Update dependency requirements (#5181)

jngrad · web-flow · commit dc87ede3f6c2 · 2025-10-16T16:05:41.000+02:00
Prepare ESPResSo for a dev-EESSI release.

Description of changes:
- bump HighFive version requirements
- allow Cython 3.1.x and Cython 3.0.4 for foss/2023b
- make Gay-Berne potential part of the default myconfig file
- fix CMake parsing of environment variable `ESPRESSO_MYCONFIG`
- limit testsuite to 3 cores on the macOS runner to avoid timeouts
diff --git a/.github/workflows/push_pull.yml b/.github/workflows/push_pull.yml
@@ -38,16 +38,17 @@ jobs:
          codesign -d -vv /usr/local/lib/libomp.dylib
          echo "::endgroup::"
          # Python dependencies
-         python3 -m venv venv
+         python -m venv venv
          . venv/bin/activate
-         pip3 install -c requirements.txt cython numpy scipy packaging
+         python -m pip install -c requirements.txt cython numpy scipy packaging
          deactivate
         shell: bash
       - name: Build and check
         uses: ./.github/actions/build_and_check
         env:
           build_procs: 3
           check_procs: 3
+          cmake_params: '-D ESPRESSO_TEST_NP=3'
           with_ccache: 'true'
           with_fftw: 'true'
           with_walberla: 'true'
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -301,7 +301,10 @@ endif()
 # Python interpreter and Cython interface library
 if(ESPRESSO_BUILD_WITH_PYTHON)
   find_package(Python 3.11 REQUIRED COMPONENTS Interpreter Development NumPy)
-  find_package(Cython 3.0.8...<3.1.0 REQUIRED)
+  find_package(Cython 3.0.4...<3.2.0 REQUIRED)
+  if(CYTHON_VERSION VERSION_LESS 3.0.8)
+    message(WARNING "We strongly recommend using Cython 3.0.8 or later")
+  endif()
   find_program(IPYTHON_EXECUTABLE NAMES jupyter ipython3 ipython)
 endif()
 
@@ -746,7 +749,7 @@ if(ESPRESSO_BUILD_WITH_HDF5)
   FetchContent_Declare(
     HighFive
     GIT_REPOSITORY https://github.com/highfive-devs/highfive.git
-    GIT_TAG        v.3.1.1
+    GIT_TAG        v3.2.0
   )
   # cmake-format: on
   FetchContent_MakeAvailable(HighFive)
diff --git a/cmake/espresso_myconfig.cmake b/cmake/espresso_myconfig.cmake
@@ -22,8 +22,8 @@
 
 # heed the environment variable "ESPRESSO_MYCONFIG"
 if(NOT ESPRESSO_MYCONFIG_FILE)
-  if(ENV{ESPRESSO_MYCONFIG})
-    set(ESPRESSO_MYCONFIG_FILE ENV{ESPRESSO_MYCONFIG})
+  if(DEFINED ENV{ESPRESSO_MYCONFIG})
+    set(ESPRESSO_MYCONFIG_FILE $ENV{ESPRESSO_MYCONFIG})
   else()
     # test whether ESPRESSO_MYCONFIG_NAME is found in the object or source dir
     find_file(ESPRESSO_MYCONFIG_FILE NAMES ${ESPRESSO_MYCONFIG_NAME}
diff --git a/requirements.txt b/requirements.txt
@@ -1,5 +1,5 @@
 # build system
-cython>=3.0.8,<3.1.0
+cython>=3.0.4,<3.2.0
 setuptools>=68.1.2
 packaging>=24.0
 # required scientific packages
diff --git a/src/config/myconfig-default.hpp b/src/config/myconfig-default.hpp
@@ -57,6 +57,7 @@
 #define LJCOS2
 #define GAUSSIAN
 #define HAT
+#define GAY_BERNE
 #define SMOOTH_STEP
 #define HERTZIAN
 #define SOFT_SPHERE
diff --git a/src/core/aosoa_pack.hpp b/src/core/aosoa_pack.hpp
@@ -90,6 +90,22 @@ struct CellStructure::AoSoA_pack {
 #endif
     }
   }
+
+  template <typename array_layout>
+  Utils::Vector3d get_vector_at(
+      Kokkos::View<double *[3], array_layout, Kokkos::HostSpace> const &view,
+      std::size_t i) const {
+    return {view(i, 0), view(i, 1), view(i, 2)};
+  }
+
+  template <typename array_layout>
+  void set_vector_at(
+      Kokkos::View<double *[3], array_layout, Kokkos::HostSpace> &view,
+      std::size_t i, Utils::Vector3d const &value) {
+    view(i, 0) = value[0];
+    view(i, 1) = value[1];
+    view(i, 2) = value[2];
+  }
 };
 
 #endif // ESPRESSO_SHARED_MEMORY_PARALLELISM
diff --git a/src/core/electrostatics/elc.hpp b/src/core/electrostatics/elc.hpp
@@ -116,28 +116,24 @@ struct elc_data {
   double space_box;
 
