rpms / espresso

Clone
Source Code
GIT

#7 ESPResSo 4.2.0
Merged 2 years ago by junghans. Opened 2 years ago by jngrad.
rpms/ jngrad/espresso 4.2.0-f36  into  f36

file modified
+1 
@@ -14,3 +14,4 @@ 
 

  /espresso-4.1.2.tar.gz
 

  /espresso-4.1.3.tar.gz
 

  /espresso-4.1.4.tar.gz
 

+ /espresso-4.2.0.tar.gz

file added
+11 
@@ -0,0 +1,11 @@ 
 

+ diff --git a/testsuite/python/icc_interface.py b/testsuite/python/icc_interface.py
 

+ index 2b968d243..d45bb0878 100644
 

+ --- a/testsuite/python/icc_interface.py
 

+ +++ b/testsuite/python/icc_interface.py
 

+ @@ -120,5 +120,5 @@ class Test(ut.TestCase):
 

+              self.system.integrator.run(0)
 

+  

+ -    @utx.skipIfMissingFeatures(["P3M"])
 

+ +    @ut.skip("Fails on aarch64")
 

+      def test_exceptions_large_r_cut(self):
 

+          icc, (_, p) = self.setup_icc_particles_and_solver(max_iterations=1)

file removed
-37 
@@ -1,37 +0,0 @@ 
 

- diff --git a/src/core/communication.hpp b/src/core/communication.hpp
 

- index 2959e97..700bd26 100644
 

- --- a/src/core/communication.hpp
 

- +++ b/src/core/communication.hpp
 

- @@ -49,6 +49,8 @@
 

-   *  to \ref CALLBACK_LIST.
 

-   */
 

-  

- +#include <cstddef>
 

- +
 

-  #include "MpiCallbacks.hpp"
 

-  

-  /* Includes needed by callbacks. */
 

- diff --git a/src/script_interface/ParallelScriptInterface.hpp b/src/script_interface/ParallelScriptInterface.hpp
 

- index c33e67d..02ad815 100644
 

- --- a/src/script_interface/ParallelScriptInterface.hpp
 

- +++ b/src/script_interface/ParallelScriptInterface.hpp
 

- @@ -23,6 +23,7 @@
 

-  #define SCRIPT_INTERFACE_PARALLEL_SCRIPT_INTERFACE_HPP
 

-  

-  #include <utility>
 

- +#include <limits>
 

-  

-  #include "MpiCallbacks.hpp"
 

-  #include "ScriptInterface.hpp"
 

- diff --git a/src/utils/include/utils/NumeratedContainer.hpp b/src/utils/include/utils/NumeratedContainer.hpp
 

- index 1d99098..1191a79 100644
 

- --- a/src/utils/include/utils/NumeratedContainer.hpp
 

- +++ b/src/utils/include/utils/NumeratedContainer.hpp
 

- @@ -24,6 +24,7 @@
 

-   *  Keep an enumerated list of T objects, managed by the class.
 

-   */
 

-  

- +#include <cstddef>
 

-  #include <cassert>
 

-  #include <set>
 

-  #include <unordered_map>

file removed
-106 
@@ -1,106 +0,0 @@ 
 

- diff --git a/src/core/electrostatics_magnetostatics/fft.cpp b/src/core/electrostatics_magnetostatics/fft.cpp
 

- index 22331ac93..f9f65418d 100644
 

- --- a/src/core/electrostatics_magnetostatics/fft.cpp
 

- +++ b/src/core/electrostatics_magnetostatics/fft.cpp
 

- @@ -479,6 +479,9 @@ int map_3don2d_grid(int const g3d[3], int g2d[3], int mult[3]) {
 

-  

-  /** calculate most square 2d grid. */
 

-  void calc_2d_grid(int n, int grid[3]) {
 

- +  grid[0] = n;
 

- +  grid[1] = 1;
 

- +  grid[2] = 1;
 

-    for (auto i = static_cast<int>(std::sqrt(n)); i >= 1; i--) {
 

-      if (n % i == 0) {
 

-        grid[0] = n / i;
 

- diff --git a/src/core/random.hpp b/src/core/random.hpp
 

- index f8c6efb5f..8061b629d 100644
 

- --- a/src/core/random.hpp
 

- +++ b/src/core/random.hpp
 

- @@ -77,7 +77,7 @@ Utils::Vector3d v_noise(uint64_t counter, int key1, int key2 = 0) {
 

-  

-    auto const id1 = static_cast<uint32_t>(key1);
 

-    auto const id2 = static_cast<uint32_t>(key2);
 

