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conda-forge / scikit-image-feedstock

A conda-smithy repository for scikit-image.
BSD 3-Clause "New" or "Revised" License
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libgomp.so.1: cannot allocate memory in static TLS block error on aarch64 python 3.8 and python 3.9 #93

Open ericpre opened 1 year ago

ericpre commented 1 year ago

Solution to issue cannot be found in the documentation.

Issue

There is the following error on aarch64 with python 3.8 and python 3.9 when import the modulre skimage.feature - other python version doesn't have the issue.

  File "/home/conda/feedstock_root/build_artifacts/hyperspy-meta_1663498680772/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.8/site-packages/skimage/feature/__init__.py", line 4, in <module>
    from ._cascade import Cascade
ImportError: /home/conda/feedstock_root/build_artifacts/hyperspy-meta_1663498680772/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.8/site-packages/skimage/feature/../../../../libgomp.so.1: cannot allocate memory in static TLS block

Context

https://github.com/conda-forge/hyperspy-feedstock/pull/66 https://app.travis-ci.com/github/conda-forge/hyperspy-feedstock/builds/255692898

import: 'hyperspy._lazy_signals'
Traceback (most recent call last):
  File "/home/conda/feedstock_root/build_artifacts/hyperspy-meta_1663498680772/test_tmp/run_test.py", line 8, in <module>
    import hyperspy._lazy_signals
  File "/home/conda/feedstock_root/build_artifacts/hyperspy-meta_1663498680772/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.8/site-packages/hyperspy/_lazy_signals.py", line 21, in <module>
    from hyperspy._signals.signal2d import LazySignal2D
  File "/home/conda/feedstock_root/build_artifacts/hyperspy-meta_1663498680772/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.8/site-packages/hyperspy/_signals/signal2d.py", line 46, in <module>
    from hyperspy.utils.peakfinders2D import (
  File "/home/conda/feedstock_root/build_artifacts/hyperspy-meta_1663498680772/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.8/site-packages/hyperspy/utils/peakfinders2D.py", line 24, in <module>
    from skimage.feature import blob_dog, blob_log, match_template, peak_local_max
  File "/home/conda/feedstock_root/build_artifacts/hyperspy-meta_1663498680772/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.8/site-packages/skimage/feature/__init__.py", line 4, in <module>
    from ._cascade import Cascade
ImportError: /home/conda/feedstock_root/build_artifacts/hyperspy-meta_1663498680772/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.8/site-packages/skimage/feature/../../../../libgomp.so.1: cannot allocate memory in static TLS block
Tests failed for hyperspy-base-1.7.2-py38h81aae68_0.tar.bz2 - moving package to /home/conda/feedstock_root/build_artifacts/broken
WARNING:conda_build.build:Tests failed for hyperspy-base-1.7.2-py38h81aae68_0.tar.bz2 - moving package to /home/conda/feedstock_root/build_artifacts/broken
TESTS FAILED: hyperspy-base-1.7.2-py38h81aae68_0.tar.bz2

