CI: draft FreeBSD source-build workflow (test run)

.github/workflows/freebsd.yml

@@ -0,0 +1,134 @@
+name: freebsd
+
+# Source build of McStas/McXtrace in a FreeBSD VM, after the approach in
+# mctools/mcpl and mctools/ncrystal (.github/workflows/freebsd.yml).
+# Tests follow {mcstas,mcxtrace}-basictest.yml (classic cogen, no KDSource/xraylib),
+# artifacts use their naming so they can sit next to the other platforms' output.
+on:
+  push:
+    branches: [main]
+  pull_request:
+  schedule:
+    - cron: '30 22 * * 0'  # 22:30 every Sunday
+  workflow_dispatch:
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - flavor: mcstas
+            build: BUILD_MCSTAS
+            mcrun: mcrun
+            mctest: mctest
+            mpilists: Tests_monitors
+            instr: BNL_H8,ISIS_CRISP,templateSANS_Mantid,NCrystal_example,ESS_BEER_MCPL,Test_MCPL_input,Test_MCPL_output,Masked_ESS_butterfly_image
+          - flavor: mcxtrace
+            build: BUILD_MCXTRACE
+            mcrun: mxrun
+            mctest: mxtest
+            mpilists: Tests
+            instr: JJ_SAXS,ESRF_BM29,Test_MCPL_input,Test_MCPL_output
+    name: freebsd.${{ matrix.flavor }}
+    runs-on: ubuntu-latest
+    env:
+      LABEL: ${{ matrix.flavor }}-classic.freebsd.freebsd-14.2.cc.mpich.python-pkg
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+        with:
+          path: src
+
+      - name: FreeBSD
+        uses: cross-platform-actions/[email protected]
+        with:
+          operating_system: freebsd
+          version: '14.2'
+          run: |
+            set -eux
+            # FreeBSD's clang does not search /usr/local, so GSL and HDF5 dirs are passed explicitly.
+            # mpich, not openmpi: the openmpi pkg keeps mpicc/mpirun outside PATH.
+            # MPI builds use base cc + mpich paths, not mpich's mpicc: mpicc links with binutils ld,
+            # which lacks LLVMgold.so for the -flto that cmake probed with cc/lld.
+            # Python modules by port origin: follows the default Python flavour (pyXYZ-) on pkg updates.
+            sudo pkg install -y cmake bison flex gsl hdf5 mpich python3 devel/py-pip devel/py-pyyaml devel/py-ply sysutils/py-psutil math/py-numpy science/py-h5py
+            # MCPL and NCrystal from PyPI (sdist builds, as in their own FreeBSD CI); McCode finds
+            # them at instrument compile time via mcpl-config / ncrystal-config on PATH.
+            python3 -mpip install --user mcpl ncrystal
+            PATH="$HOME/.local/bin:$PATH"
+            export PATH
+            mcpl-config --show buildflags
+            ncrystal-config --show buildflags
+            cmake -S ./src -B ./build \
+                -DCMAKE_INSTALL_PREFIX=$PWD/install \
+                -DCMAKE_BUILD_TYPE=Release \
+                -DMCVERSION="3.99.99" \
+                -DMCCODE_BUILD_CONDA_PKG=OFF \
+                -DMCCODE_USE_LEGACY_DESTINATIONS=OFF \
+                -DBUILD_SHARED_LIBS=ON \
+                -DCMAKE_INSTALL_LIBDIR=lib \
+                -D${{ matrix.build }}=ON \
+                -DBUILD_TOOLS=ON \
+                -DENABLE_COMPONENTS=ON \
+                -DENSURE_MCPL=OFF \
+                -DENSURE_NCRYSTAL=OFF \
+                -DENABLE_CIF2HKL=OFF \
+                -DENABLE_NEUTRONICS=OFF \
+                -DGSLFLAGS="-I/usr/local/include -Wl,-rpath,/usr/local/lib -L/usr/local/lib -lgsl -lgslcblas" \
