Release v2.0.0

- Move examples to bin
- Add sampling app with improved command-line interface for uniform
sampling
- Replace HDF5 Backend with HighFive for stable HDF5 parsing
- Add FindSBML
- Restructure thirdparty headers
- Update FindGurobi
- Update Readme
- Replace Google Test by Boost unit tests. This should speed up
building.
- Fix small bug in csvreader

Author: Fredrik Jadebeck

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "include/hops/thirdparty/HighFive"]
+	path = include/hops/thirdparty/HighFive
+	url = https://github.com/BlueBrain/HighFive.git

.travis.yml

@@ -13,22 +13,28 @@ compiler:
 before_install:
   - sudo apt-get update -y
   - sudo apt-get install -y apt-utils
-  - sudo apt-get install -y build-essential software-properties-common libssl-dev
-  - sudo apt-get install -y libeigen3-dev liblpsolve55-dev lp-solve libncursesw5-dev
-  - sudo apt-get install -y libxerces-c-dev libhdf5-dev  doxygen libncurses5-dev libsuitesparse-dev 
-  - sudo apt-get install -y libsbml5-dev git bzip2 libbz2-dev libsbml5-dev
-  - sudo apt-get install -y coinor-clp coinor-libclp-dev
-  - sudo snap install cmake --classic
+  - sudo apt-get install -y build-essential 
+  - sudo apt-get install -y software-properties-common 
+  - sudo apt-get install -y cmake 
+  - sudo apt-get install -y libeigen3-dev
+  - sudo apt-get install -y libhdf5-dev
+  - sudo apt-get install -y doxygen 
+  - sudo apt-get install -y libsbml5-dev
+  - sudo apt-get install -y libmpich-dev
+  - sudo apt-get install -y libbz2-dev
+  - sudo apt-get install -y coinor-libclp-dev 
+  - sudo apt-get install -y libboost-all-dev 
 
 script:
+  - /usr/bin/mpiexec --help
   - mkdir -p cmake-build-debug
   - cd cmake-build-debug
-  - /snap/cmake/current/bin/cmake -DHOPS_BENCHMARKS=OFF ..
+  - cmake .. -DCMAKE_BUILD_TYPE=Debug -DHOPS_BENCHMARKS=OFF -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu
   - make
   - travis_wait 30 make test
   - cd .. 
   - mkdir -p cmake-build-release
   - cd cmake-build-release
-  - /snap/cmake/current/bin/cmake -DCMAKE_BUILD_TYPE=Release -DHOPS_BENCHMARKS=OFF ..
+  - cmake .. -DCMAKE_BUILD_TYPE=Release -DHOPS_BENCHMARKS=OFF -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu
   - make
   - travis_wait 30 make test

CMakeLists.txt

@@ -9,7 +9,7 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_CURRENT_SOURCE_DIR}/cmake/")
 
 if (UNIX)
     message(STATUS "Adjusting CMAKE_PREFIX_PATH on UNIX for CLP")
-    list(APPEND CMAKE_PREFIX_PATH /usr/lib/x85_64-linux-gnu)
+    list(APPEND CMAKE_PREFIX_PATH /usr/lib/x86_64-linux-gnu)
 endif (UNIX)
 
 ########################################################################################################################
@@ -42,7 +42,6 @@ option(HOPS_TESTS "Enables compilation of unit tests. Use -DHOPS_TESTS=OFF to di
 # C++-Compiler Settings
 ########################################################################################################################
 
-# TODO update to target_compile_feature and target_compile_option
 set(CMAKE_C_FLAGS "${CMAKE_FLAGS} ${MPI_FLAGS}")
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${MPI_CXX_FLAGS}")
@@ -102,17 +101,17 @@ endif (MKL_LIBRARY_DIR)
 # HOPS
 ########################################################################################################################
 
