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Ambertools refusing assign AM1 charges to methane on macOS-13 #152

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lilyminium opened this issue Oct 21, 2024 · 5 comments
Closed

Ambertools refusing assign AM1 charges to methane on macOS-13 #152

lilyminium opened this issue Oct 21, 2024 · 5 comments
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@lilyminium
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lilyminium commented Oct 21, 2024 •
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Edited top comment for an informative overview (ignore the diagnostic comments below):

AmberTools is refusing to assign AM1 charges to methane on macOS-13. Notably this works on macOS-latest. The DGL installation was just noise -- the failing test is skipped if pyarrow is not installed, and I forgot that the pyarrow install was dependent on DGL. This is probably not really a NAGL issue but something to do with AmberTools on macOS-13.

Current environment

  • Which version are you using? (run python -c "import openff.nagl; print(openff.nagl.__version__)")
  • Which version of Python (python -V)?
  • Which operating system?
  • What is the output of pip list?
  • If you use conda, what is the output of conda list?
@lilyminium lilyminium changed the title Ambertools refusing assign charges to methane on Mac Ambertools refusing assign charges to methane on Mac with DGL installed Oct 21, 2024
@lilyminium
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Failing env with DGL:

     Name                              Version       Build                              Channel    
  ──────────────────────────────────────────────────────────────────────────────────────────────────
    absl-py                           2.1.0         pyhd8ed1ab_0                       conda-forge
    ambertools                        23.6          cuda_None_nompi_py311h9ef6679_105  conda-forge

Passing env without DGL:

   List of packages in environment: "/Users/runner/micromamba/envs/openff-nagl-test"
  
    Name                       Version       Build                              Channel    
  ───────────────────────────────────────────────────────────────────────────────────────────
    ambertools                 23.6          cuda_None_nompi_py311h9ef6679_105  conda-forge

Ok, probably not a version issue.

@lilyminium
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Passing RDKit:

   rdkit                      2024.03.6     py311h8dea741_0                    conda-forge

Failing RDKit:

     rdkit                             2024.03.6     py311h8dea741_0                    conda-forge

@lilyminium lilyminium mentioned this issue Oct 21, 2024
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@lilyminium lilyminium mentioned this issue Oct 21, 2024
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@lilyminium lilyminium changed the title Ambertools refusing assign charges to methane on Mac with DGL installed Ambertools refusing assign charges to methane on x86 Mac with DGL installed Oct 21, 2024
@lilyminium
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lilyminium commented Oct 21, 2024 •
edited
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Environment differences with whitespace removed:

Between macOS-13 runs with and without DGL:

diff failing-env.dat successful-env.dat
1c1
< failing env
---
> successful env
6,7c6
<  ──────────────────────────────────────────────────────────────────────────────────────────────────
<  absl-py 2.1.0 pyhd8ed1ab_0 conda-forge
---
>  ───────────────────────────────────────────────────────────────────────────────────────────
10,28d8
<  astunparse 1.6.3 pyhd8ed1ab_2 conda-forge
<  aws-c-auth 0.7.31 hb28a666_0 conda-forge
<  aws-c-cal 0.7.4 h8128ea2_1 conda-forge
<  aws-c-common 0.9.28 h00291cd_0 conda-forge
<  aws-c-compression 0.2.19 h8128ea2_1 conda-forge
<  aws-c-event-stream 0.4.3 hcd1ed9e_2 conda-forge
<  aws-c-http 0.8.10 h2f86973_0 conda-forge
<  aws-c-io 0.14.18 hf9a0f1c_12 conda-forge
<  aws-c-mqtt 0.10.7 h9d7d61c_0 conda-forge
<  aws-c-s3 0.6.6 hd01826e_0 conda-forge
<  aws-c-sdkutils 0.1.19 h8128ea2_3 conda-forge
<  aws-checksums 0.1.20 h8128ea2_0 conda-forge
<  aws-crt-cpp 0.28.3 hef75ebe_6 conda-forge
<  aws-sdk-cpp 1.11.379 h2e282c2_11 conda-forge
<  azure-core-cpp 1.13.0 hf8dbe3c_0 conda-forge
<  azure-identity-cpp 1.8.0 h60298e3_2 conda-forge
<  azure-storage-blobs-cpp 12.12.0 h646f05d_0 conda-forge
<  azure-storage-common-cpp 12.7.0 hf91904f_1 conda-forge
<  azure-storage-files-datalake-cpp 12.11.0 h14965f0_1 conda-forge
57d36
<  dgl 2.1.0 py310h39e7762_2 conda-forge
64d42
<  flatbuffers 24.3.25 h73e2aa4_0 conda-forge
76,79d53
<  gast 0.5.5 pyhd8ed1ab_0 conda-forge
<  gflags 2.2.2 hac325c4_1005 conda-forge
<  giflib 5.2.2 h10d778d_0 conda-forge
<  glog 0.7.1 h2790a97_0 conda-forge
82d55
<  google-pasta 0.2.0 pyhd8ed1ab_1 conda-forge
84d56
<  grpcio 1.62.2 py310h271164d_0 conda-forge
86d57
<  h5py 3.12.1 nompi_py310hafa4265_101 conda-forge
88c59
<  hdf5 1.14.3 nompi_h687a608_105 conda-forge
---
>  hdf5 1.14.4 nompi_h57e3b00_101 conda-forge
99d69
<  keras 3.6.0 pyhd8ed1ab_0 conda-forge
104c74
<  libabseil 20240116.2 cxx17_hf036a51_1 conda-forge
---
>  libabseil 20240722.0 cxx17_hac325c4_1 conda-forge
106,109d75
<  libarrow 17.0.0 hca1c1af_15_cpu conda-forge
<  libarrow-acero 17.0.0 hac325c4_15_cpu conda-forge
<  libarrow-dataset 17.0.0 hac325c4_15_cpu conda-forge
<  libarrow-substrait 17.0.0 hba007a9_15_cpu conda-forge
117d82
<  libcrc32c 1.1.2 he49afe7_0 conda-forge
123d87
<  libevent 2.1.12 ha90c15b_1 conda-forge
129,131d92
