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

John Bickar jbickar at
Thu Sep 15 20:37:05 PDT 2016

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 

I tested two different public repos cloning to AFS on corn, cardinal, 
sites1, and the "my-stanford-vbox" VM*.
corn: success
cardinal: success
sites1: success
my-stanford-vbox: success (but it failed if I tried to clone snorkel first)
corn: fail
cardinal: fail
sites1: success
my-stanford-vbox: fail

git versions:
cardinal: 1.9.1
corn: 1.9.1
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

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


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>
> on behalf of Andreas Santucci <santucci.andreas at>
> *Sent:* Thursday, September 15, 2016 1:53:44 PM
> *To:* farmshare-discuss at
> *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
> Cloning into 'cme211-asantucci'...
> Username for '': asantucci
> Password for '':
> 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
> 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
> <> 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
> 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

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