I've updated the pmwiki with some tips from my experience. Should we steer
people who have older branches from before the submodules to create new
branches from master that are submodule oriented, then merge in their
progress from the older branches? Seems logical to me, to avoid the risks
that seem to go along with deinit --all. (Wouldn't things that have since
been made into submodules have issues updating in non-submodule branches?)
Dave
On Mon, Jun 12, 2017 at 1:16 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> On Mon, Jun 12, 2017 at 1:00 PM, David Cerutti <dscerutti.gmail.com>
> wrote:
>
> > There we go! Updating the git version by installing my own straight from
> > the source was progress. I'm now watching it clone all of the various
> > submodules. Hit a snag on ambertools-test/ again, but removing the
> stuff I
> > had cloned from github and letting git v2.9.4 do the work seems to have
> > worked.
>
>
>
>
> > I'll post any more inanity that I see, but only if it's not
> > something already covered on the wiki / known to you guys.
> >
> >
> cool, may be you can update here:
> http://ambermd.org/pmwiki/index.php/Main/Submodules
>
> Hai
>
>
> > Dave
> >
> >
> >
> > On Mon, Jun 12, 2017 at 12:55 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >
> > > 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
> > > > >
> > > > _______________________________________________
> > > > 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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Received on Mon Jun 12 2017 - 18:30:02 PDT