<  libgoogle-cloud 2.29.0 hecd3d69_0 conda-forge
<  libgoogle-cloud-storage 2.29.0 h8126ed0_0 conda-forge
<  libgrpc 1.62.2 h384b2fc_0 conda-forge
137,138c98
<  liblapacke 3.9.0 22_osx64_openblas conda-forge
<  libnetcdf 4.9.2 nompi_h7334405_114 conda-forge
---
>  libnetcdf 4.9.2 nompi_h976d569_115 conda-forge
141d100
<  libparquet 17.0.0 hf1b0f52_15_cpu conda-forge
144c103
<  libprotobuf 4.25.3 hd4aba4c_1 conda-forge
---
>  libprotobuf 5.27.5 h62b0dff_2 conda-forge
146d104
<  libre2-11 2023.09.01 h81f5012_2 conda-forge
149d106
<  libthrift 0.20.0 h75589b3_1 conda-forge
151,152c108
<  libtorch 2.3.1 cpu_mkl_hcc88766_101 conda-forge
<  libutf8proc 2.8.0 hb7f2c08_0 conda-forge
---
>  libtorch 2.4.1 cpu_mkl_hdb27336_102 conda-forge
163,164d118
<  markdown 3.6 pyhd8ed1ab_0 conda-forge
<  markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge
167,168d120
<  mdurl 0.1.2 pyhd8ed1ab_0 conda-forge
<  metis 5.1.1 h73e2aa4_2 conda-forge
170d121
<  ml_dtypes 0.4.0 py310ha53a654_2 conda-forge
176d126
<  namex 0.0.8 pyhd8ed1ab_0 conda-forge
178c128
<  netcdf-fortran 4.6.1 nompi_h3f3c442_106 conda-forge
---
>  netcdf-fortran 4.6.1 nompi_h4dd9276_107 conda-forge
191,193d140
<  opt_einsum 3.4.0 pyhd8ed1ab_0 conda-forge
<  optree 0.13.0 py310hfa8da69_0 conda-forge
<  orc 2.0.2 h22b2039_0 conda-forge
205d151
<  protobuf 4.25.3 py310h533c97b_1 conda-forge
208,209d153
<  pyarrow 17.0.0 py310h58fd45c_1 conda-forge
<  pyarrow-core 17.0.0 py310h63d2070_1_cpu conda-forge
213d156
<  pygments 2.18.0 pyhd8ed1ab_0 conda-forge
222d164
<  python-flatbuffers 24.3.25 pyh59ac667_0 conda-forge
225c167
<  pytorch 2.3.1 cpu_mkl_py310heb6a33a_101 conda-forge
---
>  pytorch 2.4.1 cpu_mkl_py310h9941b98_102 conda-forge
231d172
<  re2 2023.09.01 hb168e87_2 conda-forge
235d175
<  rich 13.9.2 pyhd8ed1ab_0 conda-forge
249,254d188
<  tensorboard 2.17.1 pyhd8ed1ab_0 conda-forge
<  tensorboard-data-server 0.7.0 py310h38cfc11_2 conda-forge
<  tensorflow 2.17.0 cpu_py310h3aec5c9_0 conda-forge
<  tensorflow-base 2.17.0 cpu_py310h0919199_0 conda-forge
<  tensorflow-estimator 2.17.0 cpu_py310h0134bc7_0 conda-forge
<  termcolor 2.5.0 pyhd8ed1ab_0 conda-forge
259d192
<  torchdata 0.7.1 py310h3bfb708_7 conda-forge
268d200
<  werkzeug 3.0.4 pyhd8ed1ab_0 conda-forge
270d201
<  wrapt 1.16.0 py310h837254d_1 conda-forge