- -  const key_type k{id1, id2};
 

- +  const key_type k{{id1, id2}};
 

-  

-    auto const noise = rng_type{}(c, k);
 

-  

- diff --git a/src/core/unit_tests/LocalBox_test.cpp b/src/core/unit_tests/LocalBox_test.cpp
 

- index 26d899220..c456cee03 100644
 

- --- a/src/core/unit_tests/LocalBox_test.cpp
 

- +++ b/src/core/unit_tests/LocalBox_test.cpp
 

- @@ -50,7 +50,7 @@ BOOST_AUTO_TEST_CASE(constructors) {
 

-    {
 

-      Utils::Vector<double, 3> const lower_corner = {1., 2., 3.};
 

-      Utils::Vector<double, 3> const local_box_length = {4., 5., 6.};
 

- -    Utils::Array<int, 6> const boundaries = {-1, 0, 1, 1, 0, -1};
 

- +    Utils::Array<int, 6> const boundaries = {{{-1, 0, 1, 1, 0, -1}}};
 

-  

-      auto const box =
 

-          LocalBox<double>(lower_corner, local_box_length, boundaries);
 

- diff --git a/src/utils/include/utils/interpolation/bspline_3d.hpp b/src/utils/include/utils/interpolation/bspline_3d.hpp
 

- index b130f8fc6..9fb9f85d2 100644
 

- --- a/src/utils/include/utils/interpolation/bspline_3d.hpp
 

- +++ b/src/utils/include/utils/interpolation/bspline_3d.hpp
 

- @@ -47,8 +47,8 @@ void bspline_3d(const Vector3d &pos, const Kernel &kernel,
 

-    const auto block = detail::ll_and_dist<order>(pos, grid_spacing, offset);
 

-  

-    /* Precalc weights that are used multiple times. */
 

- -  std::array<double, order> w_y;
 

- -  std::array<double, order> w_z;
 

- +  std::array<double, order> w_y{};
 

- +  std::array<double, order> w_z{};
 

-    for (int i = 0; i < order; i++) {
 

-      w_y[i] = bspline<order>(i, block.distance[1]);
 

-      w_z[i] = bspline<order>(i, block.distance[2]);
 

- diff --git a/src/utils/tests/Array_test.cpp b/src/utils/tests/Array_test.cpp
 

- index cab5a7fb2..f55759118 100644
 

- --- a/src/utils/tests/Array_test.cpp
 

- +++ b/src/utils/tests/Array_test.cpp
 

- @@ -48,7 +48,7 @@ BOOST_AUTO_TEST_CASE(array_ctor) {
 

-  }
 

-  

-  BOOST_AUTO_TEST_CASE(iterators) {
 

- -  auto a = Array<int, 4>{{1, 2, 3, 4}};
 

- +  auto a = Array<int, 4>{{{1, 2, 3, 4}}};
 

-  

-    BOOST_CHECK(*(a.begin()) == 1);
 

-    BOOST_CHECK(*(a.cbegin()) == 1);
 

- @@ -57,7 +57,7 @@ BOOST_AUTO_TEST_CASE(iterators) {
 

-  }
 

-  

-  BOOST_AUTO_TEST_CASE(element_access) {
 

- -  auto a = Array<int, 5>{{5, 6, 7, 8, 9}};
 

- +  auto a = Array<int, 5>{{{5, 6, 7, 8, 9}}};
 

-  

-    int c = 5;
 

-    for (int i : a) {
 

- diff --git a/src/utils/tests/tuple_test.cpp b/src/utils/tests/tuple_test.cpp
 

- index 3954ebffd..870a091cf 100644
 

- --- a/src/utils/tests/tuple_test.cpp
 

- +++ b/src/utils/tests/tuple_test.cpp
 

- @@ -28,12 +28,14 @@
 

-  

-  #include "utils/tuple.hpp"
 

-  

- +#include <array>
 

- +
 

-  BOOST_AUTO_TEST_CASE(for_each) {
 

-    using Utils::for_each;
 

-  

-    /* l-value reference tuple */
 

-    {
 

- -    auto a = std::array<int, 3>{2, 3, 5};
 

- +    auto a = std::array<int, 3>{{2, 3, 5}};
 

-  

-      for_each(
 

-          [i = 0, a](int &e) mutable {
 

- @@ -71,7 +73,7 @@ BOOST_AUTO_TEST_CASE(apply) {
 

-    using Utils::apply;
 

-  

-    /* constexpr */
 

- -  { static_assert(apply(std::plus<>(), std::array<int, 2>{3, 8}) == 11, ""); }
 

