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Merged
Ed Hone (EdHone) merged 8 commits into from
Mar 24, 2026
Merged

Post-processing: Store rank and thread information in a single array #235

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3702ed5
Store rank and thread informatioN
EdHone Mar 20, 2026
b174e00
Extend getter for rank and thread
EdHone Mar 20, 2026
e5651c7
Threaded tests
EdHone Mar 20, 2026
3fc022b
Fix multithreaded data reduction
EdHone Mar 20, 2026
7d90f12
Fix threaded tests
EdHone Mar 23, 2026
9b61f06
Fix typing!
EdHone Mar 23, 2026
3537af0
Review comments
EdHone Mar 24, 2026
8045ff5
Fix broken comment
EdHone Mar 24, 2026
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3 changes: 2 additions & 1 deletion CONTRIBUTORS.md
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Expand Up @@ -4,4 +4,5 @@
|-----------------|------------------|-------------|------------|
| andrewcoughtrie | Andrew Coughtrie | Met Office | 2026-03-05 |
| mo-marqh | mark Hedley | Met Office | 2026-03-10 |
| oakleybrunt | Oakley Brunt | Met Office | 2026-03-09 |
| oakleybrunt | Oakley Brunt | Met Office | 2026-03-09 |
| EdHone | Ed Hone | Met Office | 2026-03-20 |
8 changes: 4 additions & 4 deletions post-processing/tests/data/vernier-output-test
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Expand Up @@ -6,8 +6,8 @@ Profiling on 1 thread(s).
(Size; Size/sec; Size/call; MinSize; MaxSize)
(self) (sec) (sec) (sec) ms/call ms/call

1 44.130 2.583 2.583 5.854 1 2583.167 5853.527 __test_app__
2 34.563 4.606 2.023 2.077 2 1011.582 1038.697 some_process
1 44.130 2.583 2.583 5.854 1 2583.167 5853.527 __test_app__@0
2 34.563 4.606 2.023 2.077 2 1011.582 1038.697 some_process@0

Task 2 of 2 : MPI rank ID 1
Profiling on 1 thread(s).
Expand All @@ -16,5 +16,5 @@ Profiling on 1 thread(s).
(Size; Size/sec; Size/call; MinSize; MaxSize)
(self) (sec) (sec) (sec) ms/call ms/call

1 43.991 3.009 3.009 3.069 2 1504.362 1534.740 some_process
2 37.835 5.596 2.588 6.839 1 2587.638 6839.336 __test_app__
1 43.991 3.009 3.009 3.069 2 1504.362 1534.740 some_process@0
2 37.835 5.596 2.588 6.839 1 2587.638 6839.336 __test_app__@0
21 changes: 21 additions & 0 deletions post-processing/tests/data/vernier-output-threaded/vernier-output-0
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@@ -0,0 +1,21 @@

Task 1 of 2 : MPI rank ID 0
Profiling on 4 thread(s).

# % Time Cumul Self Total # of calls Self Total Routine@
(Size; Size/sec; Size/call; MinSize; MaxSize)
(self) (sec) (sec) (sec) ms/call ms/call

1 40.000 2.000 2.000 3.000 2 1000.075 1500.115 MAIN_SUB@0
2 40.000 4.000 2.000 5.000 1 2000.140 5000.373 FULL@0
3 20.000 5.000 1.000 1.000 1 1000.073 1000.073 MAIN_SUB2@3
4 20.000 6.000 1.000 2.000 1 1000.072 2000.152 MAIN_SUB@3
5 20.000 7.001 1.000 1.000 1 1000.072 1000.072 MAIN_SUB2@0
6 20.000 8.001 1.000 1.000 1 1000.071 1000.071 MAIN_SUB2@2
7 20.000 9.001 1.000 1.000 1 1000.069 1000.069 MAIN_SUB2@1
8 20.000 10.001 1.000 2.000 1 1000.068 2000.151 MAIN_SUB@2
9 20.000 11.001 1.000 2.000 1 1000.067 2000.150 MAIN_SUB@1
10 0.000 11.001 0.000 0.000 2 0.008 0.008 __vernier__@2
11 0.000 11.001 0.000 0.000 4 0.004 0.004 __vernier__@0
12 0.000 11.001 0.000 0.000 2 0.008 0.008 __vernier__@1
13 0.000 11.001 0.000 0.000 2 0.007 0.007 __vernier__@3
21 changes: 21 additions & 0 deletions post-processing/tests/data/vernier-output-threaded/vernier-output-1
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@@ -0,0 +1,21 @@

Task 2 of 2 : MPI rank ID 1
Profiling on 4 thread(s).

