Merge branch 'tools.hopr.module' into 'master.dev'

Created module env script for hopr installation and removed cloning/building... See merge request piclas/piclas!636
piclas-framework · Apr 20, 2022 · 2c464d0 · 2c464d0
2 parents 82461d9 + 2e584b6
commit 2c464d0
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diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -173,16 +173,6 @@ build:
     - mkdir -p build ; cd build
     - git clone [email protected]:reggie2.0/reggie2.0.git reggie
     - cmake .. -DLIBS_BUILD_HDF5=OFF -DPICLAS_BUILD_POSTI=ON -DPOSTI_BUILD_SUPERB=ON -DPICLAS_READIN_CONSTANTS=ON ; make -j all
-    - if [ -n "${DO_NIGHTLY}" ] || [ -n "${DO_WEEKLY}" ]; then
-        git clone https://github.com/flexi-framework/hopr.git hopr;
-        cd hopr ; mkdir -p build ; cd build;
-        echo `pwd`;
-        cmake .. -DHOPR_BUILD_HDF5=OFF;
-        make -j all &> output.txt;
-        tail -n 20 output.txt;
-        rm output.txt;
-        ls bin/hopr;
-      fi
 
 build_maxwell:
   tags:
@@ -230,6 +220,22 @@ build_poisson:
     - git clone [email protected]:reggie2.0/reggie2.0.git reggie
     - cmake .. -DCMAKE_BUILD_TYPE=Debug -DPICLAS_EQNSYSNAME=poisson -DPICLAS_CODE_ANALYZE=ON -DPICLAS_TIMEDISCMETHOD=RK3 -DLIBS_BUILD_HDF5=OFF ; make -j all
 
+build_hopr:
+  tags:
+    - withmodules-concurrent
+  stage: build
+  script:
+    - git clone https://github.com/hopr-framework/hopr.git hopr;
+    - cd hopr ; mkdir -p build ; cd build;
+    - echo `pwd`;
+    - cmake .. -DHOPR_BUILD_HDF5=OFF;
+    - make -j all &> output.txt;
+    - tail -n 20 output.txt;
+    - rm output.txt;
+    - ls bin/hopr;
+  rules:
+    - if: '$DO_WEEKLY'
+
 # ----------------------------------------------------------------------------------------------------------------------------------------------------
 # Stage "reggie_checkin": Run most simple reggie with previous builds on check-in
 # ----------------------------------------------------------------------------------------------------------------------------------------------------

