Custom GPU init actions

custom_gpu_init_actions.sh

#!/bin/bash

# Dataproc configurations
readonly HADOOP_CONF_DIR='/etc/hadoop/conf'
readonly HIVE_CONF_DIR='/etc/hive/conf'
readonly SPARK_CONF_DIR='/etc/spark/conf'

function execute_with_retries() {
  local -r cmd=$1
  for ((i = 0; i < 10; i++)); do
    if eval "$cmd"; then
      return 0
    fi
    sleep 5
  done
  return 1
}

function set_hadoop_property() {
  local -r config_file=$1
  local -r property=$2
  local -r value=$3
  bdconfig set_property \
    --configuration_file "${HADOOP_CONF_DIR}/${config_file}" \
    --name "${property}" --value "${value}" \
    --clobber
}

function configure_yarn() {
  if [[ ! -f ${HADOOP_CONF_DIR}/resource-types.xml ]]; then
    printf '<?xml version="1.0" ?>\n<configuration/>' >"${HADOOP_CONF_DIR}/resource-types.xml"
  fi
  set_hadoop_property 'resource-types.xml' 'yarn.resource-types' 'yarn.io/gpu'

  set_hadoop_property 'capacity-scheduler.xml' \
    'yarn.scheduler.capacity.resource-calculator' \
    'org.apache.hadoop.yarn.util.resource.DominantResourceCalculator'

  set_hadoop_property 'yarn-site.xml' 'yarn.resource-types' 'yarn.io/gpu'
}

function configure_yarn_nodemanager() {
  set_hadoop_property 'yarn-site.xml' 'yarn.nodemanager.resource-plugins' 'yarn.io/gpu'
  set_hadoop_property 'yarn-site.xml' \
    'yarn.nodemanager.resource-plugins.gpu.allowed-gpu-devices' 'auto'
  set_hadoop_property 'yarn-site.xml' \
    'yarn.nodemanager.resource-plugins.gpu.path-to-discovery-executables' '/usr/bin'
  set_hadoop_property 'yarn-site.xml' \
    'yarn.nodemanager.linux-container-executor.cgroups.mount' 'true'
  set_hadoop_property 'yarn-site.xml' \
    'yarn.nodemanager.linux-container-executor.cgroups.mount-path' '/sys/fs/cgroup'
  set_hadoop_property 'yarn-site.xml' \
    'yarn.nodemanager.linux-container-executor.cgroups.hierarchy' 'yarn'
  set_hadoop_property 'yarn-site.xml' \
    'yarn.nodemanager.container-executor.class' \
    'org.apache.hadoop.yarn.server.nodemanager.LinuxContainerExecutor'
  set_hadoop_property 'yarn-site.xml' 'yarn.nodemanager.linux-container-executor.group' 'yarn'

  # Fix local dirs access permissions
  local yarn_local_dirs=()
  readarray -d ',' yarn_local_dirs < <(bdconfig get_property_value \
    --configuration_file "${HADOOP_CONF_DIR}/yarn-site.xml" \
    --name "yarn.nodemanager.local-dirs" 2>/dev/null | tr -d '\n')
  chown yarn:yarn -R "${yarn_local_dirs[@]/,/}"
}

function configure_gpu_exclusive_mode() {
  # check if running spark 3, if not, enable GPU exclusive mode
  local spark_version
  spark_version=$(spark-submit --version 2>&1 | sed -n 's/.*version[[:blank:]]\+\([0-9]\+\.[0-9]\).*/\1/p' | head -n1)
  if [[ ${spark_version} != 3.* ]]; then
    # include exclusive mode on GPU
    nvidia-smi -c EXCLUSIVE_PROCESS
  fi
}

function configure_gpu_isolation() {
  # Download GPU discovery script
  local -r spark_gpu_script_dir='/usr/lib/spark/scripts/gpu'
  mkdir -p ${spark_gpu_script_dir}
  local -r gpu_resources_url=https://raw.githubusercontent.com/apache/spark/master/examples/src/main/scripts/getGpusResources.sh
  curl -fsSL --retry-connrefused --retry 10 --retry-max-time 30 \
    "${gpu_resources_url}" -o ${spark_gpu_script_dir}/getGpusResources.sh
  chmod a+rwx -R ${spark_gpu_script_dir}

  # enable GPU isolation
  sed -i "s/yarn.nodemanager\.linux\-container\-executor\.group\=/yarn\.nodemanager\.linux\-container\-executor\.group\=yarn/g" "${HADOOP_CONF_DIR}/container-executor.cfg"
  printf '\n[gpu]\nmodule.enabled=true\n[cgroups]\nroot=/sys/fs/cgroup\nyarn-hierarchy=yarn\n' >>"${HADOOP_CONF_DIR}/container-executor.cfg"

  chmod a+rwx -R /sys/fs/cgroup/cpu,cpuacct
  chmod a+rwx -R /sys/fs/cgroup/devices
}

function main() {

    # This configuration should run on all nodes regardless of attached GPUs
    configure_yarn

    configure_yarn_nodemanager

    configure_gpu_isolation

    configure_gpu_exclusive_mode

}

main