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Posted to issues@mxnet.apache.org by GitBox <gi...@apache.org> on 2022/02/03 17:52:29 UTC
[GitHub] [incubator-mxnet] josephevans opened a new issue #20869: Upgrade numpy supported versions
josephevans opened a new issue #20869:
URL: https://github.com/apache/incubator-mxnet/issues/20869
We currently pin down numpy versions in our setup.py script:
master: `numpy<2.0.0,>1.16.0` (see https://github.com/apache/incubator-mxnet/blob/master/tools/pip/setup.py#L62)
v1.9.x: `numpy<2.0.0,>1.16.0` (see https://github.com/apache/incubator-mxnet/blob/v1.9.x/tools/pip/setup.py#L63)
Our CI system, however, pins down specific versions:
master: `numpy>=1.17,<1.20.0` (see https://github.com/apache/incubator-mxnet/blob/master/ci/docker/install/requirements#L22)
v1.9.x: `numpy>1.16.0,<1.19.0` (see https://github.com/apache/incubator-mxnet/blob/v1.9.x/ci/docker/install/requirements#L29)
The are vulnerabilities reported in numpy versions currently used in our CI system.
https://nvd.nist.gov/vuln/detail/CVE-2021-41495
https://nvd.nist.gov/vuln/detail/CVE-2021-41496
When attempting to upgrade the version of numpy, the following tests are failing:
- test_numpy_interoperability.test_np_array_function_protocol
- test_numpy_op.test_np_delete
Failing test details:
windows-cpu run in v1.9.x: https://jenkins.mxnet-ci.amazon-ml.com/blue/organizations/jenkins/mxnet-validation%2Fwindows-cpu/detail/PR-20859/2/pipeline/
```
======================================================================
[2022-02-03T01:16:31.090Z] ERROR: test_numpy_interoperability.test_np_array_function_protocol
[2022-02-03T01:16:31.090Z] ----------------------------------------------------------------------
[2022-02-03T01:16:31.090Z] Traceback (most recent call last):
[2022-02-03T01:16:31.090Z] File "C:\Python38\lib\site-packages\nose\case.py", line 198, in runTest
[2022-02-03T01:16:31.090Z] self.test(*self.arg)
[2022-02-03T01:16:31.090Z] File "C:\jenkins_slave\workspace\ut-python-cpu\tests\python\unittest\common.py", line 218, in test_new
[2022-02-03T01:16:31.090Z] orig_test(*args, **kwargs)
[2022-02-03T01:16:31.090Z] File "C:\jenkins_slave\workspace\ut-python-cpu\windows_package\python\mxnet\util.py", line 297, in _with_np_shape
[2022-02-03T01:16:31.090Z] return func(*args, **kwargs)
[2022-02-03T01:16:31.090Z] File "C:\jenkins_slave\workspace\ut-python-cpu\windows_package\python\mxnet\util.py", line 481, in _with_np_array
[2022-02-03T01:16:31.090Z] return func(*args, **kwargs)
[2022-02-03T01:16:31.090Z] File "C:\jenkins_slave\workspace\ut-python-cpu\windows_package\python\mxnet\numpy_dispatch_protocol.py", line 57, in _run_with_array_func_proto
[2022-02-03T01:16:31.090Z] raise RuntimeError('Running function {} with NumPy array function protocol failed'
[2022-02-03T01:16:31.090Z] RuntimeError: Running function test_np_array_function_protocol with NumPy array function protocol failed with exception arrays used as indices must be of integer (or boolean) type
[2022-02-03T01:16:31.090Z] -------------------- >> begin captured stdout << ---------------------
[2022-02-03T01:16:31.368Z] Dispatch test: all
[2022-02-03T01:16:31.368Z] Dispatch test: any
[2022-02-03T01:16:31.368Z] Dispatch test: sometrue
[2022-02-03T01:16:31.368Z] Dispatch test: argmin
[2022-02-03T01:16:31.368Z] Dispatch test: argmax
