Glad you got it going! It's wasn't very obvious what needed to be set, maybe it is worth explicitly stating this in the docs since it seems to have come up a couple times before too.
Bryan On Fri, Jan 15, 2016 at 12:33 PM, Andrew Weiner < andrewweiner2...@u.northwestern.edu> wrote: > Actually, I just found this [ > https://issues.apache.org/jira/browse/SPARK-1680], which after a bit of > googling and reading leads me to believe that the preferred way to change > the yarn environment is to edit the spark-defaults.conf file by adding this > line: > spark.yarn.appMasterEnv.PYSPARK_PYTHON /path/to/python > > While both this solution and the solution from my prior email work, I > believe this is the preferred solution. > > Sorry for the flurry of emails. Again, thanks for all the help! > > Andrew > > On Fri, Jan 15, 2016 at 1:47 PM, Andrew Weiner < > andrewweiner2...@u.northwestern.edu> wrote: > >> I finally got the pi.py example to run in yarn cluster mode. This was >> the key insight: >> https://issues.apache.org/jira/browse/SPARK-9229 >> >> I had to set SPARK_YARN_USER_ENV in spark-env.sh: >> export SPARK_YARN_USER_ENV="PYSPARK_PYTHON=/home/aqualab/local/bin/python" >> >> This caused the PYSPARK_PYTHON environment variable to be used in my yarn >> environment in cluster mode. >> >> Thank you for all your help! >> >> Best, >> Andrew >> >> >> >> On Fri, Jan 15, 2016 at 12:57 PM, Andrew Weiner < >> andrewweiner2...@u.northwestern.edu> wrote: >> >>> I tried playing around with my environment variables, and here is an >>> update. >>> >>> When I run in cluster mode, my environment variables do not persist >>> throughout the entire job. >>> For example, I tried creating a local copy of HADOOP_CONF_DIR in >>> /home/<username>/local/etc/hadoop/conf, and then, in spark-env.sh I the >>> variable: >>> export HADOOP_CONF_DIR=/home/<username>/local/etc/hadoop/conf >>> >>> Later, when we print the environment variables in the python code, I see >>> this: >>> >>> ('HADOOP_CONF_DIR', '/etc/hadoop/conf') >>> >>> However, when I run in client mode, I see this: >>> >>> ('HADOOP_CONF_DIR', '/home/awp066/local/etc/hadoop/conf') >>> >>> Furthermore, if I omit that environment variable from spark-env.sh >>> altogether, I get the expected error in both client and cluster mode: >>> >>> When running with master 'yarn' >>> either HADOOP_CONF_DIR or YARN_CONF_DIR must be set in the environment. >>> >>> This suggests that my environment variables are being used when I first >>> submit the job, but at some point during the job, my environment variables >>> are thrown out and someone's (yarn's?) environment variables are being used. >>> >>> Andrew >>> >>> >>> On Fri, Jan 15, 2016 at 11:03 AM, Andrew Weiner < >>> andrewweiner2...@u.northwestern.edu> wrote: >>> >>>> Indeed! Here is the output when I run in cluster mode: >>>> >>>> Traceback (most recent call last): >>>> File "pi.py", line 22, in ? >>>> raise RuntimeError("\n"+str(sys.version_info) +"\n"+ >>>> RuntimeError: >>>> (2, 4, 3, 'final', 0) >>>> [('PYSPARK_GATEWAY_PORT', '48079'), ('PYTHONPATH', >>>> '/scratch2/hadoop/yarn/local/usercache/<username>/filecache/116/spark-assembly-1.6.0-hadoop2.4.0.jar:/home/<user>/spark-1.6.0-bin-hadoop2.4/python:/home/<username>/code/libs:/scratch5/hadoop/yarn/local/usercache/<username>/appcache/application_1450370639491_0239/container_1450370639491_0239_01_000001/pyspark.zip:/scratch5/hadoop/yarn/local/usercache/<username>/appcache/application_1450370639491_0239/container_1450370639491_0239_01_000001/py4j-0.9-src.zip'), >>>> ('PYTHONUNBUFFERED', 'YES')] >>>> >>>> As we suspected, it is using Python 2.4 >>>> >>>> One thing that surprises me is that PYSPARK_PYTHON is not showing up in >>>> the list, even though I am setting it and exporting it in spark-submit >>>> *and* in spark-env.sh. Is there somewhere else I need to set this >>>> variable? Maybe in one of the hadoop conf files in my HADOOP_CONF_DIR? >>>> >>>> Andrew >>>> >>>> >>>> >>>> On Thu, Jan 14, 2016 at 1:14 PM, Bryan Cutler <cutl...