Hello community, here is the log from the commit of package lammps for openSUSE:Factory checked in at 2020-06-11 14:49:16 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/lammps (Old) and /work/SRC/openSUSE:Factory/.lammps.new.3606 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "lammps" Thu Jun 11 14:49:16 2020 rev:16 rq:805357 version:20200505 Changes: -------- --- /work/SRC/openSUSE:Factory/lammps/lammps.changes 2020-03-16 10:19:33.379617003 +0100 +++ /work/SRC/openSUSE:Factory/.lammps.new.3606/lammps.changes 2020-06-11 14:50:03.850349089 +0200 @@ -1,0 +2,56 @@ +Wed May 13 13:42:58 UTC 2020 - Christoph Junghans <[email protected]> + +- fix build on ppc64le by enabling gnu extensions, see + [gh#lammps/lammps#2079], this is a bug in older version of the + ocl package, compare [GCC#58241]. + +------------------------------------------------------------------- +Sun May 10 16:59:26 UTC 2020 - Christoph Junghans <[email protected]> + +- gcc flags an issue on leap 15.1 that is a false positive, see + [gh#lammps/lammps#2078], so disabling lammps custom no optimzation + flags, using disable_noopt.patch + +------------------------------------------------------------------- +Wed May 6 14:54:14 UTC 2020 - Christoph Junghans <[email protected]> + +- bump version to 20200505 (patch) + - update of the bundled Kokkos library to version 3.1 (Stan + Moore and the Kokkos developers, SNL) [gh#lammps/lammps#2004], + [gh#lammps/lammps#2054] + - new Kokkos styles compute orientorder/atom and coord/atom and + some related bugfixes/improvements (Stan Moore, SNL) + [gh#lammps/lammps#1895], [gh#lammps/lammps#1902], + [gh#lammps/lammps#1906], [gh#lammps/lammps#2033] + - new fix accelerate/cos and compute viscosity/cos in USER-MISC + as yet another method to compute viscosity (Zheng Gong, École + normale supérieure de Lyon) [gh#lammps/lammps#2019] + - update of the polymorphic pair style with bug fixes and a new + feature (Xiaoweng Zhou, SNL) [gh#lammps/lammps#2000] + - added option to create a dummy fix as a placeholder early in + an input to guarantee placement at the top of the list of + fixes. (Steve Plimpton, SNL) [gh#lammps/lammps#1760] + - update to fix bond/react to allow using equal style variables + a probability input (Wolfgang Verestek, U Stuttgart) + [gh#lammps/lammps#2013] + - small update to internal commands in kim_interactions to + improve KIM simulator model handling (Ronald Miller Carleton + U, Ryan S. Elliott U Minn), [gh#lammps/lammps#2014] + - many small fixes and updates to source code (mainly for the + KOKKOS package), cmake scripts, and documentation to address + issues with recent changes and minor long-standing issues. + (multiple authors) [gh#lammps/lammps#2003], + [gh#lammps/lammps#2006], [gh#lammps/lammps#2010], + [gh#lammps/lammps#2015], [gh#lammps/lammps#2022], + [gh#lammps/lammps#2023], [gh#lammps/lammps#2026], + [gh#lammps/lammps#2027], [gh#lammps/lammps#2030], + [gh#lammps/lammps#2032], [gh#lammps/lammps#2035], + [gh#lammps/lammps#2036], [gh#lammps/lammps#2041], + [gh#lammps/lammps#2043], [gh#lammps/lammps#2044], + [gh#lammps/lammps#2045], [gh#lammps/lammps#2046], + [gh#lammps/lammps#2047], [gh#lammps/lammps#2048], + [gh#lammps/lammps#2049], [gh#lammps/lammps#2051], + [gh#lammps/lammps#2053], [gh#lammps/lammps#2055] +- enable kokkos and OpenMP + +------------------------------------------------------------------- Old: ---- lammps-stable_3Mar2020.tar.gz lammps-testing-stable_3Mar2020.tar.gz New: ---- disable_noopt.patch lammps-patch_5May2020.tar.gz lammps-testing-patch_5May2020.