 #ifdef ESPRESSO_SHARED_MEMORY_PARALLELISM
-  static auto copy_aosoa_vector_elc(std::size_t i, auto &slice) {
-    return Utils::Vector3d{slice(i, 0), slice(i, 1), slice(i, 2)};
-  }
-
   /// pairwise contributions from lower and upper layers
   void dielectric_layers_contribution(BoxGeometry const &box_geo,
                                       std::size_t p1, std::size_t p2,
                                       auto &aosoa, double q1q2,
                                       auto &&kernel) const {
     if (aosoa.position(p1, 2) < space_layer) {
       auto const q_eff = delta_mid_bot * q1q2;
-      auto pos2 = copy_aosoa_vector_elc(p2, aosoa.position);
-      auto pos1 = copy_aosoa_vector_elc(p1, aosoa.position);
+      auto pos2 = aosoa.get_vector_at(aosoa.position, p2);
+      auto pos1 = aosoa.get_vector_at(aosoa.position, p1);
       pos1[2] *= -1.;
       auto const d = box_geo.get_mi_vector(pos2, pos1);
       kernel(q_eff, d);
     }
     if (aosoa.position(p1, 2) > (box_h - space_layer)) {
       auto const q_eff = delta_mid_top * q1q2;
       auto const z = 2. * box_h - aosoa.position(p1, 2);
-      auto pos2 = copy_aosoa_vector_elc(p2, aosoa.position);
-      auto pos1 = copy_aosoa_vector_elc(p1, aosoa.position);
+      auto pos2 = aosoa.get_vector_at(aosoa.position, p2);
+      auto pos1 = aosoa.get_vector_at(aosoa.position, p1);
       pos1[2] = 2. * box_h - pos1[2];
       auto const d = box_geo.get_mi_vector(pos2, pos1);
       kernel(q_eff, d);
diff --git a/src/core/electrostatics/p3m.cpp b/src/core/electrostatics/p3m.cpp
@@ -377,9 +377,7 @@ template <int cao> struct AssignCharge {
     p3m.inter_weights.zfill(n_part); // allocate buffer for parallel write
     kokkos_parallel_range_for(
         "InterpolationWeights", std::size_t{0u}, n_part, [&](auto p_index) {
-          Utils::Vector3d const p_pos{aosoa.position(p_index, 0),
-                                      aosoa.position(p_index, 1),
-                                      aosoa.position(p_index, 2)};
+          auto const p_pos = aosoa.get_vector_at(aosoa.position, p_index);
           auto constexpr memory_order =
               std::remove_reference<decltype(p3m)>::type::memory_order;
           auto const weights =
diff --git a/src/core/forces_cabana.hpp b/src/core/forces_cabana.hpp
@@ -101,15 +101,11 @@ struct ForcesKernel {
         nonbonded_ias.get_ia_param(aosoa.type(i), aosoa.type(j));
 
     ParticleForce pf{};
-    Utils::Vector3d const pos1 = {aosoa.position(i, 0), aosoa.position(i, 1),
-                                  aosoa.position(i, 2)};
-    Utils::Vector3d const pos2 = {aosoa.position(j, 0), aosoa.position(j, 1),
-                                  aosoa.position(j, 2)};
+    auto const pos1 = aosoa.get_vector_at(aosoa.position, i);
+    auto const pos2 = aosoa.get_vector_at(aosoa.position, j);
 #if defined(ESPRESSO_GAY_BERNE) or defined(ESPRESSO_DIPOLES)
-    Utils::Vector3d const dir1 = {aosoa.director(i, 0), aosoa.director(i, 1),
-                                  aosoa.director(i, 2)};
-    Utils::Vector3d const dir2 = {aosoa.director(j, 0), aosoa.director(j, 1),
-                                  aosoa.director(j, 2)};
+    auto const dir1 = aosoa.get_vector_at(aosoa.director, i);
+    auto const dir2 = aosoa.get_vector_at(aosoa.director, j);
 #endif
 
 #ifdef ESPRESSO_NPT
@@ -164,10 +160,8 @@ struct ForcesKernel {
 #ifdef ESPRESSO_DPD
     if (thermostat.thermo_switch & THERMO_DPD) {
       auto const dist2 = dist * dist;
-      Utils::Vector3d const vel1 = {aosoa.velocity(i, 0), aosoa.velocity(i, 1),
-                                    aosoa.velocity(i, 2)};
-      Utils::Vector3d const vel2 = {aosoa.velocity(j, 0), aosoa.velocity(j, 1),
-                                    aosoa.velocity(j, 2)};
+      auto const vel1 = aosoa.get_vector_at(aosoa.velocity, i);
+      auto const vel2 = aosoa.get_vector_at(aosoa.velocity, j);
       auto const force =
           dpd_pair_force(pos1, vel1, aosoa.id(i), pos2, vel2, aosoa.id(j),
                          *thermostat.dpd, box_geo, ia_params, d, dist, dist2);
diff --git a/src/core/magnetostatics/dp3m.cpp b/src/core/magnetostatics/dp3m.cpp
@@ -174,9 +174,7 @@ template <int cao> struct AssignDipole {
     dp3m.inter_weights.zfill(n_part); // allocate buffer for parallel write
     kokkos_parallel_range_for(
         "InterpolationWeights", std::size_t{0u}, n_part, [&](auto p_index) {
-          Utils::Vector3d const p_pos{aosoa.position(p_index, 0),
-                                      aosoa.position(p_index, 1),
-                                      aosoa.position(p_index, 2)};
+          auto const p_pos = aosoa.get_vector_at(aosoa.position, p_index);
           auto const weights =
               p3m_calculate_interpolation_weights<cao, memory_order>(
                   p_pos, dp3m.params.ai, dp3m.local_mesh);
diff --git a/src/core/nonbonded_interactions/gay_berne.hpp b/src/core/nonbonded_interactions/gay_berne.hpp
@@ -173,12 +173,17 @@ inline double gb_pair_energy(Utils::Quaternion<double> const &qi,
 
