Hello community, here is the log from the commit of package gromacs for openSUSE:Factory checked in at 2019-06-19 20:56:48 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/gromacs (Old) and /work/SRC/openSUSE:Factory/.gromacs.new.4811 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "gromacs" Wed Jun 19 20:56:48 2019 rev:42 rq:701640 version:2019.2 Changes: -------- --- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2018-11-13 17:13:00.282630762 +0100 +++ /work/SRC/openSUSE:Factory/.gromacs.new.4811/gromacs.changes 2019-06-19 20:57:08.973917513 +0200 @@ -1,0 +2,42 @@ +Wed May 8 15:07:49 UTC 2019 - Christoph Junghans <[email protected]> + +- version bump to 2019.2 details here: + http://manual.gromacs.org/documentation/2019.2/release-notes/2019/2019.2.html + Hightlights: + - Fix L-BGFS minimizer + - Disallow pull geometry direction-periodic with AWH + - Fixed mdrun -nsteps option + - gmx cluster -clndx indices now correct + - gmx editconf -f in.pdb -o out.pdb again preserves chain IDs + - Tools again accept .tpr files as input + - Fix segmentation fault when preparing simulated annealing inputs + - Fix error in AVX 512 detection code + - Added warning with the use of GROMOS force fields + - Prevented internal build of FFTW with clang and AVX-512 SIMD + - Updated performance guide for recent Intel processors with AVX512 instruction support + +------------------------------------------------------------------- +Tue Feb 26 10:48:25 UTC 2019 - Klaus Kämpf <[email protected]> + +- add fdupes + +------------------------------------------------------------------- +Mon Feb 25 17:51:49 UTC 2019 - Christoph Junghans <[email protected]> + +- version bump to 2019.1 details here: + http://manual.gromacs.org/documentation/2019.1/release-notes/2019/2019.1.html + Hightlights: + - Fix error with 2D/3D dynamic load balancing + - Fix incorrect LJ repulsion force switching on GPUs + - Fix segmentation fault in mdrun with domain decomposition + - Fix segmentation fault with energy minimization with the group scheme + - Correct free-energy Delta H output with mass lambda’s + - Prevent mdrun -rerun from writing incorrect free-energy output + - Fix possible division by zero in enforced-rotation code + - Fix trjconv -ndec + - Fix using index file groups when .tpr file not supplied + - Fix tune_pme + - Fixes that affect portability + - Explicitly require 64-bit platforms for OpenCL + +------------------------------------------------------------------- Old: ---- gromacs-2018.4.tar.gz manual-2018.4.pdf regressiontests-2018.4.tar.gz New: ---- gromacs-2019.2.tar.gz manual-2019.2.pdf regressiontests-2019.2.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ gromacs.spec ++++++ --- /var/tmp/diff_new_pack.jxStw2/_old 2019-06-19 20:57:18.997925862 +0200 +++ /var/tmp/diff_new_pack.jxStw2/_new 2019-06-19 20:57:19.001925865 +0200 @@ -1,8 +1,8 @@ # # spec file for package gromacs # -# Copyright (c) 2018 SUSE LINUX GmbH, Nuernberg, Germany. -# Copyright (c) 2015-2018 Christoph Junghans <[email protected]> +# Copyright (c) 2019 SUSE LINUX GmbH, Nuernberg, Germany. +# Copyright (c) 2015-2019 Christoph Junghans <[email protected]> # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -13,27 +13,41 @@ # license that conforms to the Open Source Definition (Version 