Script 'mail_helper' called by obssrc Hello community, here is the log from the commit of package gromacs for openSUSE:Factory checked in at 2021-07-03 20:50:38 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/gromacs (Old) and /work/SRC/openSUSE:Factory/.gromacs.new.2625 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "gromacs" Sat Jul 3 20:50:38 2021 rev:47 rq:903651 version:2021.2 Changes: -------- --- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2020-08-01 12:32:12.786514956 +0200 +++ /work/SRC/openSUSE:Factory/.gromacs.new.2625/gromacs.changes 2021-07-03 20:50:47.684793675 +0200 @@ -1,0 +2,41 @@ +Mon Jun 28 15:39:23 UTC 2021 - Atri Bhattacharya <[email protected]> + +- Update to version 2021.2: + * Fixes where mdrun could behave incorrectly. + * Removed a potential race condition with GPU update (issue + 4024). + * Avoided issues with global reduction observed with md-vv + (issue 4031). + * Prohibited SETTLE interactions for atoms with perturbed masses + (issue 3959). + * Rerun now writes pull output correctly (issue 4043). + * Fixes for ``gmx`` tools. + * Fix incorrect behaviour with single residue chains in pdb2gmx + (issue 4029). + * Fix grompp check for position restraints with absolute + reference (issue 3996). + * Fix error when using VMD plugin (issue 3055). + * Fix file permissions with ``gmx solvate`` and ``gmx genion`` + (issue 4040). + * Fixes that affect portability. + * Support for Intel oneAPI compiler 2021.2. + * Fixed compiler infinity math and MKL flags. + * Fix Apple OpenCL build (issue 4008). + * Fixed compilation issue with GCC 11 (issue 4039). + * Fix bond type in GROMOS force fields (issue 3995). + * Allow PME on CPU in runs with domain decomposition and GPU + update (issue 4035). +- Turn SKIP_RPATH=OFF and SKIP_INSTALL_RPATH=ON instead; skipping + rpath use entirely causes linking issues with tests, but we + still want to disable rpaths for the installed libs of course. +- Rename %{name}-bash to %{name}-bash-completion in keeping with + naming convention followed by other packages. +- Add lapack-devel to BuildRequires to use system versions of blas + and lapack. +- CMake 3.13 or higher is required; adapt BuildRequires + accordingly. +- Disable testing for i586: doesn't work with gmock. +- Adapt to updated cmake options and drop no longer applicable + ones. + +------------------------------------------------------------------- Old: ---- gromacs-2019.6.tar.gz manual-2019.6.pdf regressiontests-2019.6.tar.gz New: ---- gromacs-2021.2.tar.gz manual-2021.2.pdf regressiontests-2021.2.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ gromacs.spec ++++++ --- /var/tmp/diff_new_pack.OO9Y9F/_old 2021-07-03 20:50:50.120774943 +0200 +++ /var/tmp/diff_new_pack.OO9Y9F/_new 2021-07-03 20:50:50.120774943 +0200 @@ -1,7 +1,7 @@ # # spec file for package gromacs # -# Copyright (c) 2020 SUSE LLC +# Copyright (c) 2021 SUSE LLC # Copyright (c) 2015-2019 Christoph Junghans <[email protected]> # # All modifications and additions to the file contributed by third parties @@ -35,23 +35,24 @@ %endif Name: gromacs -Version: 2019.6 +Version: 2021.2 Release: 0 %define uversion %{version} %define sover 4 Summary: Molecular Dynamics Package -License: GPL-2.0-or-later AND Apache-2.0 +License: Apache-2.0 AND GPL-2.0-or-later Group: Productivity/Scientific/Chemistry URL: http://www.gromacs.org 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 +Source2: ftp://ftp.gromacs.org/regressiontests/regressiontests-%{uversion}.tar.gz BuildRequires: %{mpiver} BuildRequires: %{mpiver}-devel -BuildRequires: cmake >= 2.8.8 +BuildRequires: cmake >= 3.13.0 BuildRequires: fdupes BuildRequires: gcc-c++ +BuildRequires: lapack-devel BuildRequires: ocl-icd-devel BuildRequires: opencl-headers BuildRequires: pkg-config @@ -92,14 +93,16 @@ This package contains libraries for Gromacs -%package bash +%package bash-completion Summary: Bash completion for Gromacs Group: Productivity/Other Requires: %{name} = %{version}-%{release} Requires: bash-completion BuildArch: noarch +Provides: %{name}-bash = %{version} +Obsoletes: %{name}-bash < %{version} -%description bash +%description bash-completion 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 @@ -157,33 +160,29 @@ %endif mkdir nompi cd nompi -# note about rpath -# gromacs' cmake has too much rpath auto-magic, just -# force to skip it (CMAKE_SKIP_RPATH=1) and use -# LD_LIBRARY_PATH for checks below # regression are currently broken on i686, https://redmine.gromacs.org/issues/2584 # and cannot be used with GMX_BUILD_MDRUN_ONLY=ON -%{cmake} \ +%cmake \ -DCMAKE_INSTALL_PREFIX=%{_prefix} \ -DCMAKE_VERBOSE_MAKEFILE=TRUE \ -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_C_FLAGS_RELEASE:STRING="%{optflags} -fno-strict-aliasing" \ -DCMAKE_CXX_FLAGS_RELEASE:STRING="%{optflags}" \ - -DCMAKE_SKIP_RPATH=1 \ + -DCMAKE_SKIP_RPATH=OFF \ + -DCMAKE_SKIP_INSTALL_RPATH=ON \ -DGMX_SIMD=%{acce} \ -DGMX_MPI=OFF \ -DGMX_THREAD_MPI=ON \ %ifarch x86_64 - -DGMX_GPU=ON -DGMX_USE_OPENCL=ON \ + -DGMX_GPU=OpenCL \ %endif - -DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \ -DGMX_OPENMP=ON \ %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_jobs + ../../ +%cmake_build cd ../.. mkdir %{mpiver} @@ -194,18 +193,18 @@ -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_C_FLAGS_RELEASE:STRING="%{optflags} -fno-strict-aliasing" \ -DCMAKE_CXX_FLAGS_RELEASE:STRING="%{optflags}" \ - -DCMAKE_SKIP_RPATH=1 \ + -DCMAKE_SKIP_RPATH=OFF \ + -DCMAKE_SKIP_INSTALL_RPATH=ON \ -DGMX_SIMD=%{acce} \ -DGMX_BUILD_MDRUN_ONLY=ON \ -DBUILD_SHARED_LIBS=OFF \ -DGMX_MPI=ON \ %ifarch x86_64 - -DGMX_GPU=ON -DGMX_USE_OPENCL=ON \ + -DGMX_GPU=OpenCL \ %endif - -DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \ -DGMX_OPENMP=ON \ - -DGMX_LIB_INSTALL_DIR=%{_lib} ../../ -%make_jobs + ../../ +%cmake_build %install cd nompi @@ -228,16 +227,16 @@ %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/%{mpiver}/%{_lib}' make -C %{mpiver}/build %{?_smp_mflags} check +# gmock based tests don't work on i586 +%ifnarch s390x i586 +%make_build -C nompi/build check +%make_build -C %{mpiver}/build check %endif %post -n libgromacs%sover -p /sbin/ldconfig %postun -n libgromacs%sover -p /sbin/ldconfig %files -%defattr(-,root,root,-) %{_bindir}/gmx %{_bindir}/*.pl %dir %{_datadir}/gromacs @@ -250,24 +249,21 @@ %{_mandir}/man1/* %files -n libgromacs%sover -%defattr(-,root,root,-) %{_libdir}/lib*.so.* %files doc -%defattr(-,root,root,-) %doc %{_datadir}/gromacs/*.pdf %doc %{_datadir}/gromacs/README* %doc %{_datadir}/gromacs/COPYING %files %{mpiver} -%defattr(-,root,root,-) %{_bindir}/*_mpi %files devel -%defattr(-,root,root) -%{_datadir}/gromacs/template %{_datadir}/cmake %{_includedir}/gromacs/ +%{_includedir}/gmxapi/ +%{_includedir}/nblib/ %{_libdir}/*.so %{_libdir}/pkgconfig/* %ifarch x86_64 @@ -276,8 +272,7 @@ %{_datadir}/gromacs/opencl/gromacs/*/*/*.h %endif -%files bash -%defattr(-,root,root,-) +%files bash-completion %dir %{_datadir}/bash_completion.d %{_datadir}/bash_completion.d/gromacs ++++++ gromacs-2019.6.tar.gz -> gromacs-2021.2.tar.gz ++++++ /work/SRC/openSUSE:Factory/gromacs/gromacs-2019.6.tar.gz /work/SRC/openSUSE:Factory/.gromacs.new.2625/gromacs-2021.2.tar.gz differ: char 5, line 1 ++++++ manual-2019.6.pdf -> manual-2021.2.pdf ++++++ (binary differes) ++++++ regressiontests-2019.6.tar.gz -> regressiontests-2021.2.tar.gz ++++++ /work/SRC/openSUSE:Factory/gromacs/regressiontests-2019.6.tar.gz /work/SRC/openSUSE:Factory/.gromacs.new.2625/regressiontests-2021.2.tar.gz differ: char 12, line 1
