From 97a33fdde0d8bb62842d6970b52e999e27ebe05b Mon Sep 17 00:00:00 2001
From: Bill Ellis <billellis.07@gmail.com>
Date: Wed, 4 Sep 2024 14:35:08 +0100
Subject: [PATCH] added updated scripts to repo

---
 scripts/build-libmesh.sh    | 143 ++++++++++++++++++++++++++++++++++++
 scripts/setup-env-ubuntu.sh |  35 +++++++++
 scripts/ubuntu-envs.sh      |   5 ++
 3 files changed, 183 insertions(+)
 create mode 100755 scripts/build-libmesh.sh
 create mode 100755 scripts/setup-env-ubuntu.sh
 create mode 100644 scripts/ubuntu-envs.sh

diff --git a/scripts/build-libmesh.sh b/scripts/build-libmesh.sh
new file mode 100755
index 0000000..66e8c6b
--- /dev/null
+++ b/scripts/build-libmesh.sh
@@ -0,0 +1,143 @@
+#!/bin/bash
+
+set -e
+
+Help()
+{
+    # Display Help
+    echo
+    echo "Syntax: $0 [options]"
+    echo "options:"
+    echo "h      Print this help."
+    echo "w      Set working directory"
+    echo "j      Set number of compile cores"
+    echo "d      Provide HDF5 installation directory"
+    echo "f      Set MOOSE configuration flags as a string"
+    echo "r      Must supply this if user is running as root (e.g. in docker)"
+    echo "c      Allow petsc to download cmake"
+    echo "p      Set libmesh install prefix"
+    echo
+}
+
+# Defaults
+WORKDIR=
+TAG=""
+BRANCH=""
+GITSHA=""
+JOBS=1
+HDF5_DIR_IN=""
+HDF5_STR=""
+PETSC_INSTALL_DIR=""
+ENV_FILE=""
+ENV_OUTFILE=""
+ROOTUSER=false
+DOWNLOAD_CMAKE=false
+LIBMESH_PREFIX_DIR=""
+METHODS='opt dbg'
+
+# Read arguments
+while getopts "w:t:b:s:j:d:p:e:o:f:hrc" option; do
+    case $option in
+        h)
+            Help
+            exit;;
+        w)
+            WORKDIR=$(realpath $OPTARG);;
+        t)
+            TAG=$OPTARG;;
+        b)
+            BRANCH=$OPTARG;;
+        s)
+            GITSHA=$OPTARG;;
+        j)
+            JOBS=$OPTARG;;
+        d)
+            HDF5_DIR_IN=$(realpath $OPTARG);;
+        e)
+            ENV_FILE=$(realpath $OPTARG);;
+        o)
+            ENV_OUTFILE=$(realpath $OPTARG);;
+        f)
+            CONFIG_FLAGS=$OPTARG;;
+        r)
+            ROOTUSER=true;;
+	p)
+	    LIBMESH_PREFIX_DIR=$(realpath $OPTARG);;
+        \?) # Invalid option
+            echo "Error: Invalid option"
+            exit 1;;
+    esac
+done
+
+if [ "$WORKDIR" = "" ] ; then
+    echo "Please set working directory through the -w flag"
+    Help
+    exit 1
+fi
+
+if [ -n "$HDF5_DIR_IN" ]; then
+    echo "HDF5 installation location was set using HDF5_DIR=$HDF5_DIR_IN"
+    HDF5_STR="--with-hdf5=$HDF5_DIR_IN"
+fi
+
+# Set up environment variables
+export LIBMESH_DIR=$WORKDIR/libmesh
+export LIBMESH_BUILD_DIR=$LIBMESH_DIR/build
+
+# Create working directory if non-existant
+echo "Installing LIBMESH in $WORKDIR"
+if [ ! -d $WORKDIR ]; then
+    mkdir $WORKDIR
+fi
+cd $WORKDIR
+
+# Get libmesh repository if not present
+if [ ! -d ${LIBMESH_DIR} ]; then
+    git clone https://github.com/libMesh/libmesh
+fi
+
+cd $LIBMESH_DIR
+# Make libmesh build repository if not present
+if [ ! -d ${LIBMESH_BUILD_DIR} ]; then
+    mkdir $LIBMESH_BUILD_DIR
+fi
+
+# Configure Libmesh
+cd ${LIBMESH_BUILD_DIR}
+git submodule update --init --recursive
+../configure --enable-silent-rules \
+               --enable-unique-id \
+               --disable-warnings \
+               --with-thread-model=openmp \
+               --disable-maintainer-mode \
+               --enable-hdf5 \
+               --with-cxx-std-min=2017 \
+               --without-gdb-command \
+               --with-eigen \
+               --with-methods="${METHODS}" \
+               --prefix="${LIBMESH_PREFIX_DIR}" \
+               --with-future-timpi-dir="${LIBMESH_PREFIX_DIR}" \
+	       --disable-petsc \
+	       "${HDF5_STR}"
+
+make -j "${JOBS}" && make install
+
+# This is needed or it mpiexec complains because docker runs as root
+# Discussion on this issue https://github.com/open-mpi/ompi/issues/4451
+if [ "$ROOTUSER" = true ] ; then
+    export OMPI_ALLOW_RUN_AS_ROOT=1
+    export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+fi
+
+# Run tests
+#cd ${LIBMESH_DIR}/test
+#./run_tests -j${MOOSE_JOBS}
+
+# Unset those OMPI environment variables we set before
+if [ "$ROOTUSER" = true ] ; then
+    export OMPI_ALLOW_RUN_AS_ROOT=
+    export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=
+fi
+
+echo "Succesfully built Libmesh!"
+echo
diff --git a/scripts/setup-env-ubuntu.sh b/scripts/setup-env-ubuntu.sh
new file mode 100755
index 0000000..1bd888c
--- /dev/null
+++ b/scripts/setup-env-ubuntu.sh
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+set -e
+
+# Update package lists to get latest cmake
+apt-get update
+apt-get purge --auto-remove cmake
+apt-get -y --fix-missing install \
+        software-properties-common \
+        lsb-release \
+        gpg \
+        wget
+apt-get clean all
+apt-get update
+apt-get install -y --fix-missing cmake \
+        gcc \
+        g++ \
+        gfortran \
+        git \
+        libopenmpi3 \
+        python3 \
+        python3-venv \
+        python3-dev \
+        python3-distutils \
+        python-is-python3 \
+        rsync \
+        bison \
+        flex \
+        libblas-dev \
+        liblapack-dev \
+        libhdf5-dev \
+        libeigen3-dev \
+        libglfw3-dev  \
+        libtbb-dev  \
+        pkg-config
diff --git a/scripts/ubuntu-envs.sh b/scripts/ubuntu-envs.sh
new file mode 100644
index 0000000..8e7fda2
--- /dev/null
+++ b/scripts/ubuntu-envs.sh
@@ -0,0 +1,5 @@
+export CC=mpicc
+export CXX=mpicxx
+export F90=mpif90
+export F77=mpif77
+export FC=mpif90