Between macOS-13 and macOS-latest:

diff failing-env.dat successful-env-latest.dat
1c1
< failing env
---
> successful env macOS-latest
8,9c8,9
<  ambertools 23.6 cuda_None_nompi_py310h496d21a_105 conda-forge
<  arpack 3.9.1 nompi_hf81eadf_101 conda-forge
---
>  ambertools 23.6 cuda_None_nompi_py310h1865e97_105 conda-forge
>  arpack 3.9.1 nompi_h593882a_101 conda-forge
11,32c11,32
<  aws-c-auth 0.7.31 hb28a666_0 conda-forge
<  aws-c-cal 0.7.4 h8128ea2_1 conda-forge
<  aws-c-common 0.9.28 h00291cd_0 conda-forge
<  aws-c-compression 0.2.19 h8128ea2_1 conda-forge
<  aws-c-event-stream 0.4.3 hcd1ed9e_2 conda-forge
<  aws-c-http 0.8.10 h2f86973_0 conda-forge
<  aws-c-io 0.14.18 hf9a0f1c_12 conda-forge
<  aws-c-mqtt 0.10.7 h9d7d61c_0 conda-forge
<  aws-c-s3 0.6.6 hd01826e_0 conda-forge
<  aws-c-sdkutils 0.1.19 h8128ea2_3 conda-forge
<  aws-checksums 0.1.20 h8128ea2_0 conda-forge
<  aws-crt-cpp 0.28.3 hef75ebe_6 conda-forge
<  aws-sdk-cpp 1.11.379 h2e282c2_11 conda-forge
<  azure-core-cpp 1.13.0 hf8dbe3c_0 conda-forge
<  azure-identity-cpp 1.8.0 h60298e3_2 conda-forge
<  azure-storage-blobs-cpp 12.12.0 h646f05d_0 conda-forge
<  azure-storage-common-cpp 12.7.0 hf91904f_1 conda-forge
<  azure-storage-files-datalake-cpp 12.11.0 h14965f0_1 conda-forge
<  blosc 1.21.6 h7d75f6d_0 conda-forge
<  brotli 1.1.0 h00291cd_2 conda-forge
<  brotli-bin 1.1.0 h00291cd_2 conda-forge
<  brotli-python 1.1.0 py310h53e7c6a_2 conda-forge
---
>  aws-c-auth 0.7.31 hc27b277_0 conda-forge
>  aws-c-cal 0.7.4 h41dd001_1 conda-forge
>  aws-c-common 0.9.28 hd74edd7_0 conda-forge
>  aws-c-compression 0.2.19 h41dd001_1 conda-forge
>  aws-c-event-stream 0.4.3 h40a8fc1_2 conda-forge
>  aws-c-http 0.8.10 hf5a2c8c_0 conda-forge
>  aws-c-io 0.14.18 hc3cb426_12 conda-forge
>  aws-c-mqtt 0.10.7 h3acc7b9_0 conda-forge
>  aws-c-s3 0.6.6 hd16c091_0 conda-forge
>  aws-c-sdkutils 0.1.19 h41dd001_3 conda-forge
>  aws-checksums 0.1.20 h41dd001_0 conda-forge
>  aws-crt-cpp 0.28.3 h433f80b_6 conda-forge
>  aws-sdk-cpp 1.11.379 h0455a66_11 conda-forge
>  azure-core-cpp 1.13.0 hd01fc5c_0 conda-forge
>  azure-identity-cpp 1.8.0 h13ea094_2 conda-forge
>  azure-storage-blobs-cpp 12.12.0 hfde595f_0 conda-forge
>  azure-storage-common-cpp 12.7.0 hcf3b6fd_1 conda-forge
>  azure-storage-files-datalake-cpp 12.11.0 h082e32e_1 conda-forge
>  blosc 1.21.6 h5499902_0 conda-forge
>  brotli 1.1.0 hd74edd7_2 conda-forge
>  brotli-bin 1.1.0 hd74edd7_2 conda-forge
>  brotli-python 1.1.0 py310hb4ad77e_2 conda-forge
34,36c34,36
<  bzip2 1.0.8 hfdf4475_7 conda-forge
<  c-ares 1.34.2 h32b1619_0 conda-forge
<  ca-certificates 2024.8.30 h8857fd0_0 conda-forge
---
>  bzip2 1.0.8 h99b78c6_7 conda-forge
>  c-ares 1.34.2 h7ab814d_0 conda-forge
>  ca-certificates 2024.8.30 hf0a4a13_0 conda-forge
40c40
<  cairo 1.18.0 h37bd5c4_3 conda-forge
---
>  cairo 1.18.0 hb4a6bf7_3 conda-forge
42,43c42,43
<  cffi 1.17.1 py310hfce808e_0 conda-forge
<  chardet 5.2.0 py310h2ec42d9_2 conda-forge
---
>  cffi 1.17.1 py310h497396d_0 conda-forge
>  chardet 5.2.0 py310hbe9552e_2 conda-forge
50,51c50,51
<  contourpy 1.3.0 py310hfa8da69_2 conda-forge
<  coverage 7.6.3 py310h72eadd2_1 conda-forge
---
>  contourpy 1.3.0 py310h7306fd8_2 conda-forge
>  coverage 7.6.3 py310h5799be4_1 conda-forge
54c54
<  cytoolz 1.0.0 py310h837254d_1 conda-forge
---
