science/gromacs: update 2023.2 → 2024.1

*/*: chase the upgrade of BLAS / LAPACK to 3.12.0

PR:		275860

science/gromacs: Add comment

science/gromacs: Use https for MASTER_SITES and GCC for build

- Switch MASTER_SITES to https
- Fails to build with LLVM 14-17, use GCC instead

Reference:
https://github.com/Homebrew/homebrew-core/blob/c3174cdd90e026ce95010b725aa0a2f312d41bcd/Formula/g/gromacs.rb

PR:		274435
Reviewed by:	yuri (maintainer)

science/gromacs: Multiple improvements

* remove dependency on xorg: last xorg utility was retired some time ago
* add HWLOC option and pass cmake argument: hwloc2 is only used when
  this argument is supplied
* refactor OPENCL option: add OPENCL_NONE, OPENCL_ICD, OPENCL_SYCL options
* refactor SIMD option: use the AUTO value when set
* correct OPENMP option

science/gromacs: Fix tests

... by replacing the old bundled googletest with a newest release.

science/gromacs: Add TEST_DEPENDS; Remove unnecessary patch command

science/gromacs: Update 2023.1 → 2023.2

Reported by:	portscout

science/gromacs: Update 2022.4 → 2023.1

Reported by:	portscout

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

science/gromacs: Update 2022.3 -> 2022.4

Reported by:	portscout

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.

science/gromacs: Update 2022.2 -> 2022.3; Add test target

Reported by:	portscout

*/*: bump all consumers after recent boost upgrade

science: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Andreas Fehlner <fehlner@gmx.de>
  *  Brad Huntting <huntting@glarp.com>
  *  Chao Shin <quakelee@cn.FreeBSD.org>
  *  Cheng-Lung Sung <clsung@FreeBSD.org>
  *  Chia-Hsing Yu <me@davidyu.org>
  *  Chris Rees <utisoft@gmail.com>
  *  David Naylor <dbn@FreeBSD.org>
  *  Dmitry Sivachenko <demon@FreeBSD.org>
  *  Ed Schouten <ed@FreeBSD.org>
  *  Eric Freeman <freebsdports@chillibear.com>
  *  Erik B Knudsen

science/gromacs: Change WWW to https

science/gromacs: Update 2022.1 -> 2022.2

Reported by:	portscout

devel/cmake: Update to 3.23.0

Update to 3.23.0.
Fix pkg-plist: using the default share/man location

Release Notes:
  https://cmake.org/cmake/help/v3.23/release/3.23.html

PR:		262886
Exp-run by:	antoine

science/gromacs: Update 2021.5 -> 2022.1

Reported by:	portscout

textproc/libxml2: bump all LIB_DEPENDS consumers

This is a separate commit to facilitate easier cherry-picking for
quarterly.

PR: 262853, 262940, 262877, 263126
Approved by: fluffy (mentor)

textproc/libxml2: bump all dependencies

This should make sure that all dependent ports will pick
up the new version commited with a13ec21cd733f67a9fc0dc00ab45268bdc236246

science/gromacs: Update 2021.4 -> 2021.5

Reported by:	portscout

science/gromacs: Update 2021.3 -> 2021.4

Reported by:	portscout

science/gromacs: Update 2021.2 -> 2021.3

Reported by:	portscout

science/gromacs: Update 2021.1 -> 2021.2

Reported by:	portscout

Clean up some things

- Remove duplicate variables
- Remove nop variables
- Sort categories
- Remove redundant option descriptions that match the default ones

Reported by:	portscan

Remove # $FreeBSD$ from Makefiles.

science/gromacs: Update 2021 -> 2021.1

science/gromacs: Update 2020.5 -> 2021

science/gromacs: Update 2020.4 -> 2020.5

Reported by:	portscout

science/gromacs: Upgrade hwloc dep to hwloc2

hwloc2 conflicts with hwloc, so updating all dependents ASAP.

