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openPMD
CI: Add ADIOS1 (BP3) Python Test
Make sure we test ADIOS1 in Python tests.
We have known issues here that we need to fix.
Ok, so in Unittest.py these tests fail:
======================================================================
ERROR: testConstantRecords (API.APITest.APITest)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/runner/work/openPMD-api/openPMD-api/test/python/unittest/API/APITest.py", line 570, in testConstantRecords
self.makeConstantRoundTrip(ext)
File "/home/runner/work/openPMD-api/openPMD-api/test/python/unittest/API/APITest.py", line 427, in makeConstantRoundTrip
ms["int16"][SCALAR].make_constant(np.int16(234))
RuntimeError: make_constant: Only scalar values supported!
======================================================================
ERROR: testParticlePatches (API.APITest.APITest)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/runner/work/openPMD-api/openPMD-api/test/python/unittest/API/APITest.py", line 1643, in testParticlePatches
self.backend_particle_patches(ext)
File "/home/runner/work/openPMD-api/openPMD-api/test/python/unittest/API/APITest.py", line 1591, in backend_particle_patches
e.particle_patches["numParticles"][SCALAR].store(0, np.uint64(10))
RuntimeError: store: Only scalar values supported!
======================================================================
FAIL: testAttributes (API.APITest.APITest)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/runner/work/openPMD-api/openPMD-api/test/python/unittest/API/APITest.py", line 384, in testAttributes
self.attributeRoundTrip(ext)
File "/home/runner/work/openPMD-api/openPMD-api/test/python/unittest/API/APITest.py", line 277, in attributeRoundTrip
self.assertEqual(series.get_attribute("int16"), 234)
AssertionError: [234, 0] != 234
----------------------------------------------------------------------
I've now fixed the number of chunks issue uncovered by this (simple fix in the tests).
Also, this uncovered a long-standing use-after-free bug in ADIOS1, should now also be fixed.
You seem to be seeing other errors than I did, will address those next.
Ok, so in
Unittest.pythese tests fail:====================================================================== ERROR: testConstantRecords (API.APITest.APITest) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/runner/work/openPMD-api/openPMD-api/test/python/unittest/API/APITest.py", line 570, in testConstantRecords self.makeConstantRoundTrip(ext) File "/home/runner/work/openPMD-api/openPMD-api/test/python/unittest/API/APITest.py", line 427, in makeConstantRoundTrip ms["int16"][SCALAR].make_constant(np.int16(234)) RuntimeError: make_constant: Only scalar values supported! ====================================================================== ERROR: testParticlePatches (API.APITest.APITest) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/runner/work/openPMD-api/openPMD-api/test/python/unittest/API/APITest.py", line 1643, in testParticlePatches self.backend_particle_patches(ext) File "/home/runner/work/openPMD-api/openPMD-api/test/python/unittest/API/APITest.py", line 1591, in backend_particle_patches e.particle_patches["numParticles"][SCALAR].store(0, np.uint64(10)) RuntimeError: store: Only scalar values supported! ====================================================================== FAIL: testAttributes (API.APITest.APITest) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/runner/work/openPMD-api/openPMD-api/test/python/unittest/API/APITest.py", line 384, in testAttributes self.attributeRoundTrip(ext) File "/home/runner/work/openPMD-api/openPMD-api/test/python/unittest/API/APITest.py", line 277, in attributeRoundTrip self.assertEqual(series.get_attribute("int16"), 234) AssertionError: [234, 0] != 234 ----------------------------------------------------------------------
These don't look like ADIOS1-specific issues to me. More like somehow pybind appends zeroes to scalars for some reason?? I'll push a commit for some printf CI debugging, can't reproduce this locally.
Thanks for the pushes! I will pull and rebased agains the clang-format changes now.
pybind/numpy scalars are a bit special: there are zero-dimensional and I think I had to hack a little for them to work. Not sure if the ADIOS1 part contains maybe a work-around because attributes can be arrays or scalars and were patched in relatively late for us...
One definitely needs numpy 1.15+ for numpy bugs and there is this helper that would also work well: https://github.com/pybind/pybind11/pull/3544
pybind/numpy scalars are a bit special: there are zero-dimensional and I think I had to hack a little for them to work.
Yep, I saw this in the C++ side of the failing functions
Not sure if the ADIOS1 part contains maybe a work-around because attributes can be arrays or scalars and were patched in relatively late for us...
It looks to me like the errors happen before ADIOS1 even has the chance to do anything?
ERROR: testParticlePatches (API.APITest.APITest)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/runner/work/openPMD-api/openPMD-api/test/python/unittest/API/APITest.py", line 1643, in testParticlePatches
self.backend_particle_patches(ext)
File "/home/runner/work/openPMD-api/openPMD-api/test/python/unittest/API/APITest.py", line 1591, in backend_particle_patches
e.particle_patches["numParticles"][SCALAR].store(0, np.uint64(10))
RuntimeError: store: Only scalar values supported!
