Work with Jupyter on Windows and Apache Toree Kernel for compatibility with Spark

Question

I am trying to install the Apache Toree kernel to ensure intrinsic security compatibility, and I am facing some strange environmental message. This is the process that I performed:

• Install the latest version of Anaconda with Jupyter 4.1.0
• Run: pip install --pre toree
• Run: jupyter toree install --interpreters = PySpark, SparkR, Scala, SQL

Only really interested in Scala Kernel, but I installed all the interpreters. The OS is Windows 7, and there is no choice for using virtual machines or Linux.

This is the kernel.json file that I modified to use cygwin to execute the run.sh bash script:

{ "language": "scala", "display_name": "Apache Toree - Scala", "env": { "__TOREE_SPARK_OPTS__": "", "SPARK_HOME": "C:\\CDH\\spark", "__TOREE_OPTS__": "", "DEFAULT_INTERPRETER": "Scala", "PYTHONPATH": "C:\\CDH\\spark\\python:C:\\CDH\\spark\\python\\lib\\py4j-0.8.2.1-src.zip", "PYTHON_EXEC": "python" }, "argv": [ "C:\\cygwin64\\bin\\mintty.exe","-h","always","/bin/bash","-l","-e","C:\\ProgramData\\jupyter\\kernels\\apache_toree_scala\\bin\\run.sh", "--profile", "{connection_file}" ] } 

When jupyter starts, the kernel stops with an error:

 TypeError: environment can only contain strings 

Extended Journal:

 [E 10:45:56.736 NotebookApp] Failed to run command: ['C:\\cygwin64\\bin\\mintty.exe', '-h', 'always', '/bin/bash', '-l', '-e', 'C:\\ProgramData\\jupyter\\kernels\\apache_toree_scala\\bin\\run.sh', ' --profile', 'C:\\Users\\luis\\AppData\\Roaming\\jupyter\\runtime\\kernel-e02cac9b-15de-4c69-a8e5-e5b11919e1bc.json'] with kwargs: {'stdin': -1, 'stdout': None, 'cwd': 'C:\\Users\\luis\\Documents', 'stderr': None, 'env': {'TMP': 'C:\\Users\\luis\\AppData\\Local\\Temp', 'COMPUTERNAME': 'laptop', 'USERDOMAIN': 'HOME', 'SPARK_HOME': u'C:\\CDH\\spark', 'DEFLOGDIR': 'C:\\ProgramData\\McAfee\\DesktopProtection', 'PSMODULEPATH': 'C:\\Windows\\system32\\WindowsPowerShell\\v1.0\\Modules\\', 'COMMONPROGRAMFILES': 'C:\\Program Files\\Common Files', 'PROCESSOR_IDENTIFIER':'Intel64 Family 6 Model 45 Stepping 7, GenuineIntel', u'DEFAULT_INTERPRETER': u'Scala', 'PROGRAMFILES': 'C:\\Program Files', 'PROCESSOR_REVISION': '2d07', 'SYSTEMROOT': 'C:\\Windows', 'PATH': 'C:\\Users\\luis\\AppData\\Local\\Continuum\\Anaconda2\\Library\\bin;C:\\Users\\luis\\AppData\\Local\\Continuum\\Anaconda2;C:\\Users\\luis\\AppData\\Local\\Continuum\\Anaconda2\\Scripts;C:\\Users\\luis\\AppData\\Local\\Continuum\\Anaconda2\\Library\\bin;C:\\Users\\luis\\AppData\\Local\\Continuum\\Anaconda2\\Library\\bin;C:\\Program Files\\Java\\jdk1.7.0_76\\jre\\bin;C:\\Windows\\system32;C:\\Windows;C:\\Windows\\System32\\Wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0\\;C:\\Program Files (x86)\\sbt\\bin;C:\\Users\\luis\\AppData\\Local\\Continuum\\Anaconda2;C:\\Users\\luis\\AppData\\Local\\Continuum\\Anaconda2\\Scripts;C:\\Users\\luis\\AppData\\Local\\Continuum\\Anaconda2\\Library\\bin', 'PROGRAMFILES(X86)': 'C:\\Program Files (x86)', 'WINDOWS_TRACING_FLAGS': '3', 'TK_LIBRARY': 'C:\\Users\\luis\\AppData\\Local\\Continuum\\Anaconda2\\tcl\\tk8.5', u'__TOREE_SPARK_OPTS__': u'', 'TEMP': 'C:\\Users\\luis\\AppData\\Local\\Temp', 'COMMONPROGRAMFILES(X86)': 'C:\\Program Files (x86)\\Common Files', 'PROCESSOR_ARCHITECTURE': 'AMD64', 'TIX_LIBRARY': 'C:\\Users\\luis\\AppData\\Local\\Continuum\\Anaconda2\\tcl\\tix8.4.3', 'ALLUSERSPROFILE': 'C:\\ProgramData', 'LOCALAPPDATA': 'C:\\Users\\luis\\AppData\\Local', 'HOMEPATH': '\\Users\\luis', 'JAVA_HOME': 'C:\\Program Files\\java\\jdk1.7.0_76', 'JPY_INTERRUPT_EVENT': '1056', 'PROGRAMW6432': 'C:\\Program Files', 'USERNAME': 'luis', 'LOGONSERVER': '\\\\S8KROGR2', 'SBT_HOME': 'C:\\Program Files (x86)\\sbt\\', 'JPY_PARENT_PID': '1036', 'PROGRAMDATA': 'C:\\ProgramData', u'PYTHONPATH': u'C:\\CDH\\spark\\python:C:\\CDH\\spark\\python\\lib\\py4j-0.8.2.1-src.zip', 'TCL_LIBRARY': 'C:\\Users\\luis\\AppData\\Local\\Continuum\\Anaconda2\\tcl\\tcl8.5', 'VSEDEFLOGDIR': 'C:\\ProgramData\\McAfee\\DesktopProtection', 'USERDNSDOMAIN': 'HOME.ES', 'SESSIONNAME': 'RDP-Tcp#0', 'PATHEXT': '.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC', u'PYTHON_EXEC': u'python', 'CLIENTNAME': 'laptop2', u'__TOREE_OPTS__': u'', 'FP_NO_HOST_CHECK': 'NO', 'WINDIR': 'C:\\Windows', 'WINDOWS_TRACING_LOGFILE': 'C:\\BVTBin\\Tests\\installpackage\\csilogfile.log', 'HOMEDRIVE': 'C:', 'SYSTEMDRIVE': 'C:', 'COMSPEC': 'C:\\Windows\\system32\\cmd.exe', 'NUMBER_OF_PROCESSORS': '2', 'APPDATA': 'C:\\Users\\luis\\AppData\\Roaming', 'PROCESSOR_LEVEL': '6', 'COMMONPROGRAMW6432': 'C:\\Program Files\\Common Files', 'OS': 'Windows_NT', 'PUBLIC': 'C:\\Users\\Public', 'IPY_INTERRUPT_EVENT': '1056', 'USERPROFILE': 'C:\\Users\\luis'}} [E 10:45:56.744 NotebookApp] Unhandled error in API request Traceback (most recent call last): File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\notebook\base\handlers.py", line 457, in wrapper result = yield gen.maybe_future(method(self, *args, **kwargs)) File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\tornado\gen.py", line 1008, in run value = future.result() File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\tornado\concurrent.py", line 232, in result raise_exc_info(self._exc_info) File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\tornado\gen.py", line 1014, in run yielded = self.gen.throw(*exc_info) File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\notebook\services\sessions\handlers.py", line 62, in post kernel_id=kernel_id)) File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\tornado\gen.py", line 1008, in run value = future.result() File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\tornado\concurrent.py", line 232, in result raise_exc_info(self._exc_info) File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\tornado\gen.py", line 1014, in run yielded = self.gen.throw(*exc_info) File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\notebook\services\sessions\sessionmanager.py", line 79, in create_session kernel_name) File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\tornado\gen.py", line 1008, in run value = future.result() File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\tornado\concurrent.py", line 232, in result raise_exc_info(self._exc_info) File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\tornado\gen.py", line 1014, in run yielded = self.gen.throw(*exc_info) File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\notebook\services\sessions\sessionmanager.py", line 92, in start_kernel_for_session self.kernel_manager.start_kernel(path=kernel_path, kernel_name=kernel_name) File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\tornado\gen.py", line 1008, in run value = future.result() File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\tornado\concurrent.py", line 232, in result raise_exc_info(self._exc_info) File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\tornado\gen.py", line 282, in wrapper yielded = next(result) File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\notebook\services\kernels\kernelmanager.py", line 87, in start_kernel super(MappingKernelManager, self).start_kernel(**kwargs) File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\jupyter_client\multikernelmanager.py", line 110, in start_kernel km.start_kernel(**kwargs) File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\jupyter_client\manager.py", line 243, in start_kernel **kw) File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\jupyter_client\manager.py", line 189, in _launch_kernel return launch_kernel(kernel_cmd, **kw) File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\site-packages\jupyter_client\launcher.py", line 123, in launch_kernel proc = Popen(cmd, **kwargs) File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\subprocess.py", line 711, in __init__ errread, errwrite) File "C:\Users\luis\AppData\Local\Continuum\Anaconda2\lib\subprocess.py", line 959, in _execute_child startupinfo) TypeError: environment can only contain strings [E 10:45:56.766 NotebookApp] { "Origin": "http://localhost:8888", "Content-Length": "88", "Accept-Language": "es-ES,es;q=0.8", "Accept-Encoding": "gzip, deflate", "Host": "localhost:8888", "Accept": "application/json, text/javascript, */*; q=0.01", "User-Agent": "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/41.0.2272.101 Safari/537.36", "Connection": "keep-alive", "X-Requested-With": "XMLHttpRequest", "Referer": "http://localhost:8888/notebooks/Untitled3.ipynb?kernel_name=apache_toree_scala", "Content-Type": "application/json" } [E 10:45:56.796 NotebookApp] 500 POST /api/sessions (::1) 626.00ms referer=http://localhost:8888/notebooks/Untitled3.ipynb?kernel_name=apache_toree_sc ala 

