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Unable to build against GROMACS on macOS due to missing GMXRC #44

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lohedges opened this issue Apr 29, 2024 · 6 comments · Fixed by #45
Closed
1 task done

Unable to build against GROMACS on macOS due to missing GMXRC #44

lohedges opened this issue Apr 29, 2024 · 6 comments · Fixed by #45
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@lohedges
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Solution to issue cannot be found in the documentation.

  • I checked the documentation.

Issue

As reported here, I am unable to build our package against GROMACS on macOS. During a conda build I see the following error at the environment finalisation stage, after which it exits with error:

/Users/runner/miniconda3/envs/sire_build/conda-bld/sire_1714379289268/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/etc/conda/activate.d/gromacs_activate.sh: line 22: /Users/runner/miniconda3/envs/sire_build/conda-bld/sire_1714379289268/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin.SSE2/GMXRC: No such file or directory
Traceback (most recent call last):
source tree in: /Users/runner/miniconda3/envs/sire_build/conda-bld/sire_1714379289268/work
  File "/Users/runner/miniconda3/envs/sire_build/bin/conda-mambabuild", line 10, in <module>
export PREFIX=/Users/runner/miniconda3/envs/sire_build/conda-bld/sire_1714379289268/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol
export BUILD_PREFIX=/Users/runner/miniconda3/envs/sire_build/conda-bld/sire_1714379289268/_build_env
export SRC_DIR=/Users/runner/miniconda3/envs/sire_build/conda-bld/sire_1714379289268/work
    sys.exit(main())
  File "/Users/runner/miniconda3/envs/sire_build/lib/python3.10/site-packages/boa/cli/mambabuild.py", line 301, in main
    call_conda_build(action, config)
  File "/Users/runner/miniconda3/envs/sire_build/lib/python3.10/site-packages/boa/cli/mambabuild.py", line 273, in call_conda_build
    result = api.build(
  File "/Users/runner/miniconda3/envs/sire_build/lib/python3.10/site-packages/conda_build/api.py", line 250, in build
    return build_tree(
  File "/Users/runner/miniconda3/envs/sire_build/lib/python3.10/site-packages/conda_build/build.py", line 3762, in build_tree
    packages_from_this = build(
  File "/Users/runner/miniconda3/envs/sire_build/lib/python3.10/site-packages/conda_build/build.py", line 2634, in build
    utils.check_call_env(
  File "/Users/runner/miniconda3/envs/sire_build/lib/python3.10/site-packages/conda_build/utils.py", line 408, in check_call_env
    return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
  File "/Users/runner/miniconda3/envs/sire_build/lib/python3.10/site-packages/conda_build/utils.py", line 384, in _func_defaulting_env_to_os_environ
    raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/Users/runner/miniconda3/envs/sire_build/conda-bld/sire_1714379289268/work/conda_build.sh']' returned non-zero exit status 1.

In particular, note the errror:

... /bin.SSE2/GMXRC: No such file or directory

The last working build (which was only a day earlier) seemingly uses the same version of GROMACS, but a different hash:

worked:

    gromacs:                       2023.4-nompi_h9dceb8e_102            conda-forge

failed:

    gromacs:                       2023.4-nompi_hf1d43a3_102              conda-forge

If I remove GROMACS from the environment, then the build is fine. I don't see any recent merges in your PRs (last is March 28th) so I'm a bit puzzled by this.

The list of packages below are what is reported by the CI during the build. I can re-run and get it to print more info if needed.

Installed packages

Adding in variants from internal_defaults
Adding in variants from /Users/runner/work/sire/sire/sire/recipes/sire/conda_build_config.yaml
Attempting to finalize metadata for sire
conda-forge/osx-arm64                                       Using cache
conda-forge/noarch                                          Using cache
Reloading output folder: /Users/runner/miniconda3/envs/sire_build/conda-bld
Reloading output folder: /Users/runner/miniconda3/envs/sire_build/conda-bld
Reloading output folder: /Users/runner/miniconda3/envs/sire_build/conda-bld
Reloading output folder: /Users/runner/miniconda3/envs/sire_build/conda-bld
BUILD START: ['sire-2024.2.0.dev-py310h70deae4_169.tar.bz2']
Reloading output folder: /Users/runner/miniconda3/envs/sire_build/conda-bld

## Package Plan ##

  environment location: /Users/runner/miniconda3/envs/sire_build/conda-bld/sire_1714379289268/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol


The following NEW packages will be INSTALLED:

    absl-py:                       2.1.0-pyhd8ed1ab_0                     conda-forge         
    aiohttp:                       3.9.5-py310hd125d64_0                  conda-forge         
    aiosignal:                     1.3.1-pyhd8ed1ab_0                     conda-forge         
    alchemlyb:                     2.2.0-pyhd8ed1ab_0                     conda-forge         
    ambertools:                    23.3-py310h2aae41f_6                   conda-forge         
    annotated-types:               0.6.0-pyhd8ed1ab_0                     conda-forge         
    anyio:                         4.3.0-pyhd8ed1ab_0                     conda-forge         
    appnope:                       0.1.4-pyhd8ed1ab_0                     conda-forge         
    argon2-cffi:                   23.1.0-pyhd8ed1ab_0                    conda-forge         
    argon2-cffi-bindings:          21.2.0-py310h2aa6e3c_4                 conda-forge         
    arpack:                        3.8.0-nompi_ha3438d0_101               conda-forge         
    arrow:                         1.3.0-pyhd8ed1ab_0                     conda-forge         
    ase:                           3.22.1-pyhd8ed1ab_1                    conda-forge         
    asttokens:                     2.4.1-pyhd8ed1ab_0                     conda-forge         
    astunparse:                    1.6.3-pyhd8ed1ab_0                     conda-forge         
    async-lru:                     2.0.4-pyhd8ed1ab_0                     conda-forge         
    async-timeout:                 4.0.3-pyhd8ed1ab_0                     conda-forge         
    atk-1.0:                       2.38.0-hd03087b_2                      conda-forge         
    attrs:                         23.2.0-pyh71513ae_0                    conda-forge         
    aws-c-auth:                    0.7.11-ha4ce7b8_1                      conda-forge         
    aws-c-cal:                     0.6.9-h4fd42c2_3                       conda-forge         
    aws-c-common:                  0.9.12-h93a5062_0                      conda-forge         
    aws-c-compression:             0.2.17-h4fd42c2_8                      conda-forge         
    aws-c-event-stream:            0.4.1-he66824e_2                       conda-forge         
    aws-c-http:                    0.8.0-hd3d28cd_2                       conda-forge         
    aws-c-io:                      0.14.0-h8daa835_1                      conda-forge         
    aws-c-mqtt:                    0.10.1-h59ff425_0                      conda-forge         
    aws-c-s3:                      0.4.9-h7f99a2c_0                       conda-forge         
    aws-c-sdkutils:                0.1.13-h4fd42c2_1                      conda-forge         
    aws-checksums:                 0.1.17-h4fd42c2_7                      conda-forge         
    aws-crt-cpp:                   0.26.0-hfff802b_8                      conda-forge         
    aws-sdk-cpp:                   1.11.210-he93ac2d_10                   conda-forge         
    babel:                         2.14.0-pyhd8ed1ab_0                    conda-forge         
    beautifulsoup4:                4.12.3-pyha770c72_0                    conda-forge         
    biopython:                     1.83-py310hd125d64_0                   conda-forge         
    bleach:                        6.1.0-pyhd8ed1ab_0                     conda-forge         
    blinker:                       1.8.1-pyhd8ed1ab_0                     conda-forge         
    blosc:                         1.21.5-hc338f07_0                      conda-forge         
    boost:                         1.82.0-h7ed268f_6                      conda-forge         
    bracex:                        2.2.1-pyhd8ed1ab_0                     conda-forge         
    brotli:                        1.1.0-hb547adb_1                       conda-forge         
    brotli-bin:                    1.1.0-hb547adb_1                       conda-forge         
    brotli-python:                 1.1.0-py310h1253130_1                  conda-forge         
    bson:                          0.5.9-py_0                             conda-forge         
    bzip2:                         1.0.8-h93a5062_5                       conda-forge         
    c-ares:                        1.28.1-h93a5062_0                      conda-forge         
    c-blosc2:                      2.14.4-ha57e6be_1                      conda-forge         
    ca-certificates:               2024.2.2-hf0a4a13_0                    conda-forge         
    cached-property:               1.5.2-hd8ed1ab_1                       conda-forge         
    cached_property:               1.5.2-pyha770c72_1                     conda-forge         
    cachetools:                    5.3.3-pyhd8ed1ab_0                     conda-forge         
    cairo:                         1.18.0-hd1e100b_0                      conda-forge         
    certifi:                       2024.2.2-pyhd8ed1ab_0                  conda-forge         
    cffi:                          1.16.0-py310hdcd7c05_0                 conda-forge         
    cftime:                        1.6.3-py310h50ce23c_0                  conda-forge         
    chardet:                       5.2.0-py310hbe9552e_1                  conda-forge         
    charset-normalizer:            3.3.2-pyhd8ed1ab_0                     conda-forge         
    click:                         8.1.7-unix_pyh707e725_0                conda-forge         
    colorama:                      0.4.6-pyhd8ed1ab_0                     conda-forge         
    comm:                          0.2.2-pyhd8ed1ab_0                     conda-forge         
    configargparse:                1.7-pyhd8ed1ab_0                       conda-forge         
    contourpy:                     1.2.1-py310h21239e6_0                  conda-forge         
    coverage:                      7.5.0-py310h8431ef1_0                  conda-forge         
    cryptography:                  42.0.5-py310h0e6f4b3_0                 conda-forge         
    cycler:                        0.12.1-pyhd8ed1ab_0                    conda-forge         
    dargs:                         0.4.5-pyhd8ed1ab_0                     conda-forge         
    debugpy:                       1.8.1-py310h692a8b6_0                  conda-forge         
    decorator:                     5.1.1-pyhd8ed1ab_0                     conda-forge         
    deepmd-kit:                    2.2.10-cpu_py310h52574f9_mpi_openmpi_1 conda-forge         
    defusedxml:                    0.7.1-pyhd8ed1ab_0                     conda-forge         
    dill:                          0.3.8-pyhd8ed1ab_0                     conda-forge         
    eigen:                         3.4.0-h1995070_0                       conda-forge         
    entrypoints:                   0.4-pyhd8ed1ab_0                       conda-forge         
    exceptiongroup:                1.2.0-pyhd8ed1ab_2                     conda-forge         
    executing:                     2.0.1-pyhd8ed1ab_0                     conda-forge         
    expat:                         2.6.2-hebf3989_0                       conda-forge         
    fasteners:                     0.17.3-pyhd8ed1ab_0                    conda-forge         
    fftw:                          3.3.10-nompi_h3046061_108              conda-forge         
    filelock:                      3.13.4-pyhd8ed1ab_0                    conda-forge         
    flask:                         3.0.3-pyhd8ed1ab_0                     conda-forge         
    flatbuffers:                   23.5.26-h13dd4ca_1                     conda-forge         
    font-ttf-dejavu-sans-mono:     2.37-hab24e00_0                        conda-forge         
    font-ttf-inconsolata:          3.000-h77eed37_0                       conda-forge         
    font-ttf-source-code-pro:      2.038-h77eed37_0                       conda-forge         
    font-ttf-ubuntu:               0.83-h77eed37_1                        conda-forge         
    fontconfig:                    2.14.2-h82840c6_0                      conda-forge         
    fonts-conda-ecosystem:         1-0                                    conda-forge         
    fonts-conda-forge:             1-0                                    conda-forge         
    fonttools:                     4.51.0-py310hd125d64_0                 conda-forge         
    fqdn:                          1.5.1-pyhd8ed1ab_0                     conda-forge         
    freetype:                      2.12.1-hadb7bae_2                      conda-forge         
    freetype-py:                   2.3.0-pyhd8ed1ab_0                     conda-forge         
    fribidi:                       1.0.10-h27ca646_0                      conda-forge         
    frozenlist:                    1.4.1-py310hd125d64_0                  conda-forge         
