Test and Troubleshooting

Test with a tensorflow job

Distributed-shell + GPU + cgroup

 ... \
 job run \
 --env DOCKER_JAVA_HOME=/opt/java \
 --env DOCKER_HADOOP_HDFS_HOME=/hadoop-current --name distributed-tf-gpu \
 --env YARN_CONTAINER_RUNTIME_DOCKER_CONTAINER_NETWORK=calico-network \
 --worker_docker_image tf-1.13.1-gpu:0.0.1 \
 --ps_docker_image tf-1.13.1-cpu:0.0.1 \
 --input_path hdfs://${dfs_name_service}/tmp/cifar-10-data \
 --checkpoint_path hdfs://${dfs_name_service}/user/hadoop/tf-distributed-checkpoint \
 --num_ps 0 \
 --ps_resources memory=4G,vcores=2,gpu=0 \
 --ps_launch_cmd "python /test/cifar10_estimator/cifar10_main.py --data-dir=hdfs://${dfs_name_service}/tmp/cifar-10-data --job-dir=hdfs://${dfs_name_service}/tmp/cifar-10-jobdir --num-gpus=0" \
 --worker_resources memory=4G,vcores=2,gpu=1 --verbose \
 --num_workers 1 \
 --worker_launch_cmd "python /test/cifar10_estimator/cifar10_main.py --data-dir=hdfs://${dfs_name_service}/tmp/cifar-10-data --job-dir=hdfs://${dfs_name_service}/tmp/cifar-10-jobdir --train-steps=500 --eval-batch-size=16 --train-batch-size=16 --sync --num-gpus=1"

Issues:

Issue 1: Fail to start nodemanager after system reboot

2018-09-20 18:54:39,785 ERROR org.apache.hadoop.yarn.server.nodemanager.LinuxContainerExecutor: Failed to bootstrap configured resource subsystems!
org.apache.hadoop.yarn.server.nodemanager.containermanager.linux.resources.ResourceHandlerException: Unexpected: Cannot create yarn cgroup Subsystem:cpu Mount points:/proc/mounts User:yarn Path:/sys/fs/cgroup/cpu,cpuacct/hadoop-yarn
  at org.apache.hadoop.yarn.server.nodemanager.containermanager.linux.resources.CGroupsHandlerImpl.initializePreMountedCGroupController(CGroupsHandlerImpl.java:425)
  at org.apache.hadoop.yarn.server.nodemanager.containermanager.linux.resources.CGroupsHandlerImpl.initializeCGroupController(CGroupsHandlerImpl.java:377)
  at org.apache.hadoop.yarn.server.nodemanager.containermanager.linux.resources.CGroupsCpuResourceHandlerImpl.bootstrap(CGroupsCpuResourceHandlerImpl.java:98)
  at org.apache.hadoop.yarn.server.nodemanager.containermanager.linux.resources.CGroupsCpuResourceHandlerImpl.bootstrap(CGroupsCpuResourceHandlerImpl.java:87)
  at org.apache.hadoop.yarn.server.nodemanager.containermanager.linux.resources.ResourceHandlerChain.bootstrap(ResourceHandlerChain.java:58)
  at org.apache.hadoop.yarn.server.nodemanager.LinuxContainerExecutor.init(LinuxContainerExecutor.java:320)
  at org.apache.hadoop.yarn.server.nodemanager.NodeManager.serviceInit(NodeManager.java:389)
  at org.apache.hadoop.service.AbstractService.init(AbstractService.java:164)
  at org.apache.hadoop.yarn.server.nodemanager.NodeManager.initAndStartNodeManager(NodeManager.java:929)
  at org.apache.hadoop.yarn.server.nodemanager.NodeManager.main(NodeManager.java:997)
2018-09-20 18:54:39,789 INFO org.apache.hadoop.service.AbstractService: Service NodeManager failed in state INITED

Solution: Grant user yarn the access to /sys/fs/cgroup/cpu,cpuacct, which is the subfolder of cgroup mount destination.

chown :yarn -R /sys/fs/cgroup/cpu,cpuacct
chmod g+rwx -R /sys/fs/cgroup/cpu,cpuacct

If GPUs are used，the access to cgroup devices folder is neede as well

chown :yarn -R /sys/fs/cgroup/devices
chmod g+rwx -R /sys/fs/cgroup/devices

Issue 2: container-executor permission denied

2018-09-21 09:36:26,102 WARN org.apache.hadoop.yarn.server.nodemanager.containermanager.linux.privileged.PrivilegedOperationExecutor: IOException executing command:
java.io.IOException: Cannot run program "/etc/yarn/sbin/Linux-amd64-64/container-executor": error=13, Permission denied
        at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)
        at org.apache.hadoop.util.Shell.runCommand(Shell.java:938)
        at org.apache.hadoop.util.Shell.run(Shell.java:901)
        at org.apache.hadoop.util.Shell$ShellCommandExecutor.execute(Shell.java:1213)

Solution: The permission of /etc/yarn/sbin/Linux-amd64-64/container-executor should be 6050

Issue 3：How to get docker service log

Solution: we can get docker log with the following command

journalctl -u docker

Issue 4：docker can't remove containers with errors like device or resource busy

$ docker rm 0bfafa146431
Error response from daemon: Unable to remove filesystem for 0bfafa146431771f6024dcb9775ef47f170edb2f1852f71916ba44209ca6120a: remove /app/docker/containers/0bfafa146431771f6024dcb9775ef47f170edb2f152f71916ba44209ca6120a/shm: device or resource busy

Solution: to find which process leads to a device or resource busy, we can add a shell script, named find-busy-mnt.sh

#!/usr/bin/env bash

# A simple script to get information about mount points and pids and their
# mount namespaces.

if [ $# -ne 1 ];then
echo "Usage: $0 <devicemapper-device-id>"
exit 1
fi

ID=$1

MOUNTS=`find /proc/*/mounts | xargs grep $ID 2>/dev/null`

[ -z "$MOUNTS" ] &&  echo "No pids found" && exit 0

printf "PID\tNAME\t\tMNTNS\n"
echo "$MOUNTS" | while read LINE; do
PID=`echo $LINE | cut -d ":" -f1 | cut -d "/" -f3`
# Ignore self and thread-self
if [ "$PID" == "self" ] || [ "$PID" == "thread-self" ]; then
  continue
fi
NAME=`ps -q $PID -o comm=`
MNTNS=`readlink /proc/$PID/ns/mnt`
printf "%s\t%s\t\t%s\n" "$PID" "$NAME" "$MNTNS"
done

Kill the process by pid, which is found by the script

$ chmod +x find-busy-mnt.sh
./find-busy-mnt.sh 0bfafa146431771f6024dcb9775ef47f170edb2f152f71916ba44209ca6120a
# PID   NAME            MNTNS
# 5007  ntpd            mnt:[4026533598]
$ kill -9 5007

Issue 5：Yarn failed to start containers

if the number of GPUs required by applications is larger than the number of GPUs in the cluster, there would be some containers can't be created.