Re: [AMBER-Developers] I don't want to change these files... really!

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 20 Sep 2017 15:02:34 -0400

Let me preface this by saying I'm not sure what's going on with your
GIT tree, so for all of the following caveat emptor...

According to my .gitmodules, there is no module that corresponds to
'AmberTools/src/build-bot/ambertools-test' (although the directory
seems to exist). One thing you could try is to remove it.

git submodule --deinit AmberTools/src/build-bot/ambertools-test

Then pull and do another 'submodule update --init'. If it's supposed
to be there it should come back.

-Dan

On Wed, Sep 20, 2017 at 2:56 PM, David Cerutti <dscerutti.gmail.com> wrote:
> Good idea... done... still getting
>
> fatal: no submodule mapping found in .gitmodules for path
> 'AmberTools/src/build-bot/ambertools-test'
>
> for each of those commands, though...
>
> On Wed, Sep 20, 2017 at 2:55 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
>> 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
>> > >
>> > _______________________________________________
>> > AMBER-Developers mailing list
>> > AMBER-Developers.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber-developers
>> >
>> _______________________________________________
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>>
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-- 
-------------------------
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
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Received on Wed Sep 20 2017 - 12:30:03 PDT
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