Installed packages

_openmp_mutex:                 4.5-2_gnu                      conda-forge
    aom:                           3.4.0-headf329_1               conda-forge
    asciitree:                     0.3.3-py_2                     conda-forge
    asttokens:                     2.0.8-pyhd8ed1ab_0             conda-forge
    attrs:                         22.1.0-pyh71513ae_1            conda-forge
    backcall:                      0.2.0-pyh9f0ad1d_0             conda-forge
    backports:                     1.0-py_2                       conda-forge
    backports.functools_lru_cache: 1.6.4-pyhd8ed1ab_0             conda-forge
    blosc:                         1.21.1-hdfcada4_3              conda-forge
    brotli:                        1.0.9-h4e544f5_7               conda-forge
    brotli-bin:                    1.0.9-h4e544f5_7               conda-forge
    brotlipy:                      0.7.0-py39h0fd3b05_1004        conda-forge
    brunsli:                       0.1-h01db608_0                 conda-forge
    bzip2:                         1.0.8-hf897c2e_4               conda-forge
    c-ares:                        1.18.1-hf897c2e_0              conda-forge
    c-blosc2:                      2.4.1-h861a2bc_0               conda-forge
    ca-certificates:               2022.9.14-h4fd8a4c_0           conda-forge
    cached-property:               1.5.2-hd8ed1ab_1               conda-forge
    cached_property:               1.5.2-pyha770c72_1             conda-forge
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    debugpy:                       1.6.3-py39h3d8bfb9_0           conda-forge
    decorator:                     5.1.1-pyhd8ed1ab_0             conda-forge
    dill:                          0.3.5.1-pyhd8ed1ab_0           conda-forge
    entrypoints:                   0.4-pyhd8ed1ab_0               conda-forge
    execnet:                       1.9.0-pyhd8ed1ab_0             conda-forge
    executing:                     1.0.0-pyhd8ed1ab_0             conda-forge
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    fsspec:                        2022.8.2-pyhd8ed1ab_0          conda-forge
    giflib:                        5.2.1-hb9de7d4_2               conda-forge
    gmp:                           6.2.1-h7fd3ca4_0               conda-forge
    gmpy2:                         2.1.2-py39hb332cb7_0           conda-forge
    h5py:                          3.7.0-nompi_py39hb5d3840_101   conda-forge
    hdf5:                          1.12.2-nompi_h7bde11e_100      conda-forge
    hyperspy-base:                 1.7.2-py39hb9a1dbb_0           local      
    idna:                          3.3-pyhd8ed1ab_0               conda-forge
    imagecodecs:                   2022.8.8-py39h39b51ec_5        conda-forge
    imageio:                       2.21.3-pyhfa7a67d_0            conda-forge
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    jpeg:                          9e-h9cdd2b7_2                  conda-forge
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    krb5:                          1.19.3-h7c456eb_0              conda-forge
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    ld_impl_linux-aarch64:         2.36.1-h02ad14f_2              conda-forge
    lerc:                          4.0.0-h4de3ea5_0               conda-forge
    libaec:                        1.0.6-h01db608_0               conda-forge
    libavif:                       0.10.1-h4e544f5_1              conda-forge
    libblas:                       3.9.0-16_linuxaarch64_openblas conda-forge
    libbrotlicommon:               1.0.9-h4e544f5_7               conda-forge
    libbrotlidec:                  1.0.9-h4e544f5_7               conda-forge
    libbrotlienc:                  1.0.9-h4e544f5_7               conda-forge
    libcblas:                      3.9.0-16_linuxaarch64_openblas conda-forge
    libcurl:                       7.83.1-h8fd98b7_0              conda-forge
    libdeflate:                    1.14-h4e544f5_0                conda-forge
    libedit:                       3.1.20191231-he28a2e2_2        conda-forge
    libev:                         4.33-h516909a_1                conda-forge
    libffi:                        3.4.2-h3557bc0_5               conda-forge
    libgcc-ng:                     12.1.0-h3242a24_16             conda-forge
    libgfortran-ng:                12.1.0-he9431aa_16             conda-forge
    libgfortran5:                  12.1.0-h41d5c85_16             conda-forge
    libgomp:                       12.1.0-h3242a24_16             conda-forge
    liblapack:                     3.9.0-16_linuxaarch64_openblas conda-forge
    libllvm11:                     11.1.0-h6293a0b_3              conda-forge
    libnghttp2:                    1.47.0-h4173d3e_1              conda-forge
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    libpng:                        1.6.38-hf9034f9_0              conda-forge
    libsodium:                     1.0.18-hb9de7d4_1              conda-forge
    libsqlite:                     3.39.3-hf9034f9_0              conda-forge
    libssh2:                       1.10.0-h4bb3959_3              conda-forge
    libstdcxx-ng:                  12.1.0-hd01590b_16             conda-forge
    libtiff:                       4.4.0-hacef7f3_4               conda-forge