    fsspec:                        2024.3.1-pyhca7485f_0                  conda-forge         
    gast:                          0.5.4-pyhd8ed1ab_0                     conda-forge         
    gdk-pixbuf:                    2.42.11-h13c029f_0                     conda-forge         
    gemmi:                         0.6.5-py310h401b61c_0                  conda-forge         
    gettext:                       0.22.5-h8fbad5d_2                      conda-forge         
    gettext-tools:                 0.22.5-h8fbad5d_2                      conda-forge         
    gflags:                        2.2.2-hc88da5d_1004                    conda-forge         
    giflib:                        5.2.2-h93a5062_0                       conda-forge         
    glib:                          2.80.0-hfc324ee_6                      conda-forge         
    glib-tools:                    2.80.0-hb9a4d99_6                      conda-forge         
    glog:                          0.6.0-h6da1cb0_0                       conda-forge         
    gmp:                           6.3.0-hebf3989_1                       conda-forge         
    gmpy2:                         2.1.5-py310he883d71_0                  conda-forge         
    google-auth:                   2.29.0-pyhca7485f_0                    conda-forge         
    google-auth-oauthlib:          1.2.0-pyhd8ed1ab_0                     conda-forge         
    google-pasta:                  0.2.0-pyh8c360ce_0                     conda-forge         
    graphite2:                     1.3.13-hebf3989_1003                   conda-forge         
    graphviz:                      9.0.0-h3face73_1                       conda-forge         
    greenlet:                      3.0.3-py310h692a8b6_0                  conda-forge         
    griddataformats:               1.0.2-pyhd8ed1ab_0                     conda-forge         
    gromacs:                       2023.4-nompi_hf1d43a3_102              conda-forge         
    grpcio:                        1.59.3-py310hf7687f1_0                 conda-forge         
    gsd:                           3.2.1-py310h50ce23c_0                  conda-forge         
    gsl:                           2.7-h6e638da_0                         conda-forge         
    gst-plugins-base:              1.24.1-h09b4b5e_1                      conda-forge         
    gstreamer:                     1.24.1-h551c6ff_1                      conda-forge         
    gtk2:                          2.24.33-h7895bb2_4                     conda-forge         
    gts:                           0.7.6-he42f4ea_4                       conda-forge         
    gufe:                          1.0.0-pyhd8ed1ab_0                     conda-forge         
    h11:                           0.14.0-pyhd8ed1ab_0                    conda-forge         
    h2:                            4.1.0-pyhd8ed1ab_0                     conda-forge         
    h5py:                          3.11.0-nompi_py310h49e257e_100         conda-forge         
    harfbuzz:                      8.4.0-hbe0f7c0_0                       conda-forge         
    hdf4:                          4.2.15-h2ee6834_7                      conda-forge         
    hdf5:                          1.14.3-nompi_h5bb55e9_100              conda-forge         
    hpack:                         4.0.0-pyh9f0ad1d_0                     conda-forge         
    httpcore:                      1.0.5-pyhd8ed1ab_0                     conda-forge         
    httpx:                         0.27.0-pyhd8ed1ab_0                    conda-forge         
    hyperframe:                    6.0.1-pyhd8ed1ab_0                     conda-forge         
    icu:                           73.2-hc8870d7_0                        conda-forge         
    idna:                          3.7-pyhd8ed1ab_0                       conda-forge         
    importlib-metadata:            7.1.0-pyha770c72_0                     conda-forge         
    importlib_metadata:            7.1.0-hd8ed1ab_0                       conda-forge         
    importlib_resources:           6.4.0-pyhd8ed1ab_0                     conda-forge         
    ipykernel:                     6.29.3-pyh3cd1d5f_0                    conda-forge         
    ipython:                       8.22.2-pyh707e725_0                    conda-forge         
    ipywidgets:                    8.1.2-pyhd8ed1ab_0                     conda-forge         
    isoduration:                   20.11.0-pyhd8ed1ab_0                   conda-forge         
    itsdangerous:                  2.2.0-pyhd8ed1ab_0                     conda-forge         
    jax:                           0.4.26-pyhd8ed1ab_0                    conda-forge         
    jaxlib:                        0.4.23-cpu_py310h08fc835_0             conda-forge         
    jedi:                          0.19.1-pyhd8ed1ab_0                    conda-forge         
    jinja2:                        3.1.3-pyhd8ed1ab_0                     conda-forge         
    joblib:                        1.4.0-pyhd8ed1ab_0                     conda-forge         
    json5:                         0.9.25-pyhd8ed1ab_0                    conda-forge         
    jsonpointer:                   2.4-py310hbe9552e_3                    conda-forge         
    jsonschema:                    4.21.1-pyhd8ed1ab_0                    conda-forge         
    jsonschema-specifications:     2023.12.1-pyhd8ed1ab_0                 conda-forge         
    jsonschema-with-format-nongpl: 4.21.1-pyhd8ed1ab_0                    conda-forge         
    jupyter-lsp:                   2.2.5-pyhd8ed1ab_0                     conda-forge         
    jupyter_client:                8.6.1-pyhd8ed1ab_0                     conda-forge         
    jupyter_core:                  5.7.2-py310hbe9552e_0                  conda-forge         
    jupyter_events:                0.10.0-pyhd8ed1ab_0                    conda-forge         
    jupyter_server:                2.14.0-pyhd8ed1ab_0                    conda-forge         
    jupyter_server_terminals:      0.5.3-pyhd8ed1ab_0                     conda-forge         
    jupyterlab:                    4.1.8-pyhd8ed1ab_0                     conda-forge         
    jupyterlab_pygments:           0.3.0-pyhd8ed1ab_1                     conda-forge         
    jupyterlab_server:             2.27.1-pyhd8ed1ab_0                    conda-forge         
    jupyterlab_widgets:            3.0.10-pyhd8ed1ab_0                    conda-forge         
    kartograf:                     1.0.1-pyhd8ed1ab_0                     conda-forge         
    kcombu_bss:                    2023.29.01-h8a0c2ca_0                  openbiosim/label/dev
    keras:                         2.15.0-pyhd8ed1ab_0                    conda-forge         
    khronos-opencl-icd-loader:     2023.04.17-h1a8c8d9_0                  conda-forge         
    kiwisolver:                    1.4.5-py310h38f39d4_1                  conda-forge         
    krb5:                          1.21.2-h92f50d5_0                      conda-forge         
    lark-parser:                   0.12.0-pyhd8ed1ab_0                    conda-forge         
    lazy_import:                   0.2.2-pyhd8ed1ab_0                     conda-forge         
    lcms2:                         2.16-ha0e7c42_0                        conda-forge         
    lerc:                          4.0.0-h9a09cb3_0                       conda-forge         
    libabseil:                     20230802.1-cxx17_h13dd4ca_0            conda-forge         
    libaec:                        1.1.3-hebf3989_0                       conda-forge         
    libarrow:                      15.0.0-h4ce3932_0_cpu                  conda-forge         
    libarrow-acero:                15.0.0-h13dd4ca_0_cpu                  conda-forge         
    libarrow-dataset:              15.0.0-h13dd4ca_0_cpu                  conda-forge         
    libarrow-flight:               15.0.0-ha94d253_0_cpu                  conda-forge         
    libarrow-flight-sql:           15.0.0-h39a9b85_0_cpu                  conda-forge         
    libarrow-gandiva:              15.0.0-hf757142_0_cpu                  conda-forge         
    libarrow-substrait:            15.0.0-h7fd9903_0_cpu                  conda-forge         
    libasprintf:                   0.22.5-h8fbad5d_2                      conda-forge         
    libasprintf-devel:             0.22.5-h8fbad5d_2                      conda-forge         
    libblas:                       3.9.0-22_osxarm64_openblas             conda-forge         
    libboost:                      1.82.0-h72cdd8a_6                      conda-forge         
    libboost-devel:                1.82.0-hf450f58_6                      conda-forge         
    libboost-headers:              1.82.0-hce30654_6                      conda-forge         
