I encountered the same problem when trying to install Hortonworks HDP 2.1 manually. I managed to capture the container launcher script which contained the following:

#!/bin/bash

export NM_HTTP_PORT="8042"
export LOCAL_DIRS="/data/1/hadoop/yarn/local/usercache/doug/appcache/application_1406927878786_0001,/data/2/hadoop/yarn/local/usercache/doug/appcache/application_1406927878786_0001,/data/3/hadoop/yarn/local/usercache/doug/appcache/application_1406927878786_0001,/data/4/hadoop/yarn/local/usercache/doug/appcache/application_1406927878786_0001"
export JAVA_HOME="/usr/java/latest"
export NM_AUX_SERVICE_mapreduce_shuffle="AAA0+gAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA="
export CLASSPATH="$PWD:$HADOOP_CONF_DIR:$HADOOP_COMMON_HOME/share/hadoop/common/*:$HADOOP_COMMON_HOME/share/hadoop/common/lib/*:$HADOOP_HDFS_HOME/share/hadoop/hdfs/*:$HADOOP_HDFS_HOME/share/hadoop/hdfs/lib/*:$HADOOP_YARN_HOME/share/hadoop/yarn/*:$HADOOP_YARN_HOME/share/hadoop/yarn/lib/*:$HADOOP_MAPRED_HOME/share/hadoop/mapreduce/*:$HADOOP_MAPRED_HOME/share/hadoop/mapreduce/lib/*:job.jar/job.jar:job.jar/classes/:job.jar/lib/*:$PWD/*"
export HADOOP_TOKEN_FILE_LOCATION="/data/2/hadoop/yarn/local/usercache/doug/appcache/application_1406927878786_0001/container_1406927878786_0001_01_000001/container_tokens"
export NM_HOST="test02.admin.hypertable.com"
export APPLICATION_WEB_PROXY_BASE="/proxy/application_1406927878786_0001"
export JVM_PID="$$"
export USER="doug"
export HADOOP_HDFS_HOME="/usr/lib/hadoop-hdfs"
export PWD="/data/2/hadoop/yarn/local/usercache/doug/appcache/application_1406927878786_0001/container_1406927878786_0001_01_000001"
export CONTAINER_ID="container_1406927878786_0001_01_000001"
export HOME="/home/"
export NM_PORT="62404"
export LOGNAME="doug"
export APP_SUBMIT_TIME_ENV="1406928095871"
export MAX_APP_ATTEMPTS="2"
export HADOOP_CONF_DIR="/etc/hadoop/conf"
export MALLOC_ARENA_MAX="4"
export LOG_DIRS="/data/1/hadoop/yarn/logs/application_1406927878786_0001/container_1406927878786_0001_01_000001,/data/2/hadoop/yarn/logs/application_1406927878786_0001/container_1406927878786_0001_01_000001,/data/3/hadoop/yarn/logs/application_1406927878786_0001/container_1406927878786_0001_01_000001,/data/4/hadoop/yarn/logs/application_1406927878786_0001/container_1406927878786_0001_01_000001"
ln -sf "/data/1/hadoop/yarn/local/usercache/doug/filecache/10/libthrift-0.9.2.jar" "libthrift-0.9.2.jar"
ln -sf "/data/4/hadoop/yarn/local/usercache/doug/appcache/application_1406927878786_0001/filecache/13/job.xml" "job.xml"
mkdir -p jobSubmitDir
ln -sf "/data/3/hadoop/yarn/local/usercache/doug/appcache/application_1406927878786_0001/filecache/12/job.split" "jobSubmitDir/job.split"
mkdir -p jobSubmitDir
ln -sf "/data/2/hadoop/yarn/local/usercache/doug/appcache/application_1406927878786_0001/filecache/11/job.splitmetainfo" "jobSubmitDir/job.splitmetainfo"
ln -sf "/data/1/hadoop/yarn/local/usercache/doug/appcache/application_1406927878786_0001/filecache/10/job.jar" "job.jar"
ln -sf "/data/2/hadoop/yarn/local/usercache/doug/filecache/11/hypertable-0.9.8.0-apache2.jar" "hypertable-0.9.8.0-apache2.jar"
exec /bin/bash -c "$JAVA_HOME/bin/java -Dlog4j.configuration=container-log4j.properties -Dyarn.app.container.log.dir=/data/4/hadoop/yarn/logs/application_1406927878786_0001/container_1406927878786_0001_01_000001 -Dyarn.app.container.log.filesize=0 -Dhadoop.root.logger=INFO,CLA  -Xmx1024m org.apache.hadoop.mapreduce.v2.app.MRAppMaster 1>/data/4/hadoop/yarn/logs/application_1406927878786_0001/container_1406927878786_0001_01_000001/stdout 2>/data/4/hadoop/yarn/logs/application_1406927878786_0001/container_1406927878786_0001_01_000001/stderr "

The line that sets CLASSPATH was the culprit. To resolve the problem I had to set the variables HADOOP_COMMON_HOME, HADOOP_HDFS_HOME, HADOOP_YARN_HOME, and HADOOP_MAPRED_HOME in hadoop-env.sh to point to the appropriate directories under /usr/lib. In each of those directories I also had to setup the share/hadoop/... subdirectory hierarchy where the jars could be found.