run-chi.sh

#!/bin/bash
#
# Copyright (c) 2020 Peterson Yuhala, IIUN
#

#
# You must be in the graal-tee directory as root here: ie make sure PWD = graal-tee dir
# To run your app, copy the top most package folder to the SVM directory and modify the app related
# varialbles accordingly
#
#

#name of app folder in SVM directory
APP_NAME="graphchi"

#package path (same at the top of main class)
APP_PKG="edu.cmu.graphchi.apps"

#full package path (above with . replaced with /)
PKG_PATH="edu/cmu/graphchi/apps"

#pkg prefix is the first part (/subfolder) of the package name
PKG_PREFIX="edu"

#subpackages used by app on a different tree
SUB_PKG1="com"
SUB_PKG2="nom"
SUB_PKG3="ucar"

SVM_DIR="$PWD/substratevm"
SGX_DIR="$PWD/sgx"
#GRAAL_HOME="$PWD/graalvm-ce-java11-21.0.0"  # pre-built: for native image agent
#GRAAL_HOME="$PWD/sdk/latest_graalvm_home" # only useful after graal build

#JAVA_HOME="$PWD/openjdk1.8.0_282-jvmci-21.1-b01"

#export JAVA_HOME=$JAVA_HOME

#
# NB: the jdk above does not come with the native image agent.
# We downloaded a prebuilt version of graalvm-ce-java11-21.0.0 and copied
# the agent.so file to the below directory
#
AGENT_PATH="$JAVA_HOME/jre/lib/amd64/libnative-image-agent.so"

APP_DIR="$SVM_DIR/$APP_NAME"
JAVAC="$JAVA_HOME/bin/javac"
JAVA="$JAVA_HOME/bin/java"

# SGX proxies generated by graal SGX proxy generator
EDL_FILES=("/tmp/graalsgx_ecalls.edl" "/tmp/graalsgx_ocalls.edl")
TRUSTED_PROXIES=("/tmp/graalsgx_ecalls.hpp" "/tmp/graalsgx_ocalls_proxy.hpp")
UNTRUSTED_PROXIES=("/tmp/graalsgx_ocalls.hpp" "/tmp/graalsgx_ecalls_proxy.hpp")

# Ignore jvmci version check
#"warn"

#TODO put annotations in a com.oracle.svm.graalsgx package

# Give this file x permission if it does not have. Its present perm will probably be: rw-rw-r-- (664). Change to 764
# chmod 764 /path/to/graal-sdk.jar

#to find the relevant files: find . -name "filename"
#GRAAL_LIBS="$PWD/sdk/latest_graalvm_home/lib/graal/*"
#GRAALVM_LIBS="$PWD/sdk/latest_graalvm_home/lib/graalvm/*"

#SVM_LIBS="$PWD/sdk/latest_graalvm_home/lib/svm/builder/svm.jar"
#GRAAL_SDK="$PWD/sdk/mxbuild/dists/jdk1.8/graal-sdk.jar"

GRAAL_SDK="$PWD/sdk/latest_graalvm_home/jre/lib/boot/graal-sdk.jar"
#
# Graal sdk bin causes problems! do not add to the cp never add anywhere!!
# I kept it here just FYI
#

#GRAAL_SDK_BIN="$PWD/sdk/mxbuild/src/org.graalvm.nativeimage/bin"

JTRANSFORMER="$SVM_DIR/jtransformer"
JTRANS="$JTRANSFORMER/jtrans"
JAVA_ASSIST="$JTRANSFORMER/javassist-3.26.0-GA.jar"
APP_LIBS="$APP_DIR/lib/*"

LIBS="$JTRANSFORMER/json-simple-1.1.jar"

MAIN="BenchMain"

OTHERS="$APP_DIR/ucar/unidata/io/RandomAccessFile.java"
DATA="$APP_DIR/data"

#graph generator
RMAT_GEN="$APP_DIR/pers/graph_generator/*.java"

TRANSFORMER_SRC="$JTRANS/JAssistClassTransformer.java $JTRANS/AgentHelper.java $JTRANS/ClassFinder.java"

#
# class path variable
# do not add secure and unsecure jtransformer dirs to the cp else jtransformer or native img builder may see
# multiple versions of the classes. This could lead to problems.
#

