Ambertools refusing assign AM1 charges to methane on macOS-13

lilyminium commented 1 month ago

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 commented 1 month ago

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 commented 1 month ago

Passing RDKit:

   rdkit                      2024.03.6     py311h8dea741_0                    conda-forge

Failing RDKit:

     rdkit                             2024.03.6     py311h8dea741_0                    conda-forge

lilyminium commented 1 month ago

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
>  libexpat 2.6.3 hf9b8971_0 conda-forge
>  libffi 3.4.2 h3422bc3_5 conda-forge
>  libgfortran 5.0.0 13_2_0_hd922786_3 conda-forge
>  libgfortran5 13.2.0 hf226fd6_3 conda-forge
>  libglib 2.82.2 h07bd6cf_0 conda-forge
>  libgoogle-cloud 2.29.0 hfa33a2f_0 conda-forge
>  libgoogle-cloud-storage 2.29.0 h90fd6fa_0 conda-forge
>  libgrpc 1.62.2 h9c18a4f_0 conda-forge
>  libiconv 1.17 h0d3ecfb_2 conda-forge
>  libintl 0.22.5 h8414b35_3 conda-forge
>  libjpeg-turbo 3.0.0 hb547adb_1 conda-forge
>  liblapack 3.9.0 24_osxarm64_openblas conda-forge
>  liblapacke 3.9.0 24_osxarm64_openblas conda-forge
>  libnetcdf 4.9.2 nompi_he469be0_114 conda-forge
>  libnghttp2 1.58.0 ha4dd798_1 conda-forge
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lilyminium commented 1 month ago

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.

lilyminium commented 1 month ago

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.

openforcefield / openff-nagl

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

Current environment