Use Ubuntu 24.04

.github/workflows/benchmark_models.yml

@@ -35,10 +35,6 @@ jobs:
             -DBUILD_TESTS=OFF \
           && cmake --build "${AMICI_PATH}/build" --parallel -- VERBOSE=1
 
-    - name: Install parPE Python deps
-      run: |
-        pip install -r ${PARPE_BASE}/python/requirements.txt
-
     - name: Configure parpe
       run: |
         cmake \

.github/workflows/parpe_tests.yml

@@ -18,7 +18,6 @@ jobs:
       # If we are running in docker, we generally don't have SYS_PTRACE
       #  permissions  and thus, cannot use vader. Also disable Infiniband.
       PARPE_TESTS_MPIEXEC: mpiexec -n 5 --oversubscribe --allow-run-as-root --mca btl_vader_single_copy_mechanism none --mca btl ^openib --mca oob_tcp_if_include lo --mca btl_tcp_if_include lo --mca orte_base_help_aggregate 0
-
     steps:
     - uses: actions/checkout@master
     - name: chown checkout directory
@@ -58,10 +57,9 @@ jobs:
           -DBUILD_TESTS=OFF \
           && cmake --build "${AMICI_PATH}/build" --parallel -- VERBOSE=1
 
-    - name: Install parPE Python deps
+    - name: Install parPE deps
       run: |
-        pip install -r ${PARPE_BASE}/python/requirements.txt \
-          && sudo apt install lcov
+        sudo apt install lcov
 
     - name: "Install parPE deps: fides"
       run: |

.github/workflows/petab_testsuite.yml

@@ -36,10 +36,6 @@ jobs:
             -DBUILD_TESTS=OFF \
           && cmake --build "${AMICI_PATH}/build" --parallel -- VERBOSE=1
 
-    - name: Install parPE Python deps
-      run: |
-        pip install -r ${PARPE_BASE}/python/requirements.txt
-
     - name: Configure parpe
       run: |
         cmake \

cmake/CodeCoverage.cmake

@@ -41,6 +41,9 @@
 # 2017-06-02, Lars Bilke
 # - Merged with modified version from github.com/ufz/ogs
 #
+# 2024-10-13, Daniel Weindl
+# - Added "--ignore-errors mismatch" to lcov command to ignore errors with
+#   recent gcc
 #
 # USAGE:
 #
@@ -157,7 +160,7 @@ function(SETUP_TARGET_FOR_COVERAGE)
         COMMAND ${Coverage_EXECUTABLE}
 
         # Capturing lcov counters and generating report
-        COMMAND ${LCOV_PATH} --directory . --capture --output-file ${Coverage_NAME}.info
+        COMMAND ${LCOV_PATH} --directory . --capture --output-file ${Coverage_NAME}.info --ignore-errors mismatch
         COMMAND ${LCOV_PATH} --remove ${Coverage_NAME}.info ${COVERAGE_EXCLUDES} --output-file ${Coverage_NAME}.info.cleaned
         COMMAND ${GENHTML_PATH} -o ${Coverage_NAME} ${Coverage_NAME}.info.cleaned
         COMMAND ${CMAKE_COMMAND} -E remove ${Coverage_NAME}.info ${Coverage_NAME}.info.cleaned

container/charliecloud/parpe_base/Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:22.04
+FROM ubuntu:24.04
 
 COPY . /container-files
 
@@ -9,7 +9,6 @@ ENV CC clang
 ENV CXX clang++
 ENV OMPI_CC clang
 ENV OMPI_CXX clang++
-
 RUN /container-files/install_parpe.sh
 
 ENV PARPE_DIR "/parPE"

container/charliecloud/parpe_base/install.sh

@@ -39,10 +39,6 @@ apt-get install -q -y \
   unzip \
   wget
 
-# for setuptools to find:
-python3 -m pip install --upgrade pip
-pip3 install -U setuptools pkgconfig wheel
-
 echo "================= Cleaning package lists ==================="
 apt-get clean
 apt-get autoclean

container/charliecloud/parpe_base/install_parpe.sh

@@ -26,9 +26,6 @@ cmake \
 # install fides optimizer
 cd "$PARPE_BASE/ThirdParty" && ./installFides.sh
 
