I have a docker container running PySpark, hadoop and all the required dependecies. I am using spark-submit to query the minio and I want to write the output dataframe to the file. Reading the file works but writing does not. If I execute python in that container and try to create file at the same path, it works.
Am I missing some spark configuration?
This is the error I get:
File "/usr/local/spark/python/lib/pyspark.zip/pyspark/sql/readwriter.py", line 1109, in save
File "/usr/local/spark/python/lib/py4j-0.10.9-src.zip/py4j/java_gateway.py", line 1304, in __call__
File "/usr/local/spark/python/lib/pyspark.zip/pyspark/sql/utils.py", line 111, in deco
File "/usr/local/spark/python/lib/py4j-0.10.9-src.zip/py4j/protocol.py", line 326, in get_return_value
py4j.protocol.Py4JJavaError: An error occurred while calling o38.save
: java.net.ConnectException: Call From 10d3463d04ce/10.0.1.132 to localhost:9000 failed on connection exception:
java.net.ConnectException: Connection refused; For more details see: http://wiki.apache.org/hadoop/ConnectionRefused
Relevant code:
spark = SparkSession.builder.getOrCreate()
spark_context = spark.sparkContext
spark_context._jsc.hadoopConfiguration().set('fs.s3a.access.key', 'minio')
spark_context._jsc.hadoopConfiguration().set(
'fs.s3a.secret.key', AWS_SECRET_ACCESS_KEY
)
spark_context._jsc.hadoopConfiguration().set('fs.s3a.path.style.access', 'true')
spark_context._jsc.hadoopConfiguration().set(
'fs.s3a.impl', 'org.apache.hadoop.fs.s3a.S3AFileSystem'
)
spark_context._jsc.hadoopConfiguration().set('fs.s3a.endpoint', AWS_S3_ENDPOINT)
spark_context._jsc.hadoopConfiguration().set(
'fs.s3a.connection.ssl.enabled', 'false'
)
df = spark.sql(query)
df.show() # this works perfectly fine
df.coalesce(1).write.format('json').save(output_path) # here I get the error
Solution was to prepend file:// to output_path.
Related
I am trying to run a simple python script within a docker run command scheduled with Airflow.
I have followed the instructions here Airflow init.
My .env file:
AIRFLOW_UID=1000
AIRFLOW_GID=0
And the docker-compose.yaml is based on the default one docker-compose.yaml. I had to add - /var/run/docker.sock:/var/run/docker.sock as an additional volume to run docker inside of docker.
My dag is configured as followed:
""" this is an example dag """
from datetime import timedelta
from airflow import DAG
from airflow.operators.docker_operator import DockerOperator
from airflow.utils.dates import days_ago
from docker.types import Mount
default_args = {
'owner': 'airflow',
'depends_on_past': False,
'email': ['info#foo.com'],
'email_on_failure': True,
'email_on_retry': False,
'retries': 10,
'retry_delay': timedelta(minutes=5),
}
with DAG(
'msg_europe_etl',
default_args=default_args,
description='Process MSG_EUROPE ETL',
schedule_interval=timedelta(minutes=15),
start_date=days_ago(0),
tags=['satellite_data'],
) as dag:
download_and_store = DockerOperator(
task_id='download_and_store',
image='satellite_image:latest',
auto_remove=True,
api_version='1.41',
mounts=[Mount(source='/home/archive_1/archive/satellite_data',
target='/app/data'),
Mount(source='/home/dlassahn/projects/forecast-system/meteoIntelligence-satellite',
target='/app')],
command="python3 src/scripts.py download_satellite_images "
"{{ (execution_date - macros.timedelta(hours=4)).strftime('%Y-%m-%d %H:%M') }} "
"'msg_europe' ",
)
download_and_store
The Airflow log:
[2021-08-03 17:23:58,691] {docker.py:231} INFO - Starting docker container from image satellite_image:latest
[2021-08-03 17:23:58,702] {taskinstance.py:1501} ERROR - Task failed with exception
Traceback (most recent call last):
File "/home/airflow/.local/lib/python3.6/site-packages/docker/api/client.py", line 268, in _raise_for_status
response.raise_for_status()
File "/home/airflow/.local/lib/python3.6/site-packages/requests/models.py", line 943, in raise_for_status
raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 400 Client Error: Bad Request for url: http+docker://localhost/v1.41/containers/create
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/airflow/.local/lib/python3.6/site-packages/airflow/models/taskinstance.py", line 1157, in _run_raw_task
self._prepare_and_execute_task_with_callbacks(context, task)
File "/home/airflow/.local/lib/python3.6/site-packages/airflow/models/taskinstance.py", line 1331, in _prepare_and_execute_task_with_callbacks
result = self._execute_task(context, task_copy)
File "/home/airflow/.local/lib/python3.6/site-packages/airflow/models/taskinstance.py", line 1361, in _execute_task
result = task_copy.execute(context=context)
File "/home/airflow/.local/lib/python3.6/site-packages/airflow/providers/docker/operators/docker.py", line 319, in execute
return self._run_image()
