microsoft / microsoft/Graphormer

Example script hangs without output

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#111 4 comments 0 reactions 0 assignees View on GitHub

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Dominant language
Python
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Description

Hi Graphormer Team - thanks for this excellent codebase! I am opening a new issue because two similar issues have been previously closed. They are https://github.com/microsoft/Graphormer/issues/100 by @skye95git and https://github.com/microsoft/Graphormer/issues/99 by @mswzeus.

Bug

In short, despite carefully following the Graphormer installation instructions, there is no response at the console after running bash zinc.sh and interrupting the script produces a File "<frozen importlib._bootstrap>", line 107, in acquire error message.

Failed Solutions

In https://github.com/microsoft/Graphormer/issues/99, it was suggested that pip uninstall setuptools would fix the issue; however, this was not the case. Rather, running bash zinc.sh now throws terminate called after throwing an instance of 'std::bad_alloc' (which is fixed by reinstalling setuptools).

From @zhengsx in https://github.com/microsoft/Graphormer/issues/100:

We notice that similar problems occur recently, and a guess is that some recent upgrades of library lead to this problem. We're working on this problem, and maybe you can try to modify the version of cuda/torch, cu110 is recommeded.

Unfortunately, downgrading to torch.version.cuda==10.2 did not fix the issue either (i.e., bash zinc.sh still hangs). Should I find a solution, I will follow-up on this thread for future reference.

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the hang with bash zinc.sh after following the Graphormer installation instructions, then compare the reported setuptools and PyTorch/CUDA versions with issues #99 and #100. Done means identifying the dependency or environment cause and documenting or implementing a verified fix that lets the script produce output without the reported errors.

Written by the indexing model from the issue text.

Assessment

Tech stack
bash, python, pytorch
Domain
devops, machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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