Bug#992931: [Debichem-devel] Bug#992931: libopenmm7.5 does not include libOpenMMAmoeba.so, libOpenMMDrude.so, and libOpenMMRPMD.so

2021-08-26 Thread Adam Sjøgren 
Andrius writes:

> These libraries do not have sonames, thus I reckon they are not a part
> of public API.

Ah, I see - I was thinking that there would be a reason I didn't know of.

However if you run alphafold2 you get an exception where it tries to use
libOpenMMAmoeba.so. Hm.

(Unfortunately I don't have a small script to reproduce the problem.)

> On the other hand, reference libraries,
>
> libOpenMMAmoebaReference.so
> libOpenMMDrudeReference.so
> libOpenMMRPMDReference.so
>
> are provided in libopenmm-plugins binary package (>= 7.5.1+dfsg-1) at
> /usr/lib/${DEB_HOST_MULTIARCH}/openmm/plugins.
>
> If this would be of use, libOpenMM{Amoeba,Drude,RPMD}.so could be
> provided at /usr/lib/${DEB_HOST_MULTIARCH}/openmm, as
> /usr/lib/${DEB_HOST_MULTIARCH} is reserved for libraries with sonames.

Ah, ok, thanks for the explanation.

I will give it a go locally, see if that works and return.


  Thanks!

   Adam

-- 
 "I wonder if you can refuse to inherit the world." Adam Sjøgren
 "I think if you're born, it's too late."  a...@koldfront.dk

Bug#992931: [Debichem-devel] Bug#992931: libopenmm7.5 does not include libOpenMMAmoeba.so, libOpenMMDrude.so, and libOpenMMRPMD.so

2021-08-25 Thread Andrius Merkys 
Hello,

On 2021-08-25 12:12, Adam Sjøgren wrote:
> The libopenmm7.5 package does not include these three libraries, that are 
> built during compilation:
> 
>   /usr/lib/libOpenMMAmoeba.so
>libOpenMMDrude.so
>libOpenMMRPMD.so
> 
> (same folder as libOpenMM.so itself, separate from the plugins).
> 
> I was expecting them to be included in the (a?) package, e.g. something like:
> 
> --- yay/openmm-7.5.1+dfsg/debian/rules2021-07-01 12:45:26.0 
> +0200
> +++ hep/openmm-7.5.1+dfsg/debian/rules2021-08-25 10:39:41.279649991 
> +0200
> @@ -40,6 +40,9 @@
>  override_dh_auto_install:
>   dh_auto_install -O--buildsystem=cmake
>   dh_install -plibopenmm7.5  debian/tmp/usr/lib/libOpenMM.so.* 
> usr/lib/${DEB_HOST_MULTIARCH}
> + dh_install -plibopenmm7.5  debian/tmp/usr/lib/libOpenMMAmoeba.so 
> usr/lib/${DEB_HOST_MULTIARCH}
> + dh_install -plibopenmm7.5  debian/tmp/usr/lib/libOpenMMDrude.so 
> usr/lib/${DEB_HOST_MULTIARCH}
> + dh_install -plibopenmm7.5  debian/tmp/usr/lib/libOpenMMRPMD.so 
> usr/lib/${DEB_HOST_MULTIARCH}
>   dh_install -plibopenmm-dev debian/tmp/usr/lib/libOpenMM.so   
> usr/lib/${DEB_HOST_MULTIARCH}
>   dh_install -plibopenmm-plugins debian/tmp/usr/lib/plugins
> usr/lib/${DEB_HOST_MULTIARCH}/openmm
>   # cd obj-*/python && python3 setup.py install --install-layout=deb 
> --root=$(CURDIR)/debian/tmp
> 
> (not sure if that is the correct way :-))
> 
> What do you think?

These libraries do not have sonames, thus I reckon they are not a part
of public API. On the other hand, reference libraries,

libOpenMMAmoebaReference.so
libOpenMMDrudeReference.so
libOpenMMRPMDReference.so

are provided in libopenmm-plugins binary package (>= 7.5.1+dfsg-1) at
/usr/lib/${DEB_HOST_MULTIARCH}/openmm/plugins.

If this would be of use, libOpenMM{Amoeba,Drude,RPMD}.so could be
provided at /usr/lib/${DEB_HOST_MULTIARCH}/openmm, as
/usr/lib/${DEB_HOST_MULTIARCH} is reserved for libraries with sonames.

Best,
Andrius