Unable to run a basic GraphFrames example

Question

Trying to run a simple GraphFrame example using pyspark.

spark version : 2.0

graphframe version : 0.2.0

I am able to import graphframes in Jupyter:

from graphframes import GraphFrame
GraphFrame
graphframes.graphframe.GraphFrame

I get this error when I try and create a GraphFrame object:

---------------------------------------------------------------------------
Py4JJavaError                             Traceback (most recent call last)
<ipython-input-23-2bf19c66804d> in <module>()
----> 1 gr_links = GraphFrame(df_web_page, df_parent_child_link)

/Users/roopal/software/graphframes-release-0.2.0/python/graphframes/graphframe.pyc in __init__(self, v, e)
     60         self._sc = self._sqlContext._sc
     61         self._sc._jvm.org.apache.spark.ml.feature.Tokenizer()
---> 62         self._jvm_gf_api = _java_api(self._sc)
     63         self._jvm_graph = self._jvm_gf_api.createGraph(v._jdf, e._jdf)
     64 

/Users/roopal/software/graphframes-release-0.2.0/python/graphframes/graphframe.pyc in _java_api(jsc)
     32 def _java_api(jsc):
     33     javaClassName = "org.graphframes.GraphFramePythonAPI"
---> 34     return jsc._jvm.Thread.currentThread().getContextClassLoader().loadClass(javaClassName) \
     35             .newInstance()
     36 

/Users/roopal/software/spark-2.0.0-bin-hadoop2.7/python/lib/py4j-0.10.1-src.zip/py4j/java_gateway.py in __call__(self, *args)
    931         answer = self.gateway_client.send_command(command)
    932         return_value = get_return_value(
--> 933             answer, self.gateway_client, self.target_id, self.name)
    934 
    935         for temp_arg in temp_args:

/Users/roopal/software/spark-2.0.0-bin-hadoop2.7/python/pyspark/sql/utils.pyc in deco(*a, **kw)
     61     def deco(*a, **kw):
     62         try:
---> 63             return f(*a, **kw)
     64         except py4j.protocol.Py4JJavaError as e:
     65             s = e.java_exception.toString()

/Users/roopal/software/spark-2.0.0-bin-hadoop2.7/python/lib/py4j-0.10.1-src.zip/py4j/protocol.py in get_return_value(answer, gateway_client, target_id, name)
    310                 raise Py4JJavaError(
    311                     "An error occurred while calling {0}{1}{2}.\n".
--> 312                     format(target_id, ".", name), value)
    313             else:
    314                 raise Py4JError(

Py4JJavaError: An error occurred while calling o138.loadClass.
: java.lang.ClassNotFoundException: org.graphframes.GraphFramePythonAPI
    at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:237)
    at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
    at py4j.Gateway.invoke(Gateway.java:280)
    at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:128)
    at py4j.commands.CallCommand.execute(CallCommand.java:79)
    at py4j.GatewayConnection.run(GatewayConnection.java:211)
    at java.lang.Thread.run(Thread.java:745)

The python code tries to read the java class (in the jar) I guess, but cant seem to find it. Any suggestions how to fix this?

score 25 · Answer 1 · edited Jun 20 '20 at 09:12

I was able to make it work..

Depending on your spark version, all you have to do is download the graphframe jar corresponding to your version of spark here https://spark-packages.org/package/graphframes/graphframes.

Then you'll have to copy the jar downloaded to your spark jar directory

    root@93d8398b53f2:/usr/local/spark/jars# wget http://dl.bintray.com/spark-packages/maven/graphframes/graphframes/0.3.0-spark2.0-s_2.11/graphframes-0.3.0-spark2.0-s_2.11.jar

There's the little tric right here, launch pyspark with arguments for the first time so that it downloads all the graphframe's jars dependencies:

    root@93d8398b53f2:/usr/local/spark/bin# pyspark --packages graphframes:graphframes:0.3.0-spark2.0-s_2.11 --jars graphframes-0.3.0-spark2.0-s_2.11.jar