diff --git a/tools/Setup_ModuleEnv/InstallHOPR.sh b/tools/Setup_ModuleEnv/InstallHOPR.sh
@@ -0,0 +1,307 @@
+#!/bin/bash -i
+
+#==============================================================================
+# title       : InstallHOPR.sh
+# description : This script installs HOPR with specific setting in a
+#               pre-installed module env
+# date        : Apr 18, 2022
+# version     : 1.0
+# usage       : bash InstallHOPR.sh
+# notes       : Bash in run interactively via "-i" to use "module load/purge"
+#               commands
+#==============================================================================
+
+# Check privilege
+if [[ "$EUID" -ne 0 ]]; then
+  echo "Please run as root"
+  exit 1
+fi
+
+# --------------------------------------------------------------------------------------------------
+# Colors
+# --------------------------------------------------------------------------------------------------
+
+if test -t 1; then # if terminal
+  NbrOfColors=$(which tput > /dev/null && tput colors) # supports color
+  if test -n "$NbrOfColors" && test $NbrOfColors -ge 8; then
+    TERMCOLS=$(tput cols)
+    BOLD="$(tput bold)"
+    UNDERLINE="$(tput smul)"
+    STANDOUT="$(tput smso)"
+    NORMAL="$(tput sgr0)"
+    NC="$(tput sgr0)"
+    BLACK="$(tput setaf 0)"
+    RED="$(tput setaf 1)"
+    GREEN="$(tput setaf 2)"
+    YELLOW="$(tput setaf 3)"
+    BLUE="$(tput setaf 4)"
+    MAGENTA="$(tput setaf 5)"
+    CYAN="$(tput setaf 6)"
+    WHITE="$(tput setaf 7)"
+  fi
+fi
+
+# --------------------------------------------------------------------------------------------------
+# Functions
+# --------------------------------------------------------------------------------------------------
+# Function for checking modules
+check_module () {
+                 if [ -z "${2}" ]; then
+                   echo "module for ${1} not found. Exit"
+                   exit
+                 else
+                   echo "${1}: [${2}]"
+                 fi
+                }
+
+# Function for loading modules and checking if they exist in a specific combination
+load_module () {
+                 ERROR=$(module load "$1" 2>&1 | grep -in "ERROR")
+                 if [ ! -z "$ERROR" ]; then
+                   echo " "
+                   echo -e "$RED$ERROR$NC"
+                   echo -e "$RED""Failed: [module load $1]. Exit$NC"
+                   exit
+                 else
+                   module load "$1"
+                 fi
+                }
+
+# --------------------------------------------------------------------------------------------------
+# Setup
+# --------------------------------------------------------------------------------------------------
+# Check command line arguments
+RERUNMODE=0
+LOADMODULES=1
+for ARG in "$@"
+do
+
+  if [ ${ARG} == "--help" ] || [ ${ARG} == "-h" ]; then
+    echo "Input arguments:"
+    echo "--help/-h            print help information"
+    echo "--modules/-m         use modules defined in this script by the user."
+    echo "                     Otherwise, find modules automatically."
+    exit
+  fi
+
+  if [ ${ARG} == "--modules" ] || [ ${ARG} == "-m" ]; then
+    LOADMODULES=0
+    # Set desired versions
+    #CMAKEVERSION=3.15.3-d
+    #CMAKEVERSION=3.17.0-d
+    #CMAKEVERSION=3.20.3
+    CMAKEVERSION=3.21.3
+
+    #GCCVERSION=9.2.0
+    #GCCVERSION=9.3.0
+    #GCCVERSION=10.1.0
+    #GCCVERSION=10.2.0
+    GCCVERSION=11.2.0
+
+    #OPENMPIVERSION=3.1.4
+    #OPENMPIVERSION=4.0.1
+    #OPENMPIVERSION=4.0.2
+    #OPENMPIVERSION=3.1.6
+    OPENMPIVERSION=4.1.1
+
+    #HDF5VERSION=1.10.5
+    #HDF5VERSION=1.10.6
+    HDF5VERSION=1.12.1
+  fi
+
+  # Check if re-run mode is selected by the user
+  if [[ ${ARG} == "--rerun" ]] || [[ ${ARG} =~ ^-r(erun)?$ ]]; then
+    RERUNMODE=1
+  fi
+
+done
+
+HOPRVERSION='master'
+HOPRDOWNLOAD='https://github.com/hopr-framework/hopr.git'