-add_library(hops STATIC "")
+add_library(hops STATIC "" include/hops/FileReader/Hdf5Reader.hpp)
 target_include_directories(hops PUBLIC ${EIGEN3_INCLUDE_DIR})
 
 if (MKL_INCLUDE_DIR)
-    target_include_directories(hops PUBLIC ${MKL_INCLUDE_DIR})
+  target_include_directories(hops PRIVATE ${MKL_INCLUDE_DIR})
 endif (MKL_INCLUDE_DIR)
 if (MKL_LIBRARY_DIR)
-    target_link_directories(hops PUBLIC ${MKL_LIBRARY_DIR})
+  target_link_directories(hops PRIVATE ${MKL_LIBRARY_DIR})
 endif (MKL_LIBRARY_DIR)
 if (MKL_LIBRARIES)
-    target_link_libraries(hops PUBLIC ${MKL_LIBRARIES})
+  target_link_libraries(hops PRIVATE ${MKL_LIBRARIES})
 endif (MKL_LIBRARIES)
 
 add_subdirectory(include)
@@ -165,7 +164,7 @@ endif ()
 
 if (HOPS_EXAMPLES)
     message(STATUS "Enabled compilation of examples. Use -DHOPS_EXAMPLES=OFF to disable.")
-    add_subdirectory(examples)
+    add_subdirectory(bin)
 else ()
     message(STATUS "Disabled compilation of examples. Use -DHOPS_EXAMPLES=ON to enable.")
 endif ()
@@ -188,7 +187,7 @@ endif ()
 ########################################################################################################################
 
 if (HOPS_BENCHMARKS OR HOPS_EXAMPLES OR HOPS_TESTS)
-    message(STATUS "Copying resources.")
+    message(STATUS "Copying resources")
     add_subdirectory(resources)
 endif ()
 
@@ -198,6 +197,7 @@ endif ()
 
 install(DIRECTORY include/ DESTINATION include/ FILES_MATCHING PATTERN "*.hpp")
 install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/include/hops/hops.hpp DESTINATION include/hops)
+install(TARGETS hops-sampler DESTINATION bin/)
 install(TARGETS hops EXPORT hops-config LIBRARY DESTINATION "lib")
 install(EXPORT hops-config DESTINATION "lib" CONFIGURATIONS RELEASE)
 

Dockerfile

@@ -4,33 +4,42 @@ LABEL Maintainer="Johann Fredrik Jadebeck <johann.fredrik@jadebeck.dev>"
 ARG DEBIAN_FRONTEND=noninteractive
 RUN apt-get update -y
 RUN apt-get install -y apt-utils
-RUN apt-get install -y build-essential software-properties-common cmake libeigen3-dev \
-    liblpsolve55-dev lp-solve libxerces-c-dev libhdf5-dev doxygen libncurses5-dev libncursesw5-dev \
-    libsbml5-dev mpich libmpich-dev git
-RUN apt-get install -y bzip2 libbz2-dev
-RUN apt-get install -y coinor-clp coinor-libclp-dev
+RUN apt-get install -y build-essential 
+RUN apt-get install -y software-properties-common 
+RUN apt-get install -y cmake 
+RUN apt-get install -y libeigen3-dev
+RUN apt-get install -y libhdf5-dev
+RUN apt-get install -y doxygen 
+RUN apt-get install -y libsbml5-dev
+RUN apt-get install -y libmpich-dev
+#RUN apt-get install -y libbz2-dev
+#RUN apt-get install -y coinor-libclp-dev 
+RUN apt-get install -y libboost-all-dev 
 
-WORKDIR /home
+RUN useradd -ms /bin/bash hops_user
+USER hops_user
 
-ADD benchmarks /home/benchmarks
-ADD cmake /home/cmake
-ADD docs /home/docs
-ADD examples /home/examples
-ADD include /home/include
-ADD resources /home/resources
-ADD src /home/src
-ADD tests /home/tests
-ADD CMakeLists.txt /home/CMakeLists.txt
+WORKDIR /home/hops_user
 
