search

GELOG / adam-ibs

Ports the IBS/MDS/IBD functionality of Plink to Spark / ADAM
Apache License 2.0
3 stars 6 forks source link

[Ubuntu, Java 7] No configuration setting found for key 'akka.version' #52

Open davidonlaptop opened 8 years ago

davidonlaptop commented 8 years ago

La compilation fonctionne sur une machine Linux vierge (Ubuntu 14.04). Mais l'execution ne fonctionne pas:

docker run --rm -ti ubuntu:14.04

apt-get update

export JAVA_VERSION="7u85"
export JAVA_HOME="/usr/lib/jvm/java-7-openjdk-amd64"
DEBIAN_FRONTEND=noninteractive apt-get install -y openjdk-7-jdk=$JAVA_VERSION\*

apt-get install -y git
git clone https://github.com/GELOG/adam-ibs.git
cd adam-ibs/

apt-get install -y maven

mvn package

root@7d5f110a4f03:/adam-ibs# java -jar adam-ibs-core/target/adam-ibs-core-0.1.0-jar-with-dependencies.jar --help
23:33:40.516 [main] [INFO ] [c.e.m.c.Main$] : Begin with arguments : --help
      --file  <name>   Specify .ped + .map filename prefix (default 'plink')
      --genome         Calculate IBS distances between all individuals [needs
                       --file and --out]
      --make-bed       Create a new binary fileset. Specify .ped and .map files
                       [needs --file and --out]
      --out  <name>    Specify the output filename
      --show-parquet   Show shema and data sample ostored in a parquet file [needs
                       --file]
  -h, --help  <arg>    Show help message