>  cytoolz 1.0.0 py310h493c2e1_1 conda-forge
57c57
<  dgl 2.1.0 py310h39e7762_2 conda-forge
---
>  dgl 2.1.0 py310he0e4742_2 conda-forge
61,62c61,62
<  expat 2.6.3 hac325c4_0 conda-forge
<  fftw 3.3.10 nompi_h292e606_110 conda-forge
---
>  expat 2.6.3 hf9b8971_0 conda-forge
>  fftw 3.3.10 nompi_h6637ab6_110 conda-forge
64c64
<  flatbuffers 24.3.25 h73e2aa4_0 conda-forge
---
>  flatbuffers 24.3.25 hebf3989_0 conda-forge
69c69
<  fontconfig 2.14.2 h5bb23bf_0 conda-forge
---
>  fontconfig 2.14.2 h82840c6_0 conda-forge
72,73c72,73
<  fonttools 4.54.1 py310h837254d_0 conda-forge
<  freetype 2.12.1 h60636b9_2 conda-forge
---
>  fonttools 4.54.1 py310h493c2e1_0 conda-forge
>  freetype 2.12.1 hadb7bae_2 conda-forge
77,81c77,81
<  gflags 2.2.2 hac325c4_1005 conda-forge
<  giflib 5.2.2 h10d778d_0 conda-forge
<  glog 0.7.1 h2790a97_0 conda-forge
<  gmp 6.3.0 hf036a51_2 conda-forge
<  gmpy2 2.1.5 py310hade44e5_2 conda-forge
---
>  gflags 2.2.2 hf9b8971_1005 conda-forge
>  giflib 5.2.2 h93a5062_0 conda-forge
>  glog 0.7.1 heb240a5_0 conda-forge
>  gmp 6.3.0 h7bae524_2 conda-forge
>  gmpy2 2.1.5 py310heb17c8b_2 conda-forge
83,84c83,84
<  greenlet 3.1.1 py310h53e7c6a_0 conda-forge
<  grpcio 1.62.2 py310h271164d_0 conda-forge
---
>  greenlet 3.1.1 py310hb4ad77e_0 conda-forge
>  grpcio 1.62.2 py310hf7687f1_0 conda-forge
86,88c86,88
<  h5py 3.12.1 nompi_py310hafa4265_101 conda-forge
<  hdf4 4.2.15 h8138101_7 conda-forge
<  hdf5 1.14.3 nompi_h687a608_105 conda-forge
---
>  h5py 3.12.1 nompi_py310h072ed46_101 conda-forge
>  hdf4 4.2.15 h2ee6834_7 conda-forge
>  hdf5 1.14.3 nompi_hec07895_105 conda-forge
91c91
<  icu 75.1 h120a0e1_0 conda-forge
---
>  icu 75.1 hfee45f7_0 conda-forge
100,160c100,159
<  kiwisolver 1.4.7 py310hfa8da69_0 conda-forge
<  krb5 1.21.3 h37d8d59_0 conda-forge
<  lcms2 2.16 ha2f27b4_0 conda-forge
<  lerc 4.0.0 hb486fe8_0 conda-forge
<  libabseil 20240116.2 cxx17_hf036a51_1 conda-forge
<  libaec 1.1.3 h73e2aa4_0 conda-forge
<  libarrow 17.0.0 hca1c1af_15_cpu conda-forge
<  libarrow-acero 17.0.0 hac325c4_15_cpu conda-forge
<  libarrow-dataset 17.0.0 hac325c4_15_cpu conda-forge
<  libarrow-substrait 17.0.0 hba007a9_15_cpu conda-forge
<  libblas 3.9.0 22_osx64_openblas conda-forge
<  libboost 1.84.0 hbe88bda_6 conda-forge
<  libboost-python 1.84.0 py310h767a3e0_6 conda-forge
<  libbrotlicommon 1.1.0 h00291cd_2 conda-forge
<  libbrotlidec 1.1.0 h00291cd_2 conda-forge
<  libbrotlienc 1.1.0 h00291cd_2 conda-forge
<  libcblas 3.9.0 22_osx64_openblas conda-forge
<  libcrc32c 1.1.2 he49afe7_0 conda-forge
<  libcurl 8.10.1 h58e7537_0 conda-forge
<  libcxx 19.1.2 hf95d169_0 conda-forge
<  libdeflate 1.22 h00291cd_0 conda-forge
<  libedit 3.1.20191231 h0678c8f_2 conda-forge
<  libev 4.33 h10d778d_2 conda-forge
<  libevent 2.1.12 ha90c15b_1 conda-forge
<  libexpat 2.6.3 hac325c4_0 conda-forge
<  libffi 3.4.2 h0d85af4_5 conda-forge
<  libgfortran 5.0.0 13_2_0_h97931a8_3 conda-forge
<  libgfortran5 13.2.0 h2873a65_3 conda-forge
<  libglib 2.82.2 hb6ef654_0 conda-forge
<  libgoogle-cloud 2.29.0 hecd3d69_0 conda-forge
<  libgoogle-cloud-storage 2.29.0 h8126ed0_0 conda-forge
<  libgrpc 1.62.2 h384b2fc_0 conda-forge
<  libhwloc 2.11.1 default_h456cccd_1000 conda-forge
<  libiconv 1.17 hd75f5a5_2 conda-forge
<  libintl 0.22.5 hdfe23c8_3 conda-forge
<  libjpeg-turbo 3.0.0 h0dc2134_1 conda-forge