JTRANS_CP="$GRAAL_SDK:$JTRANSFORMER:$JAVA_ASSIST:$LIBS"

CP="$JTRANS_CP:$SVM_DIR:$APP_DIR:$APP_LIBS"

#clean old/stale files and objects and rebuild svm if changed
OLD_OBJS=("/tmp/*.edl" "/tmp/main_in.o" "/tmp/main_out.o" "$APP_DIR/*.class" "$SGX_DIR/Enclave/graalsgx/*.o" "$SGX_DIR/App/graalsgx/*.o" "$APP_DIR/$APP_NAME.jar")
cd $SVM_DIR
echo "--------------- Cleaning old files and objects ---------------"
for obj in "${OLD_OBJS[@]}"; do
    rm -fv $obj
done

# clean proxy files
#rm -fv $SGX_DIR/Enclave/graalsgx/edl/*
#rm -fv $SGX_DIR/Enclave/graalsgx/proxy/*
#rm -fv $SGX_DIR/App/graalsgx/proxy/*

# Adding java assist library as class path suffix
#mx --cp-sfx $JAVA_ASSIST build

# in case you encounter strange problems with mx native-image or SecurityInfo annotation absent, call the below function

function build_graal() {
    rm -r svmbuild
    mx clean
    mx build
}

build_graal

#---------------------------------- generate synthetic graph ----------------------

function generate_graph() {
    rmatFile="/home/petman/projects/graal-tee/substratevm/graphchi/data/rmat.txt"
    echo "------------------- Generating graph ------------------"
    $JAVAC -cp $CP $RMAT_GEN
    $JAVA_HOME/bin/java -cp $CP pers.graph_generator.RMATGraphGenerator $rmatFile 6250 25000

}

#generate_graph
#-----------------------------------------------------------------------------------

#exit 1

# restore app from tmp folder if present
# TO-FIX
function restore_app() {

    if [ ! -d "$SVM_DIR/$APP_NAME" ]; then
        cp -rf ./tmp/$APP_NAME $SVM_DIR
        rm -rf ./tmp/*
    fi
}
cp -rf ./tmp/$APP_NAME $SVM_DIR
rm -rf ./tmp/* 





#clean app classes
echo "--------------- Cleaning $APP_NAME classes -----------"
find $APP_DIR -name "*.class" -type f -delete

#app build options
BUILD_OPTS="-Xlint:unchecked -Xlint:deprecation"

echo "--------------- Compiling $APP_NAME application -----------"
$JAVAC -cp $CP $BUILD_OPTS $APP_DIR/$PKG_PATH/$MAIN.java $OTHERS

#--------------------------------------------------------------------------------

#clean shards
rm -rf $DATA/gen.txt.* $DATA/*.bin


#run unchanged application in jvm to generate any useful configuration files: reflection, serialization, dynamic class loading etc
echo "--------------- Running $APP_NAME on JVM to generate useful config files-----------"
mkdir -p META-INF/native-image
$JAVA_HOME/bin/java -agentlib:native-image-agent=config-output-dir=META-INF/native-image -cp $CP $APP_PKG.$MAIN 4


#clean shards
rm -rf $DATA/gen.txt.* $DATA/*.bin

#exit 1

#--------------------------------------------------------------------------------

#
# copy freshly compiled class files/app package/jar to java assist transformer module
# classes in the secure folder will be instrumented for the secure image build
# classes in the unsecure folder will be instrumented for the unsecure image build
# unannotated classes in both secure and unsecure dirs will be unchanged
#

#
# in the event of permission problems, change ownership of the project folder
# sudo chown -R ${USER} graal-tee/
#

#-------------------------------------------------------------------------------
# Clean secure and unsecure folders
rm -rf $JTRANSFORMER/secure/*
rm -rf $JTRANSFORMER/unsecure/*

#-------------------------------------------------------------------------------
echo "--------------- Copy class files to javassist transformer ---------------"

cp -rf $APP_DIR/$PKG_PREFIX $JTRANSFORMER/secure
#copy lib
cp -rf $APP_DIR/lib $JTRANSFORMER/secure

cp -rf $APP_DIR/$PKG_PREFIX $JTRANSFORMER/unsecure
#copy lib
cp -rf $APP_DIR/lib $JTRANSFORMER/secure

