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dmis-lab / BERN2

BERN2: an advanced neural biomedical namedentity recognition and normalization tool
http://bern2.korea.ac.kr
BSD 2-Clause "Simplified" License
175 stars 42 forks source link

Unable to install bern2 dependencies on Mac OS #30

Closed naveenjack closed 1 year ago

naveenjack commented 2 years ago

Hi,

I am trying to install bern2 dependencies on mac Os Montery. When I run the below commands , I am getting package not found error for cudatoolkit and faiss-gpu. And these version are not available for osx. I confirmed it through conda search and also by searching on anaconda.org search packages.

Let me know if I can run this on osx ?

Dependencies : conda install pytorch==1.9.0 cudatoolkit=10.2 -c pytorch conda install faiss-gpu libfaiss-avx2 -c conda-forge

Thanks

mjeensung commented 2 years ago

Hi,

thanks for letting us know. I hope it would work by installing faiss-cpu and cudatoolkit which is compatible with the mac os. Could you try it and let us know?

naveenjack commented 2 years ago

Hi,

Thanks for your reply. Now, I tried installing bern2 on linux machines. Since many packages are compatible this platform. As per the instruction , we need to install pytorch and cudatoolkit (conda install pytorch==1.9.0 cudatoolkit=10.2 -c pytorch). But this version is not available in pytorch channel. And getting below error:

CondaHTTPError: HTTP 403 FORBIDDEN for url https://conda.anaconda.org/pytorch/linux-64/pytorch-1.9.0-py3.7_cuda10.2_cudnn7.6.5_0.tar.bz2 Elapsed: 00:00.973224

An HTTP error occurred when trying to retrieve this URL. HTTP errors are often intermittent, and a simple retry will get you on your way.

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://repo.anaconda.com/pkgs/main/linux-64/cudatoolkit-10.2.89-hfd86e86_1.conda Elapsed: -

An HTTP error occurred when trying to retrieve this URL. HTTP errors are often intermittent, and a simple retry will get you on your way.

naveenjack commented 2 years ago

Adding more details on what I have tried. On Mac: pytorch=1.9.0 is not available in pytorch channel and cudatoolkit is also not available with 10.2 version. see below commands and result.

$> conda search pytorch=1.9.0 Loading channels: done

pytorch 1.9.0 cpu_py36h12aac5e_0 conda-forge
pytorch 1.9.0 cpu_py36h2d3ebdf_1 conda-forge
pytorch 1.9.0 cpu_py36h41aa04d_2 conda-forge
pytorch 1.9.0 cpu_py37h6234483_2 conda-forge
pytorch 1.9.0 cpu_py37h6472570_0 conda-forge
pytorch 1.9.0 cpu_py37hc5e437f_1 conda-forge
pytorch 1.9.0 cpu_py38h0529baa_2 conda-forge
pytorch 1.9.0 cpu_py38h490fcb8_1 conda-forge
pytorch 1.9.0 cpu_py39h28f9090_2 conda-forge
pytorch 1.9.0 cpu_py39h37f9f7c_1 conda-forge
pytorch 1.9.0 cpu_py39hbc4979b_0 conda-forge

$> conda search cudatoolkit=10.2 Loading channels: done No match found for: cudatoolkit=10.2. Search: cudatoolkit=10.2

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

https://anaconda.org

and use the search bar at the top of the page.

Available channel and version: $> conda search cudatoolkit Loading channels: done Name Version Build Channel
cudatoolkit 9.0 h41a26b3_0 pkgs/main

If I have to try bern2 on mac. Then which version of these version has to be installed and from which channels ?

On Linux docker image(continuumio/anaconda3) pytorch=1.9.0 cudatoolkit is not available in pytorch . And its available with different version and different channel. Please let me know which combination of version and channel has to be used on Linux platform.

(bern2) root@da0f25063715:/# conda search pytorch=1.9.0 Loading channels: done No match found for: pytorch=1.9.0. Search: pytorch=1.9.0

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

https://anaconda.org

and use the search bar at the top of the page.

cudatoolkit=10.2 : is not available in pytorch channel and its only available in pkgs/main

(bern2) root@da0f25063715:/# conda search cudatoolkit=10.2 Loading channels: done Name Version Build Channel
cudatoolkit 10.2.89 hfd86e86_0 pkgs/main
cudatoolkit 10.2.89 hfd86e86_1 pkgs/main