    libboost-python:               1.82.0-py310he53c7d2_6                 conda-forge         
    libboost-python-devel:         1.82.0-py310h7ed268f_6                 conda-forge         
    libbrotlicommon:               1.1.0-hb547adb_1                       conda-forge         
    libbrotlidec:                  1.1.0-hb547adb_1                       conda-forge         
    libbrotlienc:                  1.1.0-hb547adb_1                       conda-forge         
    libcblas:                      3.9.0-22_osxarm64_openblas             conda-forge         
    libclang-cpp15:                15.0.7-default_he012953_5              conda-forge         
    libclang13:                    18.1.3-default_h83d0a53_0              conda-forge         
    libcrc32c:                     1.1.2-hbdafb3b_0                       conda-forge         
    libcurl:                       8.7.1-h2d989ff_0                       conda-forge         
    libcxx:                        16.0.6-h4653b0c_0                      conda-forge         
    libdeflate:                    1.20-h93a5062_0                        conda-forge         
    libedit:                       3.1.20191231-hc8eb9b7_2                conda-forge         
    libev:                         4.33-h93a5062_2                        conda-forge         
    libevent:                      2.1.12-h2757513_1                      conda-forge         
    libexpat:                      2.6.2-hebf3989_0                       conda-forge         
    libffi:                        3.4.2-h3422bc3_5                       conda-forge         
    libgd:                         2.3.3-hfdf3952_9                       conda-forge         
    libgettextpo:                  0.22.5-h8fbad5d_2                      conda-forge         
    libgettextpo-devel:            0.22.5-h8fbad5d_2                      conda-forge         
    libgfortran:                   5.0.0-13_2_0_hd922786_3                conda-forge         
    libgfortran5:                  13.2.0-hf226fd6_3                      conda-forge         
    libglib:                       2.80.0-hfc324ee_6                      conda-forge         
    libgoogle-cloud:               2.12.0-hfb399a7_4                      conda-forge         
    libgrpc:                       1.59.3-h9560976_0                      conda-forge         
    libhwloc:                      2.10.0-default_h52d8fe8_1000           conda-forge         
    libiconv:                      1.17-h0d3ecfb_2                        conda-forge         
    libintl:                       0.22.5-h8fbad5d_2                      conda-forge         
    libintl-devel:                 0.22.5-h8fbad5d_2                      conda-forge         
    libjpeg-turbo:                 3.0.0-hb547adb_1                       conda-forge         
    liblapack:                     3.9.0-22_osxarm64_openblas             conda-forge         
    libllvm14:                     14.0.6-hd1a9a77_4                      conda-forge         
    libllvm15:                     15.0.7-h2621b3d_4                      conda-forge         
    libllvm18:                     18.1.3-h30cc82d_0                      conda-forge         
    libnetcdf:                     4.9.2-nompi_h291a7c2_113               conda-forge         
    libnghttp2:                    1.58.0-ha4dd798_1                      conda-forge         
    libogg:                        1.3.4-h27ca646_1                       conda-forge         
    libopenblas:                   0.3.27-openmp_h6c19121_0               conda-forge         
    libopus:                       1.3.1-h27ca646_1                       conda-forge         
    libparquet:                    15.0.0-hf6ce1d5_0_cpu                  conda-forge         
    libpng:                        1.6.43-h091b4b1_0                      conda-forge         
    libpq:                         16.2-h0f8b458_1                        conda-forge         
    libprotobuf:                   4.24.4-h810fc01_0                      conda-forge         
    libre2-11:                     2023.09.01-h741fcf5_1                  conda-forge         
    librsvg:                       2.58.0-hb3d354b_1                      conda-forge         
    libsodium:                     1.0.18-h27ca646_1                      conda-forge         
    libsqlite:                     3.45.3-h091b4b1_0                      conda-forge         
    libssh2:                       1.11.0-h7a5bd25_0                      conda-forge         
    libthrift:                     0.19.0-h026a170_1                      conda-forge         
    libtiff:                       4.6.0-h07db509_3                       conda-forge         
    libutf8proc:                   2.8.0-h1a8c8d9_0                       conda-forge         
    libuv:                         1.48.0-h93a5062_0                      conda-forge         
    libvorbis:                     1.3.7-h9f76cd9_0                       conda-forge         
    libwebp:                       1.3.2-hf30222e_1                       conda-forge         
    libwebp-base:                  1.3.2-h93a5062_1                       conda-forge         
    libxcb:                        1.15-hf346824_0                        conda-forge         
    libxml2:                       2.12.6-h0d0cfa8_2                      conda-forge         
    libzip:                        1.10.1-ha0bc3c6_3                      conda-forge         
    libzlib:                       1.2.13-h53f4e23_5                      conda-forge         
    llvm-openmp:                   18.1.3-hcd81f8e_0                      conda-forge         
    llvmlite:                      0.42.0-py310hf7687f1_1                 conda-forge         
    loguru:                        0.7.2-py310hbe9552e_1                  conda-forge         
    lomap2:                        3.0.3-pyhd8ed1ab_0                     conda-forge         
    lz4-c:                         1.9.4-hb7217d7_0                       conda-forge         
    markdown:                      3.6-pyhd8ed1ab_0                       conda-forge         
    markdown-it-py:                3.0.0-pyhd8ed1ab_0                     conda-forge         
    markupsafe:                    2.1.5-py310hd125d64_0                  conda-forge         
    matplotlib-base:               3.8.4-py310h2439c42_0                  conda-forge         
    matplotlib-inline:             0.1.7-pyhd8ed1ab_0                     conda-forge         
    mctc-lib:                      0.3.1-h1b58363_0                       conda-forge         
    mda-xdrlib:                    0.2.0-pyhd8ed1ab_0                     conda-forge         
    mdanalysis:                    2.7.0-py310h5924a0a_1                  conda-forge         
    mdtraj:                        1.9.9-py310h7c9e852_0                  conda-forge         
    mdurl:                         0.1.2-pyhd8ed1ab_0                     conda-forge         
    mistune:                       3.0.2-pyhd8ed1ab_0                     conda-forge         
    ml_dtypes:                     0.2.0-py310h5924a0a_2                  conda-forge         
    mmtf-python:                   1.1.3-pyhd8ed1ab_0                     conda-forge         
    mpc:                           1.3.1-h91ba8db_0                       conda-forge         
    mpfr:                          4.2.1-h41d338b_1                       conda-forge         
    mpi:                           1.0-openmpi                            conda-forge         
    mpiplus:                       v0.0.2-pyhd8ed1ab_0                    conda-forge         
    mpmath:                        1.3.0-pyhd8ed1ab_0                     conda-forge         
    mrcfile:                       1.5.0-pyhd8ed1ab_0                     conda-forge         
    msgpack-python:                1.0.7-py310hd137fd4_0                  conda-forge         
    multidict:                     6.0.5-py310h8e9501a_0                  conda-forge         
    munkres:                       1.1.4-pyh9f0ad1d_0                     conda-forge         
    mysql-common:                  8.3.0-hd1853d3_4                       conda-forge         
    mysql-libs:                    8.3.0-hf036fc4_4                       conda-forge         
    nbclient:                      0.10.0-pyhd8ed1ab_0                    conda-forge         
    nbconvert-core:                7.16.3-pyhd8ed1ab_1                    conda-forge         
    nbformat:                      5.10.4-pyhd8ed1ab_0                    conda-forge         
    ncurses:                       6.4.20240210-h078ce10_0                conda-forge         
    nest-asyncio:                  1.6.0-pyhd8ed1ab_0                     conda-forge         
    netcdf-fortran:                4.6.1-nompi_he6a98ad_103               conda-forge         