1.9) # published by the Open Source Initiative. -# Please submit bugfixes or comments via http://bugs.opensuse.org/ +# Please submit bugfixes or comments via https://bugs.opensuse.org/ # +# Build with OpenMPI +%if 0%{?sle_version} <= 120300 +%define mpiver openmpi +%else + %if 0%{?sle_version} <= 150000 + %define mpiver openmpi2 + %else + %define mpiver openmpi3 + %endif +%endif + Name: gromacs -Version: 2018.4 +Version: 2019.2 Release: 0 +%define uversion %{version} +%define sover 4 Summary: Molecular Dynamics Package -License: GPL-2.0-or-later +License: GPL-2.0-or-later and Apache-2.0 Group: Productivity/Scientific/Chemistry Url: http://www.gromacs.org -Source0: ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{version}.tar.gz -Source1: ftp://ftp.gromacs.org/pub/manual/manual-%{version}.pdf -Source2: http://gerrit.gromacs.org/download/regressiontests-%{version}.tar.gz +Source0: ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{uversion}.tar.gz +Source1: ftp://ftp.gromacs.org/pub/manual/manual-%{uversion}.pdf +Source2: http://gerrit.gromacs.org/download/regressiontests-%{uversion}.tar.gz +BuildRequires: %{mpiver} +BuildRequires: %{mpiver}-devel BuildRequires: cmake >= 2.8.8 BuildRequires: fdupes BuildRequires: gcc-c++ BuildRequires: ocl-icd-devel BuildRequires: opencl-headers -BuildRequires: openmpi-devel BuildRequires: pkg-config BuildRequires: pkgconfig(fftw3) BuildRoot: %{_tmppath}/%{name}-%{version}-build @@ -59,11 +73,11 @@ This package contains development libraries and header for GROMACS -%package -n libgromacs3 +%package -n libgromacs%sover Summary: Libraries for Gromacs Group: System/Libraries -%description -n libgromacs3 +%description -n libgromacs%sover 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 @@ -103,28 +117,28 @@ This package contains documentation for gromacs. -%package openmpi +%package %{mpiver} Summary: Molecular dynamics package Group: Productivity/Scientific/Chemistry Requires: %{name} = %{version} -%description openmpi +%description %{mpiver} 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 the openmpi version of GROMACS. +This package contains the %{mpiver} version of GROMACS. %prep -%setup -q +%setup -q -n %{name}-%{uversion} tar -xzf %{S:2} %build -source %{_libdir}/mpi/gcc/openmpi/bin/mpivars.sh +source %{_libdir}/mpi/gcc/%{mpiver}/bin/mpivars.sh -%ifarch i386 x86_64 +%ifarch %x86 x86_64 #increse to SSE4.1, AVX_128_FMA, AVX_256 when possible %define acce SSE2 %else @@ -149,20 +163,20 @@ -DGMX_SIMD=%{acce} \ -DGMX_MPI=OFF \ -DGMX_THREAD_MPI=ON \ -%ifnarch ppc64le +%ifarch x86_64 -DGMX_GPU=ON -DGMX_USE_OPENCL=ON \ %endif -DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \ -DGMX_OPENMP=ON \ -%ifnarch i586 - -DREGRESSIONTEST_PATH="$PWD/../../regressiontests-%{version}" \ +%ifnarch i586 %arm # regressiontest are not support on 32-bit archs: http://redmine.gromacs.org/issues/2584#note-35 + -DREGRESSIONTEST_PATH="$PWD/../../regressiontests-%{uversion}" \ %endif -DGMX_LIB_INSTALL_DIR=%{_lib} ../../ -make %{?_smp_mflags} +%make_jobs cd ../.. -mkdir openmpi -cd openmpi +mkdir %{mpiver} +cd %{mpiver} %{cmake} \ -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_VERBOSE_MAKEFILE=TRUE \ @@ -174,38 +188,42 @@ -DGMX_BUILD_MDRUN_ONLY=ON \ -DBUILD_SHARED_LIBS=OFF \ -DGMX_MPI=ON \ -%ifnarch ppc64le +%ifarch x86_64 -DGMX_GPU=ON -DGMX_USE_OPENCL=ON \ %endif -DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \ -DGMX_OPENMP=ON \ -DGMX_LIB_INSTALL_DIR=%{_lib} ../../ -make %{?