diff --git a/espresso-4.0.2.tar.gz b/espresso-4.0.2.tar.gz deleted file mode 100644 index 3809f76..0000000 --- a/espresso-4.0.2.tar.gz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:89878ab44a58e90b69d56368e961b8ca13d9307f8d4b282967a1f3071a62c740 -size 25826263 diff --git a/espresso-4.1.1.tar.gz b/espresso-4.1.1.tar.gz new file mode 100644 index 0000000..28efde2 --- /dev/null +++ b/espresso-4.1.1.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:61f19f17469522d4aa480ff5254217668ba713589c6b74576e6305920d688f90 +size 22915050 diff --git a/python3-espressomd.changes b/python3-espressomd.changes index 95e96ab..741124f 100644 --- a/python3-espressomd.changes +++ b/python3-espressomd.changes @@ -1,3 +1,31 @@ +------------------------------------------------------------------- +Fri Nov 15 16:24:45 UTC 2019 - Christoph Junghans + +- Version bump to 4.1.1 + * Restore checkpointing mechanism for the steepest descent and NPT + integrators, LB and NPT thermostats (#3245) + * Increase the minimum MPI version to 3.0; OpenMPI versions 1.6.5 and + lower are no longer supported (#3236) + * Fix `Integrator.set_isotropic_npt()`: remove the silent conversion of + the incorrect input parameter `direction=[0,0,0]` to `[1,1,1]` in the + core; the function now throws an exception for fixed-volume boxes; + this change is unlikely to break pypresso scripts since not providing + a value to `direction` or providing `[1,1,1]` were the two standard + ways to set up a box with all directions allowed to rescale (#3253) + * Fix `Integrator.set_vv()`: this function failed to set the velocity + Verlet integrator if the NPT integrator was active; this is now + resolved (#3274) + * Fix the random segmentation fault triggered by the removal of a + particle with a bond or a virtual site relationship to another + particle (#3288) + * Fix `system.part.writevtk()`: the function now writes down all + particles when using `types="all"` (#3290) + * Disable the deprecated and broken ENGINE shear torque calculation + feature; the feature will be completely removed from the core in + the upcoming 4.2 release (#3277) + * Fix unit conversion for the LB fluid viscosity (#3287) + + ------------------------------------------------------------------- Tue Apr 30 18:06:33 UTC 2019 - Christoph Junghans diff --git a/python3-espressomd.spec b/python3-espressomd.spec index c05bc2c..4cfc51f 100644 --- a/python3-espressomd.spec +++ b/python3-espressomd.spec @@ -16,23 +16,25 @@ # Please submit bugfixes or comments via https://bugs.opensuse.org/ # - -%define mpi_implem openmpi2 -%ifarch ppc64 -%define mpi_implem openmpi +# Build with OpenMPI +%if 0%{?sle_version} == 0 +%define mpiver openmpi2 +%else +%if 0%{?sle_version} <= 120300 +%define mpiver openmpi +%else + %if 0%{?sle_version} <= 150000 + %define mpiver openmpi2 + %else + %define mpiver openmpi3 + %endif %endif -%if 0%{?sle_version} == 120300 && 0%{?is_opensuse} -%define mpi_implem openmpi -%endif -%if 0%{?sle_version} == 120400 && !0%{?is_opensuse} -%define mpi_implem openmpi %endif %define pkgname espresso %define modname %{pkgname}md -%define sonum 4 Name: python3-%{modname} -Version: 4.0.2 +Version: 4.1.1 Release: 0 Summary: Parallel simulation software for soft matter research License: GPL-3.0-or-later @@ -45,7 +47,7 @@ BuildRequires: gcc-c++ # Currently libboost_mpi-devel and hdf5 use different mpi versions # BuildRequires: hdf5-devel BuildRequires: gsl-devel -BuildRequires: %{mpi_implem}-devel +BuildRequires: %{mpiver}-devel BuildRequires: python3-Cython BuildRequires: python3-devel BuildRequires: python3-numpy-devel @@ -57,6 +59,7 @@ BuildRequires: libboost_test-devel %else BuildRequires: boost-devel %endif +Obsoletes: libEspresso4 %description ESPResSo is a highly versatile software package for performing and analyzing @@ -66,18 +69,11 @@ physics, chemistry and molecular biology. It can be used to simulate systems such as polymers, liquid crystals, colloids, ferrofluids and biological systems, for example DNA and lipid membranes. -%package -n libEspresso%{sonum} -Summary: Shared libraries for ESPResSo -Group: System/Libraries - -%description -n libEspresso%{sonum} -This package provides shared libraries for ESPResSo. - %prep %setup -q -n %{pkgname} %build -source %{_libdir}/mpi/gcc/%{mpi_implem}/bin/mpivars.sh +source %{_libdir}/mpi/gcc/%{mpiver}/bin/mpivars.sh # overwrite .so linker flags on SUSE distros: drop --no-undefined # we don't install {i,}pypresso scripts as they aren't needed when installing in /usr @@ -98,29 +94,15 @@ find %{buildroot}%{_prefix} -name "gen_pxiconfig" -exec chmod +x {} \; rm -f %{buildroot}%{_libdir}/lib*.so %check -LD_LIBRARY_PATH='%{buildroot}/%{_libdir}::%{_libdir}/mpi/gcc/%{mpi_implem}/%{_lib}' make -C build check CTEST_OUTPUT_ON_FAILURE=1 %{?testargs:%{testargs}} - -%post -n libEspresso%{sonum} -p /sbin/ldconfig -%postun -n libEspresso%{sonum} -p /sbin/ldconfig +# https://github.com/espressomd/espresso/issues/3315 +%ifarch i586 +%define testargs ARGS='-E \\(MpiCallbacks_test\\|matrix_vector_product\\|collision_detection\\)' +%endif +LD_LIBRARY_PATH='%{buildroot}/%{python3_sitearch}/espressomd::%{_libdir}/mpi/gcc/%{mpiver}/%{_lib}' make -C build check CTEST_OUTPUT_ON_FAILURE=1 %{?testargs:%{testargs}} %files %license COPYING %doc README AUTHORS NEWS ChangeLog %{python3_sitearch}/espressomd -%files -n libEspresso%{sonum} -%license COPYING -%{_libdir}/libEspressoCore.so.%{sonum} -%{_libdir}/libActor.so.%{sonum} -%{_libdir}/libImmersedBoundary.so.%{sonum} -%{_libdir}/libObjectInFluid.so.%{sonum} -%{_libdir}/libAccumulators.so.%{sonum} -%{_libdir}/libConstraints.so.%{sonum} -%{_libdir}/libEspressoConfig.so.%{sonum} -%{_libdir}/libEspressoScriptInterface.so.%{sonum} -%{_libdir}/libObservables.so.%{sonum} -%{_libdir}/libShapes.so.%{sonum} -%{_libdir}/libVirtualSites.so.%{sonum} -%{_libdir}/libcluster_analysis.so.%{sonum} - %changelog \ No newline at end of file