Merge branch 'next' into hermes3-temp

.build_adios2_for_ci.sh

@@ -0,0 +1,62 @@
+#!/bin/bash
+
+set -e
+
+if test $BUILD_ADIOS2 ; then
+    if [[ ! -d $HOME/local/adios/include/adios2.h ]] || test $1 ; then
+	echo "****************************************"
+	echo "Building ADIOS2"
+	echo "****************************************"
+
+	branch=${1:-release_29}
+    if [ ! -d adios2 ]; then
+    	git clone -b $branch https://github.com/ornladios/ADIOS2.git adios2 --depth=1
+    fi
+
+	pushd adios2
+    rm -rf build
+    mkdir -p build
+    pushd build
+
+    cmake .. \
+        -DCMAKE_INSTALL_PREFIX=$HOME/local \
+        -DADIOS2_USE_MPI=ON \
+        -DADIOS2_USE_Fortran=OFF \
+        -DADIOS2_USE_Python=OFF \
+        -DADIOS2_BUILD_EXAMPLES=OFF \
+        -DCMAKE_BUILD_TYPE=Release \
+        -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
+        -DBUILD_TESTING=OFF \
+        -DADIOS2_USE_SST=OFF \
+        -DADIOS2_USE_MGARD=OFF \
+        -DADIOS2_USE_HDF5=OFF \
+        -DADIOS2_USE_BZip2=OFF \
+        -DADIOS2_USE_Blosc2=OFF \
+        -DADIOS2_USE_SZ=OFF \
+        -DADIOS2_USE_ZFP=OFF \
+        -DADIOS2_USE_DAOS=OFF \
+        -DADIOS2_USE_UCX=OFF \
+        -DADIOS2_USE_LIBPRESSIO=OFF \
+        -DADIOS2_USE_Sodium=OFF \
+        -DADIOS2_USE_ZeroMQ=OFF \
+        -DADIOS2_USE_MHS=OFF \
+        -DADIOS2_USE_DataMan=OFF
+
+	make -j 4 && make install
+	popd
+
+	echo "****************************************"
+	echo " Finished building ADIOS2"
+	echo "****************************************"
+
+    else
+
+	echo "****************************************"
+	echo " ADIOS2 already installed"
+	echo "****************************************"
+    fi
+else
+    echo "****************************************"
+    echo " ADIOS2 not requested"
+    echo "****************************************"
+fi

.build_petsc_for_ci.sh

@@ -3,12 +3,13 @@
 set -e
 
 if test $BUILD_PETSC ; then
-    if [[ ! -d $HOME/local/petsc/include/petsc ]]; then
+    if [[ ! -d $HOME/local/petsc/include/petsc ]] || test $1 ; then
 	echo "****************************************"
 	echo "Building PETSc"
 	echo "****************************************"
 
-	git clone -b release https://gitlab.com/petsc/petsc.git petsc --depth=1
+	branch=${1:-release}
+	git clone -b $branch https://gitlab.com/petsc/petsc.git petsc --depth=1
 
 	unset PETSC_DIR
 	unset PETSC_ARCH
@@ -20,7 +21,7 @@ if test $BUILD_PETSC ; then
 	    --with-scalar-type=real \
 	    --with-shared-libraries=1 \
 	    --with-debugging=0 \
-	    {C,CXX,F}OPTFLAGS="-O3 -march=native" \
+	    {C,CXX,F}OPTFLAGS="-O3" \
 	    --prefix=$HOME/local/petsc
 
 	make && make install
@@ -34,7 +35,7 @@ if test $BUILD_PETSC ; then
 	echo "Building SLEPc"
 	echo "****************************************"
 
-    git clone -b release https://gitlab.com/slepc/slepc.git slepc --depth=1
+    git clone -b $branch https://gitlab.com/slepc/slepc.git slepc --depth=1
 
     pushd slepc
 	unset SLEPC_DIR

.ci_fedora.sh

@@ -15,16 +15,19 @@ then
   #         3. docker start -a mobydick                       <=> start to run the container (initialized with docker-cp)
     if test $1 = podman ; then
 	cmd=podman
+	# For the use of testing
+	git submodule update --init # --recursive
     else
 	cmd="sudo docker"
     fi
     test . != ".$2" && mpi="$2" || mpi=openmpi
-    test . != ".$3" && version="$3" || version=latest
+    test . != ".$3" && version="$3" || version=rawhide
     time $cmd pull registry.fedoraproject.org/fedora:$version
     time $cmd create --cap-add=SYS_PTRACE --security-opt seccomp=unconfined \
+	 --shm-size 256M \
          --name mobydick registry.fedoraproject.org/fedora:$version \
 	     /tmp/BOUT-dev/.ci_fedora.sh $mpi
-    time $cmd cp ${TRAVIS_BUILD_DIR} mobydick:/tmp
+    time $cmd cp ${TRAVIS_BUILD_DIR:-$(pwd)} mobydick:/tmp/BOUT-dev
     time $cmd start -a mobydick
     exit 0
 fi
@@ -37,28 +40,34 @@ then
     cat /etc/os-release
     # Ignore weak depencies
     echo "install_weak_deps=False" >> /etc/dnf/dnf.conf
-    time dnf -y install dnf-plugins-core python3-pip cmake
+    time dnf -y install dnf5
+    time dnf5 -y install dnf5-plugins cmake python3-zoidberg python3-natsort
     # Allow to override packages - see #2073
-    time dnf copr enable -y davidsch/fixes4bout || :
-    time dnf -y upgrade
-    time dnf -y builddep bout++
+    time dnf5 copr enable -y davidsch/fixes4bout || :
+    time dnf5 -y upgrade
+    time dnf5 -y builddep bout++
     useradd test
     cp -a /tmp/BOUT-dev /home/test/
     chown -R test /home/test
     chmod u+rwX /home/test -R
     sudo -u test ${0/\/tmp/\/home\/test} $mpi
 ## If we are called as normal user, run test
 else
-    pip install --user zoidberg natsort
     . /etc/profile.d/modules.sh
     module load mpi/${1}-x86_64
     export OMPI_MCA_rmaps_base_oversubscribe=yes
+    export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe
     export TRAVIS=true
     export FLEXIBLAS=NETLIB
     cd
     cd BOUT-dev
     echo "starting configure"
-    time cmake -S . -B build -DBOUT_USE_PETSC=ON
+    time cmake -S . -B build -DBOUT_USE_PETSC=ON \
+	 -DBOUT_UPDATE_GIT_SUBMODULE=OFF \
+	 -DBOUT_USE_SYSTEM_FMT=ON \
+	 -DBOUT_USE_SYSTEM_MPARK_VARIANT=ON \
+	 -DBOUT_USE_SUNDIALS=ON
+
     time make -C build build-check -j 2
     time make -C build check
 fi