Errors with Installation

[wehos]

https://github.com/OmicsML/dance/blob/1d94be91625a352ad8510c16d5d23b9ce5e02b53/install.sh#L58

torchvision= should be replaced with torchvision==, otherwise 'install.sh' raises error Fixed by latest PR

[wehos]

The installation of dgl is not valid on HPCC systems. After the installation, dependency issue is raised:

from dance.datasets.multimodality import ModalityMatchingDataset
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/dance/datasets/__init__.py", line 1, in <module>
    from dance.datasets.multimodality import JointEmbeddingNIPSDataset, ModalityMatchingDataset, ModalityPredictionDataset
  File "/dance/datasets/multimodality.py", line 14, in <module>
    from dance.datasets.base import BaseDataset
  File "/dance/datasets/base.py", line 9, in <module>
    from dance.transforms.base import BaseTransform
  File "/dance/transforms/__init__.py", line 1, in <module>
    from dance.transforms import graph
  File "/dance/transforms/graph/__init__.py", line 1, in <module>
    from dance.transforms.graph.cell_feature_graph import CellFeatureBipartiteGraph, CellFeatureGraph, PCACellFeatureGraph
  File "/dance/transforms/graph/cell_feature_graph.py", line 1, in <module>
    import dgl
  File "/dance/lib/python3.11/site-packages/dgl/__init__.py", line 14, in <module>
    from .backend import backend_name, load_backend  # usort: skip
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/dance/lib/python3.11/site-packages/dgl/backend/__init__.py", line 122, in <module>
    load_backend(get_preferred_backend())
  File "/dance/lib/python3.11/site-packages/dgl/backend/__init__.py", line 51, in load_backend
    from .._ffi.base import load_tensor_adapter  # imports DGL C library
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/dance/lib/python3.11/site-packages/dgl/_ffi/base.py", line 50, in <module>
    _LIB, _LIB_NAME, _DIR_NAME = _load_lib()
                                 ^^^^^^^^^^^
  File "/dance/lib/python3.11/site-packages/dgl/_ffi/base.py", line 39, in _load_lib
    lib = ctypes.CDLL(lib_path[0])
          ^^^^^^^^^^^^^^^^^^^^^^^^
  File "//dance/lib/python3.11/ctypes/__init__.py", line 376, in __init__
    self._handle = _dlopen(self._name, mode)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: libcusparse.so.11: cannot open shared object file: No such file or directory

Simply reproducible with from dance.datasets.multimodality import ModalityMatchingDataset.

[wehos]

export LD_LIBRARY=~/anaconda3/lib (replacing the path with lib directory that contains module files) can solve the issue above.

We need to remind HPCC users about this. The HPC users may need to install cudatoolkit via conda (via conda install cudatoolkit=11.8 -c pytorch) and set LD_LIBRARY environ path.