+                -DNEXUSLIB=/usr/local/lib \
+                -DNEXUSINCLUDE=/usr/local/include \
+                -DMPICC=cc \
+                -DMPILIBDIR=/usr/local/lib \
+                -DMPIINCLUDEDIR=/usr/local/include
+            cmake --build ./build --config Release --parallel 2
+            cmake --install ./build --config Release
+            PATH="$PWD/install/bin:$PATH"
+            export PATH
+            cat install/share/${{ matrix.flavor }}/tools/Python/mccodelib/mccode_config.json
+            ${{ matrix.flavor }} --version
+            # RNG test (same expected checksum as the basictests)
+            ${{ matrix.mctest }} --verbose --noplots --instr=Test_RNG_rand01 --testdir=run_rngtest --suffix=classic_freebsd --uid=freebsd
+            SUM=$(find run_rngtest -name rngout.dat | xargs -n1 grep -v \# | md5 -q)
+            test "$SUM" = "6c203d69205b0656c1391555e6068c93"
+            # Basic tests
+            ${{ matrix.mctest }} --verbose --noplots --mpi=2 --instr=${{ matrix.instr }} --testdir=run_basictests --suffix=classic_freebsd_cc_mpich --uid=freebsd
+            # MPI event-list, NeXus output and mcplot loader regression tests.
+            # No SIGTERM check: the runtime installs its sighandler with OpenMPI only (MPICH uses signals).
+            python3 src/${{ matrix.flavor }}-comps/examples/${{ matrix.mpilists }}/Test_Monitor_nD_list_MPI/test_mpi_lists.py --np 2 --mcrun ${{ matrix.mcrun }} --workdir run_mpilists --sigterm-ncount 0
+            python3 src/${{ matrix.flavor }}-comps/examples/Tests_other/Test_NeXus_output/test_nexus_output.py --np 2 --mcrun ${{ matrix.mcrun }} --workdir run_nexusoutput
+            python3 src/${{ matrix.flavor }}-comps/examples/Tests_other/Test_mcplot_loader/test_mcplot_loader.py --mcrun ${{ matrix.mcrun }} --workdir run_mcplotloader
+
+      # The VM syncs the work dir back to the host on teardown, also after a failure
+      - name: 'Tar output files'
+        if: always()
+        run: |
+             set -eux
+             ls | grep run_ | xargs -n1 ./src/devel/bin/mccode-simdir-cleanfiles -d
+             tar cvfz ${LABEL}_output.tgz run_*
+
+      - name: 'Upload Artifact'
+        uses: actions/upload-artifact@v6
+        if: always()
+        with:
+          name: ${{ matrix.flavor }}-artefacts-classic.freebsd.freebsd-14.2.cc.mpich.python-pkg
+          path: ${{ env.LABEL }}_output.tgz
+
+      - name: 'Tar logs of failed tests'
+        if: always()
+        run: |
+             set -eux
+             { find run_* -name '*.failed' 2>/dev/null || true
+               grep -rl --include='*.json' --exclude='testresults_*' '"failed": true' run_* 2>/dev/null || true
+             } | sed 's#/[^/]*$##' | sort -u | while read -r d; do
+               find "$d" -maxdepth 1 -type f \( -name '*.txt' -o -name '*.failed' -o -name '*.json' \)
+             done > failed_logs.txt
+             if [ -s failed_logs.txt ]; then tar cvfz ${LABEL}_failedlogs.tgz -T failed_logs.txt; fi
+
+      - name: 'Upload failed-test logs'
+        uses: actions/upload-artifact@v6
+        if: always()
+        with:
+          name: ${{ matrix.flavor }}-failedlogs-classic.freebsd.freebsd-14.2.cc.mpich.python-pkg
+          path: ${{ env.LABEL }}_failedlogs.tgz
+          if-no-files-found: ignore