[2022-02-03T01:16:31.368Z] Dispatch test: around
[2022-02-03T01:16:31.368Z] Dispatch test: round
[2022-02-03T01:16:31.368Z] Dispatch test: round_
[2022-02-03T01:16:31.368Z] Dispatch test: argsort
[2022-02-03T01:16:31.368Z] Dispatch test: sort
[2022-02-03T01:16:31.368Z] Dispatch test: append
[2022-02-03T01:16:31.368Z] Dispatch test: broadcast_arrays
[2022-02-03T01:16:31.368Z] Dispatch test: broadcast_to
[2022-02-03T01:16:31.368Z] Dispatch test: clip
[2022-02-03T01:16:31.368Z] Dispatch test: concatenate
[2022-02-03T01:16:31.368Z] Dispatch test: copy
[2022-02-03T01:16:31.368Z] Dispatch test: cumsum
[2022-02-03T01:16:31.368Z] Dispatch test: diag
[2022-02-03T01:16:31.368Z] Dispatch test: diagonal
[2022-02-03T01:16:31.368Z] Dispatch test: diagflat
[2022-02-03T01:16:31.368Z] Dispatch test: dot
[2022-02-03T01:16:31.368Z] Dispatch test: expand_dims
[2022-02-03T01:16:31.368Z] Dispatch test: fix
[2022-02-03T01:16:31.368Z] Dispatch test: flip
[2022-02-03T01:16:31.368Z] Dispatch test: flipud
[2022-02-03T01:16:31.368Z] Dispatch test: fliplr
[2022-02-03T01:16:31.368Z] Dispatch test: inner
[2022-02-03T01:16:31.368Z] Dispatch test: insert
[2022-02-03T01:16:31.368Z] Dispatch test: max
[2022-02-03T01:16:31.368Z] Dispatch test: amax
[2022-02-03T01:16:31.368Z] Dispatch test: mean
[2022-02-03T01:16:31.368Z] Dispatch test: min
[2022-02-03T01:16:31.368Z] Dispatch test: amin
[2022-02-03T01:16:31.368Z] Dispatch test: nonzero
[2022-02-03T01:16:31.368Z] Dispatch test: ones_like
[2022-02-03T01:16:31.368Z] Dispatch test: atleast_1d
[2022-02-03T01:16:31.368Z] Dispatch test: atleast_2d
[2022-02-03T01:16:31.368Z] Dispatch test: atleast_3d
[2022-02-03T01:16:31.368Z] Dispatch test: prod
[2022-02-03T01:16:31.368Z] Dispatch test: product
[2022-02-03T01:16:31.368Z] Dispatch test: ravel
[2022-02-03T01:16:31.368Z] Dispatch test: repeat
[2022-02-03T01:16:31.368Z] Dispatch test: reshape
[2022-02-03T01:16:31.368Z] Dispatch test: roll
[2022-02-03T01:16:31.368Z] Dispatch test: split
[2022-02-03T01:16:31.368Z] Dispatch test: array_split
[2022-02-03T01:16:31.368Z] Dispatch test: hsplit
[2022-02-03T01:16:31.368Z] Dispatch test: vsplit
[2022-02-03T01:16:31.368Z] Dispatch test: dsplit
[2022-02-03T01:16:31.368Z] Dispatch test: squeeze
[2022-02-03T01:16:31.368Z] Dispatch test: stack
[2022-02-03T01:16:31.368Z] Dispatch test: std
[2022-02-03T01:16:31.368Z] Dispatch test: sum
[2022-02-03T01:16:31.368Z] Dispatch test: swapaxes
[2022-02-03T01:16:31.368Z] Dispatch test: take
[2022-02-03T01:16:31.368Z] Dispatch test: tensordot
[2022-02-03T01:16:31.368Z] Dispatch test: tile
[2022-02-03T01:16:31.368Z] Dispatch test: transpose
[2022-02-03T01:16:31.368Z] Dispatch test: unique
[2022-02-03T01:16:31.368Z] Dispatch test: unravel_index
[2022-02-03T01:16:31.368Z] Dispatch test: diag_indices_from
[2022-02-03T01:16:31.368Z] Dispatch test: delete
[2022-02-03T01:16:31.368Z]
[2022-02-03T01:16:31.628Z] --------------------- >> end captured stdout << ----------------------
[2022-02-03T01:16:31.628Z] -------------------- >> begin captured logging << --------------------
[2022-02-03T01:16:31.628Z] common: INFO: Setting module np/mx/python random seeds, use MXNET_MODULE_SEED=588078914 to reproduce.
[2022-02-03T01:16:31.628Z] common: WARNING: Error seen with seeded test, use MXNET_TEST_SEED=322621745 to reproduce.
