thanks Jason!
On Wed, Apr 28, 2021 at 4:27 PM Jason Swails <jason.swails.gmail.com> wrote:
> Amber 18 and AmberTools 20 were never meant to be unpacked into the same
> directory. If they do that, then this is the result.
>
> The updating script comes as part of AmberTools and has the Amber and
> AmberTools versions hard-coded into it. It then determines if Amber is
> present by looking for pmemd source code. There's no way a priori to
> determine what version of Amber was unpacked into it.
>
> By default, Amber18 unpacks into amber18/ and AmberTools 20 into amber20/.
> AmberTools 21 will also unpack into amber20/, and will come with an updated
> update_amber script that will try to apply updates for AmberTools 21 and
> Amber 20.
>
> This had always been "good enough", but if we start to always unpack into
> an amber/ directory (I think there was talk of this before), then we may
> have to split update_amber apart and ship Amber with the part that tells
> update_amber what version of Amber to apply updates for.
>
> It gets tricky, though, since sander (AmberTools) and pmemd (Amber) share
> many (most?) test cases and keeping these passing for more than AmberN ->
> AmberToolsN,N+1 is likely a fool's errand.
>
> All the best,
> Jason
>
> On Wed, Apr 28, 2021 at 4:08 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > I replied to this person but probably got it wrong, and now that I look
> > closer the message they got when compiled was confusing to me. If they
> have
> > amber18 and ambertools 20 , why did it offer them amber20 patches? seems
> > like it should not try to apply those to amber 18. That probably isn't
> > related to their cpptraj error but seems confusing.
> > carlos
> >
> > the section from the original post on the reflector:
> >
> > I first downloaded amber18 and ambertools20 and performed the serial
> > compilation.
> > Next, I wanted to compile the parallel version.
> >
> > I went to $AMBERHOME/AmberTools/src and issued ./configure_mpich gnu.
> > That went fine only some warnings.
> >
> > Next I went back to $AMBERHOME and issued ./configure -mpi gnu.
> > Here is where I get my error. Please see the output:
> >
> > Checking for updates...
> > Checking for available patches online. This may take a few seconds...
> >
> >
> > Available AmberTools 20 patches:
> >
> > No patches available
> >
> > Available Amber 20 patches:
> >
> > update.1, update.2, update.3, update.4, update.5, update.6, update.7,
> > update.8, update.9, update.10,update.11
> > There are patches available. Do you want to apply them now? [y/N]
> > (Recommended Y)
> > N
> > NOT updating your tree and continuing anyway.
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
>
>
> --
> Jason M. Swails
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> AMBER-Developers.ambermd.org
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>
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Received on Wed Apr 28 2021 - 14:00:02 PDT
