Accepting request 1275015 from science

OBS-URL: https://build.opensuse.org/request/show/1275015
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/lammps?expand=0&rev=25

lammps-allow-system-gtest.patch

@@ -0,0 +1,58 @@
+---
+ unittest/CMakeLists.txt |   41 +++++++++++++++++++++++++----------------
+ 1 file changed, 25 insertions(+), 16 deletions(-)
+
+Index: lammps-stable_29Aug2024_update2/unittest/CMakeLists.txt
+===================================================================
+--- lammps-stable_29Aug2024_update2.orig/unittest/CMakeLists.txt
++++ lammps-stable_29Aug2024_update2/unittest/CMakeLists.txt
+@@ -9,24 +9,33 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "GNU"
+   message(FATAL_ERROR "Need GNU C++ compiler version 6.x or later for unit testing")
+ endif()
+ 
+-message(STATUS "Downloading and building googletest framework")
+-set(GTEST_URL "https://github.com/google/googletest/archive/release-1.12.1.tar.gz" CACHE STRING "URL of googletest source")
+-set(GTEST_MD5 "e82199374acdfda3f425331028eb4e2a" CACHE STRING "MD5 sum for googletest source")
+-mark_as_advanced(GTEST_URL)
+-mark_as_advanced(GTEST_MD5)
+-set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
++set(EXTERNAL_GTEST OFF CACHE BOOL "Use system gtest")
++if (EXTERNAL_GTEST)
++  find_package(GTest REQUIRED)
++  add_library(GTest::GTest ALIAS GTest::gtest)
++  add_library(GTest::GMock ALIAS GTest::gmock)
++  add_library(GTest::GTestMain ALIAS GTest::gtest_main)
++  add_library(GTest::GMockMain ALIAS GTest::gmock_main)
++else()
++  message(STATUS "Downloading and building googletest framework")
++  set(GTEST_URL "https://github.com/google/googletest/archive/release-1.12.1.tar.gz" CACHE STRING "URL of googletest source")
++  set(GTEST_MD5 "e82199374acdfda3f425331028eb4e2a" CACHE STRING "MD5 sum for googletest source")
++  mark_as_advanced(GTEST_URL)
++  mark_as_advanced(GTEST_MD5)
++  set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
+ 
+-include(ExternalCMakeProject)
+-if(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
+-  set(cxx_strict_flags "-Wno-error -Wno-unused-command-line-argument")
++  include(ExternalCMakeProject)
++  if(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
++    set(cxx_strict_flags "-Wno-error -Wno-unused-command-line-argument")
++  endif()
++  set(INSTALL_GTEST OFF CACHE BOOL "" FORCE)
++  set(INSTALL_GMOCK OFF CACHE BOOL "" FORCE)
++  ExternalCMakeProject(googletest ${GTEST_URL} ${GTEST_MD5} googletest . "")
++  add_library(GTest::GTest ALIAS gtest)
++  add_library(GTest::GMock ALIAS gmock)
++  add_library(GTest::GTestMain ALIAS gtest_main)
++  add_library(GTest::GMockMain ALIAS gmock_main)
+ endif()
+-set(INSTALL_GTEST OFF CACHE BOOL "" FORCE)
+-set(INSTALL_GMOCK OFF CACHE BOOL "" FORCE)
+-ExternalCMakeProject(googletest ${GTEST_URL} ${GTEST_MD5} googletest . "")
+-add_library(GTest::GTest ALIAS gtest)
+-add_library(GTest::GMock ALIAS gmock)
+-add_library(GTest::GTestMain ALIAS gtest_main)
+-add_library(GTest::GMockMain ALIAS gmock_main)
+ 
+ option(SKIP_DEATH_TESTS "Do not run 'death tests' to reduce false positives in valgrind" OFF)
+ mark_as_advanced(SKIP_DEATH_TESTS)

lammps-patch_29Oct2020.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:3d347f6b512bc360505019d1c6183c969a2e1da402e31a1e26577daf5e419d95
-size 127070542

lammps-stable_29Aug2024_update2.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f8ca3f021a819ced8658055f7750e235c51b4937ddb621cf1bd7bee08e0b6266
+size 142223423

