TST, CI: add ARM64 Graviton 2 to CI (MDAnalysis#2956)

* TST, CI: add ARM64 Graviton 2 to CI

* start testing MDAnalysis on ARM64 using
new AWS Graviton 2 architecture available
in Travis CI

* testing on my fork shows only two failures
in the MDAnalysis test suite using a fairly
minimal set of dependencies; we can probably
either fix those or skip them and open an issue

* the test failures are:
`test_written_remarks_property`
`TestEncoreClustering.test_clustering_three_ensembles_two_identical`

* run time for this CI entry is about
23 minutes, which is solid for ARM; we save a lot
of time using experimental upstream wheels in some
cases and excluding (source builds of) dependencies
where possible until the ARM64 binary wheel ecosystem
matures a bit more

* MAINT: ARM64 shims

* adjust `CAffinityPropagation()` C-level function to use `double`
instead of `float` in some strategic locations that allow the
`test_clustering_three_ensembles_two_identical()` test to pass
on gcc115 ARM64 machine

* mark `test_written_remarks_property()` as a known failure on
ARM64; it fails in Travis CI on that platform, but not on gcc115
ARM64 machine; that said, this test is already known to be flaky
on Windows 32-bit (may depend on character settings on machine?)

* MAINT: MR 2956 revisions

* reduce optimization level of MDAnalysis builds on
ARM64 to avoid problems with `ap.c` causing test failures
on that architecture

* revert any source changes to `ap.c`

.disabled-travis.yml

@@ -111,6 +111,31 @@ jobs:
            INSTALL_HOLE="false"
            CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
 
+    - os: linux
+      language: python
+      arch: arm64-graviton2
+      python:
+        - "3.7"
+      dist: focal
+      virt: vm
+      group: edge
+      before_install:
+        - python -m pip install cython numpy
+        # special test SciPy wheel for ARM64:
+        - python -m pip install https://anaconda.org/multibuild-wheels-staging/scipy/1.6.0.dev0+a240c17/download/scipy-1.6.0.dev0+a240c17-cp37-cp37m-manylinux2014_aarch64.whl
+        - python -m pip install --no-build-isolation hypothesis matplotlib pytest pytest-cov pytest-xdist tqdm
+      install:
+        - cd package
+        - python setup.py install
+        - cd ../testsuite
+        - python setup.py install
+        - cd ..
+      script:
+        - cd testsuite
+        - python -m pytest ./MDAnalysisTests --disable-pytest-warnings -n 8 -rsx --cov=MDAnalysis
+      after_success:
+        - echo "Override this stage for ARM64"
+
   allow_failures:
     - env: NUMPY_VERSION=dev EVENT_TYPE="cron"
 

package/setup.py

@@ -268,8 +268,15 @@ def extensions(config):
     use_cython = config.get('use_cython', default=not is_release)
     use_openmp = config.get('use_openmp', default=True)
 
-    extra_compile_args = ['-std=c99', '-ffast-math', '-O3', '-funroll-loops',
-                          '-fsigned-zeros']  # see #2722
+    if platform.machine() == 'aarch64':
+        # reduce optimization level for ARM64 machines
+        # because of issues with test failures sourcing to:
+        # MDAnalysis/analysis/encore/clustering/src/ap.c
+        extra_compile_args = ['-std=c99', '-ffast-math', '-O1', '-funroll-loops',
+                              '-fsigned-zeros']
+    else:
+        extra_compile_args = ['-std=c99', '-ffast-math', '-O3', '-funroll-loops',
+                              '-fsigned-zeros']  # see #2722
     define_macros = []
     if config.get('debug_cflags', default=False):
         extra_compile_args.extend(['-Wall', '-pedantic'])

testsuite/MDAnalysisTests/formats/test_libdcd.py

@@ -22,6 +22,7 @@
 import sys
 import string
 import struct
+import platform
 
 import hypothesis.strategies as strategies
 from hypothesis import example, given
@@ -317,8 +318,10 @@ def write_dcd(in_name, out_name, remarks='testing', header=None):
             f_out.write(xyz=frame.xyz, box=frame.unitcell)
 
 
-@pytest.mark.xfail(os.name == 'nt' and sys.maxsize <= 2**32,
-                   reason="occasional fail on 32-bit windows")
+@pytest.mark.xfail((os.name == 'nt'
+                    and sys.maxsize <= 2**32) or
+                    platform.machine() == 'aarch64',
+                   reason="occasional fail on 32-bit windows and ARM")
 @given(remarks=strategies.text(
     alphabet=string.printable, min_size=0,
     max_size=239))  # handle the printable ASCII strings