# % Time Cumul Self Total # of calls Self Total Routine@
(Size; Size/sec; Size/call; MinSize; MaxSize)
(self) (sec) (sec) (sec) ms/call ms/call

1 40.031 2.004 2.004 5.006 1 2003.948 5005.940 FULL@0
2 39.956 4.004 2.000 3.002 2 1000.084 1500.991 MAIN_SUB@0
3 20.056 5.008 1.004 1.004 1 1003.995 1003.995 MAIN_SUB2@1
4 20.017 6.010 1.002 1.002 1 1002.034 1002.034 MAIN_SUB2@3
5 20.012 7.012 1.002 1.002 1 1001.809 1001.809 MAIN_SUB2@0
6 19.979 8.012 1.000 1.000 1 1000.149 1000.149 MAIN_SUB2@2
7 19.978 9.012 1.000 2.004 1 1000.063 2004.060 MAIN_SUB@1
8 19.978 10.012 1.000 2.002 1 1000.063 2002.101 MAIN_SUB@3
9 19.977 11.012 1.000 2.000 1 1000.038 2000.191 MAIN_SUB@2
10 0.002 11.012 0.000 0.000 2 0.052 0.052 __vernier__@2
11 0.002 11.012 0.000 0.000 2 0.052 0.052 __vernier__@1
12 0.002 11.013 0.000 0.000 2 0.052 0.052 __vernier__@3
13 0.001 11.013 0.000 0.000 4 0.007 0.007 __vernier__@0
4 changes: 2 additions & 2 deletions post-processing/tests/data/vernier-output/vernier-output-test-0
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Original file line number Diff line number Diff line change
Expand Up @@ -6,5 +6,5 @@ Profiling on 1 thread(s).
(Size; Size/sec; Size/call; MinSize; MaxSize)
(self) (sec) (sec) (sec) ms/call ms/call

1 44.130 2.583 2.583 5.854 1 2583.167 5853.527 __test_app__
2 34.563 4.606 2.023 2.077 2 1011.582 1038.697 some_process
1 44.130 2.583 2.583 5.854 1 2583.167 5853.527 __test_app__@0
2 34.563 4.606 2.023 2.077 2 1011.582 1038.697 some_process@0
4 changes: 2 additions & 2 deletions post-processing/tests/data/vernier-output/vernier-output-test-1
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Original file line number Diff line number Diff line change
Expand Up @@ -6,5 +6,5 @@ Profiling on 1 thread(s).
(Size; Size/sec; Size/call; MinSize; MaxSize)
(self) (sec) (sec) (sec) ms/call ms/call

1 43.991 3.009 3.009 3.069 2 1504.362 1534.740 some_process
2 37.835 5.596 2.588 6.839 1 2587.638 6839.336 __test_app__
1 43.991 3.009 3.009 3.069 2 1504.362 1534.740 some_process@0
2 37.835 5.596 2.588 6.839 1 2587.638 6839.336 __test_app__@0
6 changes: 3 additions & 3 deletions post-processing/tests/test_cli_tools.py
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Expand Up @@ -23,9 +23,9 @@ def setUp(self):
self.test_data_dir = Path(__file__).parent / 'data'
# pylint: disable=line-too-long
self.test_data_kgo = (
'| Routine | Total time (s) | Self (s) | Cumul time (s) | No. calls | % time | Time per call (s) |\n' +
'| __test_app__ | 6.3465 | 2.5855 | 4.0895 | 1 | 40.9825 | 6.3465 |\n' +
'| some_process | 2.573 | 2.516 | 3.8075 | 2 | 39.277 | 1.2865 |\n'
'| Routine | Total time (s) | Self (s) | Cumul time (s) | Max no. calls | % time | Time per call (s) |\n' +
'| __test_app__ | 6.3465 | 2.5855 | 4.0895 | 1 | 40.9825 | 6.3465 |\n' +
'| some_process | 2.573 | 2.516 | 3.8075 | 2 | 39.277 | 1.2865 |\n'
)
return super().setUp()

