Fatal Error when updating submodule using GIT

Question

I am trying to update the submodules of this git repositary but I keep getting a fatal errors:

[root@iptlock ProdigyView]# git submodule update --recursive
Cloning into core...
Permission denied (publickey).
fatal: The remote end hung up unexpectedly
Clone of '[email protected]:ProdigyView/ProdigyView-Core.git' into submodule path 'core' failed

Or this way

[root@iptlock root]# git clone --recursive https://github.com/ProdigyView/ProdigyView.git
Cloning into ProdigyView...
remote: Counting objects: 438, done.
remote: Compressing objects: 100% (275/275), done.
remote: Total 438 (delta 172), reused 394 (delta 128)
Receiving objects: 100% (438/438), 8.03 MiB | 5.19 MiB/s, done.
Resolving deltas: 100% (172/172), done.
Submodule 'core' ([email protected]:ProdigyView/ProdigyView-Core.git) registered for path 'core'
Cloning into core...
Permission denied (publickey).
fatal: The remote end hung up unexpectedly
Clone of '[email protected]:ProdigyView/ProdigyView-Core.git' into submodule path 'core' failed

Any ideas of why this is happening withthe submodule? The repo is this one:

https://github.com/ProdigyView/ProdigyView

(The submodule is able to be cloned if I do not try to clone it as a submodule.)

If it may help, adding the public key in github did the job for me. — i_v_harish
– i_v_harish, Commented Nov 3, 2017 at 11:30

Daniël W. Crompton · Accepted Answer · 2015-04-17 09:45:13Z

101

The issue is that git can't find the public key needed to download the repo from your server, the solution is to use the public url.

In the file .gitmodule you will find the following entry:

[submodule "example"]
    path = example
    url = [email protected]:webhat/example.git

The URL need to be changed to the public URL for the module:

[submodule "example"]
    path = example
    url = https://github.com/webhat/example.git

As you can see the prefix git@ has been changed to https:// and the infix : becomes /

EDIT: In your own repository you might need to use git:// rather than https://

The previous answer was unclear to me, so I added this.

EDIT 2: If you find you need to run git submodule sync or need to edit .git/config to get this to work, you have likely set up remotes for the submodules.

edited Apr 17, 2015 at 9:45

answered Feb 11, 2013 at 7:56

Daniël W. Crompton

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5 Comments

bfncs Over a year ago

I ran into the same problem today and Github seems to offer public cloning only via HTTPS nowadasy. The URL in your example would have been https://github.com/webhat/example.git then

Alexander Over a year ago

Repeat the procedure in .git/config

Daniël W. Crompton Over a year ago

@Alexander I didn't have an issue with .git/config after updating.

Nazareno Lorenzo Over a year ago

This worked for me, but had to run: git submodule sync before running the git submodule update --init --recursive

Trake Vital Over a year ago

Don't forget to: git submodule sync git submodule init git submodule update

Temi · Accepted Answer · 2014-05-13 14:25:49Z

54

If it can help some people:

I update my .gitmodules

[submodule "example"]
  path = example
  url = https://github.com/webhat/example.git

Then I update my .git/config too

[submodule "example"]
  url = https://github.com/webhat/example.git

Like some of you said it before (and I thank you).

Then I update my .git/modules/example/config

[remote "origin"]
  fetch = [...]
  url = https://github.com/webhat/example.git

And to finish I do

git submodule sync
git submodule init
git submodule update

answered May 13, 2014 at 14:25

Temi

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1 Comment

Onat Korucu Over a year ago

The last 3 lines (sync, init, update) helped me when I cloned a project with submodules via Sourcetree. Sourcetree successfully had configured .gitmodules but I was not able to checkout to submodule branches until I synched, initialized and updated. Then I closed and opened Sourcetree and everything was working fine.

RC_02 · Accepted Answer · 2015-09-14 02:03:06Z

7

You can manually pass in the key in Build --> "Execute shell" section of jenkins job :

ssh-agent bash -c 'ssh-add {path_to_private_key}; git submodule update --init --recursive'

Example:

ssh-agent bash -c 'ssh-add /var/lib/jenkins/.ssh/jenkins_rsa; git submodule update --init --recursive'

edited Sep 14, 2015 at 2:03

answered Sep 13, 2015 at 21:35

RC_02

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2 Comments

Vladimir Ivanov Over a year ago

This is actually useful. Even on Windows machine trying to just git submodule update gives you access denied, because no key is actually used.

Selik Over a year ago

That was the fix that helped me, kinda. I thought that maybe that's the cause and run the git commands in git bash instead of windows cmd and it asked to the password in the modal, which cmd never did. Looks like another windows bug..