+
+# --------------------------------------------------------------------------------------------------
+# Check pre-requisites
+# --------------------------------------------------------------------------------------------------
+
+# --------------------------------------------------------------------------------------------------
+#  Settings
+# --------------------------------------------------------------------------------------------------
+
+NBROFCORES=$(grep ^cpu\\scores /proc/cpuinfo | uniq |  awk '{print $4}')
+#NBROFCORES=1 # set to fixed value when errors are encountered at random (not related to missing packages)
+INSTALLDIR=/opt
+SOURCESDIR=/opt/sources
+MODULESDIR=/opt/modules/modulefiles
+TEMPLATEPATH=$(echo `pwd`/moduletemplates/utilities/hopr/hopr_temp)
+if [[ ! -f ${TEMPLATEPATH} ]]; then
+  echo "${RED}ERROR: module template not found under ${TEMPLATEPATH}${NC}. Exit."
+  exit
+fi
+
+if [ ! -d "${SOURCESDIR}" ]; then
+  mkdir -p "${SOURCESDIR}"
+fi
+
+# Check if module is available (not required here, but for following libs)
+if [[ -n $(module purge 2>&1) ]]; then
+  echo -e "${RED}module: command not found.\nThis script must be run in an interactive shell (the first line must read '#! /bin/bash' -i)${NC}"
+  exit
+fi
+
+# take the first gcc compiler installed with first compatible openmpi and hdf5
+echo " "
+if [[ $LOADMODULES -eq 1 ]]; then
+  CMAKEVERSION=$(ls ${MODULESDIR}/utilities/cmake/ | sed 's/ /\n/g' | grep -i "[0-9]\." | head -n 1 | tail -n 1)
+  GCCVERSION=$(ls ${MODULESDIR}/compilers/gcc/ | sed 's/ /\n/g' | grep -i "[0-9]\." | head -n 1 | tail -n 1)
+  OPENMPIVERSION=$(ls ${MODULESDIR}/MPI/openmpi/ | sed 's/ /\n/g' | grep -i "[0-9]\." | head -n 1 | tail -n 1)
+  HDF5VERSION=$(ls ${MODULESDIR}/libraries/hdf5/ | sed 's/ /\n/g' | grep -i "[0-9]\." | head -n 1 | tail -n 1)
+  echo -e "Modules found automatically.\n\nCMAKEVERSION=${CMAKEVERSION}\nGCCVERSION=${GCCVERSION}\nOPENMPIVERSION=${OPENMPIVERSION}\nHDF5VERSION=${HDF5VERSION}\n\nWARNING: The combination might not be possible!"
+  if [[ ${RERUNMODE} -eq 0 ]]; then
+    read -p "Press [Enter] to continue or [Crtl+c] to abort!"
+  fi
+else
+  echo "Modules defined by user. Check if the combination is possible!"
+fi
+
+check_module "cmake" "${CMAKEVERSION}"
+check_module "gcc  " "${GCCVERSION}"
+check_module "mpi  " "${OPENMPIVERSION}"
+check_module "hdf5 " "${HDF5VERSION}"
+
+HOPRMODULEFILEDIR=${MODULESDIR}/utilities/hopr/${HOPRVERSION}/gcc/${GCCVERSION}/openmpi/${OPENMPIVERSION}/hdf5
+MODULEFILE=${HOPRMODULEFILEDIR}/${HDF5VERSION}
+
+# if no HOPR module for this compiler found, install HOPR and create module
+if [ ! -e "${MODULEFILE}" ]; then
+  echo -e "$GREEN""creating HOPR-${HOPRVERSION} for GCC-${GCCVERSION} under$NC"
+  echo -e "$GREEN""$MODULEFILE$NC"
+  echo " "
+  module purge
+  load_module "cmake/${CMAKEVERSION}"
+  load_module "gcc/${GCCVERSION}"
+  load_module "openmpi/${OPENMPIVERSION}/gcc/${GCCVERSION}"
+  load_module "hdf5/${HDF5VERSION}/gcc/${GCCVERSION}/openmpi/${OPENMPIVERSION}"
+  module list
+  echo " "
+  echo -e "$GREEN""Important: If the compilation step fails, run the script again and if it still fails \n1) try compiling single, .i.e., remove -j from make -j or \n2) try make -j 2 (not all available threads)$NC"
+  echo " "
+  echo -e "This will install HOPR version ${GREEN}${HOPRVERSION}${NC} from ${HOPRDOWNLOAD} \nCompilation in parallel will be executed with ${GREEN}${NBROFCORES} threads${NC}."
+  if [[ ${RERUNMODE} -eq 0 ]]; then
+    read -p "Have the correct modules been loaded? If yes, press [Enter] to continue or [Crtl+c] to abort!"
+  fi
+
+  # Install destination
+  HOPRINSTALLDIR=/opt/hopr/${HOPRVERSION}/gcc-${GCCVERSION}/openmpi-${OPENMPIVERSION}/hdf5-${HDF5VERSION}
+
+  # Create and change to install directory
+  mkdir -p ${HOPRINSTALLDIR}
+  cd ${HOPRINSTALLDIR}
+
+  # Check if repo is already downloaded