- +  { static_assert(apply(std::plus<>(), std::array<int, 2>{{3, 8}}) == 11, ""); }
 

-  

-    /* l-value reference */
 

-    {

file modified
+22 -26 
@@ -1,32 +1,29 @@ 
 

- %global git 0
 

- %global commit f74064d62090da45a28225881008b05798703d1c
 

+ %global commit 18d49bfc4b6ca5be264f16d262338fda1f9141a7
 

  %global shortcommit %(c=%{commit}; echo ${c:0:7})
 

  

  Name:           espresso
 

- Version:        4.1.4
 

- Release:        10%{?dist}
 

+ Version:        4.2.0
 

+ Release:        1%{?dist}
 

  Summary:        Extensible Simulation Package for Research on Soft matter
 

  # segfault on s390x: https://github.com/espressomd/espresso/issues/3753
 

  # segfault on armv7hl: https://src.fedoraproject.org/rpms/espresso/pull-request/4
 

  ExcludeArch:    s390x i686 armv7hl
 

  

  License:        GPLv3+
 

- URL:            http://espressomd.org
 

- %if %{git}
 

- Source0:        https://github.com/%{name}md/%{name}/archive/%{commit}/%{name}-%{commit}.tar.gz
 

- %else
 

- Source0:       https://github.com/%{name}md/%{name}/releases/download/%{version}/%{name}-%{version}.tar.gz
 

- %endif
 

- Patch0:         %{name}-gcc11.patch
 

- Patch1:         %{name}-gcc12.patch
 

+ URL:            https://espressomd.org
 

+ Source0:        https://github.com/%{name}md/%{name}/releases/download/%{version}/%{name}-%{version}.tar.gz
 

+ # skip fragile ICC python interface test on aarch64
 

+ Patch0:         %{name}-aarch64.patch
 

  

  BuildRequires:  gcc-c++
 

- BuildRequires:  cmake3 >= 3.4
 

+ BuildRequires:  cmake3 >= 3.16
 

  BuildRequires:  /usr/bin/cython
 

  %global cython /usr/bin/cython
 

  BuildRequires:  fftw-devel
 

  BuildRequires:  python%{python3_pkgversion}-numpy
 

+ BuildRequires:  python%{python3_pkgversion}-scipy
 

  BuildRequires:  python%{python3_pkgversion}-six
 

+ BuildRequires:  python%{python3_pkgversion}-setuptools
 

  BuildRequires:  python%{python3_pkgversion}-devel
 

  BuildRequires:  boost-devel
 

  BuildRequires:  hdf5-devel
 
@@ -49,7 +46,7 @@ 
 

  in various ensembles ((N,V,E), (N,V,T), and (N,p,T)).
 

  ESPResSo contains a number of advanced algorithms, e.g.
 

      * DPD thermostat (for hydrodynamics)
 

-     * P3M, MMM2D, MMM1D, ELC for electrostatic interactions
 

+     * P3M, MMM1D, ELC for electrostatic interactions
 

      * Lattice-Boltzmann for hydrodynamics
 

  

  %package common
 
@@ -61,7 +58,7 @@ 
 

  in various ensembles ((N,V,E), (N,V,T), and (N,p,T)).
 

  ESPResSo contains a number of advanced algorithms, e.g.
 

      * DPD thermostat (for hydrodynamics)
 

-     * P3M, MMM2D, MMM1D, ELC for electrostatic interactions
 

+     * P3M, MMM1D, ELC for electrostatic interactions
 

      * Lattice-Boltzmann for hydrodynamics
 

  This package contains the license file and data files shared between the
 

  sub-packages of %{name}.
 
@@ -78,7 +75,7 @@ 
 

  in various ensembles ((N,V,E), (N,V,T), and (N,p,T)).
 

  ESPResSo contains a number of advanced algorithms, e.g.
 

      * DPD thermostat (for hydrodynamics)
 

-     * P3M, MMM2D, MMM1D, ELC for electrostatic interactions
 

+     * P3M, MMM1D, ELC for electrostatic interactions
 

      * Lattice-Boltzmann for hydrodynamics
 

  

  This package contains %{name} compiled against Open MPI.
 
@@ -98,20 +95,17 @@ 
 

  in various ensembles ((N,V,E), (N,V,T), and (N,p,T)).
 

  ESPResSo contains a number of advanced algorithms, e.g.
 