    netcdf4:                       1.6.5-nompi_py310h3aafd6c_100          conda-forge         
    networkx:                      3.3-pyhd8ed1ab_1                       conda-forge         
    nglview:                       3.1.2-pyh15ce09e_0                     conda-forge         
    nomkl:                         1.0-h5ca1d4c_0                         conda-forge         
    nose:                          1.3.7-py_1006                          conda-forge         
    notebook:                      7.1.3-pyhd8ed1ab_0                     conda-forge         
    notebook-shim:                 0.2.4-pyhd8ed1ab_0                     conda-forge         
    nspr:                          4.35-hb7217d7_0                        conda-forge         
    nss:                           3.98-h5ce2875_0                        conda-forge         
    numba:                         0.59.1-py310hdf1f89a_0                 conda-forge         
    numexpr:                       2.9.0-py310h401b61c_0                  conda-forge         
    numpy:                         1.26.4-py310hd45542a_0                 conda-forge         
    oauthlib:                      3.2.2-pyhd8ed1ab_0                     conda-forge         
    ocl_icd_wrapper_apple:         1.0.0-h27ca646_0                       conda-forge         
    openff-amber-ff-ports:         0.0.4-pyhca7485f_0                     conda-forge         
    openff-forcefields:            2024.04.0-pyhca7485f_0                 conda-forge         
    openff-interchange:            0.3.26-pyhd8ed1ab_0                    conda-forge         
    openff-interchange-base:       0.3.26-pyhd8ed1ab_0                    conda-forge         
    openff-models:                 0.1.2-pyhca7485f_0                     conda-forge         
    openff-toolkit:                0.16.0-pyhd8ed1ab_1                    conda-forge         
    openff-toolkit-base:           0.16.0-pyhd8ed1ab_1                    conda-forge         
    openff-units:                  0.2.2-pyhca7485f_0                     conda-forge         
    openff-utilities:              0.1.12-pyhd8ed1ab_0                    conda-forge         
    openjpeg:                      2.5.2-h9f1df11_0                       conda-forge         
    openmm:                        8.1.1-py310h3cbb76b_1_khronos          conda-forge         
    openmmtools:                   0.23.1-pyhd8ed1ab_0                    conda-forge         
    openmpi:                       4.1.6-h526c993_101                     conda-forge         
    openssl:                       3.2.1-h0d3ecfb_1                       conda-forge         
    opt-einsum:                    3.3.0-hd8ed1ab_2                       conda-forge         
    opt_einsum:                    3.3.0-pyhc1e730c_2                     conda-forge         
    orc:                           1.9.2-h7c018df_0                       conda-forge         
    overrides:                     7.7.0-pyhd8ed1ab_0                     conda-forge         
    packaging:                     24.0-pyhd8ed1ab_0                      conda-forge         
    packmol:                       20.2.2-h9318095_1                      conda-forge         
    pandas:                        2.2.2-py310h401b61c_0                  conda-forge         
    pandocfilters:                 1.5.0-pyhd8ed1ab_0                     conda-forge         
    panedr:                        0.8.0-pyhd8ed1ab_0                     conda-forge         
    pango:                         1.52.2-hb067d4f_0                      conda-forge         
    parmed:                        4.2.2-py310h692a8b6_1                  conda-forge         
    parso:                         0.8.4-pyhd8ed1ab_0                     conda-forge         
    patsy:                         0.5.6-pyhd8ed1ab_0                     conda-forge         
    pcre2:                         10.43-h26f9a81_0                       conda-forge         
    pdbfixer:                      1.9-pyh1a96a4e_0                       conda-forge         
    perl:                          5.32.1-7_h4614cfb_perl5                conda-forge         
    pexpect:                       4.9.0-pyhd8ed1ab_0                     conda-forge         
    pickleshare:                   0.7.5-py_1003                          conda-forge         
    pillow:                        10.3.0-py310h81a8c2e_0                 conda-forge         
    pint:                          0.23-pyhd8ed1ab_0                      conda-forge         
    pip:                           24.0-pyhd8ed1ab_0                      conda-forge         
    pixman:                        0.43.4-hebf3989_0                      conda-forge         
    pkgutil-resolve-name:          1.3.10-pyhd8ed1ab_1                    conda-forge         
    platformdirs:                  4.2.1-pyhd8ed1ab_0                     conda-forge         
    prometheus_client:             0.20.0-pyhd8ed1ab_0                    conda-forge         
    prompt-toolkit:                3.0.42-pyha770c72_0                    conda-forge         
    protobuf:                      4.24.4-py310hc08086b_0                 conda-forge         
    psutil:                        5.9.8-py310hd125d64_0                  conda-forge         
    pthread-stubs:                 0.4-h27ca646_1001                      conda-forge         
    ptyprocess:                    0.7.0-pyhd3deb0d_0                     conda-forge         
    pure_eval:                     0.2.2-pyhd8ed1ab_0                     conda-forge         
    py-cpuinfo:                    9.0.0-pyhd8ed1ab_0                     conda-forge         
    py3dmol:                       2.1.0-pyhd8ed1ab_0                     conda-forge         
    pyarrow:                       15.0.0-py310h382c99a_0_cpu             conda-forge         
    pyasn1:                        0.6.0-pyhd8ed1ab_0                     conda-forge         
    pyasn1-modules:                0.4.0-pyhd8ed1ab_0                     conda-forge         
    pybind11:                      2.12.0-py310h21239e6_0                 conda-forge         
    pybind11-global:               2.12.0-py310h21239e6_0                 conda-forge         
    pycairo:                       1.26.0-py310hea34faf_0                 conda-forge         
    pycparser:                     2.22-pyhd8ed1ab_0                      conda-forge         
    pydantic:                      2.7.1-pyhd8ed1ab_0                     conda-forge         
    pydantic-core:                 2.18.2-py310h8ffd6aa_0                 conda-forge         
    pydot:                         2.0.0-py310hbe9552e_0                  conda-forge         
    pyedr:                         0.8.0-pyhd8ed1ab_0                     conda-forge         
    pygments:                      2.17.2-pyhd8ed1ab_0                    conda-forge         
    pygtail:                       0.14.0-pyhd8ed1ab_0                    conda-forge         
    pyjwt:                         2.8.0-pyhd8ed1ab_1                     conda-forge         
    pymbar:                        4.0.3-hb6292c7_1                       conda-forge         
    pymbar-core:                   4.0.3-py310h50ce23c_1                  conda-forge         
    pyobjc-core:                   10.2-py310hb3aa912_0                   conda-forge         
    pyobjc-framework-cocoa:        10.2-py310hb3aa912_0                   conda-forge         
    pyopenssl:                     24.0.0-pyhd8ed1ab_0                    conda-forge         
    pyparsing:                     3.1.2-pyhd8ed1ab_0                     conda-forge         
    pysocks:                       1.7.1-pyha2e5f31_6                     conda-forge         
    pytables:                      3.9.2-py310h61ce8b3_2                  conda-forge         
    python:                        3.10.14-h2469fbe_0_cpython             conda-forge         
    python-constraint:             1.4.0-py_0                             conda-forge         
    python-dateutil:               2.9.0-pyhd8ed1ab_0                     conda-forge         
    python-fastjsonschema:         2.19.1-pyhd8ed1ab_0                    conda-forge         
    python-flatbuffers:            24.3.25-pyh59ac667_0                   conda-forge         
    python-hostlist:               1.21-pyh9f0ad1d_0                      conda-forge         
    python-json-logger:            2.0.7-pyhd8ed1ab_0                     conda-forge         
    python-tzdata:                 2024.1-pyhd8ed1ab_0                    conda-forge         
    python_abi:                    3.10-4_cp310                           conda-forge         
    pytng:                         0.3.1-py310ha5b23ed_1                  conda-forge         
    pytorch:                       2.1.0-cpu_generic_py310h7a13b03_0      conda-forge         
