install

#!/bin/bash

# This script is shamelessly extended from https://github.com/saalfeldlab/n5-utils, thanks @axtimwalde & co!

USERTHREADS="-1"
USERMEM="-1"

while [[ $# -gt 0 ]]; do
  case $1 in
    -t|--threads)
      USERTHREADS="$2"
      shift # past argument
      shift # past value
      ;;
    -m|--mem)
      USERMEM="$2"
      shift # past argument
      shift # past value
      ;;
    -*|--*)
      echo "Unknown option $1"
      exit 1
      ;;
  esac
done

if [ $USERTHREADS == "-1" ]; then
  echo "You did not define the number of threads for Java/Spark can use, will be set automatically. You could do it by e.g.: './install -t 8' for 8 threads."
fi

if [ $USERMEM == "-1" ]; then
  echo "You did not define the memory that Java/Spark can use, will be set automatically. You could do it by e.g.: './install -m 64' for 64GB of RAM."
fi


if [ $USERMEM == "-1" ]; then
  # check for operating system
  if [[ "$OSTYPE" == "linux-gnu" ]]; then
    echo "Assuming on Linux operating system"
    MEM=$(cat /proc/meminfo | grep MemTotal | sed s/^MemTotal:\\\s*\\\|\\\s\\+[^\\\s]*$//g)
    MEMGB=$(($MEM/1024/1024))
    MEM=$((($MEMGB/5)*4))
  elif [[ "$OSTYPE" == "darwin"* ]]; then
    echo "Assuming on MacOS X operating system"
    # sysctl returns total hardware memory size in bytes
    MEM=$(sysctl hw.memsize | grep hw.memsize | sed s/hw.memsize://g)
    MEMGB=$(($MEM/1024/1024/1024))
    MEM=$((($MEMGB/5)*4))
  else
    echo "ERROR - Operating system (arg2) must be either linux or osx to determine max memory. Please specify max memory by e.g.: './install -m 64' for 64GB of RAM"
    exit
  fi

  echo "Available memory:" $MEMGB "GB, setting Java memory limit to" $MEM "GB"
else
  MEM=$USERMEM
  echo "Setting Java memory limit to" $MEM "GB"
fi

if [ $USERTHREADS == "-1" ]; then
  # check for operating system
  if [[ "$OSTYPE" == "linux-gnu" ]]; then
    if [ $USERMEM != "-1" ]; then
      echo "Assuming on Linux operating system"
    fi
    THREADS=$(nproc --all)
  elif [[ "$OSTYPE" == "darwin"* ]]; then
    if [ $USERMEM != "-1" ]; then
      echo "Assuming on MacOS X operating system"
    fi
    # sysctl returns number of physical cores
    THREADS=$(sysctl -n hw.ncpu)
  else
    echo "ERROR - Operating system (arg2) must be either linux or osx to determine number of physical cores. Please specify physical by e.g.: './install -t 8' to use 8 threads."
    exit
  fi
  echo "Available threads:" $THREADS", setting Java/Sparks threads accordingly."
else
  THREADS=$USERTHREADS
  echo "Setting Java/Spark number of threads to" $THREADS
fi


# project version from the pom, so the shims keep pointing at the right jar after a release bump
VERSION=$(mvn -q -Denforcer.skip=true help:evaluate -Dexpression=project.version -DforceStdout)
echo "BigStitcher-Spark version: $VERSION"
INSTALL_DIR=$(pwd)
#INSTALL_DIR=${1:-$(pwd)}

echo ""
echo "Installing into $INSTALL_DIR (for local execution)"

echo 'Building the code'

# Requires Java 17 or 21 (Spark 4.0 dropped JDK 8/11). Set JAVA_HOME accordingly, e.g.:
#   export JAVA_HOME=$(/usr/libexec/java_home -v 21)   # macOS

sleep 2

mvn clean install
#echo 'Building a farjar, which can also be used for cluster/cloud execution' 
#mvn clean install -P fatjar
# Spark is 'provided' for the cluster fatjar; the local shims need it on the classpath
mvn -Dspark.scope=compile -Dmdep.outputFile=cp.txt -Dmdep.includeScope=runtime dependency:build-classpath

# function that installs one command
# $1 - command name
# $2 - java class containing the functionality
install_command () {
	echo "Installing '$1' command into" $INSTALL_DIR

	echo '#!/bin/bash' > $1
	echo '' >> $1
	echo "JAR=\$HOME/.m2/repository/net/preibisch/BigStitcher-Spark/${VERSION}/BigStitcher-Spark-${VERSION}.jar" >> $1
	echo 'java \' >> $1
	echo "  -Xmx${MEM}g -Dspark.master=local[${THREADS}] \\" >> $1
#	echo '  -XX:+UseConcMarkSweepGC \' >> $1
	# Spark 4.0 on Java 17/21 requires these JVM module-access flags (mirrors Spark's org.apache.spark.launcher.JavaModuleOptions)
	echo '  -XX:+IgnoreUnrecognizedVMOptions \' >> $1
	echo '  --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.invoke=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED \' >> $1
	echo '  --add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.util.concurrent=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED --add-opens=java.base/jdk.internal.ref=ALL-UNNAMED --add-opens=java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/sun.nio.cs=ALL-UNNAMED \' >> $1
	echo '  --add-opens=java.base/sun.security.action=ALL-UNNAMED --add-opens=java.base/sun.util.calendar=ALL-UNNAMED --add-opens=java.security.jgss/sun.security.krb5=ALL-UNNAMED \' >> $1
	echo '  -Djdk.reflect.useDirectMethodHandle=false -Dio.netty.tryReflectionSetAccessible=true \' >> $1
	echo -n '  -cp $JAR:' >> $1
	echo -n $(cat cp.txt) >> $1
	echo ' \' >> $1
	echo '  '$2' "$@"' >> $1

	chmod a+x $1
}

echo 'Installing workflow tools ...'

install_command resave "net.preibisch.bigstitcher.spark.SparkResaveN5"
install_command detect-interestpoints "net.preibisch.bigstitcher.spark.SparkInterestPointDetection"
install_command match-interestpoints "net.preibisch.bigstitcher.spark.SparkGeometricDescriptorMatching"
install_command stitching "net.preibisch.bigstitcher.spark.SparkPairwiseStitching"
install_command solver "net.preibisch.bigstitcher.spark.Solver"
install_command match-intensities "net.preibisch.bigstitcher.spark.SparkIntensityMatching"
install_command solve-intensities "net.preibisch.bigstitcher.spark.IntensitySolver"
install_command create-fusion-container "net.preibisch.bigstitcher.spark.CreateFusionContainer"
install_command fusion "net.preibisch.bigstitcher.spark.SparkFusion"
install_command nonrigid-fusion "net.preibisch.bigstitcher.spark.SparkNonRigidFusion"

echo 'Installing utils ...'

install_command split-images "net.preibisch.bigstitcher.spark.SplitDatasets"
install_command filter-views "net.preibisch.bigstitcher.spark.Filter_Views"
install_command downsample "net.preibisch.bigstitcher.spark.SparkDownsample"
install_command clear-interestpoints "net.preibisch.bigstitcher.spark.ClearInterestPoints"
install_command clear-registrations "net.preibisch.bigstitcher.spark.ClearRegistrations"
install_command transform-points "net.preibisch.bigstitcher.spark.TransformPoints"
install_command overlay-landmarks "net.preibisch.bigstitcher.spark.OverlayLandmarks"


rm cp.txt

echo "Installation finished."