Merge #3248 #3251

3248: Fix cmake install on dev branch r=KaiSzuttor a=jngrad

Porting #3228 to the dev branch

Description of changes:
- fix the CMake build system to include libraries in the list of installed files and test it in a dedicated CI job
- fix the versioning of Cython .so shared objects
- simplify the CMake tests


3251: Particle data r=jngrad a=fweik

Fixes #3157.

Description of changes:
 - Split definition of `struct Particle` from rest of particle data.


Co-authored-by: Christoph Junghans <junghans@lanl.gov>
Co-authored-by: Jean-Noël Grad <jgrad@icp.uni-stuttgart.de>
Co-authored-by: Florian Weik <fweik@icp.uni-stuttgart.de>

.gitlab-ci.yml

@@ -272,6 +272,37 @@ tutorials-samples-no-gpu:
  only:
  - schedules
 
+installation:
+ <<: *global_job_definition
+ stage: build
+ image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-10.1
+ script:
+ - export myconfig=maxset with_coverage=false make_check=false
+ - export srcdir=${CI_PROJECT_DIR} test_timeout=1800
+ - bash maintainer/CI/build_cmake.sh
+ - cd build
+ # install ESPResSo (in CI, pypresso will run up to 5 times slower when
+ # located outside the build directory, hence the larger timeout value)
+ - make install
+ # get path of installed files
+ - CI_INSTALL_DIR="/tmp/espresso-unit-tests"
+ - CI_INSTALL_PYTHON_PATH=$(dirname $(find "${CI_INSTALL_DIR}/lib" -name espressomd))
+ # deploy object-in-fluid module
+ - cp -r "src/python/object_in_fluid" "${CI_INSTALL_PYTHON_PATH}/object_in_fluid"
+ # run all tests with the installed files
+ - sed -i "s|$(pwd)/pypresso|${CI_INSTALL_DIR}/bin/pypresso|" testsuite/{python,scripts/samples,scripts/tutorials}/CTestTestfile.cmake
+ # skip long tests
+ - sed -i "/tutorial_11-ferrofluid_3/d" testsuite/scripts/tutorials/CTestTestfile.cmake
+ - make -j2 check_python_skip_long
+ - make -j2 check_samples
+ - make -j2 check_tutorials
+ tags:
+ - docker
+ - linux
+ - cuda
+ timeout: 3h
+ when: manual
+
 empty:
  <<: *global_job_definition
  stage: build

CMakeLists.txt

@@ -29,14 +29,6 @@ endif()
 enable_language(CXX)
 
 set(PROJECT_VERSION "5.0-dev")
-string(REGEX
- REPLACE "^([1-9]+)\\.[0-9]+.*$"
- "\\1"
- SOVERSION
- "${PROJECT_VERSION}")
-if(NOT ${SOVERSION} MATCHES "^[1-9]+$")
- message(FATAL_ERROR "Could not determine SOVERSION from ${PROJECT_VERSION}")
-endif(NOT ${SOVERSION} MATCHES "^[1-9]+$")
 
 #
 # CMake internal vars

doc/sphinx/conf.py.in

@@ -67,9 +67,9 @@ author = 'C. Holm, F. Weik, R. Weeber'
 # built documents.
 #
 # The short X.Y version.
-version = '@PROJECT_VERSION@'
+version = '.'.join('@PROJECT_VERSION@'.split('.')[:2])
 # The full version, including alpha/beta/rc tags.
-release = '@SOVERSION@'
+release = '@PROJECT_VERSION@'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/sphinx/installation.rst

@@ -676,7 +676,7 @@ build directory and create a new one.
 .. _make\: Compiling, testing and installing:
 
 ``make``: Compiling, testing and installing
---------------------------------------------
+-------------------------------------------
 
 The command ``make`` is mainly used to compile the source code, but it
 can do a number of other things. The generic syntax of the ``make``
@@ -701,9 +701,12 @@ targets are available:
  Deletes all files that were created during the compilation.
 
 ``install``
- Install |es|.
- Use ``make DESTDIR=/home/john install`` to install to a
- specific directory.
+ Install |es| in the path specified by the CMake variable
+ ``CMAKE_INSTALL_PREFIX``. The path can be changed by calling CMake
+ with ``cmake .. -DCMAKE_INSTALL_PREFIX=/path/to/espresso``. Do not use
+ ``make DESTDIR=/path/to/espresso install`` to install to a specific path,
+ this will cause issues with the runtime path (RPATH) and will conflict
+ with the CMake variable ``CMAKE_INSTALL_PREFIX`` if it has been set.
 
 ``doxygen``
  Creates the Doxygen code documentation in the :file:`doc/doxygen`

src/config/CMakeLists.txt

@@ -36,7 +36,6 @@ execute_process(COMMAND ${PYTHON_EXECUTABLE}
 add_library(EspressoConfig SHARED config-features.cpp)
 add_dependencies(EspressoConfig myconfig check_myconfig generate_config_features)
 install(TARGETS EspressoConfig LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)
-set_target_properties(EspressoConfig PROPERTIES SOVERSION ${SOVERSION})
 target_include_directories(EspressoConfig PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR})
 
 # Parse repository info from git if available

src/core/CMakeLists.txt

@@ -156,7 +156,6 @@ else(CUDA)
 endif(CUDA)
 
 install(TARGETS EspressoCore LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)
-set_target_properties(EspressoCore PROPERTIES SOVERSION ${SOVERSION})
 target_include_directories(EspressoCore PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 if(WITH_COVERAGE)
  target_compile_options(EspressoCore PUBLIC "$<$<CONFIG:Release>:-g>")

src/core/EspressoSystemInterface.cpp

@@ -17,10 +17,10 @@
  * along with this program. If not, see <http://www.gnu.org/licenses/>.
  */
 #include "EspressoSystemInterface.hpp"
+#include "Particle.hpp"
 #include "cells.hpp"
 #include "cuda_interface.hpp"
 #include "grid.hpp"
-#include "particle_data.hpp"
 
 /* Initialize instance pointer */
 EspressoSystemInterface *EspressoSystemInterface::m_instance = nullptr;

src/core/PartCfg.hpp

@@ -19,10 +19,10 @@
 #ifndef CORE_PART_CFG_HPP
 #define CORE_PART_CFG_HPP
 
+#include "Particle.hpp"
 #include "ParticleCache.hpp"
 #include "cells.hpp"
 #include "grid.hpp"
-#include "particle_data.hpp"
 #include "serialization/Particle.hpp"
 #include <utils/SkipIterator.hpp>