File "/home/airflow/.local/lib/python3.6/site-packages/airflow/providers/docker/operators/docker.py", line 258, in _run_image
tty=self.tty,
File "/home/airflow/.local/lib/python3.6/site-packages/docker/api/container.py", line 430, in create_container
return self.create_container_from_config(config, name)
File "/home/airflow/.local/lib/python3.6/site-packages/docker/api/container.py", line 441, in create_container_from_config
return self._result(res, True)
File "/home/airflow/.local/lib/python3.6/site-packages/docker/api/client.py", line 274, in _result
self._raise_for_status(response)
File "/home/airflow/.local/lib/python3.6/site-packages/docker/api/client.py", line 270, in _raise_for_status
raise create_api_error_from_http_exception(e)
File "/home/airflow/.local/lib/python3.6/site-packages/docker/errors.py", line 31, in create_api_error_from_http_exception
raise cls(e, response=response, explanation=explanation)
docker.errors.APIError: 400 Client Error for http+docker://localhost/v1.41/containers/create: Bad Request ("invalid mount config for type "bind": bind source path does not exist: /tmp/airflowtmp037k87u6")
Trying to set mount_tmp_dir=False yield to an Dag ImportError because of unknown Keyword Argument mount_tmp_dir. (this might be an issue for the Documentation)
Nevertheless I do not know how to configure the tmp directory correctly.
My Airflow Version: 2.1.2
There was a bug in Docker Provider 2.0.0 which prevented Docker Operator to run with Docker-In-Docker solution.
You need to upgrade to the latest Docker Provider 2.1.0
https://airflow.apache.org/docs/apache-airflow-providers-docker/stable/index.html#id1
You can do it by extending the image as described in https://airflow.apache.org/docs/docker-stack/build.html#extending-the-image with - for example - this docker file:
FROM apache/airflow
RUN pip install --no-cache-dir apache-airflow-providers-docker==2.1.0
The operator will work out-of-the-box in this case with "fallback" mode (and Warning message), but you can also disable the mount that causes the problem. More explanation from the https://airflow.apache.org/docs/apache-airflow-providers-docker/stable/_api/airflow/providers/docker/operators/docker/index.html
By default, a temporary directory is created on the host and mounted
into a container to allow storing files that together exceed the
default disk size of 10GB in a container. In this case The path to the
mounted directory can be accessed via the environment variable
AIRFLOW_TMP_DIR.
If the volume cannot be mounted, warning is printed and an attempt is
made to execute the docker command without the temporary folder
mounted. This is to make it works by default with remote docker engine
or when you run docker-in-docker solution and temporary directory is
not shared with the docker engine. Warning is printed in logs in this
case.
If you know you run DockerOperator with remote engine or via
docker-in-docker you should set mount_tmp_dir parameter to False. In
this case, you can still use mounts parameter to mount already
existing named volumes in your Docker Engine to achieve similar
capability where you can store files exceeding default disk size of
the container,
I had the same issue and all "recommended" ways of solving the issue here and setting up mount_dir params as descripted here just lead to other errors. The one solution that helped me was wrapping the invocated by docker code with the VPN (actually this hack was taken from another docker-powered DAG that used VPN and worked well).
So the final solution looks like:
#!/bin/bash
connect_to_vpn.sh &
sleep 10
python3 my_func.py
sleep 10
stop_vpn.sh
wait -n
exit $?
To connect to VPN I used openconnect. The took can be installed with apt install and supports anyconnect protocol (it was my crucial requirement).
I have an active kubernetes cluster inside Minikube VM (using VirtualBox as driver), so for deploying new containers I am able to download the images as this connection is already laid out using istio service, now if I ssh into my minikube VM first of all I am not able to wget https content but http contents are connected after setting proxies and no_proxies but if I want to access any link from inside of my containers, say simple pod with python image and urllib library and I want to connect from inside this pod and then print the contents from any link (eg.http://python.org) I am not able to do so, all I am getting is no route to host error in logs which points to some problem with the connection due to proxies.
def basic():
import urllib.request
print("inside basic funtion")
with urllib.request.urlopen('http://python.org/') as response:
html = response.read()
print(html)
this is the python code I am running from inside my container as a pipeline component.