<  liblapack 3.9.0 22_osx64_openblas conda-forge
<  liblapacke 3.9.0 22_osx64_openblas conda-forge
<  libnetcdf 4.9.2 nompi_h7334405_114 conda-forge
<  libnghttp2 1.58.0 h64cf6d3_1 conda-forge
<  libopenblas 0.3.27 openmp_h8869122_1 conda-forge
<  libparquet 17.0.0 hf1b0f52_15_cpu conda-forge
<  libpng 1.6.44 h4b8f8c9_0 conda-forge
<  libpq 16.4 h365486b_3 conda-forge
<  libprotobuf 4.25.3 hd4aba4c_1 conda-forge
<  librdkit 2024.03.6 h9a5be36_0 conda-forge
<  libre2-11 2023.09.01 h81f5012_2 conda-forge
<  libsqlite 3.46.1 h4b8f8c9_0 conda-forge
<  libssh2 1.11.0 hd019ec5_0 conda-forge
<  libthrift 0.20.0 h75589b3_1 conda-forge
<  libtiff 4.7.0 h583c2ba_1 conda-forge
<  libtorch 2.3.1 cpu_mkl_hcc88766_101 conda-forge
<  libutf8proc 2.8.0 hb7f2c08_0 conda-forge
<  libuv 1.49.2 hd79239c_0 conda-forge
<  libwebp-base 1.4.0 h10d778d_0 conda-forge
<  libxcb 1.17.0 hf1f96e2_0 conda-forge
<  libxml2 2.12.7 heaf3512_4 conda-forge
<  libzip 1.11.1 h3116616_0 conda-forge
<  libzlib 1.3.1 hd23fc13_2 conda-forge
<  lightning-utilities 0.11.8 pyhd8ed1ab_0 conda-forge
<  llvm-openmp 19.1.2 hf78d878_0 conda-forge
---
>  kiwisolver 1.4.7 py310h7306fd8_0 conda-forge
>  krb5 1.21.3 h237132a_0 conda-forge
>  lcms2 2.16 ha0e7c42_0 conda-forge
>  lerc 4.0.0 h9a09cb3_0 conda-forge
>  libabseil 20240116.2 cxx17_h00cdb27_1 conda-forge
>  libaec 1.1.3 hebf3989_0 conda-forge
>  libarrow 17.0.0 h3ba790a_15_cpu conda-forge
>  libarrow-acero 17.0.0 hf9b8971_15_cpu conda-forge
>  libarrow-dataset 17.0.0 hf9b8971_15_cpu conda-forge
>  libarrow-substrait 17.0.0 hbf8b706_15_cpu conda-forge
>  libblas 3.9.0 24_osxarm64_openblas conda-forge
>  libboost 1.84.0 h29978a0_6 conda-forge
>  libboost-python 1.84.0 py310he5c2185_6 conda-forge
>  libbrotlicommon 1.1.0 hd74edd7_2 conda-forge
>  libbrotlidec 1.1.0 hd74edd7_2 conda-forge
>  libbrotlienc 1.1.0 hd74edd7_2 conda-forge
>  libcblas 3.9.0 24_osxarm64_openblas conda-forge
>  libcrc32c 1.1.2 hbdafb3b_0 conda-forge
>  libcurl 8.10.1 h13a7ad3_0 conda-forge
>  libcxx 19.1.2 ha82da77_0 conda-forge
>  libdeflate 1.22 hd74edd7_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
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@lilyminium lilyminium mentioned this issue Oct 21, 2024
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lilyminium commented Oct 21, 2024 •
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https://github.com/openforcefield/openff-nagl/actions/runs/11432905381/job/31804077797?pr=153 Adding an explicit test for charging methane from the provided conformer is now failing without DGL as well. Again only on macOS-13

Edit: oh, right, pyarrow is not installed if DGL is not installed, so tests "passed" because they weren't run.

This was referenced Oct 21, 2024
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@lilyminium lilyminium changed the title Ambertools refusing assign charges to methane on x86 Mac with DGL installed Ambertools refusing assign AM1 charges to methane on macOS-13 Oct 21, 2024
@lilyminium lilyminium mentioned this issue Oct 22, 2024
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Closing as I think this is more of an AmberTools + macOS-13, or Toolkit + macOS-13, issue. I raised #154 to check back on this in the future.

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