Expand Down
126 changes: 108 additions & 18 deletions post-processing/tests/test_vernier_data.py
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Expand Up @@ -39,6 +39,89 @@ def test_add_empty_calliper(self):
self.assertEqual(self.test_data.data["test_calliper"].self_time, [])
self.assertEqual(self.test_data.data["test_calliper"].total_time, [])
self.assertEqual(self.test_data.data["test_calliper"].n_calls, [])
self.assertEqual(self.test_data.data["test_calliper"].rank, [])
self.assertEqual(self.test_data.data["test_calliper"].thread, [])

def test_get(self):
"""
Tests that the get method of VernierData returns the expected data.
"""
self.test_data.add_calliper("test_calliper")
self.test_data.data["test_calliper"].time_percent = [10.0, 20.0]
self.test_data.data["test_calliper"].cumul_time = [30.0, 40.0]
self.test_data.data["test_calliper"].self_time = [5.0, 15.0]
self.test_data.data["test_calliper"].total_time = [25.0, 35.0]
self.test_data.data["test_calliper"].n_calls = [2, 2]
self.test_data.data["test_calliper"].rank = [0, 1]
self.test_data.data["test_calliper"].thread = [0, 0]
calliper_data = self.test_data.get("test_calliper")
self.assertEqual(calliper_data.time_percent, [10.0, 20.0])
self.assertEqual(calliper_data.cumul_time, [30.0, 40.0])
self.assertEqual(calliper_data.self_time, [5.0, 15.0])
self.assertEqual(calliper_data.total_time, [25.0, 35.0])
self.assertEqual(calliper_data.n_calls, [2, 2])
self.assertEqual(calliper_data.rank, [0, 1])
self.assertEqual(calliper_data.thread, [0, 0])

def test_get_rank(self):
"""
Tests getter for data from a single rank
"""
self.test_data.add_calliper("test_calliper")
self.test_data.data["test_calliper"].time_percent = [10.0, 20.0]
self.test_data.data["test_calliper"].cumul_time = [30.0, 40.0]
self.test_data.data["test_calliper"].self_time = [5.0, 15.0]
self.test_data.data["test_calliper"].total_time = [25.0, 35.0]
self.test_data.data["test_calliper"].n_calls = [2, 2]
self.test_data.data["test_calliper"].rank = [0, 1]
self.test_data.data["test_calliper"].thread = [0, 0]
calliper_data = self.test_data.get("test_calliper", rank=1)
self.assertEqual(calliper_data.time_percent, [20.0])
self.assertEqual(calliper_data.cumul_time, [40.0])
self.assertEqual(calliper_data.self_time, [15.0])
self.assertEqual(calliper_data.total_time, [35.0])
self.assertEqual(calliper_data.n_calls, [2])
self.assertEqual(calliper_data.rank, [1])
self.assertEqual(calliper_data.thread, [0])

def test_get_thread(self):
"""
Tests getter for data from a single thread
"""
self.test_data.add_calliper("test_calliper")
self.test_data.data["test_calliper"].time_percent = [10.0, 20.0]
self.test_data.data["test_calliper"].cumul_time = [30.0, 40.0]
self.test_data.data["test_calliper"].self_time = [5.0, 15.0]
self.test_data.data["test_calliper"].total_time = [25.0, 35.0]
self.test_data.data["test_calliper"].n_calls = [2, 2]
self.test_data.data["test_calliper"].rank = [0, 0]
self.test_data.data["test_calliper"].thread = [0, 1]
calliper_data = self.test_data.get("test_calliper", thread=1)
self.assertEqual(calliper_data.time_percent, [20.0])
self.assertEqual(calliper_data.cumul_time, [40.0])
self.assertEqual(calliper_data.self_time, [15.0])
self.assertEqual(calliper_data.total_time, [35.0])
self.assertEqual(calliper_data.n_calls, [2])
self.assertEqual(calliper_data.rank, [0])
self.assertEqual(calliper_data.thread, [1])