lammps.changes

@@ -1,3 +1,40 @@
+-------------------------------------------------------------------
+Tue May  6 08:04:18 UTC 2025 - Atri Bhattacharya <badshah400@gmail.com>
+
+- Do not let minor tolerance issues in tests on non-x86_64 archs
+  abort builds (gh#lammps/lammps#2383, gh#lammps/lammps#2978).
+
+-------------------------------------------------------------------
+Mon May  5 16:47:47 UTC 2025 - Atri Bhattacharya <badshah400@gmail.com>
+
+- Adapt package version to reflect upstream releases; example:
+  the current version 20240829.02 reflects upstream's (weirdly but
+  consistently named) stable_29Aug2024_update2 tag.
+- Implement python packaging using python rpm macros (for now
+  default python3-* only).
+- Enable a few non-expensive modules (in terms of build
+  dependencies): compress (depends on gzip, libzstd), manybody,
+  molecule (needed for python tests), extra-molecule, and lepton.
+- Drop a few unnecessary build dependencies: intel-opencl-devel,
+  armnn-opencl-devel.
+- Add lammps-allow-system-gtest.patch to allow using system
+  installed gtest/gmock for tests. Note that upstream seems to be
+  reticent about this (gh#lammps/lammps#3540), but we have no
+  choice if we want to run tests. So, mark our patch as
+  PATCH-FEATURE-OPENSUSE for now.
+- Use pkgconfig based BuildRequires wherever possible.
+- Use ninja for build.
+- Define and use macro for shared library name consistency.
+- Disable MPI on i586 to resolve builds (missing
+  openmpi-macros-devel).
+
+-------------------------------------------------------------------
+Tue Mar 18 16:37:36 UTC 2025 - Matej Cepl <mcepl@cepl.eu>
+
+- Update to stable_29Aug2024_update2:
+  * Too many changes to list, see
+    <https://github.com/lammps/lammps/releases/tag/stable_29Aug2024>
+
 -------------------------------------------------------------------
 Mon May 15 01:02:12 UTC 2023 - Christoph Junghans <junghans@votca.org>
 

lammps.spec

@@ -1,7 +1,7 @@
 #
 # spec file for package lammps
 #
-# Copyright (c) 2022 SUSE LLC
+# Copyright (c) 2025 SUSE LLC
 # Copyright (c) 2017-2020 Christoph Junghans
 #
 # All modifications and additions to the file contributed by third parties
@@ -17,40 +17,75 @@
 #
 
 
+# kokkos >= 4.3.01 required
+%bcond_with kokkos
+%bcond_without test
+%ifarch %ix86
+# Missing openmpi-macros-devel on i586
+%bcond_with mpi
+%else
+%bcond_without mpi
+%endif
+%define shlib lib%{name}0
+%define pythons python3
+%define __builder ninja
+%define         uversion stable_29Aug2024_update2
 Name:           lammps
-Version:        20201029
+Version:        20240829.02
 Release:        0
-%define         uversion patch_29Oct2020
 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
+Source0:        https://github.com/lammps/lammps/archive/refs/tags/%{uversion}.tar.gz#/%{name}-%{uversion}.tar.gz
-Source1:        https://github.com/google/googletest/archive/release-1.10.0.tar.gz
+# PATCH-FEATURE-OPENSUSE lammps-allow-system-gtest.patch badshah400@gmail.com -- Look for system installed gtest/gmock before trying to download
+Patch0:         lammps-allow-system-gtest.patch
+BuildRequires:  clang
 BuildRequires:  cmake
-BuildRequires:  fftw3-devel
+BuildRequires:  fdupes
 BuildRequires:  gcc-c++
 BuildRequires:  gcc-fortran
-BuildRequires:  gsl-devel
+BuildRequires:  gzip
 BuildRequires:  kim-api-devel >= 2.1
-BuildRequires:  openmpi-macros-devel
+BuildRequires:  python3-build
-BuildRequires:  readline-devel
+BuildRequires:  python3-pip
-# for testing
+BuildRequires:  python3-setuptools
-BuildRequires:  kim-api-examples
+BuildRequires:  python3-wheel
-BuildRequires:  libjpeg-devel
-BuildRequires:  libpng-devel
-BuildRequires:  ocl-icd-devel
-BuildRequires:  opencl-headers
-BuildRequires:  python3-devel
 BuildRequires:  voro++-devel
-BuildRequires:  zlib-devel
+BuildRequires:  pkgconfig(OpenCL)
-# disable kokkos support until
+BuildRequires:  pkgconfig(OpenCL-CLHPP)
-# kokkos-4 is supported
+BuildRequires:  pkgconfig(OpenCL-Headers)
-# ifnarch ppc64 %ix86 %{arm}
+BuildRequires:  pkgconfig(clBLAS)
-# global         with_kokkos 1
+BuildRequires:  pkgconfig(fftw3)
-# BuildRequires:  kokkos-devel >= 3.2
+BuildRequires:  pkgconfig(gsl)
-# endif
+BuildRequires:  pkgconfig(lapack)
+BuildRequires:  pkgconfig(libjpeg)
+BuildRequires:  pkgconfig(libpng)
+BuildRequires:  pkgconfig(libzstd)
+BuildRequires:  pkgconfig(ocl-icd)
+BuildRequires:  pkgconfig(python3)
+BuildRequires:  pkgconfig(readline)
+BuildRequires:  pkgconfig(tbb)
+BuildRequires:  pkgconfig(yaml-0.1)
+BuildRequires:  pkgconfig(zlib)
 Requires:       %{name}-data
+%if "%{?__builder}" == "ninja"
+BuildRequires:  ninja
+%endif
+%if %{with kokkos}
+BuildRequires:  kokkos-devel >= 3.2
+%endif
+%if %{with mpi}
+BuildRequires:  openmpi-macros-devel
+%endif
+%if %{with test}
+BuildRequires:  kim-api-examples
+BuildRequires:  valgrind
+BuildRequires:  pkgconfig(gmock)
+BuildRequires:  pkgconfig(gmock_main)
+BuildRequires:  pkgconfig(gtest)
+BuildRequires:  pkgconfig(gtest_main)
+%endif
 
