I slightly improved the ebuild to try to compile parallelized code. Unfortunately, I cannot get it compiled (7.2.2, 7.2.5, 7.2.6 tested on x86). I have emailed usptream. Based on the comments at http://wwwkramer.in.tum.de/exelixis/software.html is seems they only support OpenMPI. Who can test that?
Created attachment 226325 [details] raxml-7.2.6.ebuild I have replaced the single-quotes with double-quotes so that ${CFLAGS} can be exapanded. Andrey, feel free to fix this in other ebuilds in the tree. I have enabled the mpi USE flag but as I said, I cannot compile against mpich2.
Upstream said: The only MPI version that works is the hybrid one, -DPARALLEL was exactly disabled for this reason and this is also the reason why no Makefile is provided.
Some more clarification from upstream: sequential version: Makefile.gcc seq+SSE3: Makefile.SSE3.gcc Pthreads: Makefile.PTHREADS.gcc Pthreads+SSE3: Makefile.SSE3.PTHREADS.gcc hybrid MPI/Pthreads: Makefile.HYBRID.gcc hybrid MPI/Pthreads+SSE3: Makefile.SSE3.HYBRID.gcc pure MPI: Makefile.MPI.gcc pure MPI+SSE3: Makefile.SSE3.MPI.gcc For MPI you will need OpenMPI, for Pthreads just the posix threads library which is installed in all Linux-based systems. I will attach an updated ebuild. I propose fixup of the 7.2.2. and 7.2.5 ebuild as well. I cannot test the OpenMPI binaries, but believe the ebuild is correct. Please commit. Maybe a test for virtual/mpi and !openmpi would be worth to print an einfo() message proposing user to place USE=-mpi into /etc/portage/package.use if (s)he has USE=mpi but has not openmpi installed. It would make the user aware of the fact that no parallel binaries are available for the machine. But as long as you keep the comments in the ebuild file it is documented.
Created attachment 226719 [details] raxml-7.2.6.ebuild
already fixed.