    pytz:                          2024.1-pyhd8ed1ab_0                    conda-forge         
    pyu2f:                         0.1.5-pyhd8ed1ab_0                     conda-forge         
    pyyaml:                        6.0.1-py310h2aa6e3c_1                  conda-forge         
    pyzmq:                         26.0.2-py310h18f1355_0                 conda-forge         
    qt-main:                       5.15.8-hf679f28_21                     conda-forge         
    rdkit:                         2023.09.6-py310h5df4984_0              conda-forge         
    re2:                           2023.09.01-h4cba328_1                  conda-forge         
    readline:                      8.2-h92ec313_1                         conda-forge         
    referencing:                   0.35.0-pyhd8ed1ab_0                    conda-forge         
    reportlab:                     4.1.0-py310hd125d64_0                  conda-forge         
    requests:                      2.31.0-pyhd8ed1ab_0                    conda-forge         
    requests-oauthlib:             2.0.0-pyhd8ed1ab_0                     conda-forge         
    rfc3339-validator:             0.1.4-pyhd8ed1ab_0                     conda-forge         
    rfc3986-validator:             0.1.1-pyh9f0ad1d_0                     conda-forge         
    rich:                          13.7.1-pyhd8ed1ab_0                    conda-forge         
    rlpycairo:                     0.2.0-pyhd8ed1ab_0                     conda-forge         
    rpds-py:                       0.18.0-py310hf632f72_0                 conda-forge         
    rsa:                           4.9-pyhd8ed1ab_0                       conda-forge         
    scikit-learn:                  1.4.2-py310h7ef31dd_0                  conda-forge         
    scipy:                         1.13.0-py310hf4b343e_0                 conda-forge         
    seaborn:                       0.13.2-hd8ed1ab_0                      conda-forge         
    seaborn-base:                  0.13.2-pyhd8ed1ab_0                    conda-forge         
    send2trash:                    1.8.3-pyh31c8845_0                     conda-forge         
    setuptools:                    65.3.0-pyhd8ed1ab_1                    conda-forge         
    setuptools-scm:                6.3.2-pyhd8ed1ab_0                     conda-forge         
    setuptools_scm:                6.3.2-hd8ed1ab_0                       conda-forge         
    six:                           1.16.0-pyh6c4a22f_0                    conda-forge         
    sleef:                         3.5.1-h156473d_2                       conda-forge         
    smirnoff99frosst:              1.1.0-pyh44b312d_0                     conda-forge         
    snappy:                        1.1.10-hd04f947_1                      conda-forge         
    sniffio:                       1.3.1-pyhd8ed1ab_0                     conda-forge         
    soupsieve:                     2.5-pyhd8ed1ab_1                       conda-forge         
    sqlalchemy:                    2.0.29-py310hd125d64_0                 conda-forge         
    stack_data:                    0.6.2-pyhd8ed1ab_0                     conda-forge         
    statsmodels:                   0.14.1-py310h50ce23c_0                 conda-forge         
    sympy:                         1.12-pypyh9d50eac_103                  conda-forge         
    tbb:                           2021.12.0-h2ffa867_0                   conda-forge         
    tbb-devel:                     2021.12.0-hf0e5eac_0                   conda-forge         
    tensorboard:                   2.15.2-pyhd8ed1ab_0                    conda-forge         
    tensorboard-data-server:       0.7.0-py310hdd3b5e7_1                  conda-forge         
    tensorflow:                    2.15.0-cpu_py310hed9d77c_2             conda-forge         
    tensorflow-base:               2.15.0-cpu_py310hb663c03_2             conda-forge         
    tensorflow-estimator:          2.15.0-cpu_py310h0d828bf_2             conda-forge         
    termcolor:                     2.4.0-pyhd8ed1ab_0                     conda-forge         
    terminado:                     0.18.1-pyh31c8845_0                    conda-forge         
    tf-keras:                      2.15.0-pyhd8ed1ab_0                    conda-forge         
    threadpoolctl:                 3.4.0-pyhc1e730c_0                     conda-forge         
    tidynamics:                    1.1.2-pyhd8ed1ab_0                     conda-forge         
    tinycss2:                      1.3.0-pyhd8ed1ab_0                     conda-forge         
    tk:                            8.6.13-h5083fa2_1                      conda-forge         
    tomli:                         2.0.1-pyhd8ed1ab_0                     conda-forge         
    torchani:                      2.2.4-cpu_py310h4c79e5c_3              conda-forge         
    tornado:                       6.4-py310hd125d64_0                    conda-forge         
    tqdm:                          4.66.2-pyhd8ed1ab_0                    conda-forge         
    traitlets:                     5.14.3-pyhd8ed1ab_0                    conda-forge         
    typeguard:                     4.2.1-pyhd8ed1ab_0                     conda-forge         
    types-python-dateutil:         2.9.0.20240316-pyhd8ed1ab_0            conda-forge         
    typing-extensions:             4.11.0-hd8ed1ab_0                      conda-forge         
    typing_extensions:             4.11.0-pyha770c72_0                    conda-forge         
    typing_utils:                  0.1.0-pyhd8ed1ab_0                     conda-forge         
    tzdata:                        2024a-h0c530f3_0                       conda-forge         
    unicodedata2:                  15.1.0-py310h2aa6e3c_0                 conda-forge         
    uri-template:                  1.3.0-pyhd8ed1ab_0                     conda-forge         
    urllib3:                       2.2.1-pyhd8ed1ab_0                     conda-forge         
    wcmatch:                       8.5-pyhd8ed1ab_0                       conda-forge         
    wcwidth:                       0.2.13-pyhd8ed1ab_0                    conda-forge         
    webcolors:                     1.13-pyhd8ed1ab_0                      conda-forge         
    webencodings:                  0.5.1-pyhd8ed1ab_2                     conda-forge         
    websocket-client:              1.8.0-pyhd8ed1ab_0                     conda-forge         
    werkzeug:                      3.0.2-pyhd8ed1ab_0                     conda-forge         
    wheel:                         0.43.0-pyhd8ed1ab_1                    conda-forge         
    widgetsnbextension:            4.0.10-pyhd8ed1ab_0                    conda-forge         
    wrapt:                         1.14.1-py310h8e9501a_1                 conda-forge         
    xmltodict:                     0.13.0-pyhd8ed1ab_0                    conda-forge         
    xorg-kbproto:                  1.0.7-h27ca646_1002                    conda-forge         
    xorg-libice:                   1.1.1-hb547adb_0                       conda-forge         
    xorg-libsm:                    1.2.4-hb547adb_0                       conda-forge         
    xorg-libx11:                   1.8.9-h570a39f_0                       conda-forge         
    xorg-libxau:                   1.0.11-hb547adb_0                      conda-forge         
    xorg-libxdmcp:                 1.1.3-h27ca646_0                       conda-forge         
    xorg-libxext:                  1.3.4-h1a8c8d9_2                       conda-forge         
    xorg-libxt:                    1.3.0-hb547adb_1                       conda-forge         
    xorg-xextproto:                7.3.0-h1a8c8d9_1003                    conda-forge         
    xorg-xproto:                   7.0.31-h27ca646_1007                   conda-forge         
    xtb:                           6.5.1-h4884bc7_1                       conda-forge         
    xtb-python:                    22.1-py310h8e9501a_0                   conda-forge         
    xz:                            5.2.6-h57fd34a_0                       conda-forge         
    yaml:                          0.2.5-h3422bc3_2                       conda-forge         
    yarl:                          1.9.4-py310hd125d64_0                  conda-forge         
    zeromq:                        4.3.5-hebf3989_1                       conda-forge         
    zipp:                          3.17.0-pyhd8ed1ab_0                    conda-forge         
    zlib:                          1.2.13-h53f4e23_5                      conda-forge         
    zlib-ng:                       2.0.7-h1a8c8d9_0                       conda-forge         
    zstd:                          1.5.5-h4f39d0f_0                       conda-forge         