PR:             252526
Submitted by:   jwb
Approved by:    yuri

science/gromacs: Turn the option FLOAT to OFF by default

This is because FLOAT=ON reduces fp accuracy, this probably shouldn't be the
default.
Also because its only user in the ports tree, science/votca, needs double fp
precision.

science/gromacs: Add the LEGACY option that installs legacy API needed by some
users

science/gromacs: Update 2020.3 -> 2020.4

Reported by:	portscout

science/gromacs: Update 2020.2 -> 2020.3

Reported by:	portscout

science/gromacs: Fix plist when MPI=on

science/gromacs: Update 2020.1 -> 2020.2

Reported by:	portscout

- 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

Clean up ports after FreeBSD 12.0 reached end-of-life.

emulators/mesen is left out for now, as it breaks on 11.3

Submitted by:	rene
Reviewed by:	jbeich, zeising
X-Differential Revision:	https://reviews.freebsd.org/D24211

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

science/gromacs: Update 2020 -> 2020.1

Reported by:	portscout

Don't both set compiler + USES=compiler

science/gromacs: Fix build on systems with older clang (clang-6)

Reported by:	fallout

Fix math/openblas and bump dependent ports

* Fix build on i386 [1]
* Fix science/code_saturne build with new openblas [2]
* Avoid installing private headers [3]
* Prevent build from optimizing for host by correcting build confg [4]
* Bump portrevision of dependent ports [5]

This is correcting issues from r523749 [1][2][4] and r515970 [3]

PR:		231371
Reported by:	build cluster [1]
Reported by:	Dima Pasechnik <dimpase+freebsd@gmail.com> [2]
Reported by:	many [5]
Reviewed by:	mat, bapt
Approved by:	implicit, since this is a build fix

science/gromacs: Change compiler requirement to c++14 along the flags that the
project supplies.

Reported by:	fallout

science/gromacs: Update 2019.5 -> 2020

Reported by:	repology

science/gromacs: Update 2019.4 -> 2019.5

Reported by:	portscout

devel/boost-*: update to 1.72.0

Changes:	http://www.boost.org/users/history/version_1_72_0.html
PR:		241449
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D22136

science/gromacs: Update 2019.3 -> 2019.4

Reported by:	portscout

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/

devel/boost-*: update to 1.71.0

Changes:	http://www.boost.org/users/history/version_1_71_0.html
PR:		238827
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D20774

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

science/gromacs: Update 2019.2 -> 2019.3

Reported by:	portscout

devel/openmp: phase out

- Expire after the last version without /usr/lib/libomp.so
- Drop SOVERSION for seamless transition (i.e., avoid conditionals)

PR:		236907
Approved by:	bapt (maintainer)
Differential Revision:	https://reviews.freebsd.org/D19767

science/gromacs: Broken on i386

Reported by:	fallout

Related to revision 499061 bump ports with USES=fortran to have them
benefit from the improved situation where libgcc_s is only used when
absolutely necessary.

Suggested by:	tijl

science/gromacs: Update 2019.1 -> 2019.2

Reported by:	portscout

devel/boost-*: update to 1.70.0

Changes:	http://www.boost.org/users/history/version_1_70_0.html
PR:		235956
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D19303

science/gromacs: Update 2019 -> 2019.1

Reported by:	portscout

science/gromacs: Update 2018.4 -> 2019

Reported by:	repology

Change cmake default behaviour to outsource.

Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".

I tried to only set insource where explictely needed.

PR:		232038
Exp-run by:	antoine

Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

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, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590

devel/boost-*: update to 1.69.0

Changes:	http://www.boost.org/users/history/version_1_69_0.html
PR:		232525
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D17645

science/gromacs: Update 2018.3 -> 2018.4

Reported by:	portscout

Add compiler:c++11-lang to USES to fix build on gcc-based archs.

Approved by:	portmgr (tier-2 blanket)

Change 20 ports from net/mpich2 to net/mpich

mpich2 is the obsolete version 2.x, mpich is at the current version 3.x

Ports:
math/scalapack science/nwchem science/quantum-espresso science/qmcpack
science/madness
science/qbox science/openmx science/jdftx science/fleur science/libgridxc
science/mdynamix science/lm science/dftbplus science/py-gpaw devel/ga
math/elpa net/charm science/gromacs math/pari math/arpack-ng-mpich

science/gromacs: Update 2018.2 -> 2018.3

Reported by:	portscout

devel/boost-*: update to 1.68.0

- Switch to C++14 for libboost_system to support C++14 consumers

Changes:	http://www.boost.org/users/history/version_1_68_0.html
PR:		229569
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D16165

Bump PORTREVISION for ports depending on the canonical version of GCC
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.

This includes ports
 - featuring USE_GCC=yes or USE_GCC=any,
 - featuring USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and those
 - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
   c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.

PR:		222542

science/gromacs: Chase the changed tarball

The upstream "rerelased" 2018.2, so updating the port.

