Issues with Setting up Aesara #1267

anirudhacharya · 2022-10-17T10:52:51Z

anirudhacharya
Oct 17, 2022

I am running into a few issues while setting up aesara on my laptop, I am raising this issue to see if others have faced the same problem and if there is a fix, or if I am doing anything wrong while setting it up.

I am using this guide to setup and test the installation.

On the latest main branch commit( c7ff283de) following things are failing -

After running python setup.py install I ran pytest tests/ from the aesara home directory and the following tests failed. I recently raised a PR and the CI system passed with all green, so clearly, these tests are only failing locally on my laptop. I am not sure if I am doing anything wrong while running the tests -

FAILED tests/test_breakpoint.py::TestPdbBreakpoint::test_infer_shape - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/test_breakpoint.py::TestPdbBreakpoint::test_grad - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/test_breakpoint.py::TestPdbBreakpoint::test_fprop - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/test_gradient.py::TestGrad::test_grad_int - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/test_gradient.py::test_subgraph_grad - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/test_gradient.py::TestConsiderConstant::test_op_removed - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/test_gradient.py::TestConsiderConstant::test_grad - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/test_gradient.py::TestZeroGrad::test_op_removed - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/test_gradient.py::TestZeroGrad::test_grad - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/test_gradient.py::TestDisconnectedGrad::test_op_removed - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/test_gradient.py::TestDisconnectedGrad::test_grad - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/test_gradient.py::test_undefined_grad_opt - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/test_gradient.py::test_jacobian_matrix - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/test_printing.py::test_pydotprint_profile - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/test_printing.py::test_debugprint - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/test_rop.py::TestRopLop::test_max - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/test_rop.py::TestRopLop::test_conv - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/test_rop.py::TestRopLop::test_flatten - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/test_rop.py::TestRopLop::test_sum - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/test_rop.py::TestRopLop::test_multiple_outputs - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
...
FAILED tests/tensor/test_elemwise.py::TestBroadcast::test_c - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/tensor/test_elemwise.py::TestBroadcast::test_c_inplace - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/tensor/test_elemwise.py::TestBroadcast::test_fill - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/tensor/test_elemwise.py::TestBroadcast::test_weird_strides - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/tensor/test_elemwise.py::TestBroadcast::test_same_inputs - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/tensor/test_elemwise.py::TestCAReduce::test_c_noopt - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/tensor/test_elemwise.py::TestCAReduce::test_infer_shape - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/tensor/test_elemwise.py::TestBitOpReduceGrad::test_all_grad - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
FAILED tests/tensor/test_elemwise.py::TestBitOpReduceGrad::test_any_grad - aesara.link.c.exceptions.CompileError: Compilation failed (return status=1):
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! KeyboardInterrupt !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
/Users/anirudhacharya/miniconda3/envs/aesara-dev/lib/python3.10/codecs.py:309: KeyboardInterrupt
(to show a full traceback on KeyboardInterrupt use --full-trace)
================================================== 231 failed, 1879 passed, 84 skipped, 25 xfailed, 1 xpassed, 2591 warnings in 2875.66s (0:47:55) ===================================================

These are not the only failures, there are more which I did not update here, because the list would be too long.

~~When I try to install the documentation dependencies with this command pip install -r requirements-rtd.txt it throws the following error~~ - no longer an issue due to this comment

Collecting pydot2
  Using cached pydot2-1.0.33.tar.gz (19 kB)
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [1 lines of output]
      error in pydot2 setup command: use_2to3 is invalid.
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

Versions and main components

Aesara version: 1.0.10
Python version: Python 3.9.12
Operating system: macOS Monterey version 12.0.1
How did you install Aesara: (conda/pip) python setup.py install ( built with the latest commit c7ff283de)

rlouf · 2022-10-17T10:56:51Z

rlouf
Oct 17, 2022
Maintainer

Can you give us specifics about you local setup? It's impossible for me to give you an answer otherwise; following the steps works on my machine.

0 replies

rlouf · 2022-10-17T10:59:12Z

rlouf
Oct 17, 2022
Maintainer

I'm also confused because the developer guide does not recommend running python setup.py install

0 replies

anirudhacharya · 2022-10-17T12:54:38Z

anirudhacharya
Oct 17, 2022
Author

@rlouf Output of python -c "import aesara; print(aesara.config)" is in this gist - https://gist.github.com/anirudhacharya/ef24e5f056690e3c9dfb820383b14804

Can you give us specifics about you local setup? It's impossible for me to give you an answer otherwise; following the steps works on my machine.