def test_get_rank_and_thread(self):
self.test_data.add_calliper("test_calliper")
self.test_data.data["test_calliper"].time_percent = [10.0, 20.0, 10.5, 20.5]
self.test_data.data["test_calliper"].cumul_time = [30.0, 40.0, 30.5, 40.5]
self.test_data.data["test_calliper"].self_time = [5.0, 15.0, 5.5, 15.5]
self.test_data.data["test_calliper"].total_time = [25.0, 35.0, 25.5, 35.5]
self.test_data.data["test_calliper"].n_calls = [2, 2, 2, 2]
self.test_data.data["test_calliper"].rank = [0, 0, 1, 1]
self.test_data.data["test_calliper"].thread = [0, 1, 0, 1]
calliper_data = self.test_data.get("test_calliper", thread=1, rank=1)
self.assertEqual(calliper_data.time_percent, [20.5])
self.assertEqual(calliper_data.cumul_time, [40.5])
self.assertEqual(calliper_data.self_time, [15.5])
self.assertEqual(calliper_data.total_time, [35.5])
self.assertEqual(calliper_data.n_calls, [2])
self.assertEqual(calliper_data.rank, [1])
self.assertEqual(calliper_data.thread, [1])

def test_filter_calliper(self):
"""
Expand Down Expand Up @@ -91,14 +174,16 @@ def test_write_txt_output_file(self):
self.test_data.data["test_calliper"].self_time = [5.0, 15.0]
self.test_data.data["test_calliper"].total_time = [25.0, 35.0]
self.test_data.data["test_calliper"].n_calls = [2]
self.test_data.data["test_calliper"].rank = [0, 1]
self.test_data.data["test_calliper"].thread = [0, 0]

# pylint: disable=unspecified-encoding
with tempfile.NamedTemporaryFile(delete=False) as tmp_file:
self.test_data.write_txt_output(Path(tmp_file.name))
contents = Path(tmp_file.name).read_text().splitlines()
# pylint: disable=line-too-long
self.assertEqual("| Routine | Total time (s) | Self (s) | Cumul time (s) | No. calls | % time | Time per call (s) |", contents[0])
self.assertEqual("| test_calliper | 30.0 | 10.0 | 35.0 | 2 | 15.0 | 15.0 |", contents[1])
self.assertEqual("| Routine | Total time (s) | Self (s) | Cumul time (s) | Max no. calls | % time | Time per call (s) |", contents[0])
self.assertEqual("| test_calliper | 30.0 | 10.0 | 35.0 | 2 | 15.0 | 15.0 |", contents[1])

def test_write_txt_output_terminal(self):
"""
Expand All @@ -111,15 +196,17 @@ def test_write_txt_output_terminal(self):
self.test_data.data["test_calliper"].self_time = [3.0, 4.0]
self.test_data.data["test_calliper"].total_time = [15.0, 55.0]
self.test_data.data["test_calliper"].n_calls = [2]
self.test_data.data["test_calliper"].rank = [0, 1]
self.test_data.data["test_calliper"].thread = [0, 0]

write_output = StringIO()
sys.stdout = write_output
self.test_data.write_txt_output()
sys.stdout = sys.__stdout__

# pylint: disable=line-too-long
self.assertEqual("| Routine | Total time (s) | Self (s) | Cumul time (s) | No. calls | % time | Time per call (s) |", write_output.getvalue().splitlines()[0])
self.assertEqual("| test_calliper | 35.0 | 3.5 | 11.0 | 2 | 45.0 | 17.5 |", write_output.getvalue().splitlines()[1])
self.assertEqual("| Routine | Total time (s) | Self (s) | Cumul time (s) | Max no. calls | % time | Time per call (s) |", write_output.getvalue().splitlines()[0])
self.assertEqual("| test_calliper | 35.0 | 3.5 | 11.0 | 2 | 45.0 | 17.5 |", write_output.getvalue().splitlines()[1])

def test_aggregate(self):
"""
Expand All @@ -133,6 +220,8 @@ def test_aggregate(self):
data1.data["calliper_a"].self_time = [5.0, 15.0]
data1.data["calliper_a"].total_time = [25.0, 35.0]
data1.data["calliper_a"].n_calls = [2, 2]
data1.data["calliper_a"].rank = [0, 1]
data1.data["calliper_a"].thread = [0, 0]

data2 = VernierData()
data2.add_calliper("calliper_a")
Expand All @@ -141,6 +230,8 @@ def test_aggregate(self):
data2.data["calliper_a"].self_time = [6.0, 16.0]
data2.data["calliper_a"].total_time = [28.0, 38.0]
data2.data["calliper_a"].n_calls = [3, 3]
data2.data["calliper_a"].rank = [0, 1]
data2.data["calliper_a"].thread = [0, 0]

