initial commit work in progress

Author: johnpapad24

install.sh

@@ -33,16 +33,16 @@ BDM_PROJECT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 
 # Detect the OS (or get the one the user specified)
 if [ -z $1 ]; then
-    BDM_DETECTED_OS=$(DetectOs)
+    BDM_DETECTED_GEN_OS=$(DetectOs2)
 else
-    BDM_DETECTED_OS=$1
+    BDM_DETECTED_GEN_OS=$1
 fi
 
 # Install all prerequisites
-$BDM_PROJECT_DIR/prerequisites.sh all ${BDM_DETECTED_OS}
+$BDM_PROJECT_DIR/prerequisites.sh all ${BDM_DETECTED_GEN_OS}
 if [ $? != 0 ]; then
    exit 1
 fi
 
 # call install script for the detected OS
-$BDM_PROJECT_DIR/util/installation/common/install.sh ${BDM_DETECTED_OS}
+$BDM_PROJECT_DIR/util/installation/common/install.sh ${BDM_DETECTED_GEN_OS}

util/installation/common/util.sh

@@ -17,6 +17,7 @@
 # (Thus reducing code duplication)
 
 SCRIPTPATH="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+SPECIFIC_OSES_SUPPORTED="ubuntu-18.04, ubuntu-20.04, ubuntu-22.04, centos-7, osx"
 
 #include echo.sh
 . $SCRIPTPATH/echo.sh
@@ -58,6 +59,29 @@ function DetectOs {
   fi
 }
 
+function DetectOs2 {
+  # detect operating system
+  if [ `uname` = "Linux" ]; then
+    # linux
+     PROCVERSION=$(cat /proc/version)
+     if echo "$PROCVERSION" | grep -Eiq 'Red Hat' ; then
+	echo rhel;
+     elif echo "$PROCVERSION" | grep -Eiq 'debian|buntu|mint|eepin' ; then
+     	echo debian;
+     elif echo "$PROCVERSION" | grep -Eiq 'SUSE|suse' ; then
+     	echo suse;
+     else
+     	echo other_distro;
+     fi
+  elif [ `uname` = "Darwin" ]; then
+    # macOS
+    echo osx
+  else
+    echo "ERROR: Operating system `uname` is not supported."
+    exit 1
+  fi
+}
+
 # This function checks if the given operating system is supported. If not, it
 # prints an error message, a list of supported systems; and exits the script.
 # Arguments:
@@ -71,10 +95,18 @@ function CheckOsSupported {
 
   local BDM_INSTALL_SRC=$1
   local BDM_OS=$2
-
-  local BDM_INSTALL_OS_SRC=$BDM_INSTALL_SRC/$BDM_OS
-
-  if [ ! -d "$BDM_INSTALL_OS_SRC" ]; then
+  local BDM_INSTALL_OS_SRC=""
+  local SPECIFIC_BDM_OS=$(DetectOs)
+
+  if echo "$SPECIFIC_OSES_SUPPORTED" | grep -Eiq "$SPECIFIC_BDM_OS" ;  then
+ 	if [ "$BDM_OS" == "osx" ]; then
+  		BDM_INSTALL_OS_SRC=$BDM_INSTALL_SRC/$BDM_OS/common
+  	else
+  		BDM_INSTALL_OS_SRC=$BDM_INSTALL_SRC/$BDM_OS/$SPECIFIC_BDM_OS
+  	fi
+  elif [ "$BDM_OS" == "osx" ] || [ "$BDM_OS" == "rhel" ] || [ "$BDM_OS" == "debian" ] || [ "$BDM_OS" == "suse" ] ; then
+    	BDM_INSTALL_OS_SRC=$BDM_INSTALL_SRC/$BDM_OS/common
+  else
     echo "ERROR: This operating system (${BDM_OS}) is not supported"
     echo "Supported operating systems are: "
     pushd $BDM_INSTALL_SRC > /dev/null
@@ -108,12 +140,27 @@ function CompileListOfPackages {
   local BDM_INSTALL_SRC="$2"
   local LOCAL_OS=$3
 
+ local SPECIFIC_BDM_OS=$(DetectOs)
+ local BDM_OS=$(DetectOs2)
   # The list of packages on Ubuntu 20.04 is identical to Ubuntu 18.04
-  if [ $LOCAL_OS == "ubuntu-20.04" ]; then
-    LOCAL_OS="ubuntu-18.04"
+  if [ $SPECIFIC_BDM_OS == "ubuntu-20.04" ]; then
+    SPECIFIC_BDM_OS="ubuntu-18.04"
   fi
 