@gmail.com> >>>> wrote: >>>> >>>>> It seems like it could be the case that some other Python version is >>>>> being invoked. To make sure, can you add something like this to the top >>>>> of >>>>> the .py file you are submitting to get some more info about how the >>>>> application master is configured? >>>>> >>>>> import sys, os >>>>> raise RuntimeError("\n"+str(sys.version_info) +"\n"+ >>>>> str([(k,os.environ[k]) for k in os.environ if "PY" in k])) >>>>> >>>>> On Thu, Jan 14, 2016 at 8:37 AM, Andrew Weiner < >>>>> andrewweiner2...@u.northwestern.edu> wrote: >>>>> >>>>>> Hi Bryan, >>>>>> >>>>>> I ran "$> python --version" on every node on the cluster, and it is >>>>>> Python 2.7.8 for every single one. >>>>>> >>>>>> When I try to submit the Python example in client mode >>>>>> * ./bin/spark-submit --master yarn --deploy-mode client >>>>>> --driver-memory 4g --executor-memory 2g --executor-cores 1 >>>>>> ./examples/src/main/python/pi.py 10* >>>>>> That's when I get this error that I mentioned: >>>>>> >>>>>> 16/01/14 10:09:10 WARN scheduler.TaskSetManager: Lost task 0.0 in >>>>>> stage 0.0 (TID 0, mundonovo-priv): org.apache.spark.SparkException: >>>>>> Error from python worker: >>>>>> python: module pyspark.daemon not found >>>>>> PYTHONPATH was: >>>>>> >>>>>> /scratch5/hadoop/yarn/local/usercache/<username>/filecache/48/spark-assembly-1.6.0-hadoop2.4.0.jar:/home/aqualab/spark-1.6.0-bin-hadoop2.4/python:/home/jpr123/hg.pacific/python-common:/home/jp >>>>>> >>>>>> r123/python-libs:/home/jpr123/lib/python2.7/site-packages:/home/zsb739/local/lib/python2.7/site-packages:/home/jpr123/mobile-cdn-analysis:/home/<username>/lib/python2.7/site-packages:/home/<username>/code/libs:/scratch5/hadoop/yarn/local/usercache/<username>/appcache/application_1450370639491_0187/container_1450370639491_0187_01_000002/pyspark.zip:/scratch5/hadoop/yarn/local/usercache/<username>/appcache/application_1450370639491_0187/container_1450370639491_0187_01_000002/py4j-0.9-src.zip >>>>>> java.io.EOFException >>>>>> at java.io.DataInputStream.readInt(DataInputStream.java:392) >>>>>> at >>>>>> org.apache.spark.api.python.PythonWorkerFactory.startDaemon(PythonWorkerFactory.scala:164) >>>>>> at [....] >>>>>> >>>>>> followed by several more similar errors that also say: >>>>>> Error from python worker: >>>>>> python: module pyspark.daemon not found >>>>>> >>>>>> >>>>>> Even though the default python appeared to be correct, I just went >>>>>> ahead and explicitly set PYSPARK_PYTHON in conf/spark-env.sh to the path >>>>>> of >>>>>> the default python binary executable. After making this change I was >>>>>> able >>>>>> to run the job successfully in client! That is, this appeared to fix the >>>>>> "pyspark.daemon not found" error when running in client mode. >>>>>> >>>>>> However, when running in cluster mode, I am still getting the same >>>>>> syntax error: >>>>>> >>>>>> Traceback (most recent call last): >>>>>> File "pi.py", line 24, in ? >>>>>> from pyspark import SparkContext >>>>>> File >>>>>> "/home/<username>/spark-1.6.0-bin-hadoop2.4/python/pyspark/__init__.py", >>>>>> line 61 >>>>>> indent = ' ' * (min(len(m) for m in indents) if indents else 0) >>>>>> ^ >>>>>> SyntaxError: invalid syntax >>>>>> >>>>>> Is it possible that the PYSPARK_PYTHON environment variable is ignored >>>>>> when jobs are submitted in cluster mode? It seems that Spark or Yarn is >>>>>> going behind my back, so to speak, and using some older version of >>>>>> python I didn't even know was installed. >>>>>> >>>>>> Thanks again for all your help thus far. We are getting close.... >>>>>> >>>>>> Andrew >>>>>> >>>>>> >>>>>> >>>>>> On Wed, Jan 13, 2016 at 6:13 PM, Bryan Cutler <cutl...