Reported by:	fallout

science/gromacs: Update 2018.1 -> 2018.2

Reported by:	portscout

science/gromacs: Update 5.0.6 -> 2018.1

Port changes:
* Take maintainership.
* Modernize the port, now using option helpers.
* Add the OPENCL option.
* Add the THREAD_MPI option that is now the default multiprocessing option.
* Add missing dependencies.

devel/boost-*: update to 1.67.0

Changes:	http://www.boost.org/users/history/version_1_67_0.html
PR:		227427
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D15030

Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).

devel/boost-*: update to 1.66.0

Changes:	http://www.boost.org/users/history/version_1_66_0.html
PR:		223922
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D13279

devel/boost-*: update to 1.65.1

Changes:	http://www.boost.org/users/history/version_1_65_1.html
PR:		218835
Approved by:	maintainer timeout (1.65.1: 2 weeks; 1.65.0: 1 month)
Tested by:	jhibbits (on powerpc64, earlier version)
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D11582

devel/boost-*: enable C++11 features

PR:		218835
Obtained from:	https://github.com/DragonFlyBSD/DeltaPorts/pull/690
Approved by:	maintainer timeout (2 months)
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D11582

Bump PORTREVISION for ports depending on the canonical version of GCC
(via Mk/bsd.default-versions.mk and lang/gcc) which has moved from
GCC 5.4 to GCC 6.4 under most circumstances.

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, c++11-lib, c++11-lang,
   c++14-lang, c++0x, c11, or gcc-c++11-lib.

PR:		219275

devel/boost-*: update to 1.64.0

Changes:	http://www.boost.org/users/history/version_1_64_0.html
PR:		218835
Approved by:	office (bapt)
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D10472

Bump PORTREVISIONs for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some
circumstances such as versions of FreeBSD or platforms).

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using using Mk/bsd.octave.mk which in turn has USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang,
   c++11-lang, c++0x, c11, or gcc-c++11-lib.

PR:		216707

devel/boost-*: update to 1.63.0

Changes:	http://www.boost.org/users/history/version_1_63_0.html
PR:		215598
Exp-run by:	antoine
Approved by:	office (bapt)
MFH:		2017Q1

Reset ports per maintainer request.

PR:		215557
Submitted by:	A.J. "Fonz" van Werven (maintainer)

Bump PORTREVISIONS for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some
circumstances such as versions of FreeBSD or platforms), part II.

The first part covered  ports with USE_GCC=yes, USE_GCC=any, or one of
gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang,
c++11-lang, c++0x, c11 requested via USES=compiler.

This adds ports with USES=fortran and ports using Mk/bsd.octave.mk
which in turn has USES=fortran.

PR:		214965
Reported by:	thierry

devel/boost-*: update to 1.62.0

- Enable `long double` C99 math usage
- Switch 9.x back to building with GCC

Changes:	http://www.boost.org/users/history/
PR:		199601
Submitted by:	Chen Xu, bapt, amdmi3, truckman (based on)
Reviewed by:	rakuco (kde) (earlier version)
Exp-run by:	antoine (3 tries), truckman (consumers only, earlier versions)
Approved by:	bapt (office)

Bump PORTREVISIONS for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some
circumstances such as versions of FreeBSD or platforms).

In particular that is ports with USE_GCC=yes, USE_GCC=any, or one of
gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang,
c++11-lang, c++0x, c11 requested via USES=compiler.

Remove ${PORTSDIR}/ from dependencies, categories r, s, t, and u.

With hat:	portmgr
Sponsored by:	Absolight

- Update to 5.0.6
- Pass maintainership to submitter
- Add distfile mirror

PR:		201921
Submitted by:	freebsd@skysmurf.nl

- Update to 5.0.5

PR:		200306
Submitted by:	tkato432@yahoo.com

Upgrade to 5.0.4.

PR:		197454
Submitted by:	Ports Fury.

Uses blaslapack.

- Update net/openmpi to 1.8.4

- Update to 5.0.2

PR:		193902
Submitted by:	tkato432@yahoo.com

science/gromacs: Fix build on DragonFly (fix from dports)

- Update net/openmpi from 1.8.2 to 1.8.3

Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)

- Upgrade to 1.5;

- Bump PORTREVISION for consumers.

math/fftw3:
- Add USES=libtool and bump dependent ports
- Add INSTALL_TARGET=install-strip
- Remove PTHREAD_CFLAGS and PTHREAD_LIBS
- Use MAKE_CMD

Chase the upgrade of net/mpich2.

Approved by:	portmgr (non staged ports)

science/gromacs: Upgrade version 4.6.5 => 5.0

PR:		191826
Submitted by:	Ports Fury