I just quote DAC's email about this (sent to me and Jason):
"The behavior of submodules depends on the version of git being used. For
example, in in git 1.7, the submodules directory has a .git directory, with
the usual contents. But with git 2.11, the .git file is just a file with
a pointer to $AMBERHOME/.git/modules/AmberTools/src/parmed (for example).
Other commands (like git submodule update --remote --merge) are not allowed
in the older version. So we probably need to ask developers to update
their git versions(?)"
Hai
On Mon, Jun 12, 2017 at 12:45 PM, David Cerutti <dscerutti.gmail.com> wrote:
> The git version I'm trying to use is 1.7.12.4
>
> Good point, though--that's probably too old!
>
>
> On Mon, Jun 12, 2017 at 12:44 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > The whole process should just as like your 1st post (ideally)
> >
> > git clone gitosis.git.ambermd.org:/amber.git <amber install directory>
> > git pull
> > git submodule update --init
> >
> > > What's your git version? if it's old, I recommend to update it and
> retry.
> >
> > You have not replied about the git version yet.
> >
> > btw, I don't have access to amber git now so will check tonight.
> > Hai
> >
> > On Mon, Jun 12, 2017 at 12:33 PM, David Cerutti <dscerutti.gmail.com>
> > wrote:
> >
> > > I've also tried
> > >
> > > git submodule foreach git pull
> > >
> > > It's complaining
> > >
> > > Entering 'AmberTools/src/ambertools-binary-build'
> > > You are not currently on a branch. Please specify which
> > > branch you want to merge with. See git-pull(1) for details.
> > >
> > > git pull <remote> <branch>
> > >
> > > Stopping at 'AmberTools/src/ambertools-binary-build'; script returned
> > > non-zero status.
> > >
> > > I can do git pull, again seeing that I'm already up-to-date, and git
> > > checkout master, to see that I'm already on master. I can also go into
> > > AmberTools/src/ambertools-binary-build/ and do
> > >
> > > git clone https://github.com/Amber-MD/ambertools-binary-build.git
> > >
> > > to see if that helps. Still no luck. That gets me:
> > >
> > > Permission denied (publickey).
> > > fatal: Could not read from remote repository.
> > >
> > > Please make sure you have the correct access rights
> > > and the repository exists.
> > > Unable to fetch in submodule path 'AmberTools/src/build-bot/
> > > ambertools-test'
> > >
> > > which is a familiar error.
> > >
> > > So, I suppose what I should be trying to do at this point is make a
> fresh
> > > clone and get its submodules initialized, but I need a protocol for
> doing
> > > that. What I'm trying to do at the moment is:
> > >
> > > git clone gitosis.git.ambermd.org:/amber.git <new amber repo>
> > > cd <new amber repo>/AmberTools/src/build-bot/
> > > git clone https://github.com/Amber-MD/ambertools-ci.git
> > > cd <new amber repo>/AmberTools/src/ambertools-binary-build/
> > > git clone https://github.com/Amber-MD/ambertools-binary-build.git
> > > cd <new amber repo>
> > > git pull
> > > git submodule update --init
> > >
> > > But, this is not working for various errors shown above.
> > >
> > > Dave
> > >
> > >
> > > On Mon, Jun 12, 2017 at 11:55 AM, David Cerutti <dscerutti.gmail.com>
> > > wrote:
> > >
> > > > Aha you were pointing me to github. I can clone that repo directly:
> > > >
> > > > git clone https://github.com/Amber-MD/ambertools-ci.git
> > > >
> > > > If I do that within AmberTools/src/build-bot/, I also get a directory
> > > > ambertools-test/ with only a .git file for its contents. Then, if I
> go
> > > > back to ${AMBERHOME} and do git pull (already up to date), git
> > submodule
> > > > update --init I get:
> > > >
> > > > fatal: Needed a single revision
> > > > Unable to find current revision in submodule path
> > > > 'AmberTools/src/build-bot/ambertools-test'
> > > >
> > > >
> > > >
> > > >
> > > > On Mon, Jun 12, 2017 at 11:39 AM, Hai Nguyen <nhai.qn.gmail.com>
> > wrote:
> > > >
> > > >> On Mon, Jun 12, 2017 at 11:32 AM, David Cerutti <
> dscerutti.gmail.com>
> > > >> wrote:
> > > >>
> > > >> > How should I clone just the one directory?
> > > >>
> > > >>
> > > >> I don't know what you meant here.
> > > >>
> > > >> What's your git version? if it's old, I recommend to update it and
> > > retry.
> > > >>
> > > >> Hai
> > > >>
> > > >>
> > > >> > I'm warying of doing a sparse
> > > >> > checkout because all that I see online tends to revolve around
> > > cloning a
> > > >> > clean repository with only portions of the original.
> > > >> >
> > > >> > On Mon, Jun 12, 2017 at 11:18 AM, Hai Nguyen <nhai.qn.gmail.com>
> > > wrote:
> > > >> >
> > > >> > > I am not sure why, but that ambertools-test repo was renamed to
> > > >> > > ambertools-ci (https://github.com/Amber-MD/ambertools-ci)
> > > >> > >
> > > >> > > Can you try git clone that repo directly to see if you got the
> > > denial?
> > > >> > >
> > > >> > > I will have a look tonight.
> > > >> > > Meanwhile, you can safely ignore that repo to continue your
> work.