First error:
2022-02-18T21:28:07.5858113Z ======================================================================
2022-02-18T21:28:07.5858385Z ERROR: testConstantRecords (API.APITest.APITest)
2022-02-18T21:28:07.5858839Z ----------------------------------------------------------------------
2022-02-18T21:28:07.5859148Z Traceback (most recent call last):
2022-02-18T21:28:07.5859803Z File "/home/runner/work/openPMD-api/openPMD-api/test/python/unittest/API/APITest.py", line 570, in testConstantRecords
2022-02-18T21:28:07.5860213Z self.makeConstantRoundTrip(ext)
2022-02-18T21:28:07.5860750Z File "/home/runner/work/openPMD-api/openPMD-api/test/python/unittest/API/APITest.py", line 427, in makeConstantRoundTrip
2022-02-18T21:28:07.5861164Z ms["int16"][SCALAR].make_constant(np.int16(234))
2022-02-18T21:28:07.5861504Z RuntimeError: make_constant: Only scalar values supported! (found 2values)
For tracing this, I added this to the CI:
.def(
"make_constant",
[](RecordComponent &rc, py::buffer &a) {
py::buffer_info buf = a.request();
auto const dtype = dtype_from_bufferformat(buf.format);
using DT = Datatype;
// allow one-element n-dimensional buffers as well
py::ssize_t numElements = 1;
if (buf.ndim > 0)
{
std::cout << "Buffer has dimensionality: " << buf.ndim
<< std::endl;
for (auto d = 0; d < buf.ndim; ++d)
{
std::cout << "Extent of dimensionality " << d << ": "
<< buf.shape.at(d) << std::endl;
numElements *= buf.shape.at(d);
}
}
Output is:
2022-02-18T21:28:07.5836071Z testConstantRecords (API.APITest.APITest) ... Buffer has dimensionality: 1
2022-02-18T21:28:07.5836391Z Extent of dimensionality 0: 2
2022-02-18T21:28:07.5836613Z ERROR
Raw log: https://pipelines.actions.githubusercontent.com/1ySCTQQQJyZRSB9lxu8ROYabgAQhsYw84NgJV467yhBP5Zcqdx/_apis/pipelines/1/runs/9483/signedlogcontent/6?urlExpires=2022-02-28T10%3A48%3A39.2682290Z&urlSigningMethod=HMACV1&urlSignature=Ir0ZKU4%2B0Y%2FW6GqAcfdsg2p5EDvsy5W6Dixw3L84di0%3D
Second error:
2022-02-18T21:28:07.5861820Z ======================================================================
2022-02-18T21:28:07.5862125Z ERROR: testParticlePatches (API.APITest.APITest)
2022-02-18T21:28:07.5862561Z ----------------------------------------------------------------------
2022-02-18T21:28:07.5862876Z Traceback (most recent call last):
2022-02-18T21:28:07.5863412Z File "/home/runner/work/openPMD-api/openPMD-api/test/python/unittest/API/APITest.py", line 1643, in testParticlePatches
2022-02-18T21:28:07.5863788Z self.backend_particle_patches(ext)
2022-02-18T21:28:07.5864332Z File "/home/runner/work/openPMD-api/openPMD-api/test/python/unittest/API/APITest.py", line 1591, in backend_particle_patches
2022-02-18T21:28:07.5864766Z e.particle_patches["numParticles"][SCALAR].store(0, np.uint64(10))
2022-02-18T21:28:07.5865127Z RuntimeError: store: Only scalar values supported! (found 8values)
Similar behavior:
2022-02-18T21:28:07.5852527Z testParticlePatches (API.APITest.APITest) ... Buffer has dimensionality: 1
2022-02-18T21:28:07.5852846Z Extent of dimensionality 0: 8
Third error:
2022-02-18T21:28:07.5865436Z ======================================================================
2022-02-18T21:28:07.5865707Z FAIL: testAttributes (API.APITest.APITest)
2022-02-18T21:28:07.5866229Z ----------------------------------------------------------------------
2022-02-18T21:28:07.5866540Z Traceback (most recent call last):
2022-02-18T21:28:07.5867070Z File "/home/runner/work/openPMD-api/openPMD-api/test/python/unittest/API/APITest.py", line 384, in testAttributes
2022-02-18T21:28:07.5867460Z self.attributeRoundTrip(ext)
2022-02-18T21:28:07.5867976Z File "/home/runner/work/openPMD-api/openPMD-api/test/python/unittest/API/APITest.py", line 277, in attributeRoundTrip
2022-02-18T21:28:07.5868476Z self.assertEqual(series.get_attribute("int16"), 234)
2022-02-18T21:28:07.5868747Z AssertionError: [234, 0] != 234
Error is:
2022-02-18T21:28:07.5827561Z testAttributes (API.APITest.APITest) ... Attribute 'char' has type: STRING
2022-02-18T21:28:07.5828770Z and value: c
2022-02-18T21:28:07.5829312Z Attribute 'pystring' has type: STRING
2022-02-18T21:28:07.5829738Z and value: howdy!
2022-02-18T21:28:07.5830225Z Attribute 'pystring2' has type: STRING
2022-02-18T21:28:07.5830611Z and value: howdy, too!
2022-02-18T21:28:07.5831006Z Attribute 'pystring3' has type: VEC_UCHAR
2022-02-18T21:28:07.5831436Z and value: [h, o, w, d, y, ,, , a, g, a, i, n, !]
2022-02-18T21:28:07.5832208Z Attribute 'pyint' has type: UCHAR
2022-02-18T21:28:07.5832768Z and value:
2022-02-18T21:28:07.5833076Z Attribute 'pyfloat' has type: DOUBLE
2022-02-18T21:28:07.5833566Z and value: 3.1416
2022-02-18T21:28:07.5833869Z Attribute 'pybool' has type: BOOL
2022-02-18T21:28:07.5834106Z and value: 0
2022-02-18T21:28:07.5834399Z Attribute 'int16' has type: VEC_UCHAR
2022-02-18T21:28:07.5834720Z and value: [�,
2022-02-18T21:28:07.5834923Z ]
2022-02-18T21:28:07.5835086Z FAIL
Summing up the above three messages: pybind11 seems to represent scalar ints as vector of uchar according to the integer's size??
I'm relatively certain that this has nothing to do with ADIOS1.
I think you have more experience with pybind11 datatypes, so I'll wait for your feedback before opening an issue.