@gmail.com> >>>>>> wrote: >>>>>> >>>>>>> Hi Andrew, >>>>>>> >>>>>>> There are a couple of things to check. First, is Python 2.7 the >>>>>>> default version on all nodes in the cluster or is it an alternate >>>>>>> install? >>>>>>> Meaning what is the output of this command "$> python --version" If >>>>>>> it is >>>>>>> an alternate install, you could set the environment variable " >>>>>>> PYSPARK_PYTHON" Python binary executable to use for PySpark in both >>>>>>> driver and workers (default is python). >>>>>>> >>>>>>> Did you try to submit the Python example under client mode? >>>>>>> Otherwise, the command looks fine, you don't use the --class option for >>>>>>> submitting python files >>>>>>> * ./bin/spark-submit --master yarn --deploy-mode client >>>>>>> --driver-memory 4g --executor-memory 2g --executor-cores 1 >>>>>>> ./examples/src/main/python/pi.py 10* >>>>>>> >>>>>>> That is a good sign that local jobs and Java examples work, probably >>>>>>> just a small configuration issue :) >>>>>>> >>>>>>> Bryan >>>>>>> >>>>>>> On Wed, Jan 13, 2016 at 3:51 PM, Andrew Weiner < >>>>>>> andrewweiner2...@u.northwestern.edu> wrote: >>>>>>> >>>>>>>> Thanks for your continuing help. Here is some additional info. >>>>>>>> >>>>>>>> *OS/architecture* >>>>>>>> output of *cat /proc/version*: >>>>>>>> Linux version 2.6.18-400.1.1.el5 ( >>>>>>>> mockbu...@x86-012.build.bos.redhat.com) >>>>>>>> >>>>>>>> output of *lsb_release -a*: >>>>>>>> LSB Version: >>>>>>>> >>>>>>>> :core-4.0-amd64:core-4.0-ia32:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-ia32:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-ia32:printing-4.0-noarch >>>>>>>> Distributor ID: RedHatEnterpriseServer >>>>>>>> Description: Red Hat Enterprise Linux Server release 5.11 >>>>>>>> (Tikanga) >>>>>>>> Release: 5.11 >>>>>>>> Codename: Tikanga >>>>>>>> >>>>>>>> *Running a local job* >>>>>>>> I have confirmed that I can successfully run python jobs using >>>>>>>> bin/spark-submit --master local[*] >>>>>>>> Specifically, this is the command I am using: >>>>>>>> *./bin/spark-submit --master local[8] >>>>>>>> ./examples/src/main/python/wordcount.py >>>>>>>> file:/home/<username>/spark-1.6.0-bin-hadoop2.4/README.md* >>>>>>>> And it works! >>>>>>>> >>>>>>>> *Additional info* >>>>>>>> I am also able to successfully run the Java SparkPi example using >>>>>>>> yarn in cluster mode using this command: >>>>>>>> * ./bin/spark-submit --class org.apache.spark.examples.SparkPi >>>>>>>> --master yarn --deploy-mode cluster --driver-memory 4g >>>>>>>> --executor-memory 2g --executor-cores 1 lib/spark-examples*.jar >>>>>>>> 10* >>>>>>>> This Java job also runs successfully when I change --deploy-mode to >>>>>>>> client. The fact that I can run Java jobs in cluster mode makes me >>>>>>>> thing >>>>>>>> that everything is installed correctly--is that a valid assumption? >>>>>>>> >>>>>>>> The problem remains that I cannot submit python jobs. Here is the >>>>>>>> command that I am using to try to submit python jobs: >>>>>>>> * ./bin/spark-submit --master yarn --deploy-mode cluster >>>>>>>> --driver-memory 4g --executor-memory 2g --executor-cores 1 >>>>>>>> ./examples/src/main/python/pi.py 10* >>>>>>>> Does that look like a correct command? I wasn't sure what to put >>>>>>>> for --class so I omitted it. At any rate, the result of the above >>>>>>>> command >>>>>>>> is a syntax error, similar to the one I posted in the original email: >>>>>>>> >>>>>>>> Traceback (most recent call last): >>>>>>>> File "pi.py", line 24, in ? >>>>>>>> from pyspark import SparkContext >>>>>>>> File >>>>>>>> "/home/<username>/spark-1.6.0-bin-hadoop2.4/python/pyspark/__init__.py", >>>>>>>> line 61 >>>>>>>> indent = ' ' * (min(len(m) for m in indents) if indents else 0) >>>>>>>> ^ >>>>>>>> SyntaxError: invalid syntax >>>>>>>> >>>>>>>> >>>>>>>> This really looks to me like a problem with the python version. >>>>>>>> Python 2.4 would throw this syntax error but Python 2.7 would not. >>>>>>>> And yet >>>>>>>> I am using Python 2.7.8. Is there any chance that Spark or Yarn is >>>>>>>> somehow >>>>>>>> using an older version of Python without my knowledge? >>>>>>>> >>>>>>>> Finally, when I try to run the same command in client mode... >>>>>>>> * ./bin/spark-submit --master yarn --deploy-mode client >>>>>>>> --driver-memory 4g --executor-memory 2g --executor-cores 1 >>>>>>>> ./examples/src/main/python/pi.py 10* >>>>>>>> I get the error I mentioned in the prior email: >>>>>>>> Error from python worker: >>>>>>>> python: module pyspark.daemon not found >>>>>>>> >>>>>>>> Any thoughts? >>>>>>>> >>>>>>>> Best, >>>>>>>> Andrew >>>>>>>> >>>>>>>> >>>>>>>> On Mon, Jan 11, 2016 at 12:25 PM, Bryan Cutler <cutl...@gmail.com> >>>>>>>> wrote: >>>>>>>> >>>>>>>>> This could be an environment issue, could you give more details >>>>>>>>> about the OS/architecture that you are using? If you are sure >>>>>>>>> everything >>>>>>>>> is installed correctly on each node following the guide on "Running >>>>>>>>> Spark >>>>>>>>> on Yarn" http://spark.apache.org/docs/latest/running-on-yarn.html >>>>>>>>> and that the spark assembly jar is reachable, then I would check to >>>>>>>>> see if >>>>>>>>> you can submit a local job to just run on one node. >>>>>>>>> >>>>>>>>> On Fri, Jan 8, 2016 at 5:22 PM, Andrew Weiner < >>>>>>>>> andrewweiner2...@u.northwestern.edu> wrote: >>>>>>>>> >>>>>>>>>> Now for simplicity I'm testing with wordcount.py from the >>>>>>>>>> provided examples, and using Spark 1.6.0 >>>>>>>>>> >>>>>>>>>> The first error I get is: >>>>>>>>>> >>>>>>>>>> 16/01/08 19:14:46 ERROR lzo.GPLNativeCodeLoader: Could not load >>>>>>>>>> native gpl library >>>>>>>>>> java.lang.UnsatisfiedLinkError: no gplcompression in >>>>>>>>>> java.library.path >>>>>>>>>> at >>>>>>>>>> java.lang.ClassLoader.loadLibrary(ClassLoader.java:1864) >>>>>>>>>> at [....] >>>>>>>>>> >>>>>>>>>> A bit lower down, I see this error: >>>>>>>>>> >>>>>>>>>> 16/01/08 19:14:48 WARN scheduler.TaskSetManager: Lost task 0.0 in >>>>>>>>>> stage 0.0 (TID 0, mundonovo-priv): org.apache.spark.SparkException: >>>>>>>>>> Error from python worker: >>>>>>>>>> python: module pyspark.daemon not found >>>>>>>>>> PYTHONPATH was: >>>>>>>>>> >>>>>>>>>> /scratch5/hadoop/yarn/local/usercache/<username>/filecache/22/spark-assembly-1.6.0-hadoop2.4.0.jar:/home/jpr123/hg.pacific/python-common:/home/jpr123/python-libs:/home/jpr123/lib/python2.7/site-packages:/home/zsb739/local/lib/python2.7/site-packages:/home/jpr123/mobile-cdn-analysis:/home/<username>/lib/python2.7/site-packages:/scratch4/hadoop/yarn/local/usercache/<username>/appcache/application_1450370639491_0136/container_1450370639491_0136_01_000002/pyspark.zip:/scratch4/hadoop/yarn/local/usercache/<username>/appcache/application_1450370639491_0136/container_1450370639491_0136_01_000002/py4j-0.9-src.zip >>>>>>>>>> java.io.EOFException >>>>>>>>>> at >>>>>>>>>> java.io.DataInputStream.readInt(DataInputStream.java:392) >>>>>>>>>> at [....] >>>>>>>>>> >>>>>>>>>> And then a few more similar pyspark.daemon not found errors... >>>>>>>>>> >>>>>>>>>> Andrew >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Jan 8, 2016 at 2:31 PM, Bryan Cutler <cutl...