pin_memory option should be explicit in cell2location

Dear developers, I was trying to run the following code:

import scvi
scvi.data.setup_anndata(adata=A1_fil, batch_key="in_tissue")
scvi.data.view_anndata_setup(A1_fil)

modA1fil = cell2location.models.Cell2location(
  A1_fil, cell_state_df=inf_aver_filraw,
  N_cells_per_location=8,
    detection_alpha=200)
modA1fil.train(max_epochs=40000,
          batch_size=None,
          train_size=1,
          use_gpu=True)`

After the print of scvi.data.view_anndata_setup(), Cell2Location recognize the GPU:

GPU available: True, used: True
TPU available: False, using: 0 TPU cores

but it does stop just afterwards with the following error: RuntimeError: cannot pin 'torch.cuda.FloatTensor' only dense CPU tensors can be pinned. I saw that it should be easily overcome if I can put pin_memory=False (see here) in cell2location model, how can I do that?

Best, Carlo

[carloelle]

yes it works smoothly!

[carloelle]

Update: I tried to re-create another conda environment following the C2L installation tutorial to see if I could overcome this error, and indeed I succeed. the previous error vanishes and it starts the training of the model using GPU. I report here the list of correct packages for future reference:

Package                 Version
----------------------- ---------
absl-py                 1.0.0
aiohttp                 3.8.1
aiosignal               1.2.0
anndata                 0.7.8
argon2-cffi             21.1.0
arviz                   0.10.0
async-timeout           4.0.1
attrs                   21.2.0
backcall                0.2.0
bleach                  4.1.0
cachetools              4.2.4
cell2location           0.6a0
certifi                 2021.10.8
cffi                    1.15.0
cftime                  1.5.1.1
charset-normalizer      2.0.8
colorama                0.4.4
commonmark              0.9.1
cycler                  0.11.0
debugpy                 1.5.1
decorator               5.1.0
defusedxml              0.7.1
descartes               1.1.0
dill                    0.3.4
docrep                  0.3.2
entrypoints             0.3
et-xmlfile              1.1.0
fastprogress            1.0.0
fonttools               4.28.2
frozenlist              1.2.0
fsspec                  2021.11.1
future                  0.18.2
google-auth             2.3.3
google-auth-oauthlib    0.4.6
grpcio                  1.42.0
h5py                    3.6.0
idna                    3.3
igraph                  0.9.8
importlib-metadata      4.8.2
ipykernel               6.6.0
ipython                 7.30.0
ipython-genutils        0.2.0
ipywidgets              7.6.5
jedi                    0.18.1
Jinja2                  3.0.3
joblib                  1.1.0
jsonschema              4.2.1
jupyter-client          7.1.0
jupyter-core            4.9.1
jupyterlab-pygments     0.1.2
jupyterlab-widgets      1.0.2
kiwisolver              1.3.2
leidenalg               0.8.8
llvmlite                0.37.0
Markdown                3.3.6
MarkupSafe              2.0.1
matplotlib              3.5.0
matplotlib-inline       0.1.3
mistune                 0.8.4
mizani                  0.7.3
multidict               5.2.0
natsort                 8.0.0
nbclient                0.5.9
nbconvert               6.3.0
nbformat                5.1.3
nest-asyncio            1.5.4
netCDF4                 1.5.8
networkx                2.6.3
notebook                6.4.6
numba                   0.54.1
numexpr                 2.8.0
numpy                   1.20.3
oauthlib                3.1.1
opencv-python           4.5.4.60
openpyxl                3.0.9
opt-einsum              3.3.0
packaging               21.3
palettable              3.3.0
pandas                  1.3.4
pandocfilters           1.5.0
parso                   0.8.3
patsy                   0.5.2
pexpect                 4.8.0
pickleshare             0.7.5
Pillow                  8.4.0
pip                     21.2.4
plotnine                0.8.0
prometheus-client       0.12.0
prompt-toolkit          3.0.23
protobuf                3.19.1
ptyprocess              0.7.0
pyasn1                  0.4.8
pyasn1-modules          0.2.8
pycparser               2.21
pyDeprecate             0.3.0
Pygments                2.10.0
pymc3                   3.10.0
pynndescent             0.5.5
pyparsing               3.0.6
pyro-api                0.1.2
pyro-ppl                1.7.0
pyrsistent              0.18.0
python-dateutil         2.8.2
python-igraph           0.9.8
pytorch-lightning       1.3.8
pytz                    2021.3
PyYAML                  5.4.1
pyzmq                   22.3.0
requests                2.26.0
requests-oauthlib       1.3.0
rich                    10.15.2
rsa                     4.8
scanpy                  1.8.2
scikit-learn            1.0.1
scipy                   1.7.3
scvi-tools              0.14.5
seaborn                 0.11.2
Send2Trash              1.8.0
setuptools              58.0.4
setuptools-scm          6.3.2
sinfo                   0.3.4
six                     1.16.0
statsmodels             0.13.1
stdlib-list             0.8.0
tables                  3.6.1
tensorboard             2.7.0
tensorboard-data-server 0.6.1
tensorboard-plugin-wit  1.8.0
terminado               0.12.1
testpath                0.5.0
texttable               1.6.4
Theano-PyMC             1.0.11
threadpoolctl           3.0.0
tomli                   1.2.2
torch                   1.10.0
torchmetrics            0.6.0
tornado                 6.1
tqdm                    4.62.3
traitlets               5.1.1
typing_extensions       4.0.1
umap-learn              0.5.2
urllib3                 1.26.7
wcwidth                 0.2.5
webencodings            0.5.1
Werkzeug                2.0.2
wheel                   0.37.0
widgetsnbextension      3.5.2
xarray                  0.20.1
xlrd                    1.2.0
yarl                    1.7.2
zipp                    3.6.0

Best, Carlo