Sruthi · Accepted Answer · 2015-08-24 22:48:06Z

6

The following steps will fix the problem.

Delete the folder of the submodule on your local.
Do git submodule sync
then git submodule update --init

Hope this helps.

answered Aug 24, 2015 at 22:48

Sruthi

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Comments

hmedia1 · Accepted Answer · 2017-08-02 04:25:26Z

6

This is happened that many times for me that I put a function in my .bash_profile (works on BSD sed / GNU / Mac):

gitfix () {
if [ -f "./.gitmodules" ] ; then
    sed -E -i.bak -e "s/(url *= *)(.*:)(.*)/\1https:\/\/github.com\/\3/g" .gitmodules \
    git submodule sync
    git submodule update --init --recursive
fi
}

A one liner:

sed -E -i.bak -e "s/(url *= *)(.*:)(.*)/\1https:\/\/github.com\/\3/g" .gitmodules ; git submodule sync ; git submodule update --init --recursive

vim search/replace:

%s/\(url\s*=\s*\)\(.*:\)\(.*\)/\1https:\/\/github.com\/\3/

Underlying solution based on Daniël 's answer

answered Aug 2, 2017 at 4:25

hmedia1

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Comments

Kio Krofovitch · Accepted Answer · 2014-08-04 17:25:24Z

I had this same issue. However, in my situation, the team wanted to use the SSH access from the .gitmodules, so modifying the URL to use http:// was not an option.

Ultimately, my issue was having an incorrect ~/.ssh/config file. The config file had some erroneous settings, so I was actually trying to access the incorrect server every time I'd really want to access [email protected]. I found this out by executing the following command:

ssh -vT [email protected]

The third line or so should say this:

debug1: Connection to github.com [<ip address>] port <port num>

If you aren't attempting to connect to github.com, then your config file is pointing you off course.

Turns out I didn't need any of the stuff in my config file anyway, so I was safe to delete it. If you want to maintain a config file, here is a good article on that:

http://nerderati.com/2011/03/17/simplify-your-life-with-an-ssh-config-file/

Also, these GitHub docs really helped me debug my issue:

https://help.github.com/articles/error-permission-denied-publickey

https://help.github.com/articles/what-ip-addresses-does-github-use-that-i-should-whitelist

MayTheSForceBeWithYou · Accepted Answer · 2020-05-15 19:20:48Z

Adding new answer instead of edit for greater visibility to anyone experience the same problem I was...

I had the exact opposite. Private Bitbucket repo & submodule for work. Always got this error...

fatal: repository 'http://bitbucket.org/companyname/submodule-repo-name.git' does not exist
fatal: clone of 'http://bitbucket.org/companyname/submodule-repo-name.git' into submodule path 
'/Users/me/path/to/repo-using-submodule/folder' failed
Failed to clone 'submodule/folder'. Retry scheduled
fatal: repository 'http://bitbucket.org/companyname/submodule-repo-name.git' does not exist
fatal: clone of 'http://bitbucket.org/companyname/submodule-repo-name.git' into submodule path 
'/Users/me/path/to/repo-using-submodule/folder' failed
Failed to clone 'submodule/folder' a second time, aborting

I had to manually go into my .git/config file and update this:

[submodule "submodule-name"]
url = https://bitbucket.org/companyname/submodule-repo.git

with this:

[submodule "submodule-name"]
url = [email protected]:companyname/submodule-repo.git

Not sure how to set this up so me and all my coworkers can use the submodule without tweaking, but got me past my several month long struggle with this.

Devin Dixon · Accepted Answer · 2011-11-19 21:00:18Z

-11

Figured it out. The path in the .gitmodule files could not download the submodule.

answered Nov 19, 2011 at 21:00

Devin Dixon

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8 Comments

Dave Lancea Over a year ago

I'm having this same issue. Could you elaborate on what was wrong and how you fixed it?

Khue Vu Over a year ago

This is how I have solved this problem: In the .gitmodules file and .git/config file, you will see url path for the submodule you want to update. If it is like git@github... change it to a valid url: git//github.com/.... it will solve the problem.

awolf Over a year ago

This answer is terribly unclear. Khune Vu's suggestion did not resolve the issue either.

Arnaldo Capo Over a year ago

After modifying the path in both places, I kept getting the same errors. I had to delete the folder of the submodule. Do git submodule sync and then git submodule update --init

hmedia1 Over a year ago

This is such a terrible answer. Not only is the file called .gitmodules not .gitmodule, but all you've done is paraphrased your original question, and given no explanation to help anyone else. Thankfully there is a great answer which Daniël W. Crompton posted, and I encourage you to change the accepted answer to that one @DevinDixon . Meanwhile, I will propose an edit to yours

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