-RUN mkdir cmake-build-debug
-RUN mkdir cmake-build-release
+ADD bin /home/hops_user/bin
+ADD benchmarks /home/hops_user/benchmarks
+ADD cmake /home/hops_user/cmake
+ADD docs /home/hops_user/docs
+ADD include /home/hops_user/include
+ADD resources /home/hops_user/resources
+ADD src /home/hops_user/src
+ADD tests /home/hops_user/tests
+ADD CMakeLists.txt /home/hops_user/CMakeLists.txt
 
-WORKDIR /home/cmake-build-debug
-RUN cmake .. -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu
-RUN make -j4
-RUN make test ARGS=j4
+RUN mkdir cmake-build-debug
+WORKDIR /home/hops_user/cmake-build-debug
+RUN cmake .. -DCMAKE_BUILD_TYPE=Debug -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu
+RUN make -j8
+RUN make test
 
-WORKDIR /home/cmake-build-release
+WORKDIR /home/hops_user/
+RUN mkdir cmake-build-release
+WORKDIR /home/hops_user/cmake-build-release
 RUN cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu
-RUN make -j4
-RUN make test ARGS=j4
+RUN make -j8
+RUN make test

README.md

@@ -14,6 +14,15 @@ Test data from the application note is downloadable at https://doi.org/10.26165/
 
 See https://modsim.github.io/hops/.
 
+## Cloning from Github
+
+HOPS contains git submodules that point to third-party libraries.
+For this reason, HOPS should be fetched recursively:
+
+```
+git clone git@github.com:modsim/hops.git --recursive
+```
+
 ## Installation
 
 HOPS uses CMake as build system.  

bin/CMakeLists.txt

@@ -0,0 +1,21 @@
+if (HOPS_MPI_SUPPORTED)
+    set(BIN_SOURCES ${EXAMPLE_SOURCES} ParallelTemperingDemo.cpp)
+endif (HOPS_MPI_SUPPORTED)
+
+foreach (BIN_SOURCE ${EXAMPLE_SOURCES})
+    get_filename_component(BIN_NAME ${EXAMPLE_SOURCE} NAME_WE)
+    add_executable(${BIN_NAME} ${EXAMPLE_SOURCE})
+    target_link_libraries(${BIN_NAME} hops)
+    target_include_directories(${BIN_NAME} PUBLIC ../include)
+endforeach (BIN_SOURCE)
+
+find_package(Boost COMPONENTS program_options REQUIRED)
+add_executable(hops-sampler hops-sampler.cpp hops-sampler.hpp)
+target_link_libraries(hops-sampler hops ${Boost_LIBRARIES})
+target_include_directories(hops-sampler PUBLIC
+        $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/../include/${LIBRARY_NAME}>
+        $<INSTALL_INTERFACE:../include/${LIBRARY_NAME}>
+        )
+
+
+

examples/ParallelTemperingDemo.cpp bin/ParallelTemperingDemo.cppexamples/ParallelTemperingDemo.cpp renamed to bin/ParallelTemperingDemo.cpp

@@ -52,7 +52,7 @@ int main(int argc, char **argv) {
         } else {
             std::unique_ptr<hops::LinearProgram> linearProgram = hops::LinearProgramFactory::createLinearProgram(
                     Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic>(A.cast<double>()),
-                    b.cast<double>());
+                    b.cast<double>();
             startingPoint = linearProgram->calculateChebyshevCenter().optimalParameters.cast<RealType>();
         }
 
@@ -124,7 +124,7 @@ int main(int argc, char **argv) {
     std::cout << "Current step size: " << markovChain->getAttribute(hops::MarkovChainAttribute::STEP_SIZE) << std::endl;
 
     auto fileWriter = hops::FileWriterFactory::createFileWriter(std::string(argv[8]) + "_" + markovChain->getName(),
-                                                                hops::FileWriterType::Csv);
+                                                                hops::FileWriterType::CSV);
     markovChain->draw(randomNumberGenerator, numberOfSamples, thinning);
     markovChain->writeHistory(fileWriter.get());
     markovChain->clearHistory();