    libuuid:                       2.32.1-hf897c2e_1000           conda-forge
    libwebp-base:                  1.2.4-h4e544f5_0               conda-forge
    libxcb:                        1.13-h3557bc0_1004             conda-forge
    libzlib:                       1.2.12-h4e544f5_3              conda-forge
    libzopfli:                     1.0.3-h01db608_0               conda-forge
    llvmlite:                      0.38.1-py39hbbff7ca_0          conda-forge
    locket:                        1.0.0-pyhd8ed1ab_0             conda-forge
    lz4-c:                         1.9.3-h01db608_1               conda-forge
    markupsafe:                    2.1.1-py39hb9a1dbb_1           conda-forge
    matplotlib-base:               3.6.0-py39h15a8d8b_0           conda-forge
    matplotlib-inline:             0.1.6-pyhd8ed1ab_0             conda-forge
    mpc:                           1.2.1-h846f343_0               conda-forge
    mpfr:                          4.1.0-h719063d_1               conda-forge
    mpmath:                        1.2.1-pyhd8ed1ab_0             conda-forge
    msgpack-python:                1.0.4-py39h110580c_0           conda-forge
    munkres:                       1.1.4-pyh9f0ad1d_0             conda-forge
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    ncurses:                       6.3-headf329_1                 conda-forge
    nest-asyncio:                  1.5.5-pyhd8ed1ab_0             conda-forge
    networkx:                      2.8.6-pyhd8ed1ab_0             conda-forge
    numba:                         0.55.2-py39h780101b_0          conda-forge
    numcodecs:                     0.10.2-py39h3d8bfb9_0          conda-forge
    numexpr:                       2.8.3-py39hed77005_0           conda-forge
    numpy:                         1.22.4-py39h451b137_0          conda-forge
    openjpeg:                      2.5.0-h9b6de37_1               conda-forge
    openssl:                       1.1.1q-h4e544f5_0              conda-forge
    packaging:                     21.3-pyhd8ed1ab_0              conda-forge
    parso:                         0.8.3-pyhd8ed1ab_0             conda-forge
    partd:                         1.3.0-pyhd8ed1ab_0             conda-forge
    pexpect:                       4.8.0-pyh9f0ad1d_2             conda-forge
    pickleshare:                   0.7.5-py_1003                  conda-forge
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    psutil:                        5.9.2-py39h0fd3b05_0           conda-forge
    pthread-stubs:                 0.4-hb9de7d4_1001              conda-forge
    ptyprocess:                    0.7.0-pyhd3deb0d_0             conda-forge
    pure_eval:                     0.2.2-pyhd8ed1ab_0             conda-forge
    py:                            1.11.0-pyh6c4a22f_0            conda-forge
    pycparser:                     2.21-pyhd8ed1ab_0              conda-forge
    pygments:                      2.13.0-pyhd8ed1ab_0            conda-forge
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    python:                        3.9.13-h2eada40_0_cpython      conda-forge
    python-dateutil:               2.8.2-pyhd8ed1ab_0             conda-forge
    python_abi:                    3.9-2_cp39                     conda-forge
    pywavelets:                    1.3.0-py39h890285e_1           conda-forge
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    readline:                      8.1.2-h38e3740_0               conda-forge
    requests:                      2.28.1-pyhd8ed1ab_1            conda-forge
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    setuptools:                    65.3.0-pyhd8ed1ab_1            conda-forge
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    sparse:                        0.13.0-pyhd8ed1ab_0            conda-forge
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    tk:                            8.6.12-hd8af866_0              conda-forge
    tomli:                         2.0.1-pyhd8ed1ab_0             conda-forge
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    wheel:                         0.37.1-pyhd8ed1ab_0            conda-forge
    xorg-libxau:                   1.0.9-h3557bc0_0               conda-forge
    xorg-libxdmcp:                 1.1.3-h3557bc0_0               conda-forge
    xz:                            5.2.6-h9cdd2b7_0               conda-forge
    yaml:                          0.2.5-hf897c2e_2               conda-forge
    zarr:                          2.12.0-pyhd8ed1ab_0            conda-forge
    zeromq:                        4.3.4-h01db608_1               conda-forge
    zfp:                           1.0.0-h4de3ea5_1               conda-forge
    zipp:                          3.8.1-pyhd8ed1ab_0             conda-forge
    zlib:                          1.2.12-h4e544f5_3              conda-forge
    zlib-ng:                       2.0.6-h4e544f5_0               conda-forge
    zstd:                          1.5.2-hc1e27d5_4               conda-forge

Environment info

Test phase when building hyperspy package: https://app.travis-ci.com/github/conda-forge/hyperspy-feedstock/builds/255692898

hmaarrfk commented 1 year ago

You can try limiting the number of threads maybe...