<pre style='margin:0'>
Renee Otten (reneeotten) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/8de14e6f9c16a64d0db5a16ec1c79b832c00dab2">https://github.com/macports/macports-ports/commit/8de14e6f9c16a64d0db5a16ec1c79b832c00dab2</a></p>
<pre style="white-space: pre; background: #F8F8F8">The following commit(s) were added to refs/heads/master by this push:
<span style='display:block; white-space:pre;color:#404040;'> new 8de14e6f9c1 gromacs: update to 2021.3
</span>8de14e6f9c1 is described below
<span style='display:block; white-space:pre;color:#808000;'>commit 8de14e6f9c16a64d0db5a16ec1c79b832c00dab2
</span>Author: Mark Abraham <Mark.J.Abraham@gmail.com>
AuthorDate: Fri Sep 10 12:59:33 2021 +0200
<span style='display:block; white-space:pre;color:#404040;'> gromacs: update to 2021.3
</span><span style='display:block; white-space:pre;color:#404040;'>
</span><span style='display:block; white-space:pre;color:#404040;'> Closes: https://trac.macports.org/ticket/63137
</span><span style='display:block; white-space:pre;color:#404040;'> Closes: https://trac.macports.org/ticket/61692
</span>---
science/gromacs/Portfile | 47 ++++++++++++++++++++++++-----------------------
1 file changed, 24 insertions(+), 23 deletions(-)
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/gromacs/Portfile b/science/gromacs/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index a5ea6ee8cf1..b2047823e4c 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/gromacs/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/gromacs/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -2,21 +2,20 @@
</span>
PortSystem 1.0
PortGroup muniversal 1.0
<span style='display:block; white-space:pre;background:#ffe0e0;'>-PortGroup cmake 1.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# this line is needed to allow use of gcc
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-configure.cxx_stdlib libstdc++
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-PortGroup cxx11 1.1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+PortGroup cmake 1.1
</span> PortGroup mpi 1.0
PortGroup linear_algebra 1.0
name gromacs
# not all versions have patches available for plumed; subport's patch will fail if not there
# find list at https://www.plumed.org/doc-v2.5/user-doc/html/_code_specific_notes.html
<span style='display:block; white-space:pre;background:#ffe0e0;'>-version 2019.2
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+version 2021.3
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision 0
</span> categories science math
<span style='display:block; white-space:pre;background:#e0ffe0;'>+platforms darwin
</span> license LGPL-2.1
maintainers {dstrubbe @dstrubbe} openmaintainer
<span style='display:block; white-space:pre;background:#ffe0e0;'>-description The World's fastest Molecular Dynamics package
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+description Molecular dynamics package designed for simulations of proteins, lipids, and nucleic acids.
</span> long_description GROMACS is a versatile package to perform molecular \
dynamics, i.e. simulate the Newtonian equations of motion for \
systems with hundreds to millions of particles. It is primarily \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -27,33 +26,35 @@ long_description GROMACS is a versatile package to perform molecular \
</span> research on non-biological systems, e.g. polymers.
platforms darwin
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage http://www.gromacs.org/
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-master_sites http://ftp.gromacs.org/pub/gromacs
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+homepage https://www.gromacs.org/
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+master_sites https://ftp.gromacs.org/pub/gromacs
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-# md5 as on http://manual.gromacs.org/documentation/2019.2/download.html
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums rmd160 e59309b1a9d0de14a547f7727d4f4915aa3a6df7 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sha256 bcbf5cc071926bc67baa5be6fb04f0986a2b107e1573e15fadcb7d7fc4fb9f7e \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- md5 9978498d904ec81f50796b3cdaa9c5df \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- size 33437869
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# md5 as on http://manual.gromacs.org/documentation/2021.3/download.html
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 74adb5fc9e2fa461d4d7ff603d0fe7e08476da20 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 e109856ec444768dfbde41f3059e3123abdb8fe56ca33b1a83f31ed4575a1cc6 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ md5 1850870fbbfb228051ee0afc1c5ddeff \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 37987972
</span>
depends_build-append \
port:pkgconfig
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_lib-append port:fftw-3-single port:libxml2 port:zlib
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_lib-append port:fftw-3-single port:hwloc port:zlib
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+compiler.cxx_standard 2017
</span>
# FIXME: enable use of avx when appropriate, instead of just SSE
<span style='display:block; white-space:pre;background:#ffe0e0;'>-configure.args-append -DGMX_SIMD:STRING="SSE4.1" -DBUILD_TESTING:BOOL=ON -DGMX_X11:BOOL=OFF -DGMX_HWLOC:BOOL=OFF -DGMX_OPENMP:BOOL=OFF
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# boost?
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+configure.args-append -DGMX_SIMD:STRING="SSE4.1" -DBUILD_TESTING:BOOL=ON -DGMX_X11:BOOL=OFF -DGMX_HWLOC:BOOL=ON -DGMX_OPENMP:BOOL=OFF
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# Ensure that GROMACS log files reflect that the build was
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# done via macports, to help users troubleshoot issues
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+configure.args-append -DGMX_VERSION_STRING_OF_FORK="macports"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# Always use libc++
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+configure.args-append -DGMX_STDLIB_CXX_FLAGS=-stdlib=libc++ -DGMX_STDLIB_LIBRARIES='-lc++abi -lc++'
</span>
variant x11 description {Enable GMX view via X11} {
configure.args-replace -DGMX_X11:BOOL=OFF -DGMX_X11:BOOL=ON
depends_lib-append port:xorg-libX11 port:xorg-libXext
}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-variant hwloc description {Enable usage of HWLOC for hardware locality} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- configure.args-replace -DGMX_HWLOC:BOOL=OFF -DGMX_HWLOC:BOOL=ON
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span> variant threads description {Enable usage of OpenMP} {
configure.args-replace -DGMX_OPENMP:BOOL=OFF -DGMX_OPENMP:BOOL=ON
}
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -101,13 +102,13 @@ subport gromacs-plumed {
</span> depends_lib-append path:${prefix}/lib/libplumedKernel.dylib:plumed
post-patch {
# I need to execute with full path since PATH variable is not properly set here
<span style='display:block; white-space:pre;background:#ffe0e0;'>-# Also notice that I am patching with runtime. Notice that
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# Also notice that I am patching with runtime. Notice that
</span> # plumed compiled for MacPorts has the hardcoded path also in the runtime patch.
# This allows the user to work with MacPorts plumed and possibly
# override the choice setting the PLUMED_KERNEL environment variable.
# Also notice that gromacs version is hardcoded here. Plumed patch is not always
# updated when gromacs is.
<span style='display:block; white-space:pre;background:#ffe0e0;'>- exec ${prefix}/bin/plumed patch --mdroot=${worksrcpath} -e gromacs-2019.2 --runtime -p
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ exec ${prefix}/bin/plumed patch --mdroot=${worksrcpath} -e gromacs-${version} --runtime -p
</span> }
notes "
PLUMED is linked with runtime binding. By setting the environment variable PLUMED_KERNEL\
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -131,5 +132,5 @@ variant double description "Build in double precision (much slower, use only if
</span> }
livecheck.type regex
<span style='display:block; white-space:pre;background:#ffe0e0;'>-livecheck.url http://ftp.gromacs.org/pub/gromacs/
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+livecheck.url https://ftp.gromacs.org/pub/gromacs/
</span> livecheck.regex ${name}-(\[0-9.\]+)${extract.suffix}
</pre><pre style='margin:0'>
</pre>