Most recent error I got-
Traceback (most recent call last):
File "/usr/local/lib/python3.7/urllib/request.py", line 1317, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/usr/local/lib/python3.7/http/client.py", line 1229, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/local/lib/python3.7/http/client.py", line 1275, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/local/lib/python3.7/http/client.py", line 1224, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/local/lib/python3.7/http/client.py", line 1016, in _send_output
self.send(msg)
File "/usr/local/lib/python3.7/http/client.py", line 956, in send
self.connect()
File "/usr/local/lib/python3.7/http/client.py", line 928, in connect
(self.host,self.port), self.timeout, self.source_address)
File "/usr/local/lib/python3.7/socket.py", line 727, in create_connection
raise err
File "/usr/local/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
TimeoutError: [Errno 110] Operation timed out
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 11, in <module>
File "<string>", line 3, in basic
File "/usr/local/lib/python3.7/urllib/request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "/usr/local/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/usr/local/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/usr/local/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/usr/local/lib/python3.7/urllib/request.py", line 1345, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/usr/local/lib/python3.7/urllib/request.py", line 1319, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [Errno 110] Operation timed out>
I have started minikube as-
minikube start --cpus 6 --memory 12288 --disk-size=80g --extra-config=apiserver.service-account-issuer=api --extra-config=apiserver.service-account-signing-key-file=/var/lib/minikube/certs/apiserver.key --extra-config=apiserver.service-account-api-audiences=api --kubernetes-version v1.14.0
after setting the env variables as well.
Update:
I created a different container just to check the curl from inside the component as- (I am using kfp libraries for creating containers)
def curl_op(text):
return dsl.ContainerOp(
name='curl',
image='tutum/curl',
command=['sh', '-c'],
arguments=['curl -x http://<proxy-server>:<proxy-port> "$0"', text]
)
so using the above argument I am able to connect to external links, which again makes it certain that i need to create the containers with proxies set.
So for running the above python code I mentioned as pipeline component.
I added the environment variables using the os library and this individual piece was able to connect to external networks.
Updated python code-
def basic():
import urllib.request
import os
proxy = 'http://proxy-path:port'
os.environ['http_proxy'] = proxy
os.environ['HTTP_PROXY'] = proxy
os.environ['https_proxy'] = proxy
os.environ['HTTPS_PROXY'] = proxy
print("inside basic funtion")
with urllib.request.urlopen('http://python.org/') as response:
html = response.read()
print(html)
And if the docker image is created from scratch without taking help of pipeline library function then we need to just add the env details into our dockerfile the usual way after the base image call-
ENV HTTP_PROXY http://proxy-path:port
ENV HTTPS_PROXY http://proxy-path:port
I am using Python 3.7 with Appium 1.15.1 on real Android Device.
When my script finish the job, I close the driver with these lines:
if p_driver:
p_driver.close()
but I get this error ouput:
File "C:\Users\Nino\AppData\Local\Programs\Python\Python37\lib\site-packages\selenium\webdriver\remote\webdriver.py", line 688, in close
self.execute(Command.CLOSE)
File "C:\Users\Nino\AppData\Local\Programs\Python\Python37\lib\site-packages\selenium\webdriver\remote\webdriver.py", line 321, in execute
self.error_handler.check_response(response)
File "C:\Users\Nino\AppData\Roaming\Python\Python37\site-packages\appium\webdriver\errorhandler.py", line 29, in check_response
raise wde
File "C:\Users\Nino\AppData\Roaming\Python\Python37\site-packages\appium\webdriver\errorhandler.py", line 24, in check_response
super(MobileErrorHandler, self).check_response(response)
File "C:\Users\Nino\AppData\Local\Programs\Python\Python37\lib\site-packages\selenium\webdriver\remote\errorhandler.py", line 242, in check_response
raise exception_class(message, screen, stacktrace)
selenium.common.exceptions.WebDriverException: Message: An unknown server-side error occurred while processing the command. Original error: Could not proxy. Proxy error: Could not proxy command to remote server. Original error: 404 - undefined
I would like to understand what I am doing wrong?
What is the way to close properly the driver?
Can you help me please?