root@7d5f110a4f03:/adam-ibs# java -jar adam-ibs-core/target/adam-ibs-core-0.1.0-jar-with-dependencies.jar --file DATA/
test --out output --make-bed
23:22:23.977 [main] [INFO ] [c.e.m.c.Main$] : Begin with arguments : --file DATA/test --out output --make-bed
23:22:25.346 [main] [ERROR] [o.a.s.SparkContext] : Error initializing SparkContext.
com.typesafe.config.ConfigException$Missing: No configuration setting found for key 'akka.version'
    at com.typesafe.config.impl.SimpleConfig.findKey(SimpleConfig.java:124) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at com.typesafe.config.impl.SimpleConfig.find(SimpleConfig.java:145) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at com.typesafe.config.impl.SimpleConfig.find(SimpleConfig.java:151) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at com.typesafe.config.impl.SimpleConfig.find(SimpleConfig.java:159) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at com.typesafe.config.impl.SimpleConfig.find(SimpleConfig.java:164) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at com.typesafe.config.impl.SimpleConfig.getString(SimpleConfig.java:206) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at akka.actor.ActorSystem$Settings.<init>(ActorSystem.scala:168) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at akka.actor.ActorSystemImpl.<init>(ActorSystem.scala:504) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at akka.actor.ActorSystem$.apply(ActorSystem.scala:141) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at akka.actor.ActorSystem$.apply(ActorSystem.scala:118) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at org.apache.spark.util.AkkaUtils$.org$apache$spark$util$AkkaUtils$$doCreateActorSystem(AkkaUtils.scala:122) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at org.apache.spark.util.AkkaUtils$$anonfun$1.apply(AkkaUtils.scala:54) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at org.apache.spark.util.AkkaUtils$$anonfun$1.apply(AkkaUtils.scala:53) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at org.apache.spark.util.Utils$$anonfun$startServiceOnPort$1.apply$mcVI$sp(Utils.scala:1991) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at scala.collection.immutable.Range.foreach$mVc$sp(Range.scala:142) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at org.apache.spark.util.Utils$.startServiceOnPort(Utils.scala:1982) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at org.apache.spark.util.AkkaUtils$.createActorSystem(AkkaUtils.scala:56) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at org.apache.spark.rpc.akka.AkkaRpcEnvFactory.create(AkkaRpcEnv.scala:245) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at org.apache.spark.rpc.RpcEnv$.create(RpcEnv.scala:52) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at org.apache.spark.SparkEnv$.create(SparkEnv.scala:247) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at org.apache.spark.SparkEnv$.createDriverEnv(SparkEnv.scala:188) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at org.apache.spark.SparkContext.createSparkEnv(SparkContext.scala:267) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at org.apache.spark.SparkContext.<init>(SparkContext.scala:424) ~[adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at com.ets.mgl804.core.AppContext$.<init>(AppContext.scala:16) [adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at com.ets.mgl804.core.AppContext$.<clinit>(AppContext.scala) [adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at com.ets.mgl804.core.cli.PlinkMethod$.<init>(PlinkMethod.scala:19) [adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at com.ets.mgl804.core.cli.PlinkMethod$.<clinit>(PlinkMethod.scala) [adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at com.ets.mgl804.core.Main$$anonfun$main$2.apply(Main.scala:26) [adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at com.ets.mgl804.core.Main$$anonfun$main$2.apply(Main.scala:23) [adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) [adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:34) [adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at com.ets.mgl804.core.Main$.main(Main.scala:22) [adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
    at com.ets.mgl804.core.Main.main(Main.scala) [adam-ibs-core-0.1.0-jar-with-dependencies.jar:na]
Exception in thread "main" java.lang.ExceptionInInitializerError
    at com.ets.mgl804.core.cli.PlinkMethod$.<init>(PlinkMethod.scala:19)
    at com.ets.mgl804.core.cli.PlinkMethod$.<clinit>(PlinkMethod.scala)
    at com.ets.mgl804.core.Main$$anonfun$main$2.apply(Main.scala:26)
    at com.ets.mgl804.core.Main$$anonfun$main$2.apply(Main.scala:23)
    at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
    at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:34)
    at com.ets.mgl804.core.Main$.main(Main.scala:22)
    at com.ets.mgl804.core.Main.main(Main.scala)
Caused by: com.typesafe.config.ConfigException$Missing: No configuration setting found for key 'akka.version'
    at com.typesafe.config.impl.SimpleConfig.findKey(SimpleConfig.java:124)
    at com.typesafe.config.impl.SimpleConfig.find(SimpleConfig.java:145)
    at com.typesafe.config.impl.SimpleConfig.find(SimpleConfig.java:151)
    at com.typesafe.config.impl.SimpleConfig.find(SimpleConfig.java:159)
    at com.typesafe.config.impl.SimpleConfig.find(SimpleConfig.java:164)
    at com.typesafe.config.impl.SimpleConfig.getString(SimpleConfig.java:206)
    at akka.actor.ActorSystem$Settings.<init>(ActorSystem.scala:168)
    at akka.actor.ActorSystemImpl.<init>(ActorSystem.scala:504)
    at akka.actor.ActorSystem$.apply(ActorSystem.scala:141)
    at akka.actor.ActorSystem$.apply(ActorSystem.scala:118)
    at org.apache.spark.util.AkkaUtils$.org$apache$spark$util$AkkaUtils$$doCreateActorSystem(AkkaUtils.scala:122)
    at org.apache.spark.util.AkkaUtils$$anonfun$1.apply(AkkaUtils.scala:54)
    at org.apache.spark.util.AkkaUtils$$anonfun$1.apply(AkkaUtils.scala:53)
    at org.apache.spark.util.Utils$$anonfun$startServiceOnPort$1.apply$mcVI$sp(Utils.scala:1991)
    at scala.collection.immutable.Range.foreach$mVc$sp(Range.scala:142)
    at org.apache.spark.util.Utils$.startServiceOnPort(Utils.scala:1982)
    at org.apache.spark.util.AkkaUtils$.createActorSystem(AkkaUtils.scala:56)
    at org.apache.spark.rpc.akka.AkkaRpcEnvFactory.create(AkkaRpcEnv.scala:245)
    at org.apache.spark.rpc.RpcEnv$.create(RpcEnv.scala:52)
    at org.apache.spark.SparkEnv$.create(SparkEnv.scala:247)
    at org.apache.spark.SparkEnv$.createDriverEnv(SparkEnv.scala:188)
    at org.apache.spark.SparkContext.createSparkEnv(SparkContext.scala:267)
    at org.apache.spark.SparkContext.<init>(SparkContext.scala:424)
    at com.ets.mgl804.core.AppContext$.<init>(AppContext.scala:16)
    at com.ets.mgl804.core.AppContext$.<clinit>(AppContext.scala)
    ... 8 more
iki-v commented 8 years ago

Le jar doit être exécute sur Spark.