Merge pull request #342 from ICB-DCM/develop

Release 0.4.6

.github/workflows/parpe_tests.yml

@@ -53,13 +53,14 @@ jobs:
           -DBUILD_TESTS=OFF \
           && cmake --build "${AMICI_PATH}/build" --parallel -- VERBOSE=1
 
-    - name: Install google test
-      run: ThirdParty/installGoogleTest.sh
-
     - name: Install parPE Python deps
       run: |
         pip install -r ${PARPE_BASE}/python/requirements.txt
 
+    - name: "Install parPE deps: fides"
+      run: |
+        sudo apt install libspdlog-dev && ${PARPE_BASE}/ThirdParty/installFides.sh
+
     - name: Configure parPE
       run: |
         cmake \
@@ -69,7 +70,8 @@ jobs:
           -DIPOPT_INCLUDE_DIRS=/usr/include/coin/ \
           -DIPOPT_LIBRARIES=/usr/lib/libipopt.so \
           -DGCOV_REPORT=TRUE \
-          -DBUILD_TESTING=TRUE
+          -DBUILD_TESTING=TRUE \
+          -DPARPE_ENABLE_FIDES=TRUE
 
     - name: Build parPE
       # with sonar build wrapper

CMakeLists.txt

@@ -1,5 +1,5 @@
-cmake_minimum_required(VERSION 3.10) # for GoogleTest
-cmake_policy(VERSION 3.10)
+cmake_minimum_required(VERSION 3.13) # pkg_search_module GLOBAL
+cmake_policy(VERSION 3.13)
 
 if(POLICY CMP0074)
   # Use package_ROOT environment variables
@@ -51,6 +51,7 @@ set(BUILD_PYTHON_MODULE FALSE CACHE BOOL "Build Python module?")
 set(BLAS "CBLAS" CACHE STRING "BLAS library to use")
 set_property(CACHE BLAS PROPERTY STRINGS "CBLAS" "MKL")
 set(PARPE_ENABLE_MPI TRUE CACHE BOOL "Use MPI?")
+set(PARPE_ENABLE_FIDES FALSE CACHE BOOL "Enable fides optimizer?")
 set(PARPE_ENABLE_IPOPT TRUE CACHE BOOL "Enable ipopt optimizer?")
 set(PARPE_ENABLE_CERES TRUE CACHE BOOL "Enable ceres optimizer?")
 set(PARPE_ENABLE_DLIB FALSE CACHE BOOL "Enable dlib optimizers?")
@@ -68,13 +69,17 @@ if(${PARPE_ENABLE_MPI})
 endif(${PARPE_ENABLE_MPI})
 # </Build options>
 
+if(${PARPE_ENABLE_FIDES})
+    find_package(Fides REQUIRED)
+endif(${PARPE_ENABLE_FIDES})
+
 find_package(PkgConfig)
 pkg_search_module(IPOPT REQUIRED IMPORTED_TARGET GLOBAL ipopt>=3.11.0 )
 
-if(${ENABLE_DLIB})
+if(${PARPE_ENABLE_DLIB})
     set(DLIB_DIR "${CMAKE_CURRENT_LIST_DIR}/ThirdParty/dlib-19.7"
         CACHE FILEPATH "DLIB base directory")
-endif(${ENABLE_DLIB})
+endif(${PARPE_ENABLE_DLIB})
 
 # PThreads
 set(THREADS_PREFER_PTHREAD_FLAG ON)
@@ -101,25 +106,6 @@ if(${BUILD_TESTING})
     set(TESTS_MPIEXEC_COMMAND
         mpiexec --allow-run-as-root --oversubscribe -n 4 CACHE STRING "")
 
-    # googletest
-    add_definitions(-DGTEST_LANGUAGE_CXX11)
-    find_package(Threads REQUIRED)
-    if ($ENV{GOOGLETEST_DIR})
-        set(GOOGLETEST_DIR $ENV{GOOGLETEST_DIR})
-    else()
-        set(GOOGLETEST_DIR "${CMAKE_CURRENT_LIST_DIR}/ThirdParty/googletest")
-    endif()
-    if (EXISTS ${GOOGLETEST_DIR})
-        set(GTestSrc ${GOOGLETEST_DIR}/googletest)
-        set(GMockSrc ${GOOGLETEST_DIR}/googlemock)
-    else ()
-        message(FATAL_ERROR "No googletest src dir found - set GOOGLETEST_DIR "
-            "or run ../ThirdParty/installGoogleTest.sh to enable!"
-            " (Or disable building tests with BUILD_TESTING=OFF)")
-    endif ()
-    include_directories(${GTestSrc} "${GTestSrc}/include"
-        ${GMockSrc} "${GMockSrc}/include")
-
     # <Coverage>
     # Create test coverage reports?
     set(GCOV_REPORT FALSE CACHE BOOL "Create GCOV report?")

CMakeModules/ParPEConfig.cmake.in

@@ -5,14 +5,16 @@ include(CMakeFindDependencyMacro)
 set(PARPE_ENABLE_MPI @PARPE_ENABLE_MPI@)
 set(PARPE_ENABLE_IPOPT @PARPE_ENABLE_IPOPT@)
 set(PARPE_ENABLE_CERES @PARPE_ENABLE_CERES@)
+set(PARPE_ENABLE_FIDES @PARPE_ENABLE_FIDES@)
 
 if(${PARPE_ENABLE_MPI})
 find_dependency(MPI REQUIRED)
 endif()
 
 if(${PARPE_ENABLE_IPOPT})
 find_dependency(PkgConfig REQUIRED)
-pkg_search_module(IPOPT REQUIRED IMPORTED_TARGET GLOBAL ipopt>=3.11.0)
+pkg_search_module(IPOPT REQUIRED IMPORTED_TARGET GLOBAL ipopt=@IPOPT_VERSION@)
+message("-- Found Ipopt version: ${IPOPT_VERSION}")
 endif()
 
 if(${PARPE_ENABLE_CERES})
@@ -21,6 +23,11 @@ find_dependency(Ceres COMPONENTS
 find_dependency(Eigen3 REQUIRED)
 endif()
 
+if(${PARPE_ENABLE_FIDES})
+find_dependency(Fides
+    HINTS "${CMAKE_SOURCE_DIR}/ThirdParty/fides-cpp/build/")
+endif()
+
 find_dependency(Amici REQUIRED)
 find_dependency(OpenMP)
 find_dependency(HDF5 COMPONENTS C CXX HL REQUIRED)

ThirdParty/installDeps.sh

@@ -15,5 +15,3 @@ cd "$script_dir"
 ./installCeres.sh
 
 ./installIpopt.sh
-
-./installGoogleTest.sh

ThirdParty/installDlib.sh

@@ -1,24 +1,32 @@
 #!/usr/bin/env bash
-# build DLIB
+# Download and build DLIB
 
 set -euo pipefail
+script_dir=$(dirname "$0")
+script_dir=$(cd "${script_dir}" && pwd)
+cd "${script_dir}"
+
+make_opts=${MAKEOPTS-}
 
 dlib_archive="dlib-19.7.tar.bz2"
-if [ ! -d "dlib-19.7" ]; then
+dlib_dir=${script_dir}/dlib-19.7
+
+if [ ! -d "${dlib_dir}" ]; then
   if [ ! -f "${dlib_archive}" ]; then
-    wget "http://dlib.net/files/${dlib_archive}" -o "${dlib_archive}"
+    wget "http://dlib.net/files/${dlib_archive}" -O "${dlib_archive}"
   fi
   tar -xjf "${dlib_archive}"
 fi
 
-cd "dlib-19.7/"
+cd "${dlib_dir}"
 mkdir -p build && cd build/
- cmake -DCMAKE_INSTALL_PREFIX="$(pwd)/install" \
-    -DDLIB_NO_GUI_SUPPORT=ON \
-    -DDLIB_GIF_SUPPORT=OFF \
-    -DDLIB_JPEG_SUPPORT=OFF \
-    -DDLIB_PNG_SUPPORT=OFF \
-    -DDLIB_LINK_WITH_SQLITE3=OFF \
-    ..
+cmake -S .. \
+  -DCMAKE_INSTALL_PREFIX="$(pwd)/install" \
+  -DDLIB_NO_GUI_SUPPORT=ON \
+  -DDLIB_GIF_SUPPORT=OFF \
+  -DDLIB_JPEG_SUPPORT=OFF \
+  -DDLIB_PNG_SUPPORT=OFF \
+  -DDLIB_LINK_WITH_SQLITE3=OFF \
+  ..
 
-make -j12 && make install
+make ${make_opts} && make install

ThirdParty/installFides.sh

@@ -0,0 +1,44 @@
+#!/usr/bin/env bash
+# Download and build fides-cpp
+
+build_blaze() {
+  cd "${script_dir}"
+
+  if [[ ! -d "${blaze_dir}" ]]; then
+    if [[ ! -f "blaze-3.8.tar.gz" ]]; then
+      wget https://bitbucket.org/blaze-lib/blaze/downloads/blaze-3.8.tar.gz
+    fi
+    tar -xzf blaze-3.8.tar.gz
+    cd blaze-3.8
+    cmake -S . -B build/ -DCMAKE_INSTALL_PREFIX="$(pwd)/build/install"
+    cd build
+    make -j2 install
+  fi
+}
+
+build_fides() {
+  if [ ! -d "${fides_dir}" ]; then
+    cd "${script_dir}"
+    git clone https://github.com/dweindl/fides-cpp.git
+    cd "${fides_dir}"
+    git checkout 9906bdac6a1966ddd4b37b96f98ad8f89770c128
+  fi
+
+  cd "${fides_dir}"
+  cmake -S . -B build -DBUILD_TESTING=OFF
+  cd build
+  make ${make_opts}
+}
+
+set -euo pipefail
+script_dir=$(dirname "$0")
+script_dir=$(cd "${script_dir}" && pwd)
+cd "${script_dir}"
+
+make_opts=${MAKEOPTS-}
+
+fides_dir=${script_dir}/fides-cpp
+blaze_dir=${script_dir}/blaze-3.8
+
+build_blaze
+build_fides

ThirdParty/installIpopt.sh

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# build Ipopt
+# Download and build Ipopt and HSL
 
 set -euo pipefail
 script_dir=$(dirname "$0")
@@ -16,6 +16,7 @@ hsl_install_dir="${ipopt_dir}/ThirdParty-HSL/install"
 
 if [[ ! -d "${ipopt_dir}" ]]; then
   if [[ ! -f "${ipopt_archive}" ]]; then
+    echo "Downloading IpOpt source archive ..."
     wget -O "${ipopt_archive}" "${ipopt_url}"
   else
     echo "Skipping download step."
@@ -26,50 +27,63 @@ if [[ ! -d "${ipopt_dir}" ]]; then
   # Handle HSL solvers
   cd "${ipopt_dir}"
   if [[ ! -d "ThirdParty-HSL" ]]; then
+    echo "Cloning ThirdParty-HSL ..."
     git clone https://github.com/coin-or-tools/ThirdParty-HSL.git
   fi
 
   cd ThirdParty-HSL
 
+  # Need some coinhsl library.
   if [[ ! -d "coinhsl" ]]; then
-    # Need some coinhsl library. Check for common ones:
-    if [[ -f "${script_dir}/coinhsl-2015.06.23.tar.gz" ]]; then
-      tar -xzf "${script_dir}/coinhsl-2015.06.23.tar.gz"
-      mv coinhsl-2015.06.23 coinhsl
-    elif [[ -f "${script_dir}/coinhsl-2014.01.10.tar.gz" ]]; then
-      tar -xzf "${script_dir}/coinhsl-2014.01.10.tar.gz"
-      mv coinhsl-2014.01.10 coinhsl
-    elif [[ -f "${script_dir}/coinhsl-2019.05.21.tar.gz" ]]; then
-      tar -xzf "${script_dir}/coinhsl-2019.05.21.tar.gz"
-      mv coinhsl-2019.05.21 coinhsl
+    # ThirdParty/coinhsl ?
+    if [[ -d "${script_dir}/coinhsl" ]]; then
+      echo "Using coinhsl from ${script_dir}/coinhsl"
+      cp -aR "${script_dir}/coinhsl" coinhsl
     else
-      echo "Did not find coinhsl/ or a known coinhsl archive."
-      echo "Name your coinhsl version."
-      read version
-      if [[ -f "${script_dir}/coinhsl-${version}.tar.gz" ]]; then
-      	tar -xzf "${script_dir}/coinhsl-${version}.tar.gz"
-      	mv coinhsl-${version} coinhsl
-      else
-      	echo "Press any key to continue"
-      	read -n 1 -s -r
-      fi
+      # Check for common ones:
+      coinhsl_archive_names="
+      coinhsl-2014.01.10
+      coinhsl-2015.06.23
+      coinhsl-2019.05.21
+      "
+      for coinhsl_archive in $coinhsl_archive_names; do
+        if [[ -f "${script_dir}/${coinhsl_archive}.tar.gz" ]]; then
+          echo "Unpacking ${script_dir}/${coinhsl_archive}.tar.gz ..."
+          tar -xzf "${script_dir}/${coinhsl_archive}.tar.gz"
+          mv "${coinhsl_archive}" coinhsl
+        fi
+      done
     fi
+
+    if [[ ! -d "coinhsl" ]]; then
+      echo "Did not find coinhsl/ or a known coinhsl archive." \
+      "IpOpt will probably not work."
+    fi
+  fi
+
+  # Use Intel MKL for lapack?
+  lapack_lflags=""
+  if [[ -v MKL_SHLIB ]]; then
+    # Will require F77=ifort when using intel compilers.
+    lapack_lflags="--with-lapack-lflags=${MKL_SHLIB}"
   fi
 
-  ./configure --prefix="${hsl_install_dir}"
-  make
+  ./configure --prefix="${hsl_install_dir}" \
+    --with-lapack "${lapack_lflags}" \
+    --disable-static --enable-shared
+  make $make_opts
   make install
-  (cd ${hsl_install_dir}/lib && test ! -e libhsl.so && ln -s libcoinhsl.so libhsl.so || true)
 
   cd "${ipopt_dir}"
+
+  PKG_CONFIG_PATH=${PKG_CONFIG_PATH-}:${hsl_install_dir}/lib/pkgconfig/ \
   ./configure --prefix="${ipopt_install_dir}" \
-    --enable-static \
-    --disable-shared \
+    --disable-static \
+    --enable-shared \
     --with-pic \
     --with-hsl \
-    --with-hsl-cflags=-I${hsl_install_dir}/include/coin-or/hsl \
-    --with-hsl-lflags="-L${hsl_install_dir}/lib/ -lcoinhsl" \
-    --disable-linear-solver-loader
+    --disable-linear-solver-loader \
+    --with-lapack "${lapack_lflags}"
   make $make_opts
   make $make_opts install
 else