Hanspeter,
Actually, gromacs got a minor update to 2016.1 so attached are
the info files and patch to build gromacs-2016.1-1 and
gromacs-mpi-2016.1-1.
Jack
ps These are also posted on fink tracker as
https://sourceforge.net/p/fink/package-submissions/4840/On Sun, Nov 13, 2016 at 1:42 PM, Jack Howarth <howarth.at.f...@gmail.com> wrote: > Hanspeter, > It has been a couple of weeks now since I emailed David Fang > about the update to the llvm39 package to add the proposed llvm-clang, > libomp-dev and libomp-shlibs split-offs required to cleanly support > packages like the gromacs/gromacs-mpi-2016-1 updates which require a > clang that supports -fopenmp without tethering the package to a > specific llvmXY release. The proposed changes are quite sensible, > straight-forward and safe... > > https://sourceforge.net/p/fink/package-submissions/4831/ > https://sourceforge.net/p/fink/package-submissions/4827/ > > Index: llvm39.info > =================================================================== > RCS file: > /cvsroot/fink/dists/10.9-libcxx/stable/main/finkinfo/languages/llvm39.info,v > retrieving revision 1.2 > diff -u -r1.2 llvm39.info > --- llvm39.info 27 Oct 2016 04:01:28 -0000 1.2 > +++ llvm39.info 13 Nov 2016 18:26:26 -0000 > @@ -1,7 +1,7 @@ > Info3: << > Package: llvm39 > Version: 3.9.0 > -Revision: 1 > +Revision: 2 > Description: Modular and reusable compiler > License: BSD > Maintainer: David Fang <fang...@users.sourceforge.net> > @@ -54,8 +54,8 @@ > > PatchFile: %n.patch > PatchFile-MD5: 6addcbd4c9fe449b3cd006eb48f5219b > -#PatchFile2: %n-clang.patch > -#PatchFile2-MD5: d2a2b4207c19b7f09f197ae9769a51d2 > +PatchFile2: %n-clang.patch > +PatchFile2-MD5: 25a45c309e14611b278c30b782f0d7e5 > #PatchFile3: %n-compiler-rt.patch > #PatchFile3-MD5: 60ed1415e15b1781f2d58c0db17aab78 > #PatchFile4: %n-polly.patch > @@ -65,7 +65,7 @@ > #PatchFile6: %n-clang-omp.patch > #PatchFile6-MD5: 8067f4cc1f58030f7746521d58c776c2 > PatchFile7: %n-clang-iomp5.patch > -PatchFile7-MD5: 33f21b006473cbdd5feced616b05903b > +PatchFile7-MD5: d5d9686fd0727c0e1cd953f585f4481d > > PatchScript: << > #!/bin/sh -ev > @@ -108,7 +108,7 @@ > pushd tools/clang > # Apply clang-omp merge before clang patch > #$patch_filter %{PatchFile6} | patch -p1 > - #$patch_filter %{PatchFile2} | patch -p1 > + $patch_filter %{PatchFile2} | patch -p1 > $patch_filter %{PatchFile7} | patch -p1 > popd > pushd tools/polly > @@ -1078,15 +1078,6 @@ > iprefix=%i/$stem > prefix=%p/$stem > > - # Pass path to libLTO.dylib with -lto_library using ld shell script > - pushd $iprefix/bin > - cat <<EOF > ./ld > -#!/bin/sh > -exec /usr/bin/ld -lto_library %p/opt/llvm-3.9/lib/libLTO.dylib "\$@" > -EOF > - chmod ugo+x ./ld > - popd > - > # convenient clang symlinks > mkdir -p %i/bin > pushd %i/bin > @@ -1112,6 +1103,26 @@ > cp %b/../build/last/*-check.log testlogs/ > cp %b/../build/last-libcxx/*-check.log testlogs/ > popd > + > +# place omp.h in %p/include/libomp for common libomp-dev package > + install -d %i/include/libomp > + pushd %i/opt/llvm-$brv/lib/clang/%v/include > + mv omp.h %i/include/libomp > + popd > + > +# place libomp.dylib in libomp subdirectory for common libomp-shlibs package > +# leave legacy copy in %p/opt/llvm-$brv/lib for clang39-shlibs > + install -d %i/lib/libomp > + pushd %i/opt/llvm-$brv/lib > + cp libomp.dylib %i/lib/libomp > + ln -s libomp.dylib %i/lib/libomp/libiomp5.dylib > + ln -s libomp.dylib %i/lib/libomp/libgomp.dylib > + popd > + install_name_tool -id %p/lib/libomp/libomp.dylib %i/lib/libomp/libomp.dylib > + > +# create compiler symlinks for common llvm-clang split-off > + ln -s clang-$brv %i/bin/llvm-clang > + ln -s clang++-$brv %i/bin/llvm-clang++ > << > SplitOff: << > Package: clang39-tools > @@ -1178,7 +1189,9 @@ > # odcctools, > # choosing to require opt-in instead of defaulting to libcxx1-dev > # libcxx1-dev, > + libomp-dev (>= %v-%r), > clang39-shlibs (= %v-%r), > + libomp-shlibs (>= %v-%r), > polly39-shlibs (= %v-%r) > << > Description: Executables and runtime for clang compiler > @@ -1186,7 +1199,6 @@ > Files: << > bin/clang* > opt/llvm-3.9/bin/clang* > - opt/llvm-3.9/bin/ld > opt/llvm-3.9/lib/clang > << > DescUsage: << > @@ -1313,6 +1325,37 @@ > << > << > SplitOff14: << > + Package: libomp-shlibs > + Description: Standard library for libomp > + Files: << > + (%m != powerpc) lib//libomp/lib*omp*.dylib > + << > + DocFiles: << > + projects/openmp/CREDITS.txt > + projects/openmp/LICENSE.txt > + << > + Shlibs: << > + (%m != powerpc) %p/lib/libomp/libomp.dylib 5.0.0 %n (>= 3.9.0-2) > + << > +<< > +SplitOff15: << > + Package: libomp-dev > + Description: Standard library header for libomp > + Depends: libomp-shlibs (= %v-%r) > + BuildDependsOnly: false > + Files: include/libomp/omp.h > + DescPackaging: << > + BuildDependsOnly set to false since clang compiler always needs > + access to omp.h at run-time. > + << > +<< > +SplitOff16: << > + Package: llvm-clang > + Description: LLVM.org clang compilers > + Depends: clang39 (= %v-%r) > + Files: bin/llvm-clang bin/llvm-clang++ > +<< > +SplitOff17: << > Package: %N-bundle > Description: Bundle of LLVM/Clang compiler tools > Type: bundle > > I would also point out that David left the details of the openmp > support in the llvmXY packaging up to me since I was working with the > upstream developers to make sure the openmp support on darwin had no > regressions compared to linux. > Please go ahead and commit the attached packaging files into the > 10.9-libc++ tree so we can have the current version of gromacs and > gromacs-mpi. Thanks in advance. > > Jack > ps This refactoring of llvm39 is *extremely* useful to other fink > package maintainers as it simplifies their task of building against a > -fopenmp-savvy clang to just adding a > > BuildDepends: llvm-clang, libomp-dev > Depends: libomp-shlibs > > which will result in the llvm-clang split-off from the most recent > llvmXY package being used. It also fully decouples the libomp.dylib > and omp.h dependencies from a specific llvmXY package. > > pos The deprecation of the ld script again is now allowed by the back > port of the llvm 4.0 changes to clang in llvm39-clang.patch which > cause the compiler to automatically emit -lto_library for the linkage > with the correct path to the libLTO.dylib bundled with the specific > llvmXY release.
gromacs.info
Description: Binary data
gromacs-mpi.info
Description: Binary data
gromacs-libxml2.patch
Description: Binary data
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