This should come up:

Ivy Default Cache set to: /root/.ivy2/cache
The jars for the packages stored in: /root/.ivy2/jars
:: loading settings :: url = jar:file:/usr/local/spark-2.0.0-bin-hadoop2.7/jars/ivy-2.4.0.jar!/org/apache/ivy/core/settings/ivysettings.xml
graphframes#graphframes added as a dependency
:: resolving dependencies :: org.apache.spark#spark-submit-parent;1.0
    confs: [default]
    found graphframes#graphframes;0.3.0-spark2.0-s_2.11 in spark-packages
    found com.typesafe.scala-logging#scala-logging-api_2.11;2.1.2 in central
    found com.typesafe.scala-logging#scala-logging-slf4j_2.11;2.1.2 in central
    found org.scala-lang#scala-reflect;2.11.0 in central
    found org.slf4j#slf4j-api;1.7.7 in central
downloading http://dl.bintray.com/spark-packages/maven/graphframes/graphframes/0.3.0-spark2.0-s_2.11/graphframes-0.3.0-spark2.0-s_2.11.jar ...
    [SUCCESSFUL ] graphframes#graphframes;0.3.0-spark2.0-s_2.11!graphframes.jar (269ms)
downloading https://repo1.maven.org/maven2/com/typesafe/scala-logging/scala-logging-api_2.11/2.1.2/scala-logging-api_2.11-2.1.2.jar ...
    [SUCCESSFUL ] com.typesafe.scala-logging#scala-logging-api_2.11;2.1.2!scala-logging-api_2.11.jar (53ms)
downloading https://repo1.maven.org/maven2/com/typesafe/scala-logging/scala-logging-slf4j_2.11/2.1.2/scala-logging-slf4j_2.11-2.1.2.jar ...
    [SUCCESSFUL ] com.typesafe.scala-logging#scala-logging-slf4j_2.11;2.1.2!scala-logging-slf4j_2.11.jar (66ms)
downloading https://repo1.maven.org/maven2/org/scala-lang/scala-reflect/2.11.0/scala-reflect-2.11.0.jar ...
    [SUCCESSFUL ] org.scala-lang#scala-reflect;2.11.0!scala-reflect.jar (1409ms)
downloading https://repo1.maven.org/maven2/org/slf4j/slf4j-api/1.7.7/slf4j-api-1.7.7.jar ...
    [SUCCESSFUL ] org.slf4j#slf4j-api;1.7.7!slf4j-api.jar (53ms)
:: resolution report :: resolve 6161ms :: artifacts dl 1877ms
    :: modules in use:
    com.typesafe.scala-logging#scala-logging-api_2.11;2.1.2 from central in [default]
    com.typesafe.scala-logging#scala-logging-slf4j_2.11;2.1.2 from central in [default]
    graphframes#graphframes;0.3.0-spark2.0-s_2.11 from spark-packages in [default]
    org.scala-lang#scala-reflect;2.11.0 from central in [default]
    org.slf4j#slf4j-api;1.7.7 from central in [default]
    ---------------------------------------------------------------------
    |                  |            modules            ||   artifacts   |
    |       conf       | number| search|dwnlded|evicted|| number|dwnlded|
    ---------------------------------------------------------------------
    |      default     |   5   |   5   |   5   |   0   ||   5   |   5   |
    ---------------------------------------------------------------------
:: retrieving :: org.apache.spark#spark-submit-parent
    confs: [default]
    5 artifacts copied, 0 already retrieved (4713kB/39ms)
Warning: Local jar /usr/local/spark-2.0.0-bin-hadoop2.7/bin/graphframes-0.3.0-spark2.0-s_2.11.jar does not exist, skipping.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel).
16/11/17 15:43:51 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
16/11/17 15:43:54 WARN Utils: Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
Welcome to
      ____              __
     / __/__  ___ _____/ /__
    _\ \/ _ \/ _ `/ __/  '_/
   /__ / .__/\_,_/_/ /_/\_\   version 2.0.0
      /_/

Using Python version 2.7.12 (default, Jul  2 2016 17:42:40)
SparkSession available as 'spark'.
>>>

Meaning it has downloaded all the dependencies required. The important thing right here is Ivy Default Cache set to: /root/.ivy2/cache, precisely the jars stored in /root/.ivy2/jars

You can exit right after, if you insist in proceeding with the python code calling GraphFrame, it will call the error:

    Py4JJavaError: An error occurred while calling o561.newInstance.
    : java.lang.NoClassDefFoundError: Could not initialize class org.graphframes.GraphFrame.

Let's see what's inside the directory /root/.ivy2/jars:

root@93d8398b53f2:/usr/local/spark/bin# ls /root/.ivy2/jars/
com.typesafe.scala-logging_scala-logging-api_2.11-2.1.2.jar  com.typesafe.scala-logging_scala-logging-slf4j_2.11-2.1.2.jar  graphframes_graphframes-0.3.0-spark2.0-s_2.11.jar  org.scala-lang_scala-reflect-2.11.0.jar  org.slf4j_slf4j-api-1.7.7.jar

Now you'll want to copy all the jars appearing in /root/.ivy2/jars to your spark's jars directory:

    root@93d8398b53f2:/usr/local/spark/jars# cp /root/.ivy2/jars/* .

Launch pyspark for the second time:

    root@93d8398b53f2:/usr/local/spark/jars# pyspark --packages graphframes:graphframes:0.3.0-spark2.0-s_2.11 --jars graphframes-0.3.0-spark2.0-s_2.11.jar

This should come up:

Ivy Default Cache set to: /root/.ivy2/cache
The jars for the packages stored in: /root/.ivy2/jars
:: loading settings :: url = jar:file:/usr/local/spark-2.0.0-bin-hadoop2.7/jars/ivy-2.4.0.jar!/org/apache/ivy/core/settings/ivysettings.xml
graphframes#graphframes added as a dependency
:: resolving dependencies :: org.apache.spark#spark-submit-parent;1.0
    confs: [default]
    found graphframes#graphframes;0.3.0-spark2.0-s_2.11 in spark-packages
    found com.typesafe.scala-logging#scala-logging-api_2.11;2.1.2 in central
    found com.typesafe.scala-logging#scala-logging-slf4j_2.11;2.1.2 in central
    found org.scala-lang#scala-reflect;2.11.0 in central
    found org.slf4j#slf4j-api;1.7.7 in central
:: resolution report :: resolve 748ms :: artifacts dl 27ms
    :: modules in use:
    com.typesafe.scala-logging#scala-logging-api_2.11;2.1.2 from central in [default]
    com.typesafe.scala-logging#scala-logging-slf4j_2.11;2.1.2 from central in [default]
    graphframes#graphframes;0.3.0-spark2.0-s_2.11 from spark-packages in [default]
    org.scala-lang#scala-reflect;2.11.0 from central in [default]
    org.slf4j#slf4j-api;1.7.7 from central in [default]
    ---------------------------------------------------------------------
    |                  |            modules            ||   artifacts   |
    |       conf       | number| search|dwnlded|evicted|| number|dwnlded|
    ---------------------------------------------------------------------
    |      default     |   5   |   0   |   0   |   0   ||   5   |   0   |
    ---------------------------------------------------------------------
:: retrieving :: org.apache.spark#spark-submit-parent
    confs: [default]
    0 artifacts copied, 5 already retrieved (0kB/24ms)
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel).
16/11/17 15:53:01 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
16/11/17 15:53:03 WARN Utils: Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
Welcome to
      ____              __
     / __/__  ___ _____/ /__
    _\ \/ _ \/ _ `/ __/  '_/
   /__ / .__/\_,_/_/ /_/\_\   version 2.0.0
      /_/

Using Python version 2.7.12 (default, Jul  2 2016 17:42:40)
SparkSession available as 'spark'.
>>>

You can now enjoy GraphFrame:

>>> # Create an Edge DataFrame with "src" and "dst" columns
... e = sqlContext.createDataFrame([
...   ("a", "b", "friend"),
...   ("b", "c", "follow"),
...   ("c", "b", "follow"),
... ], ["src", "dst", "relationship"])
>>> # Create a GraphFrame
... from graphframes import *
>>> g = GraphFrame(v, e)
>>> 
>>> # Query: Get in-degree of each vertex.
... g.inDegrees.show()
+---+--------+                                                                  
| id|inDegree|
+---+--------+
|  c|       1|
|  b|       2|
+---+--------+
>>> 
>>> # Query: Count the number of "follow" connections in the graph.
... g.edges.filter("relationship = 'follow'").count()
2       
>>> results.vertices.select("id", "pagerank").show()                            
16/11/17 16:03:45 WARN Executor: 1 block locks were not released by TID = 9059:
[rdd_337_0]
16/11/17 16:03:45 WARN Executor: 1 block locks were not released by TID = 9060:
[rdd_337_1]
+---+-------------------+
| id|           pagerank|
+---+-------------------+
|  a|               0.01|
|  b| 0.2808611427228327|
|  c|0.27995525261339177|
+---+-------------------+

I managed to make it work within a jupyter instance.. go to https://github.com/robertoNdams/jupyterlab/blob/master/README.md and look for Demo Graphframe — Gilles Essoki, Nov 12 '18 at 16:11
If pyspark was installed through Anaconda. Make sure to copy the downloaded jar file into the anaconda-pyspark installation i.e /home/user/anaconda3/lib/python3.7/site-packages/pyspark/jars/ — Rickka, May 13 '20 at 18:19

score 3 · Answer 2 · answered Jan 15 '17 at 22:12

Follow-up on @Gilles Essoki solution. Make sure you have the right Spark version and Scala version for your environment.

graphframes:(latest version)-spark(your spark version)-s_(your scala version)

I did not have to specify the jar file or copy it to the spark default jar directory when I had the right versions. Note: You need to run 'spark-shell' cmd.

%spark-shell
...
...
...
Welcome to
      ____              __
     / __/__  ___ _____/ /__
    _\ \/ _ \/ _ `/ __/  '_/
   /___/ .__/\_,_/_/ /_/\_\   version 1.6.0
      /_/
Using Scala version 2.10.5 (Java HotSpot(TM) 64-Bit Server VM, Java 1.7.0_67)

The correct version to get for this setup from SparkPackages

For my environment I had to use the following command :

%pyspark --packages graphframes:graphframes:0.3.0-spark1.6-s_2.10

score 3 · Answer 3 · answered Sep 27 '19 at 07:04

The simplest way is to start jupyter with pyspark and graphframes is to start jupyter out from pyspark with the respective packages

Just open your terminal and set the two environment variables and start pyspark with the graphframes package

export PYSPARK_DRIVER_PYTHON=jupyter
export PYSPARK_DRIVER_PYTHON_OPTS=notebook
pyspark --packages graphframes:graphframes:0.6.0-spark2.3-s_2.11

the advantage of this is also that if you later on want to run your code via spark-submit you can use the same start command

score 1 · Answer 4 · answered Sep 01 '16 at 03:52

Make sure that your PYSPARK_SUBMIT_ARGS is updated to have "--packages graphframes:graphframes:0.2.0-spark2.0" in your kernel.json ~/.ipython/kernels//kernel.json.

You probably already looked at the following link. It has more details on Jupiter setup. Basically, pyspark has to be supplied the graphframes.jar.

score 1 · Answer 5 · answered May 03 '20 at 17:17

1

For PyCharm go to configurations and add the environment variable:

Name: PYSPARK_SUBMIT_ARGS

Value: --packages graphframes:graphframes:0.2.0-spark2.0-s_2.11 pyspark-shell

I've found it doesn't work for me without the pyspark-shell at the end

answered May 03 '20 at 17:17

Shae Hanson

13
4

Unable to run a basic GraphFrames example

5 Answers5

I was able to make it work..

Linked