dvc: error on dvc get: GLIBC_2.18 not found. installed with fedora/centos

[hadoop@hostname ~]$ dvc get \
>     "https://x-token-auth:$GITHUB_TOKEN@$MODEL_REPO_URL" \
>     experiments/prod/model.pickle \
>     -o /mnt/repo/model.pickle
ERROR: failed to get 'experiments/prod/model.pickle' from 'https://x-token-auth:REDACTEDTOKEN@github.com/WPMedia/REPOURL.git' - Failed to clone repo 'https://x-token-auth:REDACTEDTOKEN@github.com/WPMedia/REPOURL.git' to '/tmp/tmpxfz0sxdedvc-repo': Cmd('git') failed due to: exit code(128)
  cmdline: git clone --no-single-branch -v https://x-token-auth:REDACTEDTOKEN@github.com/WPMedia/REPOURL.git /tmp/tmpxfz0sxdedvc-repo
  stderr: 'Cloning into '/tmp/tmpxfz0sxdedvc-repo'...
/usr/libexec/git-core/git-remote-https: /lib64/libc.so.6: version `GLIBC_2.18' not found (required by /usr/lib/dvc/libstdc++.so.6)
'

Please provide information about your setup DVC version(i.e. dvc --version), Platform and method of installation (pip, homebrew, pkg Mac, exe (Windows), DEB(Linux), RPM(Linux))

version: 0.58.1
used fedora/centos install (https://dvc.org/rpm/dvc.repo)
on standard emr cluster

About this issue

Original URL
State: closed
Created 5 years ago
Reactions: 1
Comments: 21 (17 by maintainers)

Commits related to this issue

erepo: fix environment before running git Fixes #2471 — committed to efiop/dvc by efiop 5 years ago

Most upvoted comments

Thanks!!

AlJohri on Oct 2, 2019

@AlJohri Patch is merged to master, I was unable to reproduce the error after patch. A new release should be available soon.

pared on Sep 30, 2019

pared on Sep 27, 2019

@AlJohri another patch on the way.

To put some context for future: We used fix_env to delete LD_LIBRARY_PATH from env if it was empty before Pyinstaller did its magic.

The problem is that gitpython did not “use” provided env, but used it to update its own git.cmd._environment. If there was no “LD_LIBRARY_PATH” in provided env, its value has not been updated.

So in theory fix env["LD_LIBRARY_PATH"]=None should work. Surprisingly it did not, thought env["LD_LIBRARY_PATH"]="" did.

Need to investigate why the first version does not work, might be another bug on our site, or something wrong with gitpython.

pared on Sep 27, 2019

I was able to reproduce the problem on vanilla EMR cluster machine.

pared on Sep 26, 2019

@AlJohri I am trying to reproduce the problem using docker and aws instance, and I am unable to, could you ssh to your instance and check what linux is it running? something like cat /etc/os-release

pared on Sep 25, 2019

Sorry, other stuff got in the way. Will try to get back to this ASAP.

efiop on Sep 23, 2019

@AlJohri Got it. I’ll also try to reproduce in the morning with some older docker image. 🙂

efiop on Sep 13, 2019

I’m not sure if I was using the latest version (I’ll check soon) but I definitely installed it on a fresh cluster so I got whatever version https://dvc.org/rpm/dvc.repo defines.

AlJohri on Sep 12, 2019