.github/workflows/mcstas-basictest.yml

@@ -86,13 +86,13 @@ jobs:
       id: setup-linux
       if: matrix.method == 'source' && runner.os == 'Linux'
       run: |
-           sudo apt -y install libgsl-dev libnexus-dev
+           sudo apt -y install libgsl-dev libhdf5-dev
 
     - name: Setup (macOS, source build)
       id: setup-macos
       if: matrix.method == 'source' && runner.os == 'macOS'
       run: |
-           brew install bison flex gfortran gsl homebrew/science/nexusformat
+           brew install bison flex gfortran gsl hdf5
 
     - name: Setup (Windows, source build)
       id: setup-Windows
@@ -161,7 +161,6 @@ jobs:
            if [ "$RUNNER_OS" == "macOS" ] && [ -f "/opt/homebrew/opt/flex/bin/flex" ]; then export HOMEBRW="/opt/homebrew/opt"; export GSLFLAGS="-lgsl -lgslcblas -L/opt/homebrew/lib -I/opt/homebrew/include"; fi
            if [ "$RUNNER_OS" == "macOS" ] && [ -f "/usr/local/opt/flex/bin/flex" ]; then export HOMEBRW="/usr/local/opt"; export GSLFLAGS="-lgsl -lgslcblas -L/usr/local/lib -I/usr/local/include"; fi
            if [ "$RUNNER_OS" == "macOS" ]; then export EXTRA_ARGS_FOR_CMAKE="-DBISON_EXECUTABLE=${HOMEBRW}/bison/bin/bison -DFLEX_EXECUTABLE=${HOMEBRW}/flex/bin/flex -DCMAKE_Fortran_COMPILER=${HOMEBRW}/gfortran/bin/gfortran"; fi
-           if [ "$RUNNER_OS" == "Linux" ]; then export EXTRA_ARGS_FOR_CMAKE="-DNEXUSLIB=/usr/lib -DNEXUSINCLUDE=/usr/include/nexus"; fi
            if [ "$RUNNER_OS" == "Windows" ]; then export MPIINC=`cygpath -m -s  "${MSMPI_INC}"`; export MPILIB=`cygpath -m -s  "${MSMPI_LIB64}"`; export EXTRA_ARGS_FOR_CMAKE="-DMPILIBDIR=${MPILIB} -DMPIINCLUDEDIR=${MPIINC}"; fi
            cmake \
                -DCMAKE_INSTALL_PREFIX=../install_mcstas \

.github/workflows/mcxtrace-basictest.yml

@@ -86,7 +86,7 @@ jobs:
       id: setup-linux
       if: matrix.method == 'source' && runner.os == 'Linux'
       run: |
-           sudo apt -y install libgsl-dev libxrl-dev libnexus-dev
+           sudo apt -y install libgsl-dev libxrl-dev libhdf5-dev
 
     - name: Setup (macOS, source build)
       id: setup-macos
@@ -95,7 +95,7 @@ jobs:
       # cause build-issues. Will soon port basictest scripts to conda
       # for Windows/Linux
       run: |
-           brew install bison flex gfortran gsl
+           brew install bison flex gfortran gsl hdf5
            #if [ "${{ matrix.os }}" != "macos-15" ];
            #then
            #  brew tap tschoonj/tap
@@ -169,7 +169,6 @@ jobs:
            if [ "$RUNNER_OS" == "macOS" ] && [ -f "/opt/homebrew/opt/flex/bin/flex" ]; then export HOMEBRW="/opt/homebrew/opt"; export GSLFLAGS="-lgsl -lgslcblas -L/opt/homebrew/lib -I/opt/homebrew/include"; export XRLFLAGS="-lxrl -L/opt/homebrew/lib -I/opt/homebrew/include"; fi
            if [ "$RUNNER_OS" == "macOS" ] && [ -f "/usr/local/opt/flex/bin/flex" ]; then export HOMEBRW="/usr/local/opt"; export GSLFLAGS="-lgsl -lgslcblas -L/usr/local/lib -I/usr/local/include"; export XRLFLAGS="-lxrl -L/usr/local/lib -I/usr/local/include"; fi
            if [ "$RUNNER_OS" == "macOS" ]; then export EXTRA_ARGS_FOR_CMAKE="-DBISON_EXECUTABLE=${HOMEBRW}/bison/bin/bison -DFLEX_EXECUTABLE=${HOMEBRW}/flex/bin/flex -DCMAKE_Fortran_COMPILER=${HOMEBRW}/gfortran/bin/gfortran"; fi
-           if [ "$RUNNER_OS" == "Linux" ]; then export EXTRA_ARGS_FOR_CMAKE="-DNEXUSLIB=/usr/lib -DNEXUSINCLUDE=/usr/include/nexus"; fi
            if [ "$RUNNER_OS" == "Windows" ]; then export MPIINC=`cygpath -m -s  "${MSMPI_INC}"`; export MPILIB=`cygpath -m -s  "${MSMPI_LIB64}"`; export EXTRA_ARGS_FOR_CMAKE="-DMPILIBDIR=${MPILIB} -DMPIINCLUDEDIR=${MPIINC}"; fi
            cmake \
                -DCMAKE_INSTALL_PREFIX=../install_mcxtrace \

3rdparty/sync.sh

@@ -27,16 +27,6 @@ else
     git clone https://github.com/mctools/ncrystal.git
 fi
 
