*/*: bump PORTREVISION after OpenMPI upgrade

biology/hhsuite: Fix build on some systems by adding missing C++ #include
statement

Reported by:	fallout

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

biology/hhsuite: Disable on 32-bit architectures following upstream advice

biology/hhsuite: fix build on armv7

PR:		266736

biology/hhsuite: Broken on armv7

Reported by:	fallout

Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)

Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.

biology/hhsuite: Fix build on some architectures

... by removing -march=native.

Reported by:	fallout

biology/hhsuite: Revert commit "Broken on systems where OpenMP isn't enabled"

IT was added by mistake.
The failures on armv7 are due to -march=native.

This reverts commit 0f20e25bb0c89821c657ce7d8424f6e6ad1c9a45.

Reported by:	pkubaj@

biology/hhsuite: Broken on systems where OpenMP isn't enabled

Reported by:	fallout

biology/hhsuite: check for omp.h on all architectures

biology/hhsuite: drop HAVE_POWER8 on powerpc64

powerpc64 uses PPC970 as a baseline.

biology/hhsuite: fix packaging on powerpc

pkg-static: Unable to access file
/wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhalign_omp:No such
file or directory
pkg-static: Unable to access file
/wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhblits_ca3m:No such
file or directory
pkg-static: Unable to access file
/wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhblits_omp:No such
file or directory
pkg-static: Unable to access file
/wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhsearch_omp:No such
file or directory

powerpc doesn't have LLVM with libomp.

biology/hhsuite: Fix build on aarch64

Approved by:	portmgr (build fix blanket)

biology/hhsuite: fix build on powerpc64*

hhsuite now supports VSX.

One more small cleanup, forgotten yesterday.
Reported by:	lwhsu

Remove # $FreeBSD$ from Makefiles.

biology/hhsuite: Update 3.2.0 -> 3.3.0

Reported by:	portscout

biology/hhsuite: fix build on powerpc64 elfv2

Use GCC instead of Clang:
/usr/lib/clang/10.0.0/include/mmintrin.h:216:19: error: use of undeclared
identifier '__builtin_ia32_punpckhbw'
    return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2);

- Update net/openmpi to 4.0.3 (openmpi 1 is deprecated)
- Remove option for net/openmpi2 from science/pnetcdf (net/openmpi2 is
deprecated and will be removed)
- Fix science/gromacs plist when MPI option is enabled
- Bump PORTREVISION for all the consumers of net/openmpi

Drop dependency on devel/openmp

- Drop if devel/llvm* was used as a substitute

Approved by:	yuri, rene (earlier version)
Differential Revision:	https://reviews.freebsd.org/D23020

devel/openmp: update to 9.0.0

- Connect tests to the framework to help QA remaining patches
- Force rebuild all consumers after https://reviews.llvm.org/D59783

Changes:	http://llvm.org/viewvc/llvm-project/openmp/tags/RELEASE_900/final/?view=log
ABI:		https://abi-laboratory.pro/tracker/timeline/llvm_openmp/

biology/hhsuite: fix build on powerpc64

This port can't use Altivec. Instead, it's possible to use GCC's translation
layer from SSE. Adjust build flags to do it.

PR:		239645
Approved by:	yuri (maintainer), tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D21160

Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330

biology/hhsuite: Fix build on platforms where SIMD instruction set doesn't exist
or isn't detected.

It forces it to default to SSE2 on amd64/i386 and relaxes the SIMD requirement
on all other platforms.

Reported by:	fallout

New port: biology/hhsuite: Remote protein homology detection suite