-# install parPE python requirements
-pip3 install -r "${PARPE_BASE}"/python/requirements.txt
-
 # build parPE
 cd "${PARPE_BASE}"
 mkdir -p build
@@ -45,7 +42,7 @@ mpi_cmd="$mpi_cmd;--mca;oob_tcp_if_include;lo"
 mpi_cmd="$mpi_cmd;--mca;btl_tcp_if_include;lo;"
 mpi_cmd="$mpi_cmd;--mca;orte_base_help_aggregate;0"
 
-CC=mpicc CXX=mpiCC cmake \
+cmake \
       -DPARPE_BUILD_OPTIMIZED=OFF \
       -DPARPE_ENABLE_FIDES=ON \
       -DIPOPT_INCLUDE_DIRS=/usr/include/coin/ \

src/parpeamici/CMakeLists.txt

@@ -37,11 +37,22 @@ target_include_directories(${PROJECT_NAME}
 )
 
 target_link_libraries(${PROJECT_NAME}
-    PUBLIC parpeoptimization
     PUBLIC parpeloadbalancer
     PUBLIC parpecommon
     PUBLIC Upstream::amici
     PUBLIC ${Boost_SERIALIZATION_LIBRARY_RELEASE}
+    # For not fully understood reasons, `parpeoptimization` needs to come last.
+    # There was an issue with the Ubuntu 24.04 ipopt package, which is pulling
+    # in libdmumps_seq-5.6.so, which exports dummy MPI_* symbols that cause
+    # problems when building parpe with MPI. Run-time resolution would pick up
+    # the incorrect MPI symbols. We need to make sure that MPI::MPI_C linker
+    # flags come first, but CMake first lists all direct dependencies, and only
+    # then the transitive dependencies (in this case, in an unfortunate order).
+    # INTERFACE_LINK_LIBRARIES_DIRECT did not help.
+    # Note that in this case, parpe should *not* be compiled with the MPI
+    # compiler wrappers (mpicc, mpicxx), because this will prevent CMake from
+    # adding the MPI linker flags.
+    PUBLIC parpeoptimization
 )
 
 if (${OpenMP_FOUND})

tests/parpe.supp

@@ -84,7 +84,7 @@
    libhwloc
    Memcheck:Leak
    match-leak-kinds: all
-   fun:calloc
+   fun:*alloc
    ...
    obj:/usr/lib/x86_64-linux-gnu/libhwloc.so.15.*.*
    ...
@@ -447,7 +447,7 @@
    fun:_ZN2H58PredTypeC1El
    fun:_ZN2H58PredType13makePredTypesEv
    fun:_ZN2H58PredType12getPredTypesEv
-   obj:/usr/lib/x86_64-linux-gnu/libhdf5_serial_cpp.so.103.3.0
+   obj:/usr/lib/x86_64-linux-gnu/libhdf5_serial_cpp.so.*
 }
 
 
@@ -518,3 +518,18 @@
    fun:orte_init
    ...
 }
+
+
+{
+   fides_cpp
+   Memcheck:BadSize
+   fun:posix_memalign
+   fun:_ZN5blaze15alignedAllocateEmm
+   fun:_ZN5blaze16AlignedAllocatorIdE8allocateEm
+   fun:_ZN5blaze13DynamicMatrixIdLb0ENS_16AlignedAllocatorIdEENS_8GroupTagILm0EEEEC1EmmmmRKS2_NS5_13UninitializedE
+   fun:_ZN5blaze13DynamicMatrixIdLb0ENS_16AlignedAllocatorIdEENS_8GroupTagILm0EEEEC1EmmmRKS2_NS5_13UninitializedE
+   fun:_ZN5blaze13DynamicMatrixIdLb0ENS_16AlignedAllocatorIdEENS_8GroupTagILm0EEEEC1EmmRKS2_
+   fun:_ZN5blaze13DynamicMatrixIdLb0ENS_16AlignedAllocatorIdEENS_8GroupTagILm0EEEEC1ERKS5_
+   fun:_ZN5fides9Optimizer11do_minimizeEv
+   ...
+}