   return E(r_eff(dist)) - E(r_eff(ia_params.gay_berne.cut));
 }
+
 inline ParticleForce gb_pair_force(Utils::Quaternion<double> const &qi,
                                    Utils::Quaternion<double> const &qj,
                                    IA_parameters const &ia_params,
                                    Utils::Vector3d const &d, double dist) {
+  if (dist >= ia_params.gay_berne.cut) {
+    return {};
+  }
   auto const ui = Utils::convert_quaternion_to_director(qi);
   auto const uj = Utils::convert_quaternion_to_director(qj);
   return gb_pair_force(ui, uj, ia_params, d, dist);
 }
+
 #endif // ESPRESSO_GAY_BERNE
diff --git a/src/core/short_range_cabana.hpp b/src/core/short_range_cabana.hpp
@@ -58,21 +58,13 @@ commit_particle(Particle const &p, auto const index,
   aosoa.charge(index) = p.q();
 #endif
   aosoa.type(index) = p.type();
-  auto const &pos = p.pos();
-  aosoa.position(index, 0) = pos[0];
-  aosoa.position(index, 1) = pos[1];
-  aosoa.position(index, 2) = pos[2];
+  aosoa.set_vector_at(aosoa.position, index, p.pos());
 #ifdef ESPRESSO_DPD
-  auto const &vel = p.v();
-  aosoa.velocity(index, 0) = vel[0];
-  aosoa.velocity(index, 1) = vel[1];
-  aosoa.velocity(index, 2) = vel[2];
+  aosoa.set_vector_at(aosoa.velocity, index, p.v());
 #endif
 #if defined(ESPRESSO_GAY_BERNE) or defined(ESPRESSO_DIPOLES)
-  auto const &director = Utils::convert_quaternion_to_director(p.quat());
-  aosoa.director(index, 0) = director[0];
-  aosoa.director(index, 1) = director[1];
-  aosoa.director(index, 2) = director[2];
+  aosoa.set_vector_at(aosoa.director, index,
+                      Utils::convert_quaternion_to_director(p.quat()));
 #endif
 #ifdef ESPRESSO_DIPOLES
   aosoa.dipm(index) = p.dipm();
diff --git a/testsuite/python/CMakeLists.txt b/testsuite/python/CMakeLists.txt
@@ -487,4 +487,6 @@ add_custom_target(
     --resource-spec-file ${ESPRESSO_CTEST_RESOURCE_SPEC_FILE}
     ${ESPRESSO_CTEST_ARGS} --output-on-failure)
 add_dependencies(check_python pypresso python_test_data)
+
 add_dependencies(check check_python)
+add_dependencies(espresso_packaging_dependencies python_test_data)
diff --git a/testsuite/python/constraint_shape_based.py b/testsuite/python/constraint_shape_based.py
@@ -1059,6 +1059,7 @@ def test_exceptions(self):
             np.copy(system.box_l), 0.75 * 0.5 * box_l, atol=1e-7)
         with self.assertRaisesRegex(RuntimeError, "constraints property"):
             pickle.dumps(constraint)
+        self.assertIsNone(constraint.call_method("unknown"))
 
 
 if __name__ == "__main__":
diff --git a/testsuite/python/field_test.py b/testsuite/python/field_test.py
@@ -171,6 +171,7 @@ def test_potential_field(self):
             F.default_scale = 2.0
         with self.assertRaisesRegex(RuntimeError, "Parameter 'particle_scales' is read-only"):
             F.particle_scales = {0: 0.0}
+        self.assertIsNone(F.call_method("unknown"))
 
         for i in itertools.product(*map(range, 3 * [10])):
             x = (h * i)
@@ -232,6 +233,7 @@ def test_force_field(self):
             F.default_scale = 2.0
         with self.assertRaisesRegex(RuntimeError, "Parameter 'particle_scales' is read-only"):
             F.particle_scales = {0: 0.0}
+        self.assertIsNone(F.call_method("unknown"))
 
         for i in itertools.product(*map(range, 3 * [10])):
             x = (h * i)