-  local BDM_INSTALL_OS_SRC=$BDM_INSTALL_SRC/$LOCAL_OS
+  local BDM_INSTALL_OS_SRC=""
+
+  if echo "$SPECIFIC_OSES_SUPPORTED" | grep -Eiq "$SPECIFIC_BDM_OS" ;  then
+  	if [ "$BDM_OS" == "osx" ]; then
+  		BDM_INSTALL_OS_SRC=$BDM_INSTALL_SRC/$BDM_OS/common
+  	else
+  		BDM_INSTALL_OS_SRC=$BDM_INSTALL_SRC/$BDM_OS/$SPECIFIC_BDM_OS
+  	fi
+  elif [ "$BDM_OS" == "osx" ] || [ "$BDM_OS" == "rhel" ] || [ "$BDM_OS" == "debian" ] || [ "$BDM_OS" == "suse" ]; then
+    	BDM_INSTALL_OS_SRC=$BDM_INSTALL_SRC/$BDM_OS/common
+  else
+    echo "ERROR: This operating system (${BDM_OS}) is not supported"
+    exit 1;
+  fi
 
   BDM_PKG_LIST=""
   if [ $1 == "all" ]; then
@@ -179,7 +226,65 @@ function CleanBuild {
   else
     mkdir -p $BUILD_DIR
   fi
+  cd $BDM_PROJECT_DIR
+  BDM_PROJECT_DIR_2=$(pwd)
   cd $BUILD_DIR
+
+  CLEAN_BUILD_OS=$(DetectOs2)
+ 
+  GCC_VER=$(gcc --version | grep gcc) || true
+  #GCC_VER=$(gcc --version | grep gcc | grep -oE ' |\S+' | awk '{print $NF}' | cut -d '.' -f 1-2)
+  if [ -n "${GCC_VER}" ]; then
+  	read -ra tokens <<< $GCC_VER
+  	result=()
+  	current_token=""
+	for token in "${tokens[@]}"; do
+	    if [[ -n $current_token ]]; then 
+			current_token+=" $token"
+		if [[ $current_token == *')' ]]; then
+			result+=("$current_token")
+			current_token=""
+		fi
+	    else
+		if [[ $token == '('* && $token != *')' ]]; then
+			current_token="$token"
+                else
+			result+=("$token")
+		fi
+	   fi
+	done 
+        if [[ -n $current_token ]]; then
+		result+=("$current_token")
+	fi 
+        GCC_VER=${result[2]}
+        GCC_VER=$( echo $GCC_VER | cut -d '.' -f 1-2)
+ fi
+  if [ "$CLEAN_BUILD_OS"!="osx" ]; then
+   if [ -z "${GCC_VER}" ] || [ `echo "$GCC_VER >= 12" | bc -q` -ne 0 ]  ||  [ `echo "$GCC_VER < 9" | bc -q` -ne 0 ]; then
+
+
+    if  $(command -v gcc-11 > /dev/null)  &&  $(command -v g++-11 > /dev/null)  &&  $(command -v gfortran-11 > /dev/null); then
+
+      echo "******************************************************************"
+      echo "Found suitable gcc version installed (gcc-11) via your
+distribution's package manager.
+Using that."
+      echo "******************************************************************";
+
+      export CC=gcc-11
+      export CXX=g++-11
+      export FC=gfortran-11
+      export OMPI_CC=gcc-11
+      export OMPI_CXX=g++-11
+      export OMPI_FC=gfortran-11
+      export QMAKE_CC=gcc-11
+      export QMAKE_CXX=g++-11
+      export LINK=g++-11
+      
+   fi
+  fi
+  fi
+  
   echo "CMAKEFLAGS $BDM_CMAKE_FLAGS"
   cmake $BDM_CMAKE_FLAGS ..
   make -j$(CPUCount) && make install
@@ -217,15 +322,28 @@ function CallOSSpecificScript {
   shift
   local BDM_SCRIPT_FILE="$1"
   shift
-  local BDM_LOCAL_OS=$(DetectOs)
+  local SPECIFIC_BDM_OS=$(DetectOs)
+  local BDM_OS=$(DetectOs2)
   local BDM_SCRIPT_ARGUMENTS=$@
   local BDM_INSTALL_SRC=$BDM_PROJECT_DIR/util/installation
 
