Thanks Dave and apologies if this is a duplicate message:
It turns out I was able to compile ambertools 25 and pmemd 24 for cpu’s ands gpu’s outside of spack (after sorting out a gcc/cuda compatibility issue).
So I'll try to sort this out with the spack people: The problem is even on the spack develop branch they are only up to v 20 with autotools which is why I wrote my own spack package which uses cmake and which worked until the current version.
Jerry
From: David A Case <dacase1.gmail.com>
Date: Friday, October 24, 2025 at 8:52 PM
To: Greenberg, Jerry <jpg.sdsc.edu>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Problem compiling ambertools25/amber24
On Wed, Oct 22, 2025, Greenberg, Jerry via AMBER wrote:
>
>I am trying to compile amber 24/ambertools 25 via spack (using a spack
>package that I wrote, which I modified from the package I wrote to
>successfully compile amber 22).
Hi Jerry: I'd like to know exactly what you mean by "amber 24/ambertools
25": have you downloaded Amber 24 since May of this year? You can tell
because the download will expand into a pmemd24_src folder. Building pmemd
is now completely independent of building AmberTools25.
(Of course, this change will problem mean that your spack package will need
considerable updates...)
To clarify: the *code* inside pmemd24_src is the same as the patched
version of the old (pre-May 2025) download of Amber24. It's just the
packaging that has changed.
>-- Running update_amber...
>PatchingError: .patches/Amber24_Unapplied_Patches/update.2 failed to apply. No changes made from this patch
You should also try compiling from truly fresh directories, which would not
have anything like Amber24_Unapplied_Patches there. Plus, the pmemd24_src
folder already has all the patches that were made for the older Amber24.
Our hope is this: AmberTools25 is still a complex package, and using spack
to handle dependencies, etc. might make good sense. Amber24 (in its new
version inside pmemd24_src) has many fewer dependencies, and might not need
only a very simple spack file, or maybe none at all.
...good luck...let me know if you need more info.
...dac
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Received on Thu Nov 06 2025 - 09:30:03 PST
