[Bug 497622] Review Request: apbs - adaptive poisson boltzmann solver

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https://bugzilla.redhat.com/show_bug.cgi?id=497622





--- Comment #30 from Tim Fenn <fenn at stanford.edu>  2009-07-25 20:19:11 EDT ---
(In reply to comment #26)
> apbs has support for:
>   --with-mpich=PATH       toplevel MPICH directory
>   --with-mpich2=PATH      toplevel MPICH2 directory
>   --with-lam=PATH         toplevel LAM-MPI directory
>   --with-openmpi          enable OpenMPI compilation
> so I suggest you add these to the package in the future.
> 

Will do.

> I have suggested an MPI packaging draft and an environment modules packaging
> draft, which would standardize the way MPI stuff is packaged.
> 
> - Add BR: arpack-devel and --with-arpack to enable support for ARPACK.
> 
> - Add BR: python-devel and --with-python to enable support for Python.
> 

Done, and moved relevant binaries from tools into a -tools subpackage

> - Remove maloc in the %prep phase after %setup to make sure it isn't used.
> 

done.

> - There are tests in examples/, run them in %check with
> 
> %check
> for dir in examples/*/;
>  do make -C $dir test
> done
> 

some of the directories don't contain makefiles, so instead I'm using:

%check
ln -s %{buildroot}%{_bindir}/apbs bin/apbs
make -C examples test
make -C examples test-opal

This works, but the resulting examples take ~4hrs to run on my AMD opteron 275.
I can cut it down to a 1-2 of the examples...

> 
> rpmlint output:
> apbs.x86_64: W: unused-direct-shlib-dependency
> /usr/lib64/libapbsmainroutines.so.1.0.0 /usr/lib64/libblas.so.3
> apbs-devel.x86_64: W: no-documentation
> 2 packages and 0 specfiles checked; 0 errors, 2 warnings.
> 
> - Fix the unused-direct-shlib-dependency with
> https://fedoraproject.org/wiki/Common_Rpmlint_issues#unused-direct-shlib-dependency
> 

done.

> 
> - License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD.
> - License tag can be either "LGPLv2+ and BSD" or "LGPLv2+".
> 

went with the former.

> - I strongly suggest using
>  %{_libdir}/libapbs.so.*
>  %{_libdir}/libapbsmainroutines.so.*
> instead of
>  %{_libdir}/*apbs.so.*
>  %{_libdir}/*mainroutines.so.*
> and the same thing for the .so files in -devel. Also use
>  %{_bindir}/apbs
>  %{_bindir}/psize.py
> instead of 
>  %{_bindir}/*
> 

done.

> MUST: Clean section exists. OK
> - The current clean section is a bit silly, don't you think?
>  rm -rf %{_builddir}/pmgZ
>  rm -rf %{_builddir}/aqua
>  rm -rf %{buildroot}
> Drop the two first lines.
> 

oops, fixed.

> MUST: Large documentation files must go in a -doc subpackage. NEEDSWORK
> - doc/programmer/html is 14 MB, and needs to go in a -doc subpackage.
> - examples/ is also 14 MB, but I don't think it should go in as it would need
> some work since the Makefiles are autogenerated and will need quite a lot of
> modification to work on an installed system.
> 

done.

> 
> SHOULD: If the package does not include license text(s) as separate files from
> upstream, the packager should query upstream to include it. NEEDSWORK
> - Included COPYING is BSD, LGPLv2+ COPYING is missing.
> 

done.

Spec URL: http://www.stanford.edu/~fenn/packs/apbs.spec
SRPM URL: http://www.stanford.edu/~fenn/packs/apbs-1.1.0-5.fc10.src.rpm

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