 %description
 LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale
@@ -65,8 +100,8 @@ LAMMPS runs on single processors or in parallel using message-passing
 techniques and a spatial-decomposition of the simulation domain. The code is
 designed to be easy to modify or extend with new functionality.
 
-%package -n liblammps0
+%package -n %{shlib}
-Summary:        LAMMPS library
+Summary:        A molecular dynamics simulator library
 Group:          System/Libraries
 
 %description -n liblammps0
@@ -88,7 +123,7 @@ This package contains the library of LAMMPS package.
 Summary:        Development headers and libraries for LAMMPS
 Group:          Development/Libraries/C and C++
 Requires:       %{name} = %{version}
-Requires:       liblammps0 = %{version}
+Requires:       %{shlib} = %{version}
 
 %description devel
 LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale
@@ -105,15 +140,16 @@ designed to be easy to modify or extend with new functionality.
 
 This package contains development headers and libraries for LAMMPS.
 
-%package -n python3-%{name}
+%package -n %{pythons}-%{name}
 Summary:        LAMMPS python module
 Group:          Development/Languages/Python
-Requires:       liblammps0 = %{version}
+Requires:       %{shlib} = %{version}
+BuildArch:      noarch
 # File conflict, old package contained python3 module
 Conflicts:      python-%{name} <= %{version}
 Provides:       python-%{name}:%{python3_sitearch}/%{name}.py
 
-%description -n python3-%{name}
+%description -n %{pythons}-%{name}
 LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale
 Atomic/Molecular Massively Parallel Simulator.
 
@@ -149,64 +185,96 @@ designed to be easy to modify or extend with new functionality.
 This subpackage contains LAMMPS's potential files
 
 %prep
-%setup -a 1 -q -n %{name}-%{uversion}
+%autosetup -p1 -n %{name}-%{uversion}
 