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... 

done
Reloading output folder: /Users/runner/miniconda3/envs/sire_build/conda-bld
Reloading output folder: /Users/runner/miniconda3/envs/sire_build/conda-bld

## Package Plan ##

  environment location: /Users/runner/miniconda3/envs/sire_build/conda-bld/sire_1714379289268/_build_env


The following NEW packages will be INSTALLED:

    brotli:                    1.1.0-hb547adb_1           conda-forge
    brotli-bin:                1.1.0-hb547adb_1           conda-forge
    bzip2:                     1.0.8-h93a5062_5           conda-forge
    c-ares:                    1.28.1-h93a5062_0          conda-forge
    ca-certificates:           2024.2.2-hf0a4a13_0        conda-forge
    cairo:                     1.18.0-hd1e100b_0          conda-forge
    cctools_osx-arm64:         986-hd11630f_0             conda-forge
    certifi:                   2024.2.2-pyhd8ed1ab_0      conda-forge
    chardet:                   5.2.0-py310hbe9552e_1      conda-forge
    clang:                     18.1.3-default_h4cf2255_0  conda-forge
    clang-18:                  18.1.3-default_he012953_0  conda-forge
    clang_impl_osx-arm64:      18.1.3-hda94301_11         conda-forge
    clang_osx-arm64:           18.1.3-h54d7cd3_11         conda-forge
    clangxx:                   18.1.3-default_h4cf2255_0  conda-forge
    clangxx_impl_osx-arm64:    18.1.3-h1ba0cb9_11         conda-forge
    clangxx_osx-arm64:         18.1.3-h54d7cd3_11         conda-forge
    cmake:                     3.29.2-h50fd54c_0          conda-forge
    compiler-rt:               18.1.3-h3808999_0          conda-forge
    compiler-rt_osx-arm64:     18.1.3-h3808999_0          conda-forge
    contourpy:                 1.2.1-py310h21239e6_0      conda-forge
    curl:                      8.7.1-h2d989ff_0           conda-forge
    cycler:                    0.12.1-pyhd8ed1ab_0        conda-forge
    expat:                     2.6.2-hebf3989_0           conda-forge
    font-ttf-dejavu-sans-mono: 2.37-hab24e00_0            conda-forge
    font-ttf-inconsolata:      3.000-h77eed37_0           conda-forge
    font-ttf-source-code-pro:  2.038-h77eed37_0           conda-forge
    font-ttf-ubuntu:           0.83-h77eed37_1            conda-forge
    fontconfig:                2.14.2-h82840c6_0          conda-forge
    fonts-conda-ecosystem:     1-0                        conda-forge
    fonts-conda-forge:         1-0                        conda-forge
    fonttools:                 4.51.0-py310hd125d64_0     conda-forge
    freetype:                  2.12.1-hadb7bae_2          conda-forge
    freetype-py:               2.3.0-pyhd8ed1ab_0         conda-forge
    gemmi:                     0.6.5-py310h401b61c_0      conda-forge
    gettext:                   0.22.5-h8fbad5d_2          conda-forge
    gettext-tools:             0.22.5-h8fbad5d_2          conda-forge
    git:                       2.44.0-pl5321h015987d_0    conda-forge
    greenlet:                  3.0.3-py310h692a8b6_0      conda-forge
    icu:                       73.2-hc8870d7_0            conda-forge
    kiwisolver:                1.4.5-py310h38f39d4_1      conda-forge
    krb5:                      1.21.2-h92f50d5_0          conda-forge
    lcms2:                     2.16-ha0e7c42_0            conda-forge
    ld64_osx-arm64:            711-h5e7191b_0             conda-forge
    lerc:                      4.0.0-h9a09cb3_0           conda-forge
    libasprintf:               0.22.5-h8fbad5d_2          conda-forge
    libasprintf-devel:         0.22.5-h8fbad5d_2          conda-forge
    libblas:                   3.9.0-22_osxarm64_openblas conda-forge
    libboost:                  1.84.0-h8e0f962_2          conda-forge
    libboost-python:           1.84.0-py310h1359cc7_2     conda-forge
    libbrotlicommon:           1.1.0-hb547adb_1           conda-forge
    libbrotlidec:              1.1.0-hb547adb_1           conda-forge
    libbrotlienc:              1.1.0-hb547adb_1           conda-forge
    libcblas:                  3.9.0-22_osxarm64_openblas conda-forge
    libclang-cpp18.1:          18.1.3-default_he012953_0  conda-forge
    libcurl:                   8.7.1-h2d989ff_0           conda-forge
    libcxx:                    16.0.6-h4653b0c_0          conda-forge
    libdeflate:                1.20-h93a5062_0            conda-forge
    libedit:                   3.1.20191231-hc8eb9b7_2    conda-forge
    libev:                     4.33-h93a5062_2            conda-forge
    libexpat:                  2.6.2-hebf3989_0           conda-forge
    libffi:                    3.4.2-h3422bc3_5           conda-forge
    libgettextpo:              0.22.5-h8fbad5d_2          conda-forge
    libgettextpo-devel:        0.22.5-h8fbad5d_2          conda-forge
    libgfortran:               5.0.0-13_2_0_hd922786_3    conda-forge
    libgfortran5:              13.2.0-hf226fd6_3          conda-forge
    libglib:                   2.80.0-hfc324ee_6          conda-forge
    libiconv:                  1.17-h0d3ecfb_2            conda-forge
    libintl:                   0.22.5-h8fbad5d_2          conda-forge
    libintl-devel:             0.22.5-h8fbad5d_2          conda-forge
    libjpeg-turbo:             3.0.0-hb547adb_1           conda-forge
    liblapack:                 3.9.0-22_osxarm64_openblas conda-forge
    libllvm18:                 18.1.3-h30cc82d_0          conda-forge
    libnghttp2:                1.58.0-ha4dd798_1          conda-forge
    libopenblas:               0.3.27-openmp_h6c19121_0   conda-forge
    libpng:                    1.6.43-h091b4b1_0          conda-forge
    libsqlite:                 3.45.3-h091b4b1_0          conda-forge
    libssh2:                   1.11.0-h7a5bd25_0          conda-forge
    libtiff:                   4.6.0-h07db509_3           conda-forge
    libtool:                   2.4.7-hb7217d7_0           conda-forge
    libuv:                     1.48.0-h93a5062_0          conda-forge
    libwebp-base:              1.4.0-h93a5062_0           conda-forge
    libxcb:                    1.15-hf346824_0            conda-forge
    libxml2:                   2.12.6-h0d0cfa8_2          conda-forge
    libzlib:                   1.2.13-h53f4e23_5          conda-forge
    llvm-openmp:               18.1.3-hcd81f8e_0          conda-forge
    llvm-tools:                18.1.3-h30cc82d_0          conda-forge
    make:                      4.3-he57ea6c_1             conda-forge
    matplotlib-base:           3.8.4-py310h2439c42_0      conda-forge
    munkres:                   1.1.4-pyh9f0ad1d_0         conda-forge
    ncurses:                   6.4.20240210-h078ce10_0    conda-forge
    numpy:                     1.26.4-py310hd45542a_0     conda-forge
    openjpeg:                  2.5.2-h9f1df11_0           conda-forge
    openssl:                   3.2.1-h0d3ecfb_1           conda-forge
    packaging:                 24.0-pyhd8ed1ab_0          conda-forge
    pandas:                    2.2.2-py310h401b61c_0      conda-forge
    pcre2:                     10.43-h26f9a81_0           conda-forge
    perl:                      5.32.1-7_h4614cfb_perl5    conda-forge
    pillow:                    10.3.0-py310h81a8c2e_0     conda-forge
    pip:                       24.0-pyhd8ed1ab_0          conda-forge
    pixman:                    0.43.4-hebf3989_0          conda-forge
    pthread-stubs:             0.4-h27ca646_1001          conda-forge
    pycairo:                   1.26.0-py310hea34faf_0     conda-forge
    pyparsing:                 3.1.2-pyhd8ed1ab_0         conda-forge
    python:                    3.10.14-h2469fbe_0_cpython conda-forge
    python-dateutil:           2.9.0-pyhd8ed1ab_0         conda-forge
    python-tzdata:             2024.1-pyhd8ed1ab_0        conda-forge
    python_abi:                3.10-4_cp310               conda-forge
    pytz:                      2024.1-pyhd8ed1ab_0        conda-forge
    rdkit:                     2024.03.1-py310h0e77dd1_0  conda-forge
    rdkit-dev:                 2024.03.1-h745495a_0       conda-forge
    readline:                  8.2-h92ec313_1             conda-forge
    reportlab:                 4.1.0-py310hd125d64_0      conda-forge
    rhash:                     1.4.4-hb547adb_0           conda-forge
    rlpycairo:                 0.2.0-pyhd8ed1ab_0         conda-forge
    setuptools:                69.5.1-pyhd8ed1ab_0        conda-forge
    sigtool:                   0.1.3-h44b9a77_0           conda-forge
    six:                       1.16.0-pyh6c4a22f_0        conda-forge
    sqlalchemy:                2.0.29-py310hd125d64_0     conda-forge
    tapi:                      1100.0.11-he4954df_0       conda-forge
    tk:                        8.6.13-h5083fa2_1          conda-forge
    typing-extensions:         4.11.0-hd8ed1ab_0          conda-forge
    typing_extensions:         4.11.0-pyha770c72_0        conda-forge
    tzdata:                    2024a-h0c530f3_0           conda-forge
    unicodedata2:              15.1.0-py310h2aa6e3c_0     conda-forge
    wheel:                     0.43.0-pyhd8ed1ab_1        conda-forge
    xorg-libxau:               1.0.11-hb547adb_0          conda-forge
    xorg-libxdmcp:             1.1.3-h27ca646_0           conda-forge
    xz:                        5.2.6-h57fd34a_0           conda-forge
    zlib:                      1.2.13-h53f4e23_5          conda-forge
    zlib-ng:                   2.0.7-h1a8c8d9_0           conda-forge
    zstd:                      1.5.5-h4f39d0f_0           conda-forge

Environment info

N/A
@lohedges lohedges added the bug Something isn't working label Apr 29, 2024
@lohedges
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This looks like a result of the running changing from osx-64 to osx-arm64, so presumably it's the arm64 package that is broken. Apologies for not noticing this initially. We've not changed our CI script, so presumably the default GitHub macOS runner has changed.

@mabraham
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Nothing has changed here, yet, but #43 is open so presumably there are moves afoot to support OSX+ARM and maybe changes have happened and GROMACS is behind?

@xiki-tempula
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I think the gromacs-2023.4=nompi_hf1d43a3_102 is just broken.

conda create -n gmx -c conda-forge gromacs
conda activate gmx

gives

/Users/zwu/miniconda3/envs/gmx/etc/conda/activate.d/gromacs_activate.sh:.:22: no such file or directory: /Users/zwu/miniconda3/envs/gmx/bin.SSE2/GMXRC

On my M1 mac

@xiki-tempula xiki-tempula mentioned this issue May 3, 2024
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@mattwthompson
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#43 is for Linux ARM, #34 (merged a while back) is for macOS ARM. I swear the

I'm experiencing the same things on my M1/M2 mac as Zhiyi and Lester

I naively poked around and found that editing my $CONDA_PREFIX/bin/gmx to look for arm64 gets it running for me

$ $ uname -m && gmx --version
arm64
                   :-) GROMACS - gmx, 2023.3-conda_forge (-:

Executable:   /Users/mattthompson/micromamba/envs/openff-interchange-dev/bin.ARM_NEON_ASIMD/gmx
Data prefix:  /Users/mattthompson/micromamba/envs/openff-interchange-dev
Working dir:  /Users/mattthompson/software/openff-interchange
Command line:
  gmx --version

GROMACS version:    2023.3-conda_forge
Precision:          mixed
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     disabled
GPU support:        disabled
SIMD instructions:  ARM_NEON_ASIMD
CPU FFT library:    fftw-3.3.10
GPU FFT library:    none
Multi-GPU FFT:      none
TNG support:        enabled
Hwloc support:      disabled
Tracing support:    disabled
C compiler:         /Users/runner/miniforge3/conda-bld/gromacs_1701183648835/_build_env/bin/arm64-apple-darwin20.0.0-clang Clang 16.0.6
C compiler flags:   -Wno-unknown-pragmas -Wno-missing-field-initializers -O3 -DNDEBUG
C++ compiler:       /Users/runner/miniforge3/conda-bld/gromacs_1701183648835/_build_env/bin/arm64-apple-darwin20.0.0-clang++ Clang 16.0.6
C++ compiler flags: -Wno-unknown-pragmas -Wno-reserved-identifier -Wno-missing-field-initializers -Weverything -Wno-c++98-compat -Wno-c++98-compat-pedantic -Wno-source-uses-openmp -Wno-c++17-extensions -Wno-documentation-unknown-command -Wno-covered-switch-default -Wno-switch-enum -Wno-extra-semi-stmt -Wno-weak-vtables -Wno-shadow -Wno-padded -Wno-reserved-id-macro -Wno-double-promotion -Wno-exit-time-destructors -Wno-global-constructors -Wno-documentation -Wno-format-nonliteral -Wno-used-but-marked-unused -Wno-float-equal -Wno-conditional-uninitialized -Wno-conversion -Wno-disabled-macro-expansion -Wno-unused-macros -Wno-unsafe-buffer-usage -Wno-cast-function-type-strict -O3 -DNDEBUG
BLAS library:       External - detected on the system
LAPACK library:     External - detected on the system

@mattwthompson
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Cool, ZW found the same thing 🙂

@lohedges
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lohedges commented May 3, 2024

Ah great, thanks for debugging and fixing this. I only encountered this on our CI. I use Linux locally so there was no (easy) way to debug.

@xiki-tempula xiki-tempula mentioned this issue May 6, 2024
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Fix the osx-arm64 build xiki-tempula/gromacs-feedstock
4 participants
@mabraham @lohedges @xiki-tempula @mattwthompson