Step1: you should get the appium session dictionary first:
session_instance = webdriver.Remote(str(url), caps_dic)
where url is your appium server url. something like: "http://127.0.0.1:4723/wd/hub"
and caps_dic is a dictionary of all your desired capabilities
Step2: you run the quit() method on session:
session_instance[session].quit()
So the whole snippet is:
session_instance = webdriver.Remote(str(url), caps_dic)
session_instance[session].quit()
I'm trying to start a dask cluster over SSH, but I am encountering a strange errors like these:
Exception in thread Thread-6:
Traceback (most recent call last):
File "/home/localuser/miniconda3/lib/python3.6/threading.py", line 916, in _bootstrap_inner
self.run()
File "/home/localuser/miniconda3/lib/python3.6/threading.py", line 864, in run
self._target(*self._args, **self._kwargs)
File "/home/localuser/miniconda3/lib/python3.6/site-packages/distributed/deploy/ssh.py", line 57, in async_ssh
banner_timeout=20) # Helps prevent timeouts when many concurrent ssh connections are opened.
File "/home/localuser/miniconda3/lib/python3.6/site-packages/paramiko/client.py", line 329, in connect
to_try = list(self._families_and_addresses(hostname, port))
File "/home/localuser/miniconda3/lib/python3.6/site-packages/paramiko/client.py", line 200, in _families_and_addresses
hostname, port, socket.AF_UNSPEC, socket.SOCK_STREAM)
File "/home/localuser/miniconda3/lib/python3.6/socket.py", line 745, in getaddrinfo
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known
I'm starting the cluster like this:
$ dask-ssh --ssh-private-key ~/.ssh/cluster_id_rsa \
--hostfile ~/dask-hosts.txt \
--remote-python "~/miniconda3/bin/python3.6"
My dask-hosts.txt looks like this:
localuser#127.0.0.1
remoteuser#10.10.4.200
...
remoteuser#10.10.4.207
I get the same error with/without the localhost line.
I have checked the ssh setup, I can login to all the nodes using a public key setup (the key is unencrypted, to avoid decryption prompts). What am I missing?
The error indicates that name resolution is the culprit. Most likely this is happening because of the inclusion of usernames in your dask-hosts.txt. According to its documentation, the host file should contain only hostnames/IP addresses:
–hostfile PATH Textfile with hostnames/IP addresses
You can use --ssh-username to set a username (although only a single one).
When i run this script from user jenkins (Linux Mint) i get this error, and when running it from my user it works. Jenkins user is created with jenkins service. I have installed virtualenv.
import unittest
from selenium import webdriver
from selenium.webdriver.support.ui import WebDriverWait
DRIVER = None
def getOrCreateWebdriver():
global DRIVER
DRIVER = DRIVER or webdriver.Firefox()
return DRIVER
class LoginTest(unittest.TestCase):
def setUp(self):
self.browser = getOrCreateWebdriver()
def test_Loggin(self):pass
browser = self.browser
def tearDown(self):
self.browser.close()
if __name__ == '__main__':
unittest.main(verbosity=2)
From user jenkins when i run this script i get error :
test_Loggin (__main__.LoginTest) ... ERROR
/usr/lib/python3.4/unittest/case.py:602: ResourceWarning: unclosed file <_io.BufferedWriter name='/dev/null'>
outcome.errors.clear()
======================================================================
ERROR: test_Loggin (__main__.LoginTest)
----------------------------------------------------------------------
Traceback (most recent call last):
File "Test.py", line 16, in setUp
self.browser = getOrCreateWebdriver()
File "Test.py", line 10, in getOrCreateWebdriver
DRIVER = DRIVER or webdriver.Firefox()
File "/usr/local/lib/python3.4/dist-packages/selenium/webdriver/firefox/webdriver.py", line 64, in __init__
self.binary, timeout),
File "/usr/local/lib/python3.4/dist-packages/selenium/webdriver/firefox/extension_connection.py", line 51, in __init__
self.binary.launch_browser(self.profile)
File "/usr/local/lib/python3.4/dist-packages/selenium/webdriver/firefox/firefox_binary.py", line 70, in launch_browser
self._wait_until_connectable()
File "/usr/local/lib/python3.4/dist-packages/selenium/webdriver/firefox/firefox_binary.py", line 100, in _wait_until_connectable
raise WebDriverException("The browser appears to have exited "
selenium.common.exceptions.WebDriverException: Message: The browser appears to have exited before we could connect. If you specified a log_file in the FirefoxBinary constructor, check it for details.
When you're logged in as yourself, you need to do echo $DISPLAY and note the display info it prints. Subsequently when you login as jenkins service you need to do xhost +, DISPLAY=[display-info]; export DISPLAY. (display-info is what you got from echo $DISPLAY, ignore the square brackets, they shouldn't be specified in the command)
Hopefully this should work. I don't have similar env to test, just mentioning what i recollect having done it quite sometime back.