Add arm support (#7500)

Fixes # .

### Description

Add arm support

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: YunLiu <[email protected]>
Co-authored-by: Eric Kerfoot <[email protected]>

Author: KumoLiu

Dockerfile

@@ -16,6 +16,10 @@ FROM ${PYTORCH_IMAGE}
 
 LABEL maintainer="[email protected]"
 
+# TODO: remark for issue [revise the dockerfile](https://github.com/zarr-developers/numcodecs/issues/431)
+WORKDIR /opt
+RUN git clone --recursive https://github.com/zarr-developers/numcodecs.git && pip wheel numcodecs
+
 WORKDIR /opt/monai
 
 # install full deps

requirements-dev.txt

@@ -26,7 +26,7 @@ mypy>=1.5.0
 ninja
 torchvision
 psutil
-cucim>=23.2.0; platform_system == "Linux"
+cucim-cu12; platform_system == "Linux" and python_version >= "3.9" and python_version <= "3.10"
 openslide-python
 imagecodecs; platform_system == "Linux" or platform_system == "Darwin"
 tifffile; platform_system == "Linux" or platform_system == "Darwin"
@@ -46,7 +46,7 @@ pynrrd
 pre-commit
 pydicom
 h5py
-nni; platform_system == "Linux"
+nni; platform_system == "Linux" and "arm" not in platform_machine and "aarch" not in platform_machine
 optuna
 git+https://github.com/Project-MONAI/MetricsReloaded@monai-support#egg=MetricsReloaded
 onnx>=1.13.0

setup.cfg

@@ -59,7 +59,7 @@ all =
     tqdm>=4.47.0
     lmdb
     psutil
-    cucim>=23.2.0
+    cucim-cu12; python_version >= '3.9' and python_version <= '3.10'
     openslide-python
     tifffile
     imagecodecs
@@ -111,7 +111,7 @@ lmdb =
 psutil =
     psutil
 cucim =
-    cucim>=23.2.0
+    cucim-cu12
 openslide =
     openslide-python
 tifffile =

tests/test_convert_to_onnx.py

@@ -12,6 +12,7 @@
 from __future__ import annotations
 
 import itertools
+import platform
 import unittest
 
 import torch
@@ -29,6 +30,12 @@
 TESTS = list(itertools.product(TORCH_DEVICE_OPTIONS, [True, False], [True, False]))
 TESTS_ORT = list(itertools.product(TORCH_DEVICE_OPTIONS, [True]))
 
+ON_AARCH64 = platform.machine() == "aarch64"
+if ON_AARCH64:
+    rtol, atol = 1e-1, 1e-2
+else:
+    rtol, atol = 1e-3, 1e-4
+
 onnx, _ = optional_import("onnx")
 
 
@@ -56,8 +63,8 @@ def test_unet(self, device, use_trace, use_ort):
                 device=device,
                 use_ort=use_ort,
                 use_trace=use_trace,
-                rtol=1e-3,
-                atol=1e-4,
+                rtol=rtol,
+                atol=atol,
             )
         else:
             # https://github.com/pytorch/pytorch/blob/release/1.9/torch/onnx/__init__.py#L182
@@ -72,8 +79,8 @@ def test_unet(self, device, use_trace, use_ort):
                 device=device,
                 use_ort=use_ort,
                 use_trace=use_trace,
-                rtol=1e-3,
-                atol=1e-4,
+                rtol=rtol,
+                atol=atol,
             )
         self.assertTrue(isinstance(onnx_model, onnx.ModelProto))
 
@@ -107,8 +114,8 @@ def test_seg_res_net(self, device, use_ort):
             device=device,
             use_ort=use_ort,
             use_trace=True,
-            rtol=1e-3,
-            atol=1e-4,
+            rtol=rtol,
+            atol=atol,
         )
         self.assertTrue(isinstance(onnx_model, onnx.ModelProto))
 

tests/test_dynunet.py

@@ -11,6 +11,7 @@
 
 from __future__ import annotations
 
+import platform
 import unittest
 from typing import Any, Sequence
 
@@ -24,6 +25,12 @@
 
 InstanceNorm3dNVFuser, _ = optional_import("apex.normalization", name="InstanceNorm3dNVFuser")
 
+ON_AARCH64 = platform.machine() == "aarch64"
+if ON_AARCH64:
+    rtol, atol = 1e-2, 1e-2
+else:
+    rtol, atol = 1e-4, 1e-4
+
 device = "cuda" if torch.cuda.is_available() else "cpu"
 
 strides: Sequence[Sequence[int] | int]
@@ -159,7 +166,7 @@ def test_consistency(self, input_param, input_shape, _):
                         with eval_mode(net_fuser):
                             result_fuser = net_fuser(input_tensor)
 
-                        assert_allclose(result, result_fuser, rtol=1e-4, atol=1e-4)
+                        assert_allclose(result, result_fuser, rtol=rtol, atol=atol)
 
 
 class TestDynUNetDeepSupervision(unittest.TestCase):

tests/test_rand_affine.py

@@ -147,7 +147,7 @@ def test_rand_affine(self, input_param, input_data, expected_val):
         g.set_random_state(123)
         result = g(**input_data)
         g.rand_affine_grid.affine = torch.eye(4, dtype=torch.float64)  # reset affine
-        test_resampler_lazy(g, result, input_param, input_data, seed=123)
+        test_resampler_lazy(g, result, input_param, input_data, seed=123, rtol=_rtol)
         if input_param.get("cache_grid", False):
             self.assertTrue(g._cached_grid is not None)
         assert_allclose(result, expected_val, rtol=_rtol, atol=1e-4, type_test="tensor")

tests/test_rand_affined.py

@@ -234,7 +234,9 @@ def test_rand_affined(self, input_param, input_data, expected_val, track_meta):
                 lazy_init_param["keys"], lazy_init_param["mode"] = key, mode
                 resampler = RandAffined(**lazy_init_param).set_random_state(123)
                 expected_output = resampler(**call_param)
-                test_resampler_lazy(resampler, expected_output, lazy_init_param, call_param, seed=123, output_key=key)
+                test_resampler_lazy(
+                    resampler, expected_output, lazy_init_param, call_param, seed=123, output_key=key, rtol=_rtol
+                )
             resampler.lazy = False
 
         if input_param.get("cache_grid", False):

tests/test_spatial_resampled.py

@@ -11,6 +11,7 @@
 
 from __future__ import annotations
 
+import platform
 import unittest
 
 import numpy as np
@@ -23,6 +24,12 @@
 from tests.lazy_transforms_utils import test_resampler_lazy
 from tests.utils import TEST_DEVICES, assert_allclose
 
+ON_AARCH64 = platform.machine() == "aarch64"
+if ON_AARCH64:
+    rtol, atol = 1e-1, 1e-2
+else:
+    rtol, atol = 1e-3, 1e-4
+
 TESTS = []
 
 destinations_3d = [
@@ -104,7 +111,7 @@ def test_flips_inverse(self, img, device, dst_affine, kwargs, expected_output):
 
         # check lazy
         lazy_xform = SpatialResampled(**init_param)
-        test_resampler_lazy(lazy_xform, output_data, init_param, call_param, output_key="img")
+        test_resampler_lazy(lazy_xform, output_data, init_param, call_param, output_key="img", rtol=rtol, atol=atol)
 
         # check inverse
         inverted = xform.inverse(output_data)["img"]