aggregated = VernierData()
aggregated.aggregate([data1, data2])
Expand Down Expand Up @@ -174,6 +265,8 @@ def test_aggregate_inconsistent(self):
data1.data["calliper_a"].self_time = [5.0, 15.0]
data1.data["calliper_a"].total_time = [25.0, 35.0]
data1.data["calliper_a"].n_calls = [2, 2]
data1.data["calliper_a"].rank = [0, 1]
data1.data["calliper_a"].thread = [0, 0]

data2 = VernierData()
data2.add_calliper("calliper_b")
Expand All @@ -182,6 +275,8 @@ def test_aggregate_inconsistent(self):
data2.data["calliper_b"].self_time = [6.0, 16.0]
data2.data["calliper_b"].total_time = [28.0, 38.0]
data2.data["calliper_b"].n_calls = [3, 3]
data2.data["calliper_b"].rank = [0, 1]
data2.data["calliper_b"].thread = [0, 0]

with self.assertRaises(ValueError):
aggregated = VernierData()
Expand All @@ -203,19 +298,6 @@ def test_aggregate_inconsistent_ok(self):
self.assertIn("calliper_a", aggregated.data)
self.assertIn("calliper_b", aggregated.data)

def test_get(self):
"""
Test that the get method of the VernierData class works as expected.
"""
data1 = VernierData()
data1.add_calliper("calliper_a")
data1.data["calliper_a"].time_percent = [10.0, 20.0]
data1.data["calliper_a"].cumul_time = [30.0, 40.0]
data1.data["calliper_a"].self_time = [5.0, 15.0]
data1.data["calliper_a"].total_time = [25.0, 35.0]
data1.data["calliper_a"].n_calls = [2, 2]
self.assertEqual(len(data1.get("calliper_a")), 2)


class TestVernierCollation(unittest.TestCase):
"""
Expand All @@ -233,6 +315,8 @@ def _add_data(self):
data1.data["calliper_a"].self_time = [5.0, 15.0]
data1.data["calliper_a"].total_time = [25.0, 35.0]
data1.data["calliper_a"].n_calls = [2, 2]
data1.data["calliper_a"].rank = [0, 1]
data1.data["calliper_a"].thread = [0, 0]

data2 = VernierData()
data2.add_calliper("calliper_a")
Expand All @@ -241,6 +325,8 @@ def _add_data(self):
data2.data["calliper_a"].self_time = [6.0, 16.0]
data2.data["calliper_a"].total_time = [28.0, 38.0]
data2.data["calliper_a"].n_calls = [3, 3]
data2.data["calliper_a"].rank = [0, 1]
data2.data["calliper_a"].thread = [0, 0]

self.collation.add_data('test1', data1)
self.collation.add_data('test2', data2)
Expand All @@ -262,7 +348,7 @@ def test_remove_data(self):
self.collation.remove_data('test1')
self.assertEqual(len(self.collation), 1)

def test_get(self):
def test_get__collation(self):
"""
Test that the get method of VernierCollation returns the expected
VernierData instance.
Expand All @@ -284,13 +370,17 @@ def test_internal_consistency(self):
data_inc.data["calliper_a"].self_time = [5.0, 15.0]
data_inc.data["calliper_a"].total_time = [25.0, 35.0]
data_inc.data["calliper_a"].n_calls = [2, 2]
data_inc.data["calliper_a"].rank = [0, 1]
data_inc.data["calliper_a"].thread = [0, 0]

data_inc.add_calliper("calliper_b")
data_inc.data["calliper_b"].time_percent = [15.0, 25.0]
data_inc.data["calliper_b"].cumul_time = [35.0, 45.0]
data_inc.data["calliper_b"].self_time = [6.0, 16.0]
data_inc.data["calliper_b"].total_time = [28.0, 38.0]
data_inc.data["calliper_b"].n_calls = [3, 3]
data_inc.data["calliper_b"].rank = [0, 1]
data_inc.data["calliper_b"].thread = [0, 0]

with self.assertRaises(ValueError) as test_exception:
self.collation.add_data('test3', data_inc)
Expand Down
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