search

openmm / NNPOps

High-performance operations for neural network potentials
Other
81 stars 17 forks source link

Readme example appears broken #72

Closed scal444 closed 1 year ago

scal444 commented 1 year ago

Running the readme example code, replacing molecule.mol2 with a water pdb (example_input.zip), I get this exception

Traceback (most recent call last):
  File "/home/kevin/benchmarks/nnpops/run.py", line 22, in <module>
    nnp.aev_computer = TorchANISymmetryFunctions(nnp.species_converter, nnp.aev_computer, species).to(device)
  File "/home/kevin/programs/conda/envs/openmm-8-beta-linux/lib/python3.10/site-packages/NNPOps/SymmetryFunctions.py", line 90, in __init__
    species = converter((atomicNumbers, torch.empty(0))).species[0].tolist()
AttributeError: 'tuple' object has no attribute 'species'

It looks like SpeciesConverter returns a tuple (code), but TorchANISymmetryFunctions expects some other structure (code)

raimis commented 1 year ago

Most likely you are using a broken TorchANI version. Make sure you got 2.2.2.

scal444 commented 1 year ago

My environment is from the openmm beta, torchani 2.2.2. Unless I'm misreading (see the links I'm looking at in the post), this error comes from mismatch between return types / expected types purely within NNPOps, 

conda list
# packages in environment at /home/kevin/programs/conda/envs/openmm-8-beta-linux:
#
# Name                    Version                   Build  Channel
_ipython_minor_entry_point 8.7.0                hb6b4a82_0    conda-forge
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
asttokens                 2.2.0              pyhd8ed1ab_0    conda-forge
astunparse                1.6.3              pyhd8ed1ab_0    conda-forge
attrs                     22.1.0             pyh71513ae_1    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
blas                      1.1                    openblas    conda-forge
blosc                     1.21.1               h83bc5f7_3    conda-forge
brotlipy                  0.7.0           py310h5764c6d_1004    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2022.9.24            ha878542_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
certifi                   2022.9.24          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310h255011f_1    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
cryptography              38.0.2          py310h600f1e7_1    conda-forge
cudatoolkit               11.6.0              hecad31d_10    conda-forge
cudnn                     8.4.1.50             hed8a83a_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
exceptiongroup            1.0.0rc9           pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
h5py                      3.7.0           nompi_py310h416281c_101    conda-forge
hdf5                      1.12.2          nompi_h4df4325_100    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        4.11.4          py310hff52083_0    conda-forge
importlib_metadata        4.11.4               hd8ed1ab_0    conda-forge
iniconfig                 1.1.1              pyh9f0ad1d_0    conda-forge
intel-openmp              2022.1.0          h9e868ea_3769  
ipython                   8.7.0              pyh41d4057_0    conda-forge
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.19.3               h08a2579_0    conda-forge
lark-parser               0.12.0             pyhd8ed1ab_0    conda-forge
ld_impl_linux-64          2.39                 hc81fddc_0    conda-forge
libblas                   3.9.0           16_linux64_openblas    conda-forge
libcblas                  3.9.0           16_linux64_openblas    conda-forge
libcurl                   7.85.0               h2283fc2_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgfortran-ng            12.2.0              h69a702a_19    conda-forge
libgfortran5              12.2.0              h337968e_19    conda-forge
libgomp                   12.2.0              h65d4601_19    conda-forge
liblapack                 3.9.0           16_linux64_openblas    conda-forge
libnghttp2                1.47.0               hff17c54_1    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.21          pthreads_h78a6416_3    conda-forge
libprotobuf               3.21.8               h6239696_0    conda-forge
libsqlite                 3.39.4               h753d276_0    conda-forge
libssh2                   1.10.0               hf14f497_3    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libzlib                   1.2.13               h166bdaf_4    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
magma                     2.5.4                hc72dce7_3    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mdgym-cpp                 0.0.1                    pypi_0    pypi
mdtraj                    1.9.7           py310h902c554_4    conda-forge
mkl                       2022.1.0           hc2b9512_224  
nccl                      2.14.3.1             h0800d71_0    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
ninja                     1.11.0               h924138e_0    conda-forge
nnpops                    0.2             cuda112py310h8b99da5_5    conda-forge
numexpr                   2.8.4           py310h757a811_0  
numpy                     1.23.4          py310h53a5b5f_0    conda-forge
ocl-icd                   2.3.1                h7f98852_0    conda-forge
ocl-icd-system            1.0.0                         1    conda-forge
openblas                  0.3.21          pthreads_h320a7e8_3    conda-forge
openmm                    8.0.0beta       py310h2996cf7_2    conda-forge/label/openmm_rc
openmm-ml                 1.0beta            pyh79ba5db_2    conda-forge/label/openmm_rc
openmm-torch              1.0beta         cuda112py310h02d4f52_1    conda-forge/label/openmm-torch_rc
openssl                   3.0.7                h166bdaf_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.5.2           py310h769672d_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pip                       22.3               pyhd8ed1ab_0    conda-forge
pluggy                    1.0.0           py310hff52083_3    conda-forge
prompt-toolkit            3.0.33             pyha770c72_0    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.13.0             pyhd8ed1ab_0    conda-forge
pyopenssl                 22.1.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pytables                  3.7.0           py310hb60b9b2_3    conda-forge
pytest                    7.2.0           py310hff52083_0    conda-forge
python                    3.10.6          ha86cf86_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.10                    2_cp310    conda-forge
pytorch                   1.12.1          cuda112py310he33e0d6_201    conda-forge
pytz                      2022.6             pyhd8ed1ab_0    conda-forge
readline                  8.1.2                h0f457ee_0    conda-forge
requests                  2.28.1             pyhd8ed1ab_1    conda-forge
scipy                     1.9.3           py310hdfbd76f_2    conda-forge
setuptools                59.5.0          py310hff52083_0    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                h9b69904_2    conda-forge
snappy                    1.1.9                hbd366e4_2    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
torchani                  2.2.2           cuda112py310h98dee98_6    conda-forge
traitlets                 5.6.0              pyhd8ed1ab_0    conda-forge
typing_extensions         4.4.0              pyha770c72_0    conda-forge
tzdata                    2022e                h191b570_0    conda-forge
urllib3                   1.26.11            pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zipp                      3.10.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h166bdaf_4    conda-forge
zstd                      1.5.2                h6239696_4    conda-forge