The steps I followed for my local setup -

conda env create -n aesara-dev -f environment.yml
conda activate aesara-dev
pip install -r requirements.txt
pre-commit install
Installed numba and jax based on this - https://aesara.readthedocs.io/en/latest/install.html#installing-aesara
1. conda install numba
2. conda install jax -c conda-forge
Build and install from source - python setup.py install. How else do you suggest I build and install from the source code? I have also tried pip install -e .

For running aesara tests I followed this - how to test that aesara works properly.

python -c "import numpy; numpy.test()"

====================================================================================== short test summary info =======================================================================================
ERROR array_api/tests/test_set_functions.py - hypothesis.errors.InvalidArgument: Array module numpy.array_api has no attribute __array_api_version__, which is required when inferring api_version....
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
1295 deselected, 5 warnings, 1 error in 5.81s

python -c "import scipy; scipy.test()"

====================================================================================== short test summary info =======================================================================================
ERROR linalg/tests/test_decomp.py::test_aligned_mem - TypeError: Skip.__init__() got multiple values for argument 'reason' - maybe you meant pytest.mark.skipif?
ERROR optimize/tests/test_linprog.py::TestLinprogSimplexDefault::test_bug_10466 - TypeError: Skip.__init__() got multiple values for argument 'reason' - maybe you meant pytest.mark.skipif?
ERROR optimize/tests/test_linprog.py::TestLinprogSimplexBland::test_bug_10466 - TypeError: Skip.__init__() got multiple values for argument 'reason' - maybe you meant pytest.mark.skipif?
ERROR optimize/tests/test_linprog.py::TestLinprogSimplexNoPresolve::test_bug_10466 - TypeError: Skip.__init__() got multiple values for argument 'reason' - maybe you meant pytest.mark.skipif?
ERROR optimize/tests/test_linprog.py::TestLinprogIPDense::test_bug_10466 - TypeError: Skip.__init__() got multiple values for argument 'reason' - maybe you meant pytest.mark.skipif?
ERROR optimize/tests/test_linprog.py::TestLinprogIPSparse::test_bug_10466 - TypeError: Skip.__init__() got multiple values for argument 'reason' - maybe you meant pytest.mark.skipif?
ERROR optimize/tests/test_linprog.py::TestLinprogIPSparsePresolve::test_bug_10466 - TypeError: Skip.__init__() got multiple values for argument 'reason' - maybe you meant pytest.mark.skipif?
ERROR optimize/tests/test_linprog.py::TestLinprogRSCommon::test_bug_10466 - TypeError: Skip.__init__() got multiple values for argument 'reason' - maybe you meant pytest.mark.skipif?
ERROR optimize/tests/test_linprog.py::TestLinprogRSBland::test_bug_10466 - TypeError: Skip.__init__() got multiple values for argument 'reason' - maybe you meant pytest.mark.skipif?
ERROR optimize/tests/test_linprog.py::TestLinprogHiGHSSimplexDual::test_bug_10466 - TypeError: Skip.__init__() got multiple values for argument 'reason' - maybe you meant pytest.mark.skipif?
ERROR optimize/tests/test_linprog.py::TestLinprogHiGHSIPM::test_bug_10466 - TypeError: Skip.__init__() got multiple values for argument 'reason' - maybe you meant pytest.mark.skipif?
======================================= 32567 passed, 2077 skipped, 11134 deselected, 105 xfailed, 9 xpassed, 148179 warnings, 11 errors in 441.60s (0:07:21) ========================================

AESARA_FLAGS='' pytest tests/ - It fails with the log pasted in the issue description.

0 replies

anirudhacharya · 2022-10-17T14:49:56Z

anirudhacharya
Oct 17, 2022
Author

When I try to install the documentation dependencies with this command pip install -r requirements-rtd.txt it throws the following error

Collecting pydot2
  Using cached pydot2-1.0.33.tar.gz (19 kB)
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [1 lines of output]
      error in pydot2 setup command: use_2to3 is invalid.
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

This is no longer an issue. I am able to build the documentation without installing pydot2. I work with Python version 3.9. And pydot library and not pydot2 is used for that version of Python.

0 replies

anirudhacharya · 2022-10-17T16:34:38Z

anirudhacharya
Oct 17, 2022
Author

The other test failures due Compilation Failed issue still exists, I am trying to triage it.

0 replies

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Issues with Setting up Aesara #1267

anirudhacharya Oct 17, 2022

Versions and main components

Replies: 5 comments

rlouf Oct 17, 2022 Maintainer

rlouf Oct 17, 2022 Maintainer

anirudhacharya Oct 17, 2022 Author

anirudhacharya Oct 17, 2022 Author

anirudhacharya Oct 17, 2022 Author

anirudhacharya
Oct 17, 2022

rlouf
Oct 17, 2022
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anirudhacharya
Oct 17, 2022
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anirudhacharya
Oct 17, 2022
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anirudhacharya
Oct 17, 2022
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