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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Received on Wed Apr 28 2021 - 13:30:03 PDT