_smp_mflags} +%make_jobs %install -make -C nompi/build install DESTDIR=%{buildroot} -make -C openmpi/build install DESTDIR=%{buildroot} -%fdupes %{buildroot}%{_prefix} +cd nompi +%cmake_install +cd ../%{mpiver} +%cmake_install +cd .. #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 +mkdir -p %{buildroot}%{_datadir}/bash_completion.d #concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs) -cat %{buildroot}%{_bindir}/gmx-completion{,?*}.bash > %{buildroot}%{_sysconfdir}/bash_completion.d/gromacs +cat %{buildroot}%{_bindir}/gmx-completion{,?*}.bash > %{buildroot}%{_datadir}/bash_completion.d/gromacs rm -f %{buildroot}%{_bindir}/gmx-completion* cp %{S:1} %{buildroot}%{_datadir}/gromacs +%fdupes -s %{buildroot} + %check #s390x is too slow for tests %ifnarch s390x LD_LIBRARY_PATH=%{buildroot}/%{_libdir} make -C nompi/build %{?_smp_mflags} check -LD_LIBRARY_PATH='%{buildroot}/%{_libdir}::%{_libdir}/mpi/gcc/openmpi/%{_lib}' make -C openmpi/build %{?_smp_mflags} check +LD_LIBRARY_PATH='%{buildroot}/%{_libdir}::%{_libdir}/mpi/gcc/%{mpiver}/%{_lib}' make -C %{mpiver}/build %{?_smp_mflags} check %endif -%post -n libgromacs3 -p /sbin/ldconfig -%postun -n libgromacs3 -p /sbin/ldconfig +%post -n libgromacs%sover -p /sbin/ldconfig +%postun -n libgromacs%sover -p /sbin/ldconfig %files %defattr(-,root,root,-) @@ -213,12 +231,14 @@ %{_bindir}/*.pl %dir %{_datadir}/gromacs %{_datadir}/gromacs/top -%ifnarch ppc64le +%ifarch x86_64 %{_datadir}/gromacs/opencl +%exclude %{_datadir}/gromacs/opencl/gromacs/*/*.h +%exclude %{_datadir}/gromacs/opencl/gromacs/*/*/*.h %endif %{_mandir}/man1/* -%files -n libgromacs3 +%files -n libgromacs%sover %defattr(-,root,root,-) %{_libdir}/lib*.so.* @@ -228,7 +248,7 @@ %doc %{_datadir}/gromacs/README* %doc %{_datadir}/gromacs/COPYING -%files openmpi +%files %{mpiver} %defattr(-,root,root,-) %{_bindir}/*_mpi @@ -239,9 +259,15 @@ %{_includedir}/gromacs/ %{_libdir}/*.so %{_libdir}/pkgconfig/* +%ifarch x86_64 +%dir %{_datadir}/gromacs/opencl +%{_datadir}/gromacs/opencl/gromacs/*/*.h +%{_datadir}/gromacs/opencl/gromacs/*/*/*.h +%endif %files bash %defattr(-,root,root,-) -%config %{_sysconfdir}/bash_completion.d/gromacs +%dir %{_datadir}/bash_completion.d +%{_datadir}/bash_completion.d/gromacs %changelog ++++++ _constraints ++++++ --- /var/tmp/diff_new_pack.jxStw2/_old 2019-06-19 20:57:19.025925885 +0200 +++ /var/tmp/diff_new_pack.jxStw2/_new 2019-06-19 20:57:19.029925889 +0200 @@ -2,7 +2,7 @@ <constraints> <hardware> <physicalmemory> - <size unit="M">1500</size> + <size unit="G">2</size> </physicalmemory> <disk> <size unit="G">2</size> ++++++ gromacs-2018.4.tar.gz -> gromacs-2019.2.tar.gz ++++++ /work/SRC/openSUSE:Factory/gromacs/gromacs-2018.4.tar.gz /work/SRC/openSUSE:Factory/.gromacs.new.4811/gromacs-2019.2.tar.gz differ: char 5, line 1 ++++++ manual-2018.4.pdf -> manual-2019.2.pdf ++++++ (binary differes) ++++++ regressiontests-2018.4.tar.gz -> regressiontests-2019.2.tar.gz ++++++ /work/SRC/openSUSE:Factory/gromacs/regressiontests-2018.4.tar.gz /work/SRC/openSUSE:Factory/.gromacs.new.4811/regressiontests-2019.2.tar.gz differ: char 12, line 1
