May be try
git submodule foreach git clean -fdx .
git submodule foreach git checkout .
I will read your email mor carefully tonight.
Hai
On Wed, Sep 20, 2017 at 2:49 PM David Cerutti <dscerutti.gmail.com> wrote:
> 2.9.5...
>
> >From the location it looks like some submodule may not be properly
> addressing everything from the root directory. I was in src/pmemd/src/cuda
> when I did "git submodule update --init," which should be just fine, but it
> said it was searching for something in AmberTools/src/... as if it were a
> subdirectory of pmemd/src/cuda. I went back up to the root amber
> directory. Still got the error, albeit now saying
>
> fatal: No url found for submodule path
> 'AmberTools/src/build-bot/ambertools-test' in .gitmodules
>
> If my clone is borked, I don't know how best to get the good changes out of
> it and into a pristine clone before pushing.
>
> Dave
>
>
> On Wed, Sep 20, 2017 at 2:41 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > Not sure why you're getting that error - sounds like your GIT tree may
> > be borked in some way. What version of GIT are you using?
> >
> > -Dan
> >
> > On Wed, Sep 20, 2017 at 2:32 PM, David Cerutti <dscerutti.gmail.com>
> > wrote:
> > > I had been doing "git submodule update --remote --merge," but I tried
> > > submodule update --init again, and I'm getting
> > >
> > > fatal: No url found for submodule path
> > > 'src/pmemd/src/cuda/AmberTools/src/build-bot/ambertools-test' in
> > .gitmodules
> > >
> > >
> > > On Wed, Sep 20, 2017 at 2:29 PM, Daniel Roe <daniel.r.roe.gmail.com>
> > wrote:
> > >
> > >> Make sure your submodules are up to date:
> > >>
> > >> git submodule update --init
> > >>
> > >> With some versions of git this is needed to bring them in line.
> > >>
> > >> -Dan
> > >>
> > >> On Wed, Sep 20, 2017 at 2:22 PM, David Cerutti <dscerutti.gmail.com>
> > >> wrote:
> > >> > I'm hoping someone can help me to understand what's going on with my
> > >> merges
> > >> > from SpeedBoostSM into master. I'm preparing to commit my
> performance
> > >> > enhancements, and the merge goes more or less smoothly except that,
> > >> after I
> > >> > merge from commit d3db6730442cee05bc7c048b0bb89213d9a6000f of
> > >> SpeedBoostSM
> > >> > (the point at which I deemed things in a suitable state--I've made
> > other
> > >> > commits since then to continue progress), I am still getting the
> > >> following:
> > >> >
> > >> > On branch master
> > >> > Your branch is ahead of 'origin/master' by 59 commits.
> > >> > (use "git push" to publish your local commits)
> > >> > Changes not staged for commit:
> > >> > (use "git add <file>..." to update what will be committed)
> > >> > (use "git checkout -- <file>..." to discard changes in working
> > >> directory)
> > >> > modified: ../../../../AmberTools/src/
> > ambertools-binary-build
> > >> (new
> > >> > commits)
> > >> > modified: ../../../../AmberTools/src/cpptraj (new commits)
> > >> >
> > >> > Untracked files:
> > >> > ...
> > >> >
> > >> > It's the business of ambertools-binary-build bearing "changes"
> (which,
> > >> for
> > >> > all I can tell with git diff, are perhaps one whitespace
> > character)--same
> > >> > with the cpptraj directory. When I checkout these files /
> directories
> > >> from
> > >> > master I still see "Changes not staged for commit."
> > >> >
> > >> > Hai pointed out a similar issue in one of my previous commits
> > involving
> > >> the
> > >> > test cases. I'm not sure what it is, but something seems to be
> > >> > persistently lacing these files with some miniscule tweak that I
> can't
> > >> help
> > >> > but make--I'm not doing anything to these files deliberately. Can
> > anyone
> > >> > suggest what might be going on?
> > >> >
> > >> > Cheers,
> > >> >
> > >> > Dave
> > >> > _______________________________________________
> > >> > AMBER-Developers mailing list
> > >> > AMBER-Developers.ambermd.org
> > >> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> > >>
> > >>
> > >>
> > >> --
> > >> -------------------------
> > >> Daniel R. Roe
> > >> Laboratory of Computational Biology
> > >> National Institutes of Health, NHLBI
> > >> 5635 Fishers Ln, Rm T900
> > >> Rockville MD, 20852
> > >> https://www.lobos.nih.gov/lcb
> > >>
> > >> _______________________________________________
> > >> 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
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe
> > Laboratory of Computational Biology
> > National Institutes of Health, NHLBI
> > 5635 Fishers Ln, Rm T900
> > Rockville MD, 20852
> > https://www.lobos.nih.gov/lcb
> >
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
> _______________________________________________
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Received on Wed Sep 20 2017 - 12:00:05 PDT