+  CLONEDIR=${HOPRINSTALLDIR}/hopr
+  if [[ -d ${CLONEDIR} ]]; then
+    # Inquiry: Continue the installation with the existing files OR remove them all and start fresh
+    while true; do
+      echo " "
+      echo "${YELLOW}${CLONEDIR} already exists.${NC}"
+      echo "${YELLOW}Do you want to continue the installation (y/n)?${NC}"
+      # Inquiry
+      if [[ ${RERUNMODE} -eq 0 ]]; then
+        read -p "${YELLOW}Otherwise the directory will be removed and a fresh installation will be performed. [Y/n]${NC}" yn
+      else
+        yn=y
+      fi
+      # Select case
+      case $yn in
+          [Yy]* ) echo "Continuing... "; break;;
+          [Nn]* ) rm -rf ${CLONEDIR} ; break;;
+          * ) echo "Please answer yes or no.";;
+      esac
+    done
+  fi
+
+  # Check if git repo exists/is available
+  # echo "Checking git repository ${HOPRDOWNLOAD}"
+  # wget ${HOPRDOWNLOAD} --no-check-certificate -o /dev/null
+  # ERRORCODE=$?
+  # if [ ${ERRORCODE} -ne 0 ]; then
+  #   echo " "
+  #   echo -e "$RED""Failed to find git repository: [wget ${HOPRDOWNLOAD} --no-check-certificate -o /dev/null]$NC"
+  #   exit
+  # fi
+
+  # Clone git repository
+  if [[ -d ${CLONEDIR} ]]; then
+    cd ${CLONEDIR}
+    git fetch
+    git pull origin ${HOPRVERSION}
+  else
+    git clone ${HOPRDOWNLOAD}
+    cd ${CLONEDIR}
+  fi
+  echo `pwd`
+
+
+  # Check if extraction failed
+  ERRORCODE=$?
+  if [ ${ERRORCODE} -ne 0 ]; then
+    echo " "
+    echo -e "$RED""Failed to download [git clone ${HOPRDOWNLOAD}] or update [git pull origin ${HOPRVERSION}]$NC"
+    exit
+  else
+    HOPRBUILDDIR=${CLONEDIR}/build
+    rm -rf ${HOPRBUILDDIR}
+    mkdir -p ${HOPRBUILDDIR}
+    cd ${HOPRBUILDDIR}
+  fi
+
+  # CMAKE COMPILE FLAGS DEPEND ON THE CHOSEN HOPR VERSION!
+  #if [ "$PARAVIEWVERSION" == "5.2.0" ] || [ "$PARAVIEWVERSION" == "5.3.0" ] || [ "$PARAVIEWVERSION" == "5.4.0" ]; then
+    cmake -DCMAKE_BUILD_TYPE=Release \
+          -DLIBS_USE_MPI=ON \
+          -DLIBS_BUILD_HDF5=OFF \
+          ${CLONEDIR}
+  #else
+    #echo -e "$RED""ERROR: Set the correct cmake compile flags for the HOPR version [$HOPRVERSION] in InstallHOPR.sh$NC"
+    #exit
+  #fi
+
+  # Compile source files with NBROFCORES threads
+  make -j${NBROFCORES} 2>&1 | tee make.out
+
+  # Check if compilation failed
+  if [ ${PIPESTATUS[0]} -ne 0 ]; then
+    echo " "
+    echo -e "$RED""Failed: [make -j${NBROFCORES} 2>&1 | tee make.out]$NC"
+    exit
+  else
+    make install 2>&1 | tee install.out
+  fi
+
+
+  #ERRORCODE=$?
+  #echo ${ERRORCODE}
+  #echo `pwd`
+  #ls -l
+    #read -p "Download okay?"
+
+
+  # create modulefile if the installation seems successful (check if mpicc, mpicxx, mpifort exists in installdir)
+  if [ -e "${HOPRBUILDDIR}/bin/hopr" ]; then
+    if [ ! -d "${HOPRMODULEFILEDIR}" ]; then
+      mkdir -p ${HOPRMODULEFILEDIR}
+    fi
+    cp ${TEMPLATEPATH} ${MODULEFILE}
+    sed -i 's/hoprversion/'${HOPRVERSION}'/gI' ${MODULEFILE}
+    sed -i 's/CMAKEVERSIONFLAG/'${CMAKEVERSION}'/gI' ${MODULEFILE}
+    sed -i 's/GCCVERSIONFLAG/'${GCCVERSION}'/gI' ${MODULEFILE}
+    sed -i 's/MPIVERSIONFLAG/'${OPENMPIVERSION}'/gI' ${MODULEFILE}
+    sed -i 's/HDF5VERSIONFLAG/'${HDF5VERSION}'/gI' ${MODULEFILE}
+    sed -i 's\HOPRTOPDIR\'${HOPRBUILDDIR}'\gI' ${MODULEFILE}
+  else
+    echo -e "$RED""No module file created for HOPR-${HOPRVERSION} for GCC-${GCCVERSION}$NC"
+    echo -e "$RED""no installation found in ${HOPRBUILDDIR}/bin$NC"
+  fi
+else
+  echo -e "$YELLOW""HOPR-${HOPRVERSION} already created: module file exists under ${MODULEFILE}$NC"
+fi
diff --git a/tools/Setup_ModuleEnv/README.md b/tools/Setup_ModuleEnv/README.md
@@ -44,7 +44,7 @@ This cleans the created module file and build directory of the version currently
 ## 6. HDF5 from [https://support.hdfgroup.org/ftp/HDF5/releases/](https://support.hdfgroup.org/ftp/HDF5/releases/)
        sudo ./InstallHDF5.sh
 