-if [ -d nexus-code ]; then
-    echo Updating existing NeXus clone
-    cd nexus-code
-    git pull
-    cd ..
-else
-    echo Cloning NeXus
-    git clone https://github.com/nexusformat/code nexus-code
-fi
-
 if [ -d xraylib ]; then
     echo Updating existing xraylib clone
     cd xraylib

buildscripts/build_pkg_ghostbsd

@@ -39,5 +39,4 @@ export MCINSTALL_PREFIX=/usr/local
 
 ./mkdist mcstas-ncrystal ${1} 3rdparty/ncrystal-package "" ghostbsd "" -- pkg
 ./mkdist mcstas-mcpl ${1} 3rdparty/mcpl-package "" ghostbsd "" -- pkg
-./mkdist mcstas-nexus ${1} 3rdparty/nexus-package "" ghostbsd "" -- pkg
 

cmake/Modules/InstallMCCODE.cmake

@@ -99,7 +99,7 @@ macro(installMCCODE)
 
   # update definitions to match choices
   if (USE_NEXUS)
-    AppendDef(HAVE_NEXUS="-DUSE_NEXUS -lNeXus")
+    AppendDef(HAVE_NEXUS="-DUSE_NEXUS -lhdf5")
     AppendDef(USE_NEXUS)
   endif()
 

cmake/Modules/MCUtil.cmake

@@ -61,12 +61,6 @@ macro(setupMCCODE FLAVOR)
     set(WINDOWS true)
   endif()
 
-  # Set Nexus linking flag
-  if(USE_NEXUS)
-    set(CMAKE_C_FLAGS  "${CMAKE_C_FLAGS}  -lNeXus")
-    set(CMAKE_C_LFLAGS "${CMAKE_C_LFLAGS} -lNeXus")
-  endif()
-
   # Set 32-bit flags
   if(ARCH EQUAL "i386")
     set(CMAKE_C_FLAGS  "-m32")

cmake/Modules/PlatformDefaults.cmake

@@ -223,17 +223,17 @@ function( detect_platform_variables resultvarname )
   provide_var( MPICC )
 
 
-  #NeXus-flags:
+  #NeXus-flags: NeXus output is written with HDF5 (NEXUSLIB/NEXUSINCLUDE: where libhdf5 and hdf5.h are)
   if ( NOT NEXUSFLAGS )
-    set(NEXUSFLAGS "-DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -lNeXus -lhdf5")#?? should probably have another value
+    set(NEXUSFLAGS "-DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -lhdf5")
     if ( MCCODE_BUILD_CONDA_PKG )
-      set( NEXUSFLAGS "-DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -I\$\{CONDA_PREFIX\}/include/nexus -I\$\{CONDA_PREFIX\}/include -Wl,-rpath,$\{CONDA_PREFIX\}/lib -L\$\{CONDA_PREFIX\}/lib -lNeXus -lhdf5" )
+      set( NEXUSFLAGS "-DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -I\$\{CONDA_PREFIX\}/include -Wl,-rpath,$\{CONDA_PREFIX\}/lib -L\$\{CONDA_PREFIX\}/lib -lhdf5" )
     endif()
     if ( WINDOWS )
       if ( "${CMAKE_C_COMPILER_ID}" STREQUAL "MSVC" )
-        set( NEXUSFLAGS " /DUSE_NEXUS /DNX_COMPRESSION=NX_COMP_LZW_LVL1 /DH5_BUILT_AS_DYNAMIC_LIB /I\$\{CONDA_PREFIX\}/Library/include/nexus /I\$\{CONDA_PREFIX\}/Library/include /link /LIBPATH:\$\{CONDA_PREFIX\}/Library/lib NeXus.lib hdf5.lib" )
+        set( NEXUSFLAGS " /DUSE_NEXUS /DNX_COMPRESSION=NX_COMP_LZW_LVL1 /DH5_BUILT_AS_DYNAMIC_LIB /I\$\{CONDA_PREFIX\}/Library/include /link /LIBPATH:\$\{CONDA_PREFIX\}/Library/lib hdf5.lib" )
       else()
-	set( NEXUSFLAGS "-DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -DH5_BUILT_AS_DYNAMIC_LIB -I\$\{CONDA_PREFIX\}/Library/include/nexus -I\$\{CONDA_PREFIX\}/Library/include -Wl,-rpath,$\{CONDA_PREFIX\}/Library/lib -L\$\{CONDA_PREFIX\}/Library/lib -lNeXus -lhdf5" )
+	set( NEXUSFLAGS "-DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -DH5_BUILT_AS_DYNAMIC_LIB -I\$\{CONDA_PREFIX\}/Library/include -Wl,-rpath,$\{CONDA_PREFIX\}/Library/lib -L\$\{CONDA_PREFIX\}/Library/lib -lhdf5" )
       endif()
     endif()
     if ( NEXUSLIB )
@@ -261,6 +261,10 @@ function( detect_platform_variables resultvarname )
   if ( DARWIN )
     set(MCCODE_CFLAGS "${MCCODE_CFLAGS} -D_DARWIN_C_SOURCE")
   endif()
+  if ( CMAKE_SYSTEM_NAME STREQUAL "FreeBSD" )
+    #_POSIX_C_SOURCE (set in generated code) hides XSI, e.g. gettimeofday, on FreeBSD
+    set(MCCODE_CFLAGS "${MCCODE_CFLAGS} -D_XOPEN_SOURCE=700")
+  endif()
   if ( WINDOWS )
     if ("${CMAKE_C_COMPILER_ID}" STREQUAL "MSVC")
       if ( MCCODE_BUILD_CONDA_PKG )