 %build
+%if %{with mpi}
 %setup_openmpi
+%endif
 
-%{cmake} \
+pushd cmake
-  -C ../cmake/presets/all_on.cmake \
+%cmake \
-  -C ../cmake/presets/nolib.cmake \
+  -DCMAKE_INSTALL_SYSCONFDIR=%{_sysconfdir} \
   -DCMAKE_TUNE_FLAGS='%{?tune_flags}' \
   -DBUILD_TOOLS=ON \
   -DBUILD_LAMMPS_SHELL=$(pkg-config readline && echo ON) \
+  -DBUILD_MPI=%{?with_mpi:ON}%{!?with_mpi:OFF} \
   -DBUILD_OMP=ON \
-  %{?with_kokkos:-DPKG_KOKKOS=ON -DEXTERNAL_KOKKOS=ON} \
+  -DDOWNLOAD_POTENTIALS=OFF \
-  -DBUILD_MPI=ON \
+  -DENABLE_TESTING:BOOL=%{?with_test:ON}%{!?with_test:OFF} \
-  -DPKG_PYTHON=ON \
+  -DEXTERNAL_GTEST:BOOL=ON \
-  -DPKG_KIM=ON \
-  -DPKG_VORONOI=ON \
-  -DPKG_GPU=ON -DGPU_API=OpenCL \
   -DFFT=FFTW3 \
-  -DPYTHON_INSTDIR=%{python3_sitearch} \
+  -DGPU_API=OpenCL \
-  -DCMAKE_INSTALL_SYSCONFDIR=/etc \
+  -DPKG_COMPRESS=ON \
-%ifnarch x86_64 %ix86
+  -DPKG_EXTRA-MOLECULE=ON \
-  -DPKG_USER-INTEL=OFF \
+  -DPKG_GPU=ON \
-%endif
+  -DPKG_KIM=ON \
-  -DENABLE_TESTING=ON \
+  -DPKG_KSPACE=OFF \
-  -DGTEST_URL=%{S:1} \
+  -DPKG_LEPTON=ON \
-  ../cmake
+  -DPKG_MANYBODY=ON \
+  -DPKG_MOLECULE=ON \
+  -DPKG_PHONON=OFF \
+  -DPKG_PYTHON=ON \
+  -DPKG_VORONOI=ON \
+  -DPYTHON_EXECUTABLE=%{_bindir}/python%{python3_version} \
+  -DUSE_STATIC_OPENCL_LOADER=OFF \
+  -DUSE_SPGLIB:BOOL=OFF \
+  %{?with_kokkos:-DPKG_KOKKOS=ON -DEXTERNAL_KOKKOS=ON} \
+%{nil}
 %cmake_build
+popd
+cd python
+%pyproject_wheel
 
 %install
+pushd cmake
 %cmake_install
-rm -rf %{buildroot}%{_datadir}/{applications,icons}/
+popd
 
+pushd python
+%pyproject_install
+popd
+
+%fdupes %{buildroot}%{_datadir}/%{name}/
+%fdupes %{buildroot}%{python3_sitelib}/%{name}/
+
+%if %{with test}
 %check
+%if %{with mpi}
 %setup_openmpi
+%endif
 
-# https://github.com/lammps/lammps/issues/2383, inject -msse2 on %ix86 to make test pass
+pushd cmake
-%ifarch %ix86
+# Do not cause failing tests on non-x86_64 archs to abort builds
-%ctest --exclude-regex 'AtomStyle|Fortran' || true
+# as these are due to minor numerical tolerance differences which
-%ctest --tests-regex 'AtomStyle|Fortran' || true
+# upstream does not intend to fix. See, for instance,
+# * https://github.com/lammps/lammps/issues/2383
+# * https://github.com/lammps/lammps/issues/2978
+%ifnarch x86_64
+%ctest || true
 %else
 %ctest
 %endif
+popd
 
-%post -n liblammps0 -p /sbin/ldconfig
+%endif
-%postun -n liblammps0 -p /sbin/ldconfig
+
+%ldconfig_scriptlets -n %{shlib}
 
 %files
 %doc README
 %license LICENSE
 %{_bindir}/l{mp,ammps}*
-%{_mandir}/man1/lmp.1.*
+%{_mandir}/man1/lmp.1%{?ext_man}
 %{_bindir}/msi2lmp
-%{_mandir}/man1/msi2lmp.1.*
+%{_mandir}/man1/msi2lmp.1%{?ext_man}
 %{_bindir}/binary2txt
 %{_bindir}/chain.x
+%{_bindir}/micelle2d.x
+%{_bindir}/phana
+%{_bindir}/stl_bin2txt
 
-%files -n liblammps0
+%files -n %{shlib}
 %{_libdir}/liblammps.so.*
 
 %files devel
@@ -216,12 +284,13 @@ rm -rf %{buildroot}%{_datadir}/{applications,icons}/
 %{_libdir}/pkgconfig/liblammps.pc
 %{_libdir}/cmake/LAMMPS
 
-%files -n python3-%{name}
-%{python3_sitearch}/%{name}.py
-
 %files data
 %license LICENSE
 %{_datadir}/%{name}
 %config %{_sysconfdir}/profile.d/lammps.*
 
+%files -n %{pythons}-%{name}
+%{python3_sitelib}/%{name}/
+%{python3_sitelib}/%{name}-*.*-info
+
 %changelog

release-1.10.0.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:9dc9157a9a1551ec7a7e43daea9a694a0bb5fb8bec81235d8a1e6ef64c716dcb
-size 904349