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

Alex Chekholko chekh at stanford.edu
Fri Sep 16 10:11:10 PDT 2016


Hi all,

I recommend you work around AFS problems by not using AFS.  Use your 
user_data directory instead:

https://web.stanford.edu/group/farmshare/cgi-bin/wiki/index.php/User_Guide#Directory_paths

Regards,
Alex

On 09/16/2016 09:49 AM, Nick Henderson wrote:
> I also want to confirm |git| issues on |corn.stanford.edu
> <http://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
>     <mailto:farmshare-discuss-bounces at lists.stanford.edu>>
>     > on behalf of Andreas Santucci <santucci.andreas at gmail.com
>     <mailto:santucci.andreas at gmail.com>>
>     > *Sent:* Thursday, September 15, 2016 1:53:44 PM
>     > *To:* farmshare-discuss at lists.stanford.edu
>     <mailto: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
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     > _______________________________________________
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>     <mailto:farmshare-discuss at lists.stanford.edu>
>     > https://mailman.stanford.edu/mailman/listinfo/farmshare-discuss
>     >
>
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>
>>
>
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-- 
Alex Chekholko chekh at stanford.edu 347-401-4860



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