Ivadomed: Installation timeout error when collecting torch 1.5.0 package

[mariehbourget]

Issue description

I tried to install ivadomed on rosenberg for the first time (no cached packages) with the instruction in RTD. I get a timeout error when collecting torch, both with a venv in python 3.6 and python 3.8.

torch error python 3.6

ERROR: Could not install packages due to an OSError: HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Max retries exceeded with url: /packages/13/70/54e9fb010fe1547bc4774716f11ececb81ae5b306c05f090f4461ee13205/torch-1.5.0-cp36-cp36m-manylinux1_x86_64.whl (Caused by ReadTimeoutError("HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Read timed out. (read timeout=15)",))

torch error python 3.8

ERROR: Could not install packages due to an OSError: HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Max retries exceeded with url: /packages/ec/77/6de2895b3f0953f5e4bd9c7bb3f04552124051d1c0eb66697354aa510bf9/torch-1.5.0-cp38-cp38-manylinux1_x86_64.whl (Caused by ReadTimeoutError("HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Read timed out. (read timeout=15)"))

Steps to reproduce

1. Login to rosenberg
2. virtualenv venv-ivadomed --python=python3.8 (or python 3.6)
3. source venv-ivadomed/bin/activate
4. git clone https://github.com/neuropoly/ivadomed.git
5. cd ivadomed
6. pip install -e .
7. The installation stops after the timeout error when collecting torch 1.5.0.

Note: the same issue happens on my laptop (Ubuntu 20.04 in WSL1) if ~/.cache/pip is not present (torch was already cached there).

Temporary fix

I managed to install ivadomed in roserberg in a new 3.8 venv by first installing torch with pip install torch==1.5.0 (no error in that case when collecting the package), then doing the pip install -e . in ivadomed.

Has anyone run into this issue before?

[ssinad]

Can you describe the steps to reproduce this error?

On Tue, Apr 6, 2021 at 8:22 AM mariehbourget @.*>
wrote:

Issue description

I tried to install ivadomed on rosenberg for the first time (no cached
packages) with the instruction in RTD. I get a timeout error when
collecting torch, both with a venv in python 3.6 and python 3.8.
torch error python 3.6

ERROR: Could not install packages due to an OSError: HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Max retries exceeded with url: /packages/13/70/54e9fb010fe1547bc4774716f11ececb81ae5b306c05f090f4461ee13205/torch-1.5.0-cp36-cp36m-manylinux1_x86_64.whl (Caused by ReadTimeoutError("HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Read timed out. (read timeout=15)",))

torch error python 3.8

ERROR: Could not install packages due to an OSError: HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Max retries exceeded with url: /packages/ec/77/6de2895b3f0953f5e4bd9c7bb3f04552124051d1c0eb66697354aa510bf9/torch-1.5.0-cp38-cp38-manylinux1_x86_64.whl (Caused by ReadTimeoutError("HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Read timed out. (read timeout=15)"))

I managed to install everything in a new 3.8 venv by first installing
torch with pip install torch==1.5.0 (no error in that case when
collecting the package), then doing the pip install -e . in ivadomed.

Has anyone run into this issue before?

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[mariehbourget]

Can you describe the steps to reproduce this error?

I updated the first comment with more details.

[gisellemartel]

Issue description

I tried to install ivadomed on rosenberg for the first time (no cached packages) with the instruction in RTD. I get a timeout error when collecting torch, both with a venv in python 3.6 and python 3.8.

torch error python 3.6

ERROR: Could not install packages due to an OSError: HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Max retries exceeded with url: /packages/13/70/54e9fb010fe1547bc4774716f11ececb81ae5b306c05f090f4461ee13205/torch-1.5.0-cp36-cp36m-manylinux1_x86_64.whl (Caused by ReadTimeoutError("HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Read timed out. (read timeout=15)",))

torch error python 3.8

ERROR: Could not install packages due to an OSError: HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Max retries exceeded with url: /packages/ec/77/6de2895b3f0953f5e4bd9c7bb3f04552124051d1c0eb66697354aa510bf9/torch-1.5.0-cp38-cp38-manylinux1_x86_64.whl (Caused by ReadTimeoutError("HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Read timed out. (read timeout=15)"))

Steps to reproduce

1. Login to rosenberg
2. virtualenv venv-ivadomed --python=python3.8 (or python 3.6)
3. source venv-ivadomed/bin/activate
4. git clone https://github.com/neuropoly/ivadomed.git
5. cd ivadomed
6. pip install -e .
7. The installation stops after the timeout error when collecting torch 1.5.0.

Note: the same issue happens on my laptop (Ubuntu 20.04 in WSL1) if ~/.cache/pip is not present (torch was already cached there).

Temporary fix

I managed to install ivadomed in roserberg in a new 3.8 venv by first installing torch with pip install torch==1.5.0 (no error in that case when collecting the package), then doing the pip install -e . in ivadomed.

Has anyone run into this issue before?

I noticed that you mentioned you got it to work with 3.8 with the torch install workaround. Were you able to find a temporary fix for version 3.6?

[mariehbourget]

I noticed that you mentioned you got it to work with 3.8 with the torch install workaround. Were you able to find a temporary fix for version 3.6?

I have not tried with 3.6.

However, I tried changing the default timeout (as was suggested in meeting, ref: https://stackoverflow.com/questions/50305112/pip-install-timeout-issue/61472212#61472212).
So, in a new 3.8 environment without previously cached packages , I ran: pip --default-timeout=1000 install -e . in ivadomed
It took ~7-8 minutes to collect the torch package but after that, the installation was successful.

We should maybe try it on 3.6 and 3.7, and add a note about this in the documentation.