Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

Nick Eubank nickeubank at gmail.com
Fri Sep 16 10:08:22 PDT 2016


It's not too new -- I was having this problem in July (there's actually a
thread about it in the archives of this mailing list)

(A different ) Nick

On Fri, Sep 16, 2016 at 9:50 AM Nick Henderson <nwh at stanford.edu> wrote:

> 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
>> >
>>
>> _______________________________________________
>> farmshare-discuss mailing list
>> farmshare-discuss at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/farmshare-discuss
>>
>> _______________________________________________
> farmshare-discuss mailing list
> farmshare-discuss at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/farmshare-discuss
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/farmshare-discuss/attachments/20160916/40ae7593/attachment-0001.html>


More information about the farmshare-discuss mailing list