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[farmshare-discuss] Git Clone fatal error (sha1 file, timeout)

Nick Henderson nwh at stanford.edu
Fri Sep 16 09:49:25 PDT 2016


I also want to confirm git issues on corn.stanford.edu.

I was able to clone a small repo directly in my afs home dir:

https://github.com/nwh/cme211-test-repo

However, the clone times out on my course notes repo:

https://github.com/CME211/notes

$ git clone https://github.com/CME211/notes
Cloning into 'notes'...
remote: Counting objects: 1244, done.
remote: Compressing objects: 100% (198/198), done.
remote: Total 1244 (delta 97), reused 0 (delta 0), pack-reused 1042
Receiving objects: 100% (1244/1244), 17.75 MiB | 3.61 MiB/s, done.
Resolving deltas: 100% (506/506), done.
Checking connectivity... done.
error: unable to create file challenge/cpp_assignment/u.data
(Connection timed out)
error: unable to create file challenge/cpp_assignment/u.data.short
(Connection timed out)
fatal: cannot create directory at 'challenge/even_fib': Connection timed out
warning: unable to unlink .git/index.lock: Connection timed out
warning: Clone succeeded, but checkout failed.
You can inspect what was checked out with 'git status'
and retry the checkout with 'git checkout -f HEAD'

Very similar behavior when cloning via SSH.

This is a new issue. I have been cloning directly into my AFS for quite a
long time with no issue.

We would really appreciate attention to this issue. I am the instructor for
CME211. We teach the students to use git and keep track of their work on
GitHub. Asking all students to clone to /tmp is not a good solution for us.
In previous years, all of our students cloned directly to their home
folders on AFS with no issue.

Thanks so much,
Nick

On Thu, Sep 15, 2016 at 8:37 PM John Bickar jbickar at stanford.edu
<http://mailto:jbickar@stanford.edu> wrote:

Hrm. It's not necessarily AFS, per se, but something with the config on
> corn and cardinal, plus something in the git repo or git itself that
> causes the clone to fail. I (and the rest of my team) clone from github
> (public and private repos, using primarily the SSH protocol) to AFS
> hundreds of times daily, so it's not simply that git and AFS don't work
> together.
>
> I tested two different public repos cloning to AFS on corn, cardinal,
> sites1, and the "my-stanford-vbox" VM*.
>
> https://github.com/SU-SWS/Stanford-Drupal-Profile.git:
> corn: success
> cardinal: success
> sites1: success
> my-stanford-vbox: success (but it failed if I tried to clone snorkel first)
>
> https://github.com/HazyResearch/snorkel.git:
> corn: fail
> cardinal: fail
> sites1: success
> my-stanford-vbox: fail
>
> git versions:
> cardinal: 1.9.1
> corn: 1.9.1
> sites1: 1.7.10.4
> my-stanford-vbox: 1.9.1
>
> My best guess would be a mismatch in versions of OpenAFS or git among
> the different servers, but I couldn't figure out what version of OpenAFS
> was running on each of the servers I tried (using the instructions at
> https://uit.stanford.edu/service/afs/install).
>
> It may also be a difference in the size of the repo: snorkel is 235M,
> Stanford-Drupal-Profile is 534K.
>
> Maybe the above will help our friends in Research Computing troubleshoot
> this issue.
>
> -John Bickar
> Stanford Web Services
>
>
> * https://code.stanford.edu/devops-tools/my-stanford-vbox
>
>
>
>
> On 9/15/16 6:06 PM, Charles E Yates wrote:
> > Clone to /tmp then copy to where you want it.  Seems git clone and afs
> > don't play well together.
> > ------------------------------------------------------------------------
> > *From:* farmshare-discuss <farmshare-discuss-bounces at lists.stanford.edu>
> > on behalf of Andreas Santucci <santucci.andreas at gmail.com>
> > *Sent:* Thursday, September 15, 2016 1:53:44 PM
> > *To:* farmshare-discuss at lists.stanford.edu
> > *Subject:* [farmshare-discuss] Git Clone fatal error (sha1 file, timeout)
> >
> > Dear Farmshare Mailing List,
> >
> > I am quite consistently encountering a connection time-out when trying
> > to clone git repositories on Corn, regardless whether I attempt to clone
> > via SSH or HTTPS.
> >
> > _*Using HTTPS:*_
> > santucci at corn12:~$ git clone
> https://github.com/CME211/cme211-asantucci.git
> > Cloning into 'cme211-asantucci'...
> > Username for 'https://github.com': asantucci
> > Password for 'https://asantucci@github.com':
> > remote: Counting objects: 52, done.
> > remote: Compressing objects: 100% (24/24), done.
> > _*fatal: error when closing sha1 file: Connection timed out
> >
> > *_
> > _*Using * *SSH**:**
> > *_
> > santucci at corn12:~$ git clone git at github.com:CME211/cme211-asantucci.git
> > Cloning into 'cme211-asantucci'...
> > remote: Counting objects: 52, done.
> > remote: Compressing objects: 100% (24/24), done.
> > remote: Total 52 (delta 9), reused 0 (delta 0), pack-reused 24
> > Receiving objects: 100% (52/52), 10.18 MiB | 1.31 MiB/s, done.
> > Resolving deltas: 100% (15/15), done.
> > Checking connectivity... done.
> > error: unable to create file hw1/alignments3.txt (Connection timed out)
> > ... (More connection time-outs here) ...
> > _*fatal: unable to checkout working tree
> > warning: unable to unlink .git/index.lock: Connection timed out
> > warning: Clone succeeded, but checkout failed.
> > *_You can inspect what was checked out with 'git status'
> > and retry the checkout with 'git checkout -f HEAD'
> >
> > Attempts to follow the instructions above (retrying the checkout) leads
> > only to more time-outs.
> >
> > _*Last Ditch Effort: Adding SSH Keys to GitHub Account:
> > *_
> > I've also tried to follow some of the instructions listed here on GitHub
> > <https://help.github.com/categories/ssh/> pertaining to adding SSH Keys
> > or GPG Keys manually to a GitHub account.
> >
> > _*Question:*_
> > What is the correct way to remedy this error? Executing the same
> > commands from a local machine causes no problems. I apologize that the
> > repository listed above is private. For a public repo which also causes
> > the same error, try:
> >
> > git clone https://github.com/HazyResearch/snorkel.git
> >
> > Thank you for your time and attention, please let me know if I can add
> > any clarifying details.
> >
> > Andreas Santucci
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > farmshare-discuss mailing list
> > farmshare-discuss at lists.stanford.edu
> > https://mailman.stanford.edu/mailman/listinfo/farmshare-discuss
> >
>
> _______________________________________________
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> farmshare-discuss at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/farmshare-discuss
>
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