science/pnetcdf: Add LICENSE

science/pnetcdf: Update to 1.14.0

- Add mpich and openmpi flavors

Changes:	https://github.com/Parallel-NetCDF/PnetCDF/blob/master/RELEASE_NOTES
		https://github.com/Parallel-NetCDF/PnetCDF/commits/master

*/*: Remove GNU_CONFIGURE_MANPREFIX=${PREFIX}/share after
9fd7ee1cdf6cbd5528159b58a966e1a40e2909a9

science/pnetcdf: Clean up Makefile

science/pnetcdf: Update WWW and clean up pkg-descr

science/pnetcdf: Update manpage location
(003a571d1d6585196545295efc181514f171c4c4, r523104)

*/*: bump PORTREVISION after OpenMPI upgrade

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

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science/pnetcdf: Remove outdated post-patch:

science/pnetcdf: fix build on non amd64 / i386 architectures

1. Set the default to OPENMPI on everywhere to fix:
====> You must select one and only one option from the MPI single
=====> No option was selected (and one must be)
2. Then exclude it on other 32-bit architectures, not just i386.

science/pnetcdf: Fix build on i386

Use MPICH option for i386. PnetCDF requires MPI_Offset >= 8 but Open MPI sets
MPI_Offset to 4 on 32-bit architecture regardless of LFS. See
https://github.com/open-mpi/ompi/issues/3195 for details

science/pnetcdf: Clean up (should be part of
3100961a1a18df741ae58dd1394bb38e13fead88)

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/pnetcdf: Update to 1.12.3

- Update MASTER_SITES
- Update WWW

Changes:	https://github.com/Parallel-NetCDF/Parallel-NetCDF.github.io/tree/master/Release_notes

Remove # $FreeBSD$ from Makefiles.

Simplify Makefile

- Use shared OPENMPI_DESC
- Remove OPENMPI3 option

Cosmetic change

Fix Makefile.

Update GCC_DEFAULT from 9 to 10.

A few (mostly Fortran-based) ports need to be patched because GCC 10
is stricter.  A handful of ports need to be restricted to GCC 9 because
they fail with 10.

5 ports still fail with GCC 10.  However, seeing as this work has been
ongoing since 2020-05-24, it is simply time to make the commit and
notify the affected maintainers.

While here, pet portlint (Makevar order).

PR:		246700
Submitted by:	gerald
Approved by:	antoine (after many, many, -exp runs)

- 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

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

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

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

Change from MPICH2 to MPICH option

- Bump PORTREVISION for dependency and package change

PR:		231634
Submitted by:	yuri

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

Add OPENMPI3 option

- Change default from OPENMPI to OPENMPI3
- Bump PORTREVISION for dependency change

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

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

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

Add OPENMPI2 option

Update to 1.8.1

Changes:	http://trac.mcs.anl.gov/projects/parallel-netcdf/wiki/ReleaseNotes-1.8.1

- Update DESTDIR support: use usptream patch with modified MANDIR
(prefix/share/man -> prefix/man)
- Update WWW: use https://

Obtained from:	http://trac.mcs.anl.gov/projects/parallel-netcdf/changeset/2745

- Update to 1.8.0

Changes:	http://trac.mcs.anl.gov/projects/parallel-netcdf/wiki/ReleaseNotes-1.8.0

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

- Update to 1.7.0
- Use CONFLICTS_INSTALL instead of CONFLICTS
- Convert to options target helper
- Pet portlint: fix diff header of patch files
- Sort PLIST

Changes:	http://trac.mcs.anl.gov/projects/parallel-netcdf/wiki/ReleaseNotes-1.7.0

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

With hat:	portmgr
Sponsored by:	Absolight

- Update to 1.10.2

- Update to 1.10.0
- Add SLURM to OPTIONS_DEFAULT (it's enabled by default in the configure script)

- Update to 1.6.1

Changes:	http://trac.mcs.anl.gov/projects/parallel-netcdf/wiki/ReleaseNotes-1.6.1

- Update to 1.6.0

Changes:	http://trac.mcs.anl.gov/projects/parallel-netcdf/wiki/ReleaseNotes-1.6.0

- Update net/openmpi to 1.8.4

- 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.

- Update net/openmpi from 1.8.1 to 1.8.2

- Convert net/openmpi to USES=libtool and bump dependent ports
- Add INSTALL_TARGET=install-strip
- Use BROKEN_sparc64

Approved by:	portmgr (implicit, bump unstaged port)

- Fix PLIST [1]
- Bump PORTREVISION for package change
- Cleanup Makefile
- Reformat pkg-descr

Reported by:	swills [1]

- Update to 1.5.0

Changes:	http://trac.mcs.anl.gov/projects/parallel-netcdf/wiki/ReleaseNotes-1.5.0

- Update openmpi from 1.6.5 to 1.8 (new stable version)
- Convert USE_BZIP2 to USES

- Simplify Makefile

- Use USES=tar:bzip2

Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3.  This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.

Part II, Bump PORTREVISIONs.