# the source files are probably not needed
# NB: maybe this is not needed
#find $JTRANSFORMER/secure -type f -name '*.java' -delete
#find $JTRANSFORMER/unsecure -type f -name '*.java' -delete
#-------------------------------------------------------------------------------

# temp directory to hold app folder just in case we accidentally delete them
# after all the movements :-)
mkdir -p tmp
mv $APP_DIR ./tmp

# build java assist class transformer
$JAVA_HOME/bin/javac -cp $CP -Xlint:unchecked $TRANSFORMER_SRC

#
# run java assist class transformer
# the arg0: jtransformer parent dir arg1: app pkg name
#

#|------------------------------------Start Instrumentation---------------------------------
#|
echo "--------------- Instrumenting classes in jassist transformer ---------------"
$JAVA_HOME/bin/java -cp $JTRANS_CP:$JTRANS jtrans.JAssistClassTransformer $JTRANSFORMER $PKG_PREFIX
#|
#|------------------------------------End Instrumentation---------------------------------

#exit 1 

# native image build options
SVM_OPTS="--allow-incomplete-classpath -H:+UseOnlyWritableBootImageHeap"
GC_OPTS="-R:PercentTimeInIncrementalCollection=10"
#NATIVE_IMG_OPTS="--shared --no-fallback --allow-incomplete-classpath --initialize-at-build-time=java.util.Random"
NATIVE_IMG_OPTS="--shared --no-fallback -R:MaxHeapSize=2g"
ISO_OPTS="-H:-SpawnIsolates"
ERROR_OPTS="-H:+ReportExceptionStackTraces"

# replace app folder with secure-transforms
echo "--------------- Moving transformed classes for secure image gen ---------------"
#rm -rf $APP_DIR
mkdir -p $APP_NAME
cp -R $JTRANSFORMER/secure/* $APP_DIR
#specific to graphchi
cp -R ./tmp/$APP_NAME/$SUB_PKG1 $APP_DIR
cp -R ./tmp/$APP_NAME/$SUB_PKG2 $APP_DIR
cp -R ./tmp/$APP_NAME/$SUB_PKG3 $APP_DIR

#$JAVA_HOME/bin/native-image $APP_PKG.Main
#TODO: build image directly from secure/unsecure folders without copying
#exit 1
# build secure image
mx native-image -cp $CP $NATIVE_IMG_OPTS $ERROR_OPTS --sgx-in $APP_PKG.$MAIN
#rm Main.class

# mv unsecure-transforms to app folder for unsecure image
echo "--------------- Moving transformed classes for unsecure image gen ---------------"
#rm -rf $APP_DIR
cp -R $JTRANSFORMER/unsecure/* $APP_DIR

#build unsecure image
mx native-image -cp $CP $NATIVE_IMG_OPTS --sgx-out $APP_PKG.$MAIN
#rm Main.class
#exit 1
# move newly created object files to sgx module
echo "--------------- Moving generated images to SGX module ---------------"
mv /tmp/main_in.o $SGX_DIR/Enclave/graalsgx/
mv /tmp/main_out.o $SGX_DIR/App/graalsgx/

# copy generated headers to sgx module; graal entry points are defined here
mv $SVM_DIR/*.h $SGX_DIR/Include/

# create proxy directories
mkdir -p $SGX_DIR/Enclave/graalsgx/edl
mkdir -p $SGX_DIR/Enclave/graalsgx/proxy
mkdir -p $SGX_DIR/App/graalsgx/proxy

# copy generated files to sgx module: edl files and ecall/ocall definitions and proxies
echo "--------------- Copying generated proxies to SGX module  --------------"
for file in "${EDL_FILES[@]}"; do
    mv $file $SGX_DIR/Enclave/graalsgx/edl
done

for file in "${TRUSTED_PROXIES[@]}"; do
    mv $file $SGX_DIR/Enclave/graalsgx/proxy
done

for file in "${UNTRUSTED_PROXIES[@]}"; do
    mv $file $SGX_DIR/App/graalsgx/proxy
done
# clean other files
rm -fv $SVM_DIR/*.so

# move app folder back to original location
rm -rf $APP_NAME
cp -rf ./tmp/$APP_NAME $SVM_DIR
rm -rf ./tmp/*