>From my limited knowledge, only limited options such as network mode, volumes, portmaps can be passed through. See https://github.com/apache/spark/pull/3074/files.
https://issues.apache.org/jira/browse/SPARK-8734 is open for exposing all docker options to spark. -Mao On Thu, Jan 28, 2016 at 1:55 PM, Sathish Kumaran Vairavelu < vsathishkuma...@gmail.com> wrote: > Thank you., I figured it out. I have set executor memory to minimal and it > works., > > Another issue has come.. I have to pass --add-host option while running > containers in slave nodes.. Is there any option to pass docker run > parameters from spark? > On Thu, Jan 28, 2016 at 12:26 PM Mao Geng <m...@sumologic.com> wrote: > >> Sathish, >> >> I guess the mesos resources are not enough to run your job. You might >> want to check the mesos log to figure out why. >> >> I tried to run the docker image with "--conf spark.mesos.coarse=false" >> and "true". Both are fine. >> >> Best, >> Mao >> >> On Wed, Jan 27, 2016 at 5:00 PM, Sathish Kumaran Vairavelu < >> vsathishkuma...@gmail.com> wrote: >> >>> Hi, >>> >>> On the same Spark/Mesos/Docker setup, I am getting warning "Initial Job >>> has not accepted any resources; check your cluster UI to ensure that >>> workers are registered and have sufficient resources". I am running in >>> coarse grained mode. Any pointers on how to fix this issue? Please help. I >>> have updated both docker.properties and spark-default.conf with >>> spark.mesos.executor.docker.image >>> and other properties. >>> >>> >>> Thanks >>> >>> Sathish >>> >>> On Wed, Jan 27, 2016 at 9:58 AM Sathish Kumaran Vairavelu < >>> vsathishkuma...@gmail.com> wrote: >>> >>>> Thanks a lot for your info! I will try this today. >>>> On Wed, Jan 27, 2016 at 9:29 AM Mao Geng <m...@sumologic.com> wrote: >>>> >>>>> Hi Sathish, >>>>> >>>>> The docker image is normal, no AWS profile included. >>>>> >>>>> When the driver container runs with --net=host, the driver host's AWS >>>>> profile will take effect so that the driver can access the protected s3 >>>>> files. >>>>> >>>>> Similarly, Mesos slaves also run Spark executor docker container in >>>>> --net=host mode, so that the AWS profile of Mesos slaves will take effect. >>>>> >>>>> Hope it helps, >>>>> Mao >>>>> >>>>> On Jan 26, 2016, at 9:15 PM, Sathish Kumaran Vairavelu < >>>>> vsathishkuma...@gmail.com> wrote: >>>>> >>>>> Hi Mao, >>>>> >>>>> I want to check on accessing the S3 from Spark docker in Mesos. The >>>>> EC2 instance that I am using has the AWS profile/IAM included. Should we >>>>> build the docker image with any AWS profile settings or --net=host docker >>>>> option takes care of it? >>>>> >>>>> Please help >>>>> >>>>> >>>>> Thanks >>>>> >>>>> Sathish >>>>> >>>>> On Tue, Jan 26, 2016 at 9:04 PM Mao Geng <m...@sumologic.com> wrote: >>>>> >>>>>> Thank you very much, Jerry! >>>>>> >>>>>> I changed to "--jars >>>>>> /opt/spark/lib/hadoop-aws-2.7.1.jar,/opt/spark/lib/aws-java-sdk-1.7.4.jar" >>>>>> then it worked like a charm! >>>>>> >>>>>> From Mesos task logs below, I saw Mesos executor downloaded the jars >>>>>> from the driver, which is a bit unnecessary (as the docker image already >>>>>> has them), but that's ok - I am happy seeing Spark + Mesos + Docker + S3 >>>>>> worked together! >>>>>> >>>>>> Thanks, >>>>>> Mao >>>>>> >>>>>> 16/01/27 02:54:45 INFO Executor: Using REPL class URI: >>>>>> http://172.16.3.98:33771 >>>>>> 16/01/27 02:55:12 INFO CoarseGrainedExecutorBackend: Got assigned task 0 >>>>>> 16/01/27 02:55:12 INFO Executor: Running task 0.0 in stage 0.0 (TID 0) >>>>>> 16/01/27 02:55:12 INFO Executor: Fetching >>>>>> http://172.16.3.98:3850/jars/hadoop-aws-2.7.1.jar with timestamp >>>>>> 1453863280432 >>>>>> 16/01/27 02:55:12 INFO Utils: Fetching >>>>>> http://172.16.3.98:3850/jars/hadoop-aws-2.7.1.jar to >>>>>> /tmp/spark-7b8e1681-8a62-4f1d-9e11-fdf8062b1b08/fetchFileTemp1518118694295619525.tmp >>>>>> 16/01/27 02:55:12 INFO Utils: Copying >>>>>> /tmp/spark-7b8e1681-8a62-4f1d-9e11-fdf8062b1b08/-19880839621453863280432_cache >>>>>> to /./hadoop-aws-2.7.1.jar >>>>>> 16/01/27 02:55:12 INFO Executor: Adding file:/./hadoop-aws-2.7.1.jar to >>>>>> class loader >>>>>> 16/01/27 02:55:12 INFO Executor: Fetching >>>>>> http://172.16.3.98:3850/jars/aws-java-sdk-1.7.4.jar with timestamp >>>>>> 1453863280472 >>>>>> 16/01/27 02:55:12 INFO Utils: Fetching >>>>>> http://172.16.3.98:3850/jars/aws-java-sdk-1.7.4.jar to >>>>>> /tmp/spark-7b8e1681-8a62-4f1d-9e11-fdf8062b1b08/fetchFileTemp8868621397726761921.tmp >>>>>> 16/01/27 02:55:12 INFO Utils: Copying >>>>>> /tmp/spark-7b8e1681-8a62-4f1d-9e11-fdf8062b1b08/8167072821453863280472_cache >>>>>> to /./aws-java-sdk-1.7.4.jar >>>>>> 16/01/27 02:55:12 INFO Executor: Adding file:/./aws-java-sdk-1.7.4.jar >>>>>> to class loader >>>>>> >>>>>> On Tue, Jan 26, 2016 at 5:40 PM, Jerry Lam <chiling...@gmail.com> >>>>>> wrote: >>>>>> >>>>>>> Hi Mao, >>>>>>> >>>>>>> Can you try --jars to include those jars? >>>>>>> >>>>>>> Best Regards, >>>>>>> >>>>>>> Jerry >>>>>>> >>>>>>> Sent from my iPhone >>>>>>> >>>>>>> On 26 Jan, 2016, at 7:02 pm, Mao Geng <m...@sumologic.com> wrote: >>>>>>> >>>>>>> Hi there, >>>>>>> >>>>>>> I am trying to run Spark on Mesos using a Docker image as executor, >>>>>>> as mentioned >>>>>>> http://spark.apache.org/docs/latest/running-on-mesos.html#mesos-docker-support >>>>>>> . >>>>>>> >>>>>>> I built a docker image using the following Dockerfile (which is >>>>>>> based on >>>>>>> https://github.com/apache/spark/blob/master/docker/spark-mesos/Dockerfile >>>>>>> ): >>>>>>> >>>>>>> FROM mesosphere/mesos:0.25.0-0.2.70.ubuntu1404 >>>>>>> >>>>>>> # Update the base ubuntu image with dependencies needed for Spark >>>>>>> RUN apt-get update && \ >>>>>>> apt-get install -y python libnss3 openjdk-7-jre-headless curl >>>>>>> >>>>>>> RUN curl >>>>>>> http://www.carfab.com/apachesoftware/spark/spark-1.6.0/spark-1.6.0-bin-hadoop2.6.tgz >>>>>>> | tar -xzC /opt && \ >>>>>>> ln -s /opt/spark-1.6.0-bin-hadoop2.6 /opt/spark >>>>>>> ENV SPARK_HOME /opt/spark >>>>>>> ENV MESOS_NATIVE_JAVA_LIBRARY /usr/local/lib/libmesos.so >>>>>>> >>>>>>> Then I successfully ran spark-shell via this docker command: >>>>>>> docker run --rm -it --net=host <registry>/<image>:<tag> >>>>>>> /opt/spark/bin/spark-shell --master mesos://<master_host>:5050 --conf >>>>>>> <registry>/<image>:<tag> >>>>>>> >>>>>>> So far so good. Then I wanted to call sc.textFile to load a file >>>>>>> from S3, but I was blocked by some issues which I couldn't figure out. >>>>>>> I've >>>>>>> read >>>>>>> https://dzone.com/articles/uniting-spark-parquet-and-s3-as-an-alternative-to >>>>>>> and >>>>>>> http://blog.encomiabile.it/2015/10/29/apache-spark-amazon-s3-and-apache-mesos, >>>>>>> learned that I need to add hadood-aws-2.7.1 and aws-java-sdk-2.7.4 into >>>>>>> the >>>>>>> executor and driver's classpaths, in order to access s3 files. >>>>>>> >>>>>>> So, I added following lines into Dockerfile and build a new image. >>>>>>> RUN curl >>>>>>> https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk/1.7.4/aws-java-sdk-1.7.4.jar >>>>>>> -o /opt/spark/lib/aws-java-sdk-1.7.4.jar >>>>>>> RUN curl >>>>>>> http://central.maven.org/maven2/org/apache/hadoop/hadoop-aws/2.7.1/hadoop-aws-2.7.1.jar >>>>>>> -o /opt/spark/lib/hadoop-aws-2.7.1.jar >>>>>>> >>>>>>> Then I started spark-shell again with below command: >>>>>>> docker run --rm -it --net=host <registry>/<image>:<tag> >>>>>>> /opt/spark/bin/spark-shell --master mesos://<master_host>:5050 --conf >>>>>>> <registry>/<image>:<tag> --conf >>>>>>> spark.executor.extraClassPath=/opt/spark/lib/hadoop-aws-2.7.1.jar:/opt/spark/lib/aws-java-sdk-1.7.4.jar >>>>>>> --conf >>>>>>> spark.driver.extraClassPath=/opt/spark/lib/hadoop-aws-2.7.1.jar:/opt/spark/lib/aws-java-sdk-1.7.4.jar >>>>>>> >>>>>>> But below command failed when I ran it in spark-shell: >>>>>>> scala> sc.textFile("s3a://<bucket_name>/<file_name>").count() >>>>>>> [Stage 0:> >>>>>>> (0 + 2) / 2]16/01/26 23:05:23 WARN TaskSetManager: Lost task 0.0 in >>>>>>> stage >>>>>>> 0.0 (TID 0, ip-172-16-14-203.us-west-2.compute.internal): >>>>>>> java.lang.RuntimeException: java.lang.ClassNotFoundException: Class >>>>>>> org.apache.hadoop.fs.s3a.S3AFileSystem not found >>>>>>> at >>>>>>> org.apache.hadoop.conf.Configuration.getClass(Configuration.java:2074) >>>>>>> at >>>>>>> org.apache.hadoop.fs.FileSystem.getFileSystemClass(FileSystem.java:2578) >>>>>>> at >>>>>>> org.apache.hadoop.fs.FileSystem.createFileSystem(FileSystem.java:2591) >>>>>>> at org.apache.hadoop.fs.FileSystem.access$200(FileSystem.java:91) >>>>>>> at >>>>>>> org.apache.hadoop.fs.FileSystem$Cache.getInternal(FileSystem.java:2630) >>>>>>> at org.apache.hadoop.fs.FileSystem$Cache.get(FileSystem.java:2612) >>>>>>> at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:370) >>>>>>> at org.apache.hadoop.fs.Path.getFileSystem(Path.java:296) >>>>>>> at >>>>>>> org.apache.hadoop.mapred.LineRecordReader.<init>(LineRecordReader.java:107) >>>>>>> at >>>>>>> org.apache.hadoop.mapred.TextInputFormat.getRecordReader(TextInputFormat.java:67) >>>>>>> at org.apache.spark.rdd.HadoopRDD$$anon$1.<init>(HadoopRDD.scala:237) >>>>>>> at org.apache.spark.rdd.HadoopRDD.compute(HadoopRDD.scala:208) >>>>>>> at org.apache.spark.rdd.HadoopRDD.compute(HadoopRDD.scala:101) >>>>>>> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306) >>>>>>> at org.apache.spark.rdd.RDD.iterator(RDD.scala:270) >>>>>>> at >>>>>>> org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38) >>>>>>> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306) >>>>>>> at org.apache.spark.rdd.RDD.iterator(RDD.scala:270) >>>>>>> at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66) >>>>>>> at org.apache.spark.scheduler.Task.run(Task.scala:89) >>>>>>> at >>>>>>> org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:213) >>>>>>> at >>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) >>>>>>> at >>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) >>>>>>> at java.lang.Thread.run(Thread.java:745) >>>>>>> Caused by: java.lang.ClassNotFoundException: Class >>>>>>> org.apache.hadoop.fs.s3a.S3AFileSystem not found >>>>>>> at >>>>>>> org.apache.hadoop.conf.Configuration.getClassByName(Configuration.java:1980) >>>>>>> at >>>>>>> org.apache.hadoop.conf.Configuration.getClass(Configuration.java:2072) >>>>>>> ... 23 more >>>>>>> >>>>>>> I checked hadoop-aws-2.7.1.jar, >>>>>>> the org.apache.hadoop.fs.s3a.S3AFileSystem class file is in it. I also >>>>>>> checked the Environment page of driver's Web UI at 4040 port, both >>>>>>> hadoop-aws-2.7.1.jar and aws-java-sdk-1.7.4.jar are in the >>>>>>> Classpath Entries (system path). And following code ran fine in >>>>>>> spark-shell: >>>>>>> scala> val clazz = >>>>>>> Class.forName("org.apache.hadoop.fs.s3a.S3AFileSystem") >>>>>>> clazz: Class[_] = class org.apache.hadoop.fs.s3a.S3AFileSystem >>>>>>> >>>>>>> scala> clazz.getClassLoader() >>>>>>> res2: ClassLoader = sun.misc.Launcher$AppClassLoader@770848b9 >>>>>>> >>>>>>> So, I am confused why the task failed with >>>>>>> "java.lang.ClassNotFoundException" >>>>>>> Exception? Is there something wrong in the command line options I >>>>>>> used to start spark-shell, or in the docker image, or in the "s3a://" >>>>>>> url? >>>>>>> Or is something related to the Docker executor of Mesos? I studied a bit >>>>>>> https://github.com/apache/spark/blob/branch-1.6/core/src/main/scala/org/apache/spark/scheduler/cluster/mesos/MesosSchedulerBackend.scala >>>>>>> but didn't understand it well... >>>>>>> >>>>>>> Appreciate if anyone will shed some lights on me. >>>>>>> >>>>>>> Thanks, >>>>>>> Mao Geng >>>>>>> >>>>>>> >>>>>> >>