@gmail.com> >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> Hi Andrew, >>>>>>>>>>> >>>>>>>>>>> I know that older versions of Spark could not run PySpark on >>>>>>>>>>> YARN in cluster mode. I'm not sure if that is fixed in 1.6.0 >>>>>>>>>>> though. Can >>>>>>>>>>> you try setting deploy-mode option to "client" when calling >>>>>>>>>>> spark-submit? >>>>>>>>>>> >>>>>>>>>>> Bryan >>>>>>>>>>> >>>>>>>>>>> On Thu, Jan 7, 2016 at 2:39 PM, weineran < >>>>>>>>>>> andrewweiner2...@u.northwestern.edu> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hello, >>>>>>>>>>>> >>>>>>>>>>>> When I try to submit a python job using spark-submit (using >>>>>>>>>>>> --master yarn >>>>>>>>>>>> --deploy-mode cluster), I get the following error: >>>>>>>>>>>> >>>>>>>>>>>> /Traceback (most recent call last): >>>>>>>>>>>> File "loss_rate_by_probe.py", line 15, in ? >>>>>>>>>>>> from pyspark import SparkContext >>>>>>>>>>>> File >>>>>>>>>>>> >>>>>>>>>>>> "/scratch5/hadoop/yarn/local/usercache/<username>/filecache/18/spark-assembly-1.3.1-hadoop2.4.0.jar/pyspark/__init__.py", >>>>>>>>>>>> line 41, in ? >>>>>>>>>>>> File >>>>>>>>>>>> >>>>>>>>>>>> "/scratch5/hadoop/yarn/local/usercache/<username>/filecache/18/spark-assembly-1.3.1-hadoop2.4.0.jar/pyspark/context.py", >>>>>>>>>>>> line 219 >>>>>>>>>>>> with SparkContext._lock: >>>>>>>>>>>> ^ >>>>>>>>>>>> SyntaxError: invalid syntax/ >>>>>>>>>>>> >>>>>>>>>>>> This is very similar to this post from 2014 >>>>>>>>>>>> < >>>>>>>>>>>> http://apache-spark-user-list.1001560.n3.nabble.com/SparkContext-lock-Error-td18233.html >>>>>>>>>>>> > >>>>>>>>>>>> , but unlike that person I am using Python 2.7.8. >>>>>>>>>>>> >>>>>>>>>>>> Here is what I'm using: >>>>>>>>>>>> Spark 1.3.1 >>>>>>>>>>>> Hadoop 2.4.0.2.1.5.0-695 >>>>>>>>>>>> Python 2.7.8 >>>>>>>>>>>> >>>>>>>>>>>> Another clue: I also installed Spark 1.6.0 and tried to submit >>>>>>>>>>>> the same >>>>>>>>>>>> job. I got a similar error: >>>>>>>>>>>> >>>>>>>>>>>> /Traceback (most recent call last): >>>>>>>>>>>> File "loss_rate_by_probe.py", line 15, in ? >>>>>>>>>>>> from pyspark import SparkContext >>>>>>>>>>>> File >>>>>>>>>>>> >>>>>>>>>>>> "/scratch5/hadoop/yarn/local/usercache/<username>/appcache/application_1450370639491_0119/container_1450370639491_0119_01_000001/pyspark.zip/pyspark/__init__.py", >>>>>>>>>>>> line 61 >>>>>>>>>>>> indent = ' ' * (min(len(m) for m in indents) if indents >>>>>>>>>>>> else 0) >>>>>>>>>>>> ^ >>>>>>>>>>>> SyntaxError: invalid syntax/ >>>>>>>>>>>> >>>>>>>>>>>> Any thoughts? >>>>>>>>>>>> >>>>>>>>>>>> Andrew >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> View this message in context: >>>>>>>>>>>> http://apache-spark-user-list.1001560.n3.nabble.com/SparkContext-SyntaxError-invalid-syntax-tp25910.html >>>>>>>>>>>> Sent from the Apache Spark User List mailing list archive at >>>>>>>>>>>> Nabble.com. >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> --------------------------------------------------------------------- >>>>>>>>>>>> To unsubscribe, e-mail: user-unsubscr...@spark.apache.org >>>>>>>>>>>> For additional commands, e-mail: user-h...@spark.apache.org >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >
