Hello community,
here is the log from the commit of package gromacs for openSUSE:Factory checked in at 2016-09-01 14:02:34
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/gromacs (Old)
and /work/SRC/openSUSE:Factory/.gromacs.new (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "gromacs"
Changes:
--------
--- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2015-10-20 00:05:19.000000000 +0200
+++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2016-09-01 14:02:36.000000000 +0200
@@ -1,0 +2,17 @@
+Wed Aug 24 15:24:30 UTC 2016 - junghans@votca.org
+
+- version bump to 2015 details here:
+ http://manual.gromacs.org/documentation/2016/ReleaseNotes/index.html
+- Highlights:
+ - As always, we’ve got several useful performance improvements, with or without GPUs. CPU-side SIMD and threading enhancements will make GPU-accelerated simulations faster even if we’d left the GPU code alone! Thanks to these and additional GPU kernel improvements, in GPU-accelerated runs expect around 15% improvement in throughput. (And not just for plain vanilla MD, either... the pull code now supports OpenMP threading throughout, and multi-simulations have less coupling between simulations.)
+ - We have a new C++11 portability layer permitting us to accelerate in SIMD on the CPU lots of minor routines. These will also often improve runs that use accelerators or many nodes through better load balancing. POWER8, ARM64, AVX512 (KNL), and more are fully SIMD accelerated now because they are supported in the new portability layer!
+ - We made further SIMD acceleration of bonded interactions which reduces their calculation time by about a factor of 2. This improves load balance at high parallelization by a factor of 2, and shows significantly better scaling.
+ - Similarly, SIMD acceleration of SETTLE reduces the time for constraints by a factor of 3 to 5 - which has a strong effect for GPU runs.
+ - OpenCL GPU support is now available with all combinations of MPI, thread-MPI and GPU sharing (ie. the same as CUDA). Kernel performance has improved by up to 60%. AMD GPUs benefit the most, OpenCL on NVIDIA is generally still slow.
+ - Tools in the new analysis framework can handle trajectories that are subsets of the simulation system.
+ - New pull coordinate geometries angle-axis, dihedral, and normal angle.
+ - Checkpoint restarts work only in the cases where the implementation can always do what the user wants.
+ - The version numbering has changed to be the year of the release, plus (in future) a patch number. GROMACS 2016 will be the initial release from this branch, then GROMACS 2016.1 will have the set of bugs that have been fixed in GROMACS 2016, etc.
+
+
+-------------------------------------------------------------------
@@ -8 +24,0 @@
-
Old:
----
gromacs-5.1.tar.gz
manual-5.1.pdf
regressiontests-5.1.tar.gz
New:
----
gromacs-2016.tar.gz
manual-2016.pdf
regressiontests-2016.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ gromacs.spec ++++++
--- /var/tmp/diff_new_pack.PLO56N/_old 2016-09-01 14:02:42.000000000 +0200
+++ /var/tmp/diff_new_pack.PLO56N/_new 2016-09-01 14:02:42.000000000 +0200
@@ -1,7 +1,7 @@
#
# spec file for package gromacs
#
-# Copyright (c) 2015 Christoph Junghans
+# Copyright (c) 2015,2016 Christoph Junghans
# Copyright (c) 2013,2014 SUSE LINUX Products GmbH, Nuernberg, Germany.
#
# All modifications and additions to the file contributed by third parties
@@ -17,7 +17,7 @@
#
Name: gromacs
-Version: 5.1
+Version: 2016
Release: 0
Summary: Molecular Dynamics Package
License: GPL-2.0+
@@ -31,12 +31,9 @@
BuildRequires: cmake >= 2.8.8
BuildRequires: fdupes
BuildRequires: openmpi-devel
-%if %{defined fedora}
-BuildRequires: pkgconfig
-%else
BuildRequires: pkg-config
-%endif
BuildRequires: pkgconfig(fftw3)
+BuildRequires: pkgconfig(tinyxml2)
BuildRoot: %{_tmppath}/%{name}-%{version}-build
%description
@@ -60,6 +57,19 @@
This package contains development libraries and header for GROMACS
+%package -n libgromacs2
+Summary: Libraries for Gromacs
+Group: System/Libraries
+
+%description -n libgromacs2
+GROMACS is a versatile and extremely well optimized package to perform
+molecular dynamics computer simulations and subsequent trajectory analysis.
+It is developed for biomolecules like proteins, but the extremely high
+performance means it is used also in several other field like polymer chemistry
+and solid state physics.
+
+This package contains libraries for Gromacs
+
%package bash
Summary: Bash completion for Gromacs
Group: Productivity/Other
@@ -116,13 +126,12 @@
%else
%define acce None
%endif
-mkdir nompi openmpi
-cd nompi
+%define __builddir nompi
# note about rpath
-# gromacs' cmake has too rpath much auto-magin, just
+# gromacs' cmake has too much rpath auto-magic, just
# force to skip it (CMAKE_SKIP_RPATH=1) and use
-# LD_LIBRARY_PATH for make check
-cmake \
+# LD_LIBRARY_PATH for checks below
+%{cmake} \
-DCMAKE_INSTALL_PREFIX=%{_prefix} \
-DCMAKE_VERBOSE_MAKEFILE=TRUE \
-DCMAKE_BUILD_TYPE=Release \
@@ -134,16 +143,14 @@
-DGMX_THREAD_MPI=ON \
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DGMX_OPENMP=ON \
+ -DGMX_EXTERNAL_TINYXML2=ON \
-DREGRESSIONTEST_PATH="$PWD/../regressiontests-%{version}" \
- -DGMX_LIB_INSTALL_DIR=%{_lib} \
- ..
+ -DGMX_LIB_INSTALL_DIR=%{_lib}
make %{?_smp_mflags}
-cd ../openmpi
-%if %{defined fedora}
-%{_openmpi_load}
-%endif
-cmake \
+cd ..
+%define __builddir openmpi
+%{cmake} \
-DCMAKE_INSTALL_PREFIX=/usr \
-DCMAKE_VERBOSE_MAKEFILE=TRUE \
-DCMAKE_BUILD_TYPE=Release \
@@ -152,11 +159,13 @@
-DCMAKE_SKIP_RPATH=1 \
-DGMX_SIMD=%{acce} \
-DGMX_BUILD_MDRUN_ONLY=ON \
+ -DBUILD_SHARED_LIBS=OFF \
-DGMX_MPI=ON \
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DGMX_OPENMP=ON \
- -DGMX_LIB_INSTALL_DIR=%{_lib} \
- ..
+ -DGMX_EXTERNAL_TINYXML2=ON \
+ -DREGRESSIONTEST_PATH="$PWD/../regressiontests-%{version}" \
+ -DGMX_LIB_INSTALL_DIR=%{_lib}
make %{?_smp_mflags}
%install
@@ -164,7 +173,7 @@
make -C openmpi install DESTDIR=%{buildroot}
%fdupes %{buildroot}%{_prefix}
-#not need when installed in /usr
+#no need when installed in /usr
rm -f %{buildroot}%{_bindir}/GMXRC*
# Move bash completion file to correct location
mkdir -p %{buildroot}%{_sysconfdir}/bash_completion.d
@@ -175,27 +184,29 @@
cp %{S:1} %{buildroot}%{_datadir}/gromacs
%check
-%if %{defined fedora}
-%{_openmpi_unload}
-%endif
LD_LIBRARY_PATH=%{buildroot}/%{_libdir} make -C nompi %{?_smp_mflags} check
+LD_LIBRARY_PATH=%{buildroot}/%{_libdir} make -C openmpi %{?_smp_mflags} check
-%post -p /sbin/ldconfig
-%postun -p /sbin/ldconfig
+%post -n libgromacs2 -p /sbin/ldconfig
+%postun -n libgromacs2 -p /sbin/ldconfig
%files
%defattr(-,root,root,-)
-%{_bindir}/*
-%exclude %{_bindir}/*_mpi
-%{_datadir}/gromacs
-%exclude %{_datadir}/gromacs/template
-%exclude %{_datadir}/gromacs/*.pdf
-%{_libdir}/lib*.so.*
+%{_bindir}/gmx
+%{_bindir}/*.pl
+%dir %{_datadir}/gromacs
+%{_datadir}/gromacs/top
%{_mandir}/man1/*
+%files -n libgromacs2
+%defattr(-,root,root,-)
+%{_libdir}/lib*.so.*
+
%files doc
%defattr(-,root,root,-)
%doc %{_datadir}/gromacs/*.pdf
+%doc %{_datadir}/gromacs/README*
+%doc %{_datadir}/gromacs/COPYING
%files openmpi
%defattr(-,root,root,-)
@@ -212,5 +223,3 @@
%files bash
%defattr(-,root,root,-)
%config %{_sysconfdir}/bash_completion.d/gromacs
-
-%changelog
++++++ gromacs-5.1.tar.gz -> gromacs-2016.tar.gz ++++++
/work/SRC/openSUSE:Factory/gromacs/gromacs-5.1.tar.gz /work/SRC/openSUSE:Factory/.gromacs.new/gromacs-2016.tar.gz differ: char 5, line 1
++++++ manual-5.1.pdf -> manual-2016.pdf ++++++
(binary differes)
++++++ regressiontests-5.1.tar.gz -> regressiontests-2016.tar.gz ++++++
/work/SRC/openSUSE:Factory/gromacs/regressiontests-5.1.tar.gz /work/SRC/openSUSE:Factory/.gromacs.new/regressiontests-2016.tar.gz differ: char 15, line 1