PR:		182136
Supported by:	Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by:	bdrewery (two -exp runs)

- Cleanup Makefile

- Update to 1.4.1
- Add MPICH2 option
- Convert to new options helper
- Support STAGEDIR

Changes:	http://trac.mcs.anl.gov/projects/parallel-netcdf/wiki/ReleaseNotes-1.4.1
		http://trac.mcs.anl.gov/projects/parallel-netcdf/wiki/ReleaseNotes-1.4.0

Convert all USE_FORTRAN=yes to "USES=fortran, USE_GCC=yes".  In most cases
USE_GCC=yes has been omitted though.

Remove USE_FORTRAN handling from bsd.port.mk and bsd.gcc.mk.

Minor cleanups in some ports like USE_GMAKE, NOPORTDOCS,...

Exp-run:	bdrewery
Approved by:	portmgr (bdrewery)

Update to libmpc version 1.0.1 which brings the following fixes:

 - Switched to automake 1.11.6, see CVE-2012-3386.
 - #14669: Fixed extraction of CC from gmp.h.
 - Fixed case of intermediate zero real or imaginary part in mpc_fma,
   found by hydra with GMP_CHECK_RANDOMIZE=1346362345.

This is on top of the following changes from version 1.0

 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
   invariant sections) for the documentation.
 - 100% of all lines are covered by tests
 - Renamed functions
   . mpc_mul_2exp to mpc_mul_2ui
   . mpc_div_2exp to mpc_div_2ui

Add NO_STAGE all over the place in preparation for the staging support (cat:
science)

- Remove leading indefinite article from COMMENT

- Use USES=gmake

- Update to 1.3.1
- Cleanup Makefile header

Changes:	http://trac.mcs.anl.gov/projects/parallel-netcdf/wiki/ReleaseNotes-1.3.1

- Update to 1.3.0
- Convert to new options framework
- Pet portlint
- Cosmetic change
- Take maintainership

Changes:       
http://trac.mcs.anl.gov/projects/parallel-netcdf/wiki/ReleaseNotes-1.3.0

Chase the upgrade of MPICH2.

Since I'm there, pet portlint where needed, e.g. by removing oblsolete
MD5 checksums.

PR:             ports/154715

Update to 1.2.0

PR:             ports/150665
Submitted by:   KATO Tsuguru <tkato432 at yahoo.com>

- Update to 1.1.1

PR:             143442
Submitted by:   Ports Fury

- Chase relocation of net/mpich2

- Bump PORTREVISION if needed

- Fix some portlint errors.

- Update to 1.1.0

PR:             140486
Submitted by:   Ports Fury

- Fix MASTER_SITES

- Update to 1.0.3

PR:             139772
Submitted by:   Ports Fury

Bump PORTREVISION for everything that sets USE_FORTRAN=yes which now
implies lang/gcc44 up from lang/gcc43.

Approved by:    portmgr

Leverage USE_FORTRAN instead of accomplishing the same manually.

Reset quakelee@cn.FreeBSD.org due to maintainer-timeouts and no response
to email.

Hat:    portmgr

Bump portrevision due to upgrade of devel/gettext.

The affected ports are the ones with gettext as a run-dependency
according to ports/INDEX-7 (5007 of them) and the ones with USE_GETTEXT
in Makefile (29 of them).

PR:             ports/124340
Submitted by:   edwin@
Approved by:    portmgr (pav)

- Mark BROKEN on 7.x

- Set --mandir and --infodir in CONFIGURE_ARGS if the configure script
  supports them.  This is determined by running ``configure --help'' in
  do-configure target and set the shell variable _LATE_CONFIGURE_ARGS
  which is then passed to CONFIGURE_ARGS.
- Remove --mandir and --infodir in ports' Makefile where applicable
  Few ports use REINPLACE_CMD to achieve the same effect, remove them too.
- Correct some manual pages location from PREFIX/man to MANPREFIX/man
- Define INFO_PATH where necessary
- Document that .info files are installed in a subdirectory relative to
  PREFIX/INFO_PATH and slightly change add-plist-info to use INFO_PATH and
  subdirectory detection.

PR:             ports/111470
Approved by:    portmgr
Discussed with: stas (Mk/*), gerald (info related stuffs)
Tested by:      pointyhat exp run

- Add a new dependence of gfortran42
- Bump PORTREVISION

PR:             113047
Submitted by:   CHAO Shin <quakelee@cn.FreeBSD.org> (maintainer)

- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.

Parallel-NetCDF is a library providing high-performance I/O while still
maintaining file-format compatibility with Unidata's NetCDF. NetCDF gives
scientific programmers a space-efficient and portable means for storing data.
However, it does so in a serial manner, making it difficult to achieve high
I/O performance. By making some small changes to the API specified by NetCDF,
we can use MPI-IO and its collective operations.

WWW: http://trac.mcs.anl.gov/projects/parallel-netcdf

PR:             ports/112265
Submitted by:   Chao Shin <quakelee at cn.FreeBSD.org>