I ran the highlighted command:

 C:\\cygwin64\\bin\\mintty.exe -h always /bin/bash -l -e C:\\ProgramData\\jupyter\\kernels\\apache_toree_scala\\bin\\run.sh 

And it works. This only happens in the context of jupyter server execution.

Can anyone run this kernel on a Window machine?

Answer 1

I have the same problem: python on win 10, Anaconda, spark 2.0.2

This is the workaround I came up with for this: use conda environment switch to set environment variables instead of using jupyter to set them

• clone a separate conda environment ( http://conda.pydata.org/docs/using/envs.html#create-an-environment )
• set the environment variables needed for the torus ( http://conda.pydata.org/docs/using/envs.html#windows )

then run jupyter notebook <root dir of notebooks>

You can alternately just set constant variables constantly from windows and start the dictionary "env" from kernel.json "env":{}

I wanted to keep separate env variables when using pyspark

Answer 2

I wrote my own hacked run.cmd and was able to get it working using Spark 2.2.0 and toree-assembly-0.2.0.dev1-incubating-SNAPSHOT. I sent my decision on a TOREE-399 ticket .

Run.cmd:

 @echo off set PROG_HOME=%~dp0.. if not defined SPARK_HOME ( echo SPARK_HOME must be set to the location of a Spark distribution! exit 1 ) REM disable randomized hash for string in Python 3.3+ set PYTHONHASHSEED=0 REM The SPARK_OPTS values during installation are stored in __TOREE_SPARK_OPTS__. This allows values to be specified during REM install, but also during runtime. The runtime options take precedence over the install options. if not defined SPARK_OPTS ( set SPARK_OPTS=%__TOREE_SPARK_OPTS__% ) else ( if "%SPARK_OPTS%" == "" ( set SPARK_OPTS=%__TOREE_SPARK_OPTS__% ) ) if not defined TOREE_OPTS ( set TOREE_OPTS=%__TOREE_OPTS__% ) else ( if "%TOREE_OPTS%" == "" ( set TOREE_OPTS=%__TOREE_OPTS__% ) ) echo Starting Spark Kernel with SPARK_HOME=%SPARK_HOME% REM This doesn't work because the classpath doesn't get set properly, unless you hardcode it in SPARK_SUBMIT_OPTS using forward slashes or double backslashes, but then you can't use the SPARK_HOME and PROG_HOME variables. REM set SPARK_SUBMIT_OPTS=-cp "%SPARK_HOME%\conf\;%SPARK_HOME%\jars\*;%PROG_HOME%\lib\toree-assembly-0.2.0.dev1-incubating-SNAPSHOT.jar" -Dscala.usejavacp=true REM set TOREE_COMMAND="%SPARK_HOME%\bin\spark-submit.cmd" %SPARK_OPTS% --class org.apache.toree.Main %PROG_HOME%\lib\toree-assembly-0.2.0.dev1-incubating-SNAPSHOT.jar %TOREE_OPTS% %* REM The two important things that we must do differently on Windows are that we must add toree-assembly-0.2.0.dev1-incubating-SNAPSHOT.jar to the classpath, and we must define the java property scala.usejavacp=true. set TOREE_COMMAND=%JAVA_HOME%\bin\java -cp "%SPARK_HOME%\conf\;%SPARK_HOME%\jars\*;%PROG_HOME%\lib\toree-assembly-0.2.0.dev1-incubating-SNAPSHOT.jar" -Dscala.usejavacp=true -Xmx1g org.apache.spark.deploy.SparkSubmit %SPARK_OPTS% --class org.apache.toree.Main %PROG_HOME%\lib\toree-assembly-0.2.0.dev1-incubating-SNAPSHOT.jar %TOREE_OPTS% %* echo. echo %TOREE_COMMAND% echo. %TOREE_COMMAND% 

• The run.cmd file should be placed in C: \ ProgramData \ jupyter \ kernels \ apache_toree_scala \ Bin \
• In addition, you need to edit kernel.json in the folder above to change run.sh to run. cmd.
• If you want to allow the installation of additional Toree, you must also edit toreeapp.py to change run.sh to run.cmd.
• I did not check the correct operation of the IF statements. I suspect that they will choke on some parameters since the batch does not have a reliable IF statement.