cmake/toolchains/deb32.cmake

@@ -10,10 +10,8 @@ set(MPICC "mpicc")
 set(MPILIB "mpi")
 set(OACCFLAGS "-fast -Minfo=accel -acc=gpu -gpu=managed -DOPENACC")
 set(MPIRUN "mpirun")
-set(NEXUSLIB "/usr/lib")
-set(NEXUSINCLUDE "/usr/include/nexus")
-# Packages are built before libnexus-dev/libhdf5-dev are installed: set the
+# Packages are built before libhdf5-dev is installed: set the
 # full flags. Debian's serial HDF5 is in /usr/include/hdf5/serial, linked as libhdf5_serial
-set(NEXUSFLAGS "-Wl,-rpath,/usr/lib -L/usr/lib -DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -lNeXus -lhdf5_serial -I/usr/include/nexus -I/usr/include/hdf5/serial")
+set(NEXUSFLAGS "-Wl,-rpath,/usr/lib -L/usr/lib -DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -lhdf5_serial -I/usr/include/hdf5/serial")
 set(MCCODE_CFLAGS "-fno-PIC -fPIE -flto -O3 -mtune=native -march=native -fno-math-errno -ftree-vectorize -g -DNDEBUG -D_POSIX_SOURCE -std=c99 -lm")
 set(EDITOR "gedit")

cmake/toolchains/deb64.cmake

@@ -10,10 +10,8 @@ set(MPICC "mpicc")
 set(OACCFLAGS "-fast -Minfo=accel -acc=gpu -gpu=managed -DOPENACC")
 set(MPILIB "mpi")
 set(MPIRUN "mpirun")
-set(NEXUSLIB "/usr/lib")
-set(NEXUSINCLUDE "/usr/include/nexus")
-# Packages are built before libnexus-dev/libhdf5-dev are installed: set the
+# Packages are built before libhdf5-dev is installed: set the
 # full flags. Debian's serial HDF5 is in /usr/include/hdf5/serial, linked as libhdf5_serial
-set(NEXUSFLAGS "-Wl,-rpath,/usr/lib -L/usr/lib -DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -lNeXus -lhdf5_serial -I/usr/include/nexus -I/usr/include/hdf5/serial")
+set(NEXUSFLAGS "-Wl,-rpath,/usr/lib -L/usr/lib -DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -lhdf5_serial -I/usr/include/hdf5/serial")
 set(MCCODE_CFLAGS "-fno-PIC -fPIE -flto -O3 -mtune=native -march=native -fno-math-errno -ftree-vectorize -g -DNDEBUG -D_POSIX_SOURCE -std=c99 -lm")
 set(EDITOR "gedit")

cmake/toolchains/deb64arm.cmake

@@ -10,10 +10,8 @@ set(MPICC "mpicc")
 set(MPILIB "mpi")
 set(OACCFLAGS "-fast -Minfo=accel -acc=gpu -gpu=managed -DOPENACC")
 set(MPIRUN "mpirun")
-set(NEXUSLIB "/usr/lib")
-set(NEXUSINCLUDE "/usr/include/nexus")
-# Packages are built before libnexus-dev/libhdf5-dev are installed: set the
+# Packages are built before libhdf5-dev is installed: set the
 # full flags. Debian's serial HDF5 is in /usr/include/hdf5/serial, linked as libhdf5_serial
-set(NEXUSFLAGS "-Wl,-rpath,/usr/lib -L/usr/lib -DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -lNeXus -lhdf5_serial -I/usr/include/nexus -I/usr/include/hdf5/serial")
+set(NEXUSFLAGS "-Wl,-rpath,/usr/lib -L/usr/lib -DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -lhdf5_serial -I/usr/include/hdf5/serial")
 set(MCCODE_CFLAGS "-fno-PIC -fPIE -flto -O3 -mtune=native -march=native -fno-math-errno -ftree-vectorize -g -DNDEBUG -D_POSIX_SOURCE -std=c99 -lm")
 set(EDITOR "gedit")

cmake/toolchains/freebsd32.cmake

@@ -9,5 +9,5 @@ set(TOOLS_CC "clang")
 set(MPICC "mpicc")
 set(MPILIB "mpi")
 set(MPIRUN "mpirun")
-set(MCCODE_CFLAGS "-fno-PIC -fPIE -flto -O3 -mtune=native -march=native -fno-math-errno -ftree-vectorize -g -DNDEBUG -D_POSIX_SOURCE -std=c99 -lm")
+set(MCCODE_CFLAGS "-fno-PIC -fPIE -flto -O3 -mtune=native -march=native -fno-math-errno -ftree-vectorize -g -DNDEBUG -D_POSIX_SOURCE -D_XOPEN_SOURCE=700 -std=c99 -lm")
 set(EDITOR "gedit")

cmake/toolchains/freebsd64.cmake

@@ -9,5 +9,5 @@ set(TOOLS_CC "clang")
 set(MPICC "mpicc")
 set(MPIRUN "mpirun")
 set(MPILIB "mpi")
-set(MCCODE_CFLAGS "-fno-PIC -fPIE -flto -O3 -mtune=native -march=native -fno-math-errno -ftree-vectorize -g -DNDEBUG -D_POSIX_SOURCE -std=c99 -lm")
+set(MCCODE_CFLAGS "-fno-PIC -fPIE -flto -O3 -mtune=native -march=native -fno-math-errno -ftree-vectorize -g -DNDEBUG -D_POSIX_SOURCE -D_XOPEN_SOURCE=700 -std=c99 -lm")
 set(EDITOR "gedit")

cmake/toolchains/ghostbsd.cmake

@@ -9,5 +9,5 @@ set(TOOLS_CC "clang")
 set(MPICC "mpicc")
 set(MPIRUN "mpirun")
 set(MPILIB "mpi")
-set(MCCODE_CFLAGS "-fno-PIC -fPIE -flto -O3 -mtune=native -march=native -fno-math-errno -ftree-vectorize -g -DNDEBUG -D_POSIX_SOURCE -std=c99 -lm")
+set(MCCODE_CFLAGS "-fno-PIC -fPIE -flto -O3 -mtune=native -march=native -fno-math-errno -ftree-vectorize -g -DNDEBUG -D_POSIX_SOURCE -D_XOPEN_SOURCE=700 -std=c99 -lm")
 set(EDITOR "gedit")

cmake/toolchains/mac-silicon.cmake

@@ -16,6 +16,6 @@ set(XRLFLAGS "-IGETPATH(miniconda3/include) -Wl,-rpath,GETPATH(miniconda3/lib) -
 set(MPIRUN "mpirun")
 set(MPILIB "mpi")
 set(NEXUSLIB "GETPATH(miniconda3/lib)")
-set(NEXUSINCLUDE "GETPATH(miniconda3/include/nexus)")
+set(NEXUSINCLUDE "GETPATH(miniconda3/include)")
 set(MCCODE_CFLAGS "-g -O2 -DNDEBUG -lm -std=c99")
 set(EDITOR "open")

cmake/toolchains/mac.cmake

@@ -16,6 +16,6 @@ set(XRLFLAGS "-IGETPATH(miniconda3/include) -Wl,-rpath,GETPATH(miniconda3/lib) -
 set(MPIRUN "mpirun")
 set(MPILIB "mpi")
 set(NEXUSLIB "GETPATH(miniconda3/lib)")
-set(NEXUSINCLUDE "GETPATH(miniconda3/include/nexus)")
+set(NEXUSINCLUDE "GETPATH(miniconda3/include)")
 set(MCCODE_CFLAGS "-g -O2 -DNDEBUG -lm -std=c99")
 set(EDITOR "open")