   # detect os
-  local BDM_INSTALL_OS_SRC=$BDM_INSTALL_SRC/$BDM_LOCAL_OS
+  local BDM_INSTALL_OS_SRC=""
+
+  if echo "$SPECIFIC_OSES_SUPPORTED" | grep -Eiq "$SPECIFIC_BDM_OS" ;  then
+        if [ "$BDM_OS" == "osx" ]; then
+          	BDM_INSTALL_OS_SRC=$BDM_INSTALL_SRC/$BDM_OS/common
+        else
+  		BDM_INSTALL_OS_SRC=$BDM_INSTALL_SRC/$BDM_OS/$SPECIFIC_BDM_OS
+  	fi
+  elif [ "$BDM_OS" == "osx" ] || [ "$BDM_OS" == "rhel" ] || [ "$BDM_OS" == "debian" ] || [ "$BDM_OS" == "suse" ]; then
+    	BDM_INSTALL_OS_SRC=$BDM_INSTALL_SRC/$BDM_OS/common
+  else
+    echo "ERROR: This operating system (${BDM_OS}) is not supported"
+    exit 1;
+  fi
 
   # check if this system is supported
-  CheckOsSupported $BDM_INSTALL_SRC $BDM_LOCAL_OS
 
   # check if script exists for the detected OS
   local BDM_SCRIPTPATH=$BDM_INSTALL_OS_SRC/$BDM_SCRIPT_FILE
@@ -390,7 +508,7 @@ function EchoFinishInstallation {
   EchoNewStep "For other shells, or for more information, see:"
   EchoNewStep "   ${BDM_ECHO_UNDERLINE}https://biodynamo.org/docs/userguide/first_steps/"
   echo
-  # any warnings about users' post-install shell 
+  # any warnings about users' post-install shell
   # configuration may be added to the function called below
   WarnPossibleBadShellConfigs || true
 }

…allation/ubuntu-22.04/package_list_extra …llation/debian/common/package_list_extrautil/installation/ubuntu-22.04/package_list_extra renamed to util/installation/debian/common/package_list_extra util/installation/ubuntu-22.04/package_list_extra renamed to util/installation/debian/common/package_list_extra

@@ -0,0 +1,32 @@
+
+curl
+freeglut3-dev
+g++
+gcc
+gcc-11
+g++-11
+gfortran-11
+git
+libblas-dev
+libbz2-dev
+liblapack-dev
+libnuma-dev
+libomp5
+libomp-dev
+libopenmpi-dev
+libpthread-stubs0-dev
+make
+wget
+zlib1g-dev
+python3-dev
+libbz2-dev
+libffi-dev
+liblzma-dev
+libreadline-dev
+libsqlite3-dev
+libssl-dev
+python3-openssl
+tk-dev
+xz-utils
+zlib1g-dev
+patch

util/installation/debian/common/package_list_required

@@ -25,7 +25,7 @@ Arguments:
   exit 1
 fi
 
-BDM_PROJECT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/../../.."
+BDM_PROJECT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/../../../.."
 
 # Required to add Kitware ppa below
 sudo apt-get update
@@ -40,17 +40,15 @@ sudo apt-get install apt-transport-https
 # Update
 sudo apt-get update
 
-
-# Install required packages
-sudo apt-get install -y \
-  $(cat $BDM_PROJECT_DIR/util/installation/ubuntu-18.04/package_list_required)
-  
 CMAKE_VER=3.19.3
 CMAKE_SH="cmake-${CMAKE_VER}-linux-x86_64.sh"
 curl -L -O  https://github.com/Kitware/CMake/releases/download/v${CMAKE_VER}/${CMAKE_SH}
 sudo bash "${CMAKE_SH}" --prefix=/usr/local --skip-license
 rm "${CMAKE_SH}"
 
+# Install required packages
+sudo apt-get install -y \
+  $(cat $BDM_PROJECT_DIR/util/installation/debian/common/package_list_required)
 
 if [ -n "${PYENV_ROOT}" ]; then
   unset PYENV_ROOT
@@ -80,10 +78,10 @@ pyenv shell $PYVERS
 # Install optional packages
 if [ $1 == "all" ]; then
   # Don't install --user: the packages should end up in the PYENV_ROOT directory
-  python -m pip install -r $BDM_PROJECT_DIR/util/installation/ubuntu-18.04/pip_packages.txt
+  python -m pip install -r $BDM_PROJECT_DIR/util/installation/debian/common/pip_packages.txt
 
   sudo apt-get install -y \
-    $(cat $BDM_PROJECT_DIR/util/installation/ubuntu-18.04/package_list_extra)
+    $(cat $BDM_PROJECT_DIR/util/installation/debian/common/package_list_extra)
 fi
 
 exit 0