Open Rhys-McAlister opened 6 months ago
Hi Rhys, thank you so much for the using our tool and sharing the feedback! I will try to reproduce the error and loop back shortly.
Hi Rhys, thank you so much for the using our tool and sharing the feedback! I will try to reproduce the error and loop back shortly.
Thanks!
Hi Rhys,
Thank you for your patience! Would you mind trying these commands instead to see if it works?
conda create -n graph-mamba python==3.9
conda activate graph-mamba
pip install torch==1.13.0
pip install torch-scatter torch-sparse -f https://data.pyg.org/whl/torch-1.13.0+cu117.html
pip install torch_geometric==2.0.4
pip install transformers==4.36.2
pip install torchmetrics==0.10.3
pip install openbabel-wheel
pip install fsspec
pip install rdkit
pip install pytorch-lightning yacs
pip install performer-pytorch
pip install tensorboardX
pip install ogb
pip install wandb
pip install causal-conv1d==1.0.2
pip install mamba-ssm==1.0.1
The mamba installation (last two lines) might be a bit tricky. Please feel free to refer to the common issues such as cuda dependency in their repo https://github.com/state-spaces/mamba or we could look into it together.
Thank you for the response, you were correct those two last lines were tricky.
`Collecting causal-conv1d==1.0.2 Using cached causal_conv1d-1.0.2.tar.gz (6.4 kB) Preparing metadata (setup.py) ... error error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [13 lines of output]
/tmp/pip-install-_txvuxlg/causal-conv1d_6c9aaf7a6ea4488f91528d397f701b26/setup.py:78: UserWarning: causal_conv1d was requested, but nvcc was not found. Are you sure your environment has nvcc available? If you're installing within a container from https://hub.docker.com/r/pytorch/pytorch, only images whose names contain 'devel' will provide nvcc.
warnings.warn(
Traceback (most recent call last):
File "
torch.__version__ = 1.13.0+cu117
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed
× Encountered error while generating package metadata. ╰─> See above for output.
note: This is an issue with the package mentioned above, not pip. hint: See above for details. Collecting mamba-ssm==1.0.1 Downloading mamba_ssm-1.0.1.tar.gz (28 kB) Preparing metadata (setup.py) ... error error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [13 lines of output]
/tmp/pip-install-dy2v6xzo/mamba-ssm_45311b26096b450c9b61a4164acc8b62/setup.py:77: UserWarning: mamba_ssm was requested, but nvcc was not found. Are you sure your environment has nvcc available? If you're installing within a container from https://hub.docker.com/r/pytorch/pytorch, only images whose names contain 'devel' will provide nvcc.
warnings.warn(
Traceback (most recent call last):
File "
torch.__version__ = 1.13.0+cu117
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed
× Encountered error while generating package metadata. ╰─> See above for output.
note: This is an issue with the package mentioned above, not pip. hint: See above for details.`
Any help with this would be much appreciated. I have had a look through the steps in this repo originally but haven't had much success.
Thanks in advance
Gotcha, this issue seems relevant. Could you type in nvidia-smi
or nvcc --version
in command line to check your cuda version?
Thank you for the response, you were correct those two last lines were tricky.
`Collecting causal-conv1d==1.0.2 Using cached causal_conv1d-1.0.2.tar.gz (6.4 kB) Preparing metadata (setup.py) ... error error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully. │ exit code: 1 ╰─> [13 lines of output] /tmp/pip-install-_txvuxlg/causal-conv1d_6c9aaf7a6ea4488f91528d397f701b26/setup.py:78: UserWarning: causal_conv1d was requested, but nvcc was not found. Are you sure your environment has nvcc available? If you're installing within a container from https://hub.docker.com/r/pytorch/pytorch, only images whose names contain 'devel' will provide nvcc. warnings.warn( Traceback (most recent call last): File "", line 2, in File "", line 34, in File "/tmp/pip-install-_txvuxlg/causal-conv1d_6c9aaf7a6ea4488f91528d397f701b26/setup.py", line 112, in if bare_metal_version >= Version("11.8"): NameError: name 'bare_metal_version' is not defined
torch.__version__ = 1.13.0+cu117 [end of output]
note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed
× Encountered error while generating package metadata. ╰─> See above for output.
note: This is an issue with the package mentioned above, not pip. hint: See above for details. Collecting mamba-ssm==1.0.1 Downloading mamba_ssm-1.0.1.tar.gz (28 kB) Preparing metadata (setup.py) ... error error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully. │ exit code: 1 ╰─> [13 lines of output] /tmp/pip-install-dy2v6xzo/mamba-ssm_45311b26096b450c9b61a4164acc8b62/setup.py:77: UserWarning: mamba_ssm was requested, but nvcc was not found. Are you sure your environment has nvcc available? If you're installing within a container from https://hub.docker.com/r/pytorch/pytorch, only images whose names contain 'devel' will provide nvcc. warnings.warn( Traceback (most recent call last): File "", line 2, in File "", line 34, in File "/tmp/pip-install-dy2v6xzo/mamba-ssm_45311b26096b450c9b61a4164acc8b62/setup.py", line 111, in if bare_metal_version >= Version("11.8"): NameError: name 'bare_metal_version' is not defined
torch.__version__ = 1.13.0+cu117 [end of output]
note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed
× Encountered error while generating package metadata. ╰─> See above for output.
note: This is an issue with the package mentioned above, not pip. hint: See above for details.`
Any help with this would be much appreciated. I have had a look through the steps in this repo originally but haven't had much success.
Thanks in advance
I have the same issue, and my system is ubuntu, when I type the command "nvcc -V", it shows no nvcc, so I install the cudatoolkit in my computer, after I install the cudatoolkit, then the "nvcc -V" is ok, then I set "CUDA_HOME=/usr/local/cuda-X.X", now I can install mamba-ssm. I did not know if this is useful for your system
The most straightforward method I found for installing nvcc
was to utilize the conda package within the environment. You can install it using the following command:
conda install nvidia/label/cuda-11.7.1::cuda-nvcc
There are also other versions available: https://anaconda.org/nvidia/cuda-nvcc
Thank you for your comments!
Attempting to use the install commands in the readme and finding the below error:
Platform: WSL
`conda clean --all Retrieving notices: ...working... done Channels:
PackagesNotFoundError: The following packages are not available from current channels:
Current channels:
To search for alternate channels that may provide the conda package you're looking for, navigate to
and use the search bar at the top of the page.
EnvironmentNameNotFound: Could not find conda environment: graph-mamba You can list all discoverable environments with
conda info --envs
.`