-## 7. ParaViewfrom [https://www.paraview.org/download/](https://www.paraview.org/download/)
+## 7. ParaView from [https://www.paraview.org/download/](https://www.paraview.org/download/)
 The installation of ParaView is not mandatory for piclas/hopr. The pre-requisites for Ubuntu are installed via
 
        sudo ./InstallPackagesParaView.sh
@@ -53,4 +53,7 @@ and Paraview itself is installed via
 
       sudo ./InstallParaview.sh
 
+## 8. HOPR from [https://github.com/hopr-framework/hopr](https://github.com/hopr-framework/hopr)
+This installation is optional and creates a module for HOPR by running
 
+      sudo ./InstallHOPR.sh
diff --git a/tools/Setup_ModuleEnv/moduletemplates/utilities/hopr/hopr_temp b/tools/Setup_ModuleEnv/moduletemplates/utilities/hopr/hopr_temp
@@ -0,0 +1,30 @@
+#%Module1.0#####################################################################
+##
+## modules hopr/hoprversion
+##
+## modulefiles/utilities/hopr/hoprversion
+##
+proc ModulesHelp { } {
+        global version modroot
+
+        puts stderr "hopr-hoprversion - sets the Environment for HOPR-hoprversion"
+}
+
+module-whatis   "Sets the environment for using hopr-hoprversion"
+
+conflict hopr
+
+prereq cmake/CMAKEVERSIONFLAG
+prereq gcc/GCCVERSIONFLAG
+prereq openmpi/MPIVERSIONFLAG/gcc/GCCVERSIONFLAG
+prereq hdf5/HDF5VERSIONFLAG/gcc/GCCVERSIONFLAG/openmpi/MPIVERSIONFLAG
+
+# for Tcl script use only
+set     topdir          HOPRTOPDIR
+set     version         hoprversion
+set     sys             linux64
+
+prepend-path    PATH            $topdir/bin
+prepend-path    LD_LIBRARY_PATH $topdir/lib
+prepend-path    HOPR_PATH       $topdir/bin/hopr
+#set-alias       paraviewmpi "paraview --mpi$