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ lammps.spec ++++++ --- /var/tmp/diff_new_pack.HDe0kN/_old 2020-06-11 14:50:08.254363224 +0200 +++ /var/tmp/diff_new_pack.HDe0kN/_new 2020-06-11 14:50:08.258363237 +0200 @@ -2,7 +2,7 @@ # spec file for package lammps # # Copyright (c) 2020 SUSE LLC -# Copyright (c) 2017-2019 Christoph Junghans +# Copyright (c) 2017-2020 Christoph Junghans # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -33,15 +33,17 @@ %endif Name: lammps -Version: 20200303 +Version: 20200505 Release: 0 -%define uversion stable_3Mar2020 +%define uversion patch_5May2020 Summary: Molecular Dynamics Simulator License: GPL-2.0-only AND GPL-3.0-or-later Group: Productivity/Scientific/Chemistry URL: https://lammps.sandia.gov Source0: https://github.com/lammps/lammps/archive/%{uversion}.tar.gz#/%{name}-%{uversion}.tar.gz Source1: https://github.com/lammps/lammps-testing/archive/%{uversion}.tar.gz#/%{name}-testing-%{uversion}.tar.gz +# PATCH-FIX-UPSTREAM disable_noopt.patch, gcc flags a false positive [gh#lammps/lammps#2078] +Patch0: disable_noopt.patch BuildRequires: %{mpiver} BuildRequires: %{mpiver}-devel BuildRequires: cmake @@ -58,6 +60,10 @@ BuildRequires: python-devel BuildRequires: voro++-devel BuildRequires: zlib-devel +%ifnarch ppc64 %ix86 +%global with_kokkos 1 +BuildRequires: kokkos-devel >= 3.1 +%endif Requires: %{name}-data BuildRoot: %{_tmppath}/%{name}-%{version}-build @@ -157,6 +163,12 @@ %prep %setup -a 1 -q -n %{name}-%{uversion} +%patch0 -p1 +# see [gh#lammps/lammps#2079], this is a bug in older version +# of the ocl package, compare [GCC#58241] +%ifarch ppc64le +sed -i '/CMAKE_CXX_EXTENSIONS/s/OFF/ON/' cmake/CMakeLists.txt +%endif %build source %{_libdir}/mpi/gcc/%{mpiver}/bin/mpivars.sh @@ -164,8 +176,11 @@ %{cmake} \ -C ../cmake/presets/all_on.cmake \ -C ../cmake/presets/nolib.cmake \ + -DCMAKE_Fortran_COMPILER="$(type -p gfortran)" \ -DBUILD_TOOLS=ON \ - -DBUILD_LIB=ON -DBUILD_MPI=ON -DPKG_PYTHON=ON \ + -DBUILD_OMP=ON \ + %{?with_kokkos:-DPKG_KOKKOS=ON -DEXTERNAL_KOKKOS=ON} \ + -DBUILD_MPI=ON -DPKG_PYTHON=ON \ -DPKG_KIM=ON -DENABLE_TESTING=ON -DPKG_VORONOI=ON \ -DPKG_GPU=ON -DGPU_API=OpenCL -DFFT=FFTW3 \ -DPYTHON_INSTDIR=%{python_sitearch} -DCMAKE_INSTALL_SYSCONFDIR=/etc \ @@ -173,19 +188,19 @@ -DPKG_USER-INTEL=OFF \ %endif -DLAMMPS_TESTING_SOURCE_DIR=$(echo $PWD/../lammps-testing-*) ../cmake -%make_jobs +%cmake_build %install %cmake_install %check -LD_LIBRARY_PATH='%{buildroot}/%{_libdir}:%{_libdir}/mpi/gcc/%{mpiver}/%{_lib}' make -C build %{?_smp_mflags} test CTEST_OUTPUT_ON_FAILURE=1 +export LD_LIBRARY_PATH='%{buildroot}%{_libdir}:%{_libdir}/mpi/gcc/%{mpiver}/%{_lib}' +%ctest %post -n liblammps0 -p /sbin/ldconfig %postun -n liblammps0 -p /sbin/ldconfig %files -%defattr(-,root,root) %doc README %license LICENSE %{_bindir}/lmp @@ -196,24 +211,19 @@ %{_bindir}/chain.x %files -n liblammps0 -%defattr(-,root,root,-) %{_libdir}/liblammps.so.* %files devel -%defattr(-,root,root) %license LICENSE %{_includedir}/%{name} %{_libdir}/liblammps.so %{_libdir}/pkgconfig/liblammps.pc -%dir %{_datadir}/cmake/Modules -%{_datadir}/cmake/Modules/FindLAMMPS.cmake +%{_libdir}/cmake/LAMMPS %files -n python-%{name} -%defattr(-,root,root,-) %{python_sitearch}/%{name}.py %files data -%defattr(-,root,root,-) %license LICENSE %{_datadir}/%{name} %config %{_sysconfdir}/profile.d/lammps.* ++++++ disable_noopt.patch ++++++ >From afd769314b67d9614e70d80c4e8fade41b367899 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer <[email protected]> Date: Sun, 10 May 2020 14:06:56 -0400 Subject: [PATCH] define _noopt macro with -D_FORTIFY_SOURCE to be empty to avoid false positives --- src/lmptype.h | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/src/lmptype.h b/src/lmptype.h index 5c19ab7483..1513fe5782 100644 --- a/src/lmptype.h +++ b/src/lmptype.h @@ -206,10 +206,13 @@ typedef int bigint; #define _noalias #endif -// declaration to turn off optimization for specific functions -// and avoid compiler warnings about variable tracking +// Declaration to turn off optimization for specific noncritical +// functions and avoid compiler warnings about variable tracking. +// Disable for broken -D_FORTIFY_SOURCE feature. -#if defined(__clang__) +#if defined(_FORTIFY_SOURCE) && (_FORTIFY_SOURCE > 0) +#define _noopt +#elif defined(__clang__) # define _noopt __attribute__((optnone)) #elif defined(__INTEL_COMPILER) # define _noopt