> > > >> > >
> > > >> > > Hai
> > > >> > >
> > > >> > > On Mon, Jun 12, 2017 at 11:08 AM, David Cerutti <
> > > dscerutti.gmail.com>
> > > >> > > wrote:
> > > >> > >
> > > >> > > > Hello devs,
> > > >> > > >
> > > >> > > > Has anyone seen this problem? It looks like a git permissions
> > > >> issue,
> > > >> > but
> > > >> > > > that is very odd since I can do a clean
> > > >> > > >
> > > >> > > > git clone gitosis.git.ambermd.org:/amber.git <amber install
> > > >> directory>
> > > >> > > >
> > > >> > > > without problems. However, if I then do
> > > >> > > >
> > > >> > > > git pull
> > > >> > > > git submodule update --init
> > > >> > > >
> > > >> > > > Submodule 'AmberTools/src/ambertools-binary-build' (
> > > >> > > > https://github.com/Amber-MD/ambertools-binary-build)
> registered
> > > for
> > > >> > path
> > > >> > > > 'AmberTools/src/ambertools-binary-build'
> > > >> > > > Submodule 'AmberTools/src/build-bot/ambertools-test'
> > > >> > > > (git.github.com:Amber-MD/ambertools-test)
> > > >> > > > registered for path 'AmberTools/src/build-bot/
> ambertools-test'
> > > >> > > > Submodule 'AmberTools/src/build-bot/docker-amber-build-box'
> > > >> > > > (git.github.com:Amber-MD/docker-amber-build-box)
> > > >> > > > registered for path 'AmberTools/src/build-bot/dock
> > > >> er-amber-build-box'
> > > >> > > > Submodule 'AmberTools/src/cphstats' (git.github.com:
> /Amber-MD/
> > > >> > > > cphstats.git)
> > > >> > > > registered for path 'AmberTools/src/cphstats'
> > > >> > > > Submodule 'AmberTools/src/cpptraj' (git.github.com:/Amber-MD/
> > > >> > > cpptraj.git)
> > > >> > > > registered for path 'AmberTools/src/cpptraj'
> > > >> > > > Submodule 'AmberTools/src/parmed' (git.github.com:
> > /ParmEd/ParmEd
> > > >> .git)
> > > >> > > > registered for path 'AmberTools/src/parmed'
> > > >> > > > Submodule 'AmberTools/src/pdb4amber' (git.github.com:
> /Amber-MD/
> > > >> > > pdb4amber)
> > > >> > > > registered for path 'AmberTools/src/pdb4amber'
> > > >> > > > Submodule 'AmberTools/src/pytraj' (git.github.com:/Amber-MD/
> > > >> > pytraj.git)
> > > >> > > > registered for path 'AmberTools/src/pytraj'
> > > >> > > > Cloning into 'AmberTools/src/ambertools-binary-build'...
> > > >> > > > remote: Counting objects: 1700, done.
> > > >> > > > remote: Compressing objects: 100% (71/71), done.
> > > >> > > > remote: Total 1700 (delta 60), reused 65 (delta 32),
> pack-reused
> > > >> 1597
> > > >> > > > Receiving objects: 100% (1700/1700), 246.98 KiB, done.
> > > >> > > > Resolving deltas: 100% (1012/1012), done.
> > > >> > > > Submodule path 'AmberTools/src/ambertools-binary-build':
> > checked
> > > >> out
> > > >> > > > '18c419831a106b836ed60bf2296c241a44a4714e'
> > > >> > > > Cloning into 'AmberTools/src/build-bot/ambertools-test'...
> > > >> > > > Permission denied (publickey).
> > > >> > > > fatal: Could not read from remote repository.
> > > >> > > >
> > > >> > > > Please make sure you have the correct access rights
> > > >> > > > and the repository exists.
> > > >> > > > Clone of 'git.github.com:Amber-MD/ambertools-test' into
> > submodule
> > > >> path
> > > >> > > > 'AmberTools/src/build-bot/ambertools-test' failed
> > > >> > > > [cerutti.casegroup1 amber3]$ ls AmberTools/src/build-bot/
> > > >> > > >
> > > >> > > > It looks like a permissions issue, but I'm not certain. The
> > > >> directory
> > > >> > > > AmberTools/src/build-bot/ certainly exists, and I'm assuming
> > that
> > > it
> > > >> > > wants
> > > >> > > > to clone a new directory ambertools-test/ into that, but at
> > > present
> > > >> I
> > > >> > > don't
> > > >> > > > see ambertools-test/. I've been trying to clone a new repo
> > > because
> > > >> > I've
> > > >> > > > been having this same problem when I try to update the current
> > > repo
> > > >> > I've
> > > >> > > > been working in. Am I missing something obvious?
> > > >> > > >
> > > >> > > > Thanks!
> > > >> > > >
> > > >> > > > Dave
> > > >> > > > _______________________________________________
> > > >> > > > AMBER-Developers mailing list
> > > >> > > > AMBER-Developers.ambermd.org
> > > >> > > > http://lists.ambermd.org/mailman/listinfo/amber-developers
> > > >> > > >
> > > >> > > _______________________________________________
> > > >> > > AMBER-Developers mailing list
> > > >> > > AMBER-Developers.ambermd.org
> > > >> > > http://lists.ambermd.org/mailman/listinfo/amber-developers
> > > >> > >
> > > >> > _______________________________________________
> > > >> > AMBER-Developers mailing list
> > > >> > AMBER-Developers.ambermd.org
> > > >> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> > > >> >
> > > >> _______________________________________________
> > > >> AMBER-Developers mailing list
> > > >> AMBER-Developers.ambermd.org
> > > >> http://lists.ambermd.org/mailman/listinfo/amber-developers
> > > >>
> > > >
> > > >
> > > _______________________________________________
> > > AMBER-Developers mailing list
> > > AMBER-Developers.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber-developers
> > >
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
> _______________________________________________
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>
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Received on Mon Jun 12 2017 - 10:00:04 PDT
