<pre style='margin:0'>
David Strubbe (dstrubbe) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/5f4ed0fe73174b552002ce6ec639ceda1482e43b">https://github.com/macports/macports-ports/commit/5f4ed0fe73174b552002ce6ec639ceda1482e43b</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 5f4ed0f gromacs: Variants for hwloc and threads, respecting choice for lapack.
</span>5f4ed0f is described below
<span style='display:block; white-space:pre;color:#808000;'>commit 5f4ed0fe73174b552002ce6ec639ceda1482e43b
</span>Author: David Strubbe <dstrubbe@macports.org>
AuthorDate: Sun Feb 11 14:47:20 2018 -0800
<span style='display:block; white-space:pre;color:#404040;'> gromacs: Variants for hwloc and threads, respecting choice for lapack.
</span><span style='display:block; white-space:pre;color:#404040;'>
</span><span style='display:block; white-space:pre;color:#404040;'> Stop opportunistic linking by adding hwloc variants. Use linear algebra portgroup setting for LAPACK as well as BLAS. Support for OpenMP threads. Put plumed patching into patch phase, not configure.
</span>---
science/gromacs/Portfile | 25 +++++++++++--------------
1 file changed, 11 insertions(+), 14 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 d3bcf35..81e5578 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;'>@@ -12,6 +12,7 @@ PortGroup linear_algebra 1.0
</span> name gromacs
# not all versions have patches available for plumed; subport's patch will fail if not there
version 2016.4
<span style='display:block; white-space:pre;background:#e0ffe0;'>+revision 1
</span> categories science math
license LGPL-2.1
maintainers dstrubbe openmaintainer
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -40,7 +41,7 @@ depends_build-append \
</span> depends_lib-append port:fftw-3-single port:libxml2 port:zlib
# 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
</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=OFF -DGMX_OPENMP:BOOL=OFF
</span> # boost?
variant x11 description {Enable GMX view via X11} {
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -48,16 +49,15 @@ variant x11 description {Enable GMX view via X11} {
</span> depends_lib-append port:xorg-libX11 port:xorg-libXext
}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-# FIXME: use threads.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-#:info:configure -- Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-#:info:configure CMake Warning at cmake/gmxManageOpenMP.cmake:78 (message):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-#:info:configure The compiler you are using does not support OpenMP parallelism. This might
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-#:info:configure hurt your performance a lot, in particular with GPUs. Try using a more
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-#:info:configure recent version, or a different compiler. For now, we are proceeding by
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-#:info:configure turning off OpenMP.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant hwloc description {Enable usage of HWLOC for hardware locality} {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ configure.args-replace -DGMX_HWLOC:BOOL=OFF -DGMX_HWLOC:BOOL=ON
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant threads description {Enable usage of OpenMP} {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ configure.args-replace -DGMX_OPENMP:BOOL=OFF -DGMX_OPENMP:BOOL=ON
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span>
compilers.choose cc cxx
<span style='display:block; white-space:pre;background:#ffe0e0;'>-#-dragonegg
</span> mpi.setup
test.run yes
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -89,9 +89,7 @@ post-test {
</span> #For more information and tips for troubleshooting, please check the GROMACS
#website at http://www.gromacs.org/Documentation/Errors
<span style='display:block; white-space:pre;background:#ffe0e0;'>-## ADDITION FOR PLUMED SUBPORT
</span> subport gromacs-plumed {
<span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span> description ${description}: \
(THIS PORT INSTALLS A VERSION OF GROMACS PATCHED WITH PLUMED)
long_description ${long_description}: \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -107,7 +105,7 @@ subport gromacs-plumed {
</span>
depends_build-append path:${prefix}/bin/plumed:plumed
depends_lib-append path:${prefix}/lib/libplumedKernel.dylib:plumed
<span style='display:block; white-space:pre;background:#ffe0e0;'>- pre-configure {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ post-patch {
</span> # I need to execute with full path since PATH variable is not properly set here
# Also notice that I am patching with runtime. Notice that
# plumed compiled for MacPorts has the hardcoded path also in the runtime patch.
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -123,14 +121,13 @@ to the path of libplumedKernel.dylib you can replace your own PLUMED library at
</span> By default, ${prefix}/lib/libplumedKernel.dylib is linked.
"
}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-## END ADDITION FOR PLUMED SUBPORT ONLY
</span>
linalg.setup noveclibfort
pre-configure {
if {[mpi_variant_isset]} {
configure.args-append -DGMX_MPI:BOOL=ON -DMPIEXEC:STRING="${mpi.exec}"
}
<span style='display:block; white-space:pre;background:#ffe0e0;'>- configure.args-append -DGMX_BLAS_USER="${linalglib}"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ configure.args-append -DGMX_BLAS_USER="${linalglib}" -DGMX_LAPACK_USER="${linalglib}"
</span> }
variant double description "Build in double precision (much slower, use only if you really need it)" {
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