      * DPD thermostat (for hydrodynamics)
 

-     * P3M, MMM2D, MMM1D, ELC for electrostatic interactions
 

+     * P3M, MMM1D, ELC for electrostatic interactions
 

      * Lattice-Boltzmann for hydrodynamics
 

  

  This package contains %{name} compiled against MPICH2.
 

  

  

  %prep
 

- %if %{git}
 

- %setup -q -n espresso-%{commit}
 

- %else
 

  %setup -q -n %{name}
 

- %endif
 

+ %ifarch aarch64
 

  %patch0 -p1
 

- %patch1 -p1
 

+ %endif
 

  

  %build
 

  %global defopts \\\
 
@@ -133,7 +127,7 @@ 
 

     module load mpi/${mpi}-%{_arch}
 

     old_LDFLAGS="${LDFLAGS}"
 

     export LDFLAGS="${LDFLAGS} -Wl,-rpath,${MPI_PYTHON3_SITEARCH}/%{name}md"
 

-    %{cmake3} %{defopts} -DLIBDIR=${MPI_LIB} -DPYTHON_INSTDIR=${MPI_PYTHON3_SITEARCH}
 

+    %{cmake3} %{defopts} -DPYTHON_INSTDIR=${MPI_PYTHON3_SITEARCH} -DWITH_CUDA=OFF -DWITH_HDF5=ON -DWITH_GSL=ON
 

     export LD_LIBRARY_PATH=$PWD/${mpi:-serial}/src/config
 

     %cmake3_build
 

     export LDFLAGS="${old_LDFLAGS}"
 
@@ -149,8 +143,7 @@ 
 

  

  %check
 

  export CTEST_OUTPUT_ON_FAILURE=1
 

- # exclude openmpi, see https://github.com/espressomd/espresso/issues/3905
 

- for mpi in mpich; do
 

+ for mpi in mpich openmpi; do
 

     module load mpi/${mpi}-%{_arch}
 

     export LD_LIBRARY_PATH=${MPI_LIB}:%{buildroot}${MPI_PYTHON3_SITEARCH}/%{name}md
 

     %cmake3_build --target check
 
@@ -158,7 +151,7 @@ 
 

  done
 

  

  %files common
 

- %doc AUTHORS README NEWS ChangeLog
 

+ %doc AUTHORS Readme.md NEWS ChangeLog
 

  %license COPYING
 

  

  %files -n python%{python3_pkgversion}-%{name}-openmpi
 
@@ -168,6 +161,9 @@ 
 

  %{python3_sitearch}/mpich/%{name}md/
 

  

  %changelog
 

+ * Fri Jul 01 2022 Jean-Noël Grad <jgrad@icp.uni-stuttgart.de> - 4.2.0-1
 

+ - Update to 4.2.0 (#2102861)
 

+ 

  * Thu Jan 20 2022 Jean-Noël Grad <jgrad@icp.uni-stuttgart.de> - 4.1.4-10
 

  - Rebuild for GCC 12.0.0

file modified
+1 -1 
@@ -1,1 +1,1 @@ 
 

- SHA512 (espresso-4.1.4.tar.gz) = c901b0f39ba8ec8a5b32d67a52b4cd0fe07c2f98a1032cfc4542bb27eba9f24d1f2d575a048e4f6256bef7be8a51cd68851e457f87038a0dc946ec5c28324a9d
 

+ SHA512 (espresso-4.2.0.tar.gz) = b80afb1bef57911fd79b88378a5b2e31b07a18d415fe17fcd5ed28fb448eeca5922f98af8df42117e9e869645765d55ecfb3aae615fa6a53c915f7d8a63081c5

Fixes bugzilla #2102861

  • bump ESPResSo version from 4.1.4 to 4.2.0
  • re-enable Open MPI testsuite
  • remove git-based build system

Pull-Request has been merged by junghans
2 years ago

Can you trigger a f36 build using fedpkg build?

Can you trigger a f36 build using fedpkg build?

done: espresso-4.2.0-1.fc37

fc37? Do you mean fc36?

Oops, that was a copy-paste error.

Should I now do fedpkg update to get it on Bohdi? If yes, should I use the following parameters?

type=bugfix
request=testing
bugs=2102861

I always use the web interface, but that sounds right

Metadata
None
No Tags
Changes Summary 6
+1 -0
file changed
.gitignore
+11
file added
espresso-aarch64.patch
-37
file removed
espresso-gcc11.patch
-106
file removed
espresso-gcc12.patch
+22 -26
file changed
espresso.spec
+1 -1
file changed
sources
Powered by Pagure 5.13.3
Documentation • File an Issue • About this Instance • SSH Hostkey/Fingerprint
© Red Hat, Inc. and others.