[2022-02-03T01:16:31.628Z] --------------------- >> end captured logging << ---------------------
[2022-02-03T01:16:31.628Z]
[2022-02-03T01:16:31.628Z] ======================================================================
[2022-02-03T01:16:31.628Z] ERROR: test_numpy_op.test_np_delete
[2022-02-03T01:16:31.628Z] ----------------------------------------------------------------------
[2022-02-03T01:16:31.628Z] Traceback (most recent call last):
[2022-02-03T01:16:31.628Z] File "C:\Python38\lib\site-packages\nose\case.py", line 198, in runTest
[2022-02-03T01:16:31.628Z] self.test(*self.arg)
[2022-02-03T01:16:31.628Z] File "C:\jenkins_slave\workspace\ut-python-cpu\tests\python\unittest\common.py", line 218, in test_new
[2022-02-03T01:16:31.628Z] orig_test(*args, **kwargs)
[2022-02-03T01:16:31.628Z] File "C:\jenkins_slave\workspace\ut-python-cpu\windows_package\python\mxnet\util.py", line 297, in _with_np_shape
[2022-02-03T01:16:31.628Z] return func(*args, **kwargs)
[2022-02-03T01:16:31.628Z] File "C:\jenkins_slave\workspace\ut-python-cpu\windows_package\python\mxnet\util.py", line 481, in _with_np_array
[2022-02-03T01:16:31.628Z] return func(*args, **kwargs)
[2022-02-03T01:16:31.628Z] File "C:\jenkins_slave\workspace\ut-python-cpu\tests\python\unittest\test_numpy_op.py", line 3635, in test_np_delete
[2022-02-03T01:16:31.628Z] expected_ret = _np.delete(a.asnumpy(), obj_onp, axis=axis)
[2022-02-03T01:16:31.628Z] File "<__array_function__ internals>", line 5, in delete
[2022-02-03T01:16:31.628Z] File "C:\Python38\lib\site-packages\numpy\lib\function_base.py", line 4406, in delete
[2022-02-03T01:16:31.628Z] keep[obj,] = False
[2022-02-03T01:16:31.628Z] IndexError: index 0 is out of bounds for axis 0 with size 0
[2022-02-03T01:16:31.628Z] -------------------- >> begin captured logging << --------------------
[2022-02-03T01:16:31.628Z] common: WARNING: Error seen with seeded test, use MXNET_TEST_SEED=2089306386 to reproduce.
[2022-02-03T01:16:31.628Z] --------------------- >> end captured logging << ---------------------
```
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[GitHub] [incubator-mxnet] josephevans commented on issue #20869: Upgrade numpy supported versions
Posted by GitBox <gi...@apache.org>.
josephevans commented on issue #20869:
URL: https://github.com/apache/incubator-mxnet/issues/20869#issuecomment-1029508694
I have created a draft PR (https://github.com/apache/incubator-mxnet/pull/20872) to work on updating, will update the list of failing tests in this issue as more information is collected.
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[GitHub] [incubator-mxnet] DickJC123 commented on issue #20869: Upgrade numpy supported versions
Posted by GitBox <gi...@apache.org>.
DickJC123 commented on issue #20869:
URL: https://github.com/apache/incubator-mxnet/issues/20869#issuecomment-1063116150
I'm not able to do a reasonable job of testing an updated version of graphviz. If we put the graphviz update in this PR, then a required revert based on either a numpy or graphviz problem would revert both modules- an unfortunate coupling.
Could you suggest a graphviz version to move to, based on some testing, and we'll make a separate PR for that?
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[GitHub] [incubator-mxnet] DickJC123 removed a comment on issue #20869: Upgrade numpy supported versions
Posted by GitBox <gi...@apache.org>.
DickJC123 removed a comment on issue #20869:
URL: https://github.com/apache/incubator-mxnet/issues/20869#issuecomment-1063116150
I'm not able to do a reasonable job of testing an updated version of graphviz. If we put the graphviz update in this PR, then a required revert based on either a numpy or graphviz problem would revert both modules- an unfortunate coupling.
Could you suggest a graphviz version to move to, based on some testing, and we'll make a separate PR for that?
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[GitHub] [incubator-mxnet] huubvh95 commented on issue #20869: Upgrade numpy supported versions
Posted by GitBox <gi...@apache.org>.
huubvh95 commented on issue #20869:
URL: https://github.com/apache/incubator-mxnet/issues/20869#issuecomment-1041857721
Is it also possible to update Graphviz in the PR? The required version for Graphviz is rather old.
See issue #20897
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