST_TIMEOUT_PER_TEST}` to set the maximal number of
-seconds a single test is allowed to take.  Default is 5 seconds.  To allow for,
-e.g., up to 10 seconds per test, run the tests with
+* Timeouts are buggy in pytest.  The use of `pytest.mark.timeout` has been
+removed. *
+
+
+## Including the large tests
+
+Setting an environment variable `PYTEST_LARGE_TESTS` to `TRUE`, will include
+tests up to arrays of `256^4` double-precision numbers. This will amount to
+about 34 GiB written to and read from disk:
 
 ```bash
 cd ${sources_dir}/scientific-computing-use-cases
-PYTEST_TIMEOUT_PER_TEST=10 ./run.sh ${path_to_output_dir}
+PYTEST_LARGE_TESTS=TRUE ./run.sh ${path_to_output_dir}
 ```
 
 

run.sh

@@ -13,7 +13,15 @@ source ${mc3_target_dir}/bin/activate py3_std || \
       echo "Please run set_up_environment.sh first.";
       exit; }
 
+
+# If we're running the large tests, allow for 24GB virtual memory instead of 8
+if [ $PYTEST_LARGE_TESTS == "TRUE" ]; then
+    vlim=32
+else
+    vlim=8
+fi
+ulimit -v "$(expr ${vlim} \* 1000 \* 1000)"
+
 # run all tests using a local tmp dir and monitor
 # timing of all tests
-ulimit -v "$(expr 8 \* 1000 \* 1000)"
 pytest -v -s --basetemp=${tmp_dir} --durations=0 tests/

tests/test_random_data_writes.py

@@ -11,13 +11,9 @@ import os
 np.random.seed(137)
 
 
-# read timeout from environment
-def _get_timeout():
-    if "PYTEST_TIMEOUT_PER_TEST" in os.environ:
-        pytest_timeout_per_test = float(os.environ["PYTEST_TIMEOUT_PER_TEST"])
-    else:
-        pytest_timeout_per_test = 5.0  # seconds
-    return pytest_timeout_per_test
+# do we want to run the large tests?
+def _run_large_tests():
+    return (os.environ.get("PYTEST_LARGE_TESTS", "false").upper() == "TRUE")
 
 
 def _get_xr_data_array(array):
@@ -33,20 +29,19 @@ def temp_dir(tmpdir_factory):
     temp_dir.remove()
 
 
-@pytest.mark.parametrize(
-    "ndim",
-    [3,
-     pytest.mark.xfail(reason="Expect out-of-memory errors")(4)])
+@pytest.mark.parametrize("ndim", [3, 4])
 @pytest.mark.parametrize(
     "N",
-    list(2 ** n for n in range(5, 6)) +
-    list(pytest.mark.xfail(reason="Expect out-of-memory errors")(2 ** n)
-         for n in range(6, 8)))
+    list(2 ** n for n in range(5, 8)) +
+    list(pytest.mark.xfail(reason="Expect out-of-memory errors")(
+            pytest.mark.skipif(
+                not _run_large_tests(),
+                reason="User did not ask for the large tests")(2 ** n))
+         for n in [8]))
 @pytest.mark.parametrize("num_chunks", [2, 8])
 @pytest.mark.parametrize("use_zarr_or_nc4", ["zarr", "nc4"])
 @pytest.mark.parametrize("only_write", [False, True])
 @pytest.mark.parametrize("threads_per_worker", [4, 1])
-@pytest.mark.timeout(_get_timeout())
 def test_large_arrays(num_chunks, N, ndim, temp_dir, use_zarr_or_nc4,
                       only_write, threads_per_worker):
     """Write random data sets to disk and re-read check for corrupted data.