I have critical data in an Amazon S3 bucket. I want to make a weekly backup of its other contents to another cloud service, or even inside S3. The best way would to sync my bucket to a new bucket inside a different region, in case of data loss.
How can I do that?
I prefer to backup locally using sync where only changes are updated. That is not the perfect backup solution but you can implement periodic updates later as you need:
s3cmd sync --delete-removed s3://your-bucket-name/ /path/to/myfolder/
If you never used s3cmd, install and configure it using:
pip install s3cmd
s3cmd --configure
Also there should be S3 backup services for $5/month but I would also check Amazon Glacier which lets you put nearly 40 GB single archive file if you use multi-part upload.
http://docs.aws.amazon.com/amazonglacier/latest/dev/uploading-archive-mpu.html#qfacts
Remember, if your S3 account is compromised, you have chance to lose all of your data as you would sync an empty folder or malformed files. So, you better write a script to archive your backup few times, for e.g by detecting start of the week.
Update 01/17/2016:
Python based AWS CLI is very mature now.
Please use: https://github.com/aws/aws-cli
Example: aws s3 sync s3://mybucket .
This script backs up an S3 bucket:
#!/usr/bin/env python
from boto.s3.connection import S3Connection
import re
import datetime
import sys
import time
def main():
s3_ID = sys.argv[1]
s3_key = sys.argv[2]
src_bucket_name = sys.argv[3]
num_backup_buckets = sys.argv[4]
connection = S3Connection(s3_ID, s3_key)
delete_oldest_backup_buckets(connection, num_backup_buckets)
backup(connection, src_bucket_name)
def delete_oldest_backup_buckets(connection, num_backup_buckets):
"""Deletes the oldest backup buckets such that only the newest NUM_BACKUP_BUCKETS - 1 buckets remain."""
buckets = connection.get_all_buckets() # returns a list of bucket objects
num_buckets = len(buckets)
backup_bucket_names = []
for bucket in buckets:
if (re.search('backup-' + r'\d{4}-\d{2}-\d{2}' , bucket.name)):
backup_bucket_names.append(bucket.name)
backup_bucket_names.sort(key=lambda x: datetime.datetime.strptime(x[len('backup-'):17], '%Y-%m-%d').date())
# The buckets are sorted latest to earliest, so we want to keep the last NUM_BACKUP_BUCKETS - 1
delete = len(backup_bucket_names) - (int(num_backup_buckets) - 1)
if delete <= 0:
return
for i in range(0, delete):
print 'Deleting the backup bucket, ' + backup_bucket_names[i]
connection.delete_bucket(backup_bucket_names[i])
def backup(connection, src_bucket_name):
now = datetime.datetime.now()
# the month and day must be zero-filled
new_backup_bucket_name = 'backup-' + str('%02d' % now.year) + '-' + str('%02d' % now.month) + '-' + str(now.day);
print "Creating new bucket " + new_backup_bucket_name
new_backup_bucket = connection.create_bucket(new_backup_bucket_name)
copy_bucket(src_bucket_name, new_backup_bucket_name, connection)
def copy_bucket(src_bucket_name, dst_bucket_name, connection, maximum_keys = 100):
src_bucket = connection.get_bucket(src_bucket_name);
dst_bucket = connection.get_bucket(dst_bucket_name);
result_marker = ''
while True:
keys = src_bucket.get_all_keys(max_keys = maximum_keys, marker = result_marker)
for k in keys:
print 'Copying ' + k.key + ' from ' + src_bucket_name + ' to ' + dst_bucket_name
t0 = time.clock()
dst_bucket.copy_key(k.key, src_bucket_name, k.key)
print time.clock() - t0, ' seconds'
if len(keys) < maximum_keys:
print 'Done backing up.'
break
result_marker = keys[maximum_keys - 1].key
if __name__ =='__main__':main()
I use this in a rake task (for a Rails app):
desc "Back up a file onto S3"
task :backup do
S3ID = "AKIAJM3FAKEFAKENRWVQ"
S3KEY = "0A5kuzV+F1pbaMjZxHQAZfakedeJd0dfakeNpry"
SRCBUCKET = "primary-mzgd"
NUM_BACKUP_BUCKETS = 2
Dir.chdir("#{Rails.root}/lib/tasks")
system "./do_backup.py #{S3ID} #{S3KEY} #{SRCBUCKET} #{NUM_BACKUP_BUCKETS}"
end
The AWS CLI supports this now.
aws s3 cp s3://first-bucket-name s3://second-bucket-name --recursive
I've tried to do this in the past, and it's still annoyingly difficult, especially with large, multi-GB, many-millions-of-files buckets. The best solution I ever found was S3S3Mirror, which was made for exactly this purpose.
It's not as trivial as just flipping a switch, but it's still better than most other DIY solutions I've tried. It's multi-threaded and will copy the files much faster than similar single-threaded approaches.
One suggestion: Set it up on a separate EC2 instance, and once you run it, just shut that machine off but leave the AMI there. Then, when you need to re-run, fire the machine up again and you're all set. This is nowhere near as nice as a truly automated solution, but is manageable for monthly or weekly backups.
The best way would be to have the ability to sync my bucket with a new bucket in a different region in case of a data loss.
As of 24 Mar 2015, this is possible using the Cross-Region Replication feature of S3.
One of the listed Use-case Scenarios is "compliance requirements", which seems to match your use-case of added protection of critical data against data loss:
Although, by default, Amazon S3 stores your data across multiple geographically distant Availability Zones, compliance requirements might dictate that you store data at even further distances. Cross-region replication allows you to replicate data between distant AWS regions to satisfy these compliance requirements.
See How to Set Up Cross-Region Replication for setup instructions.
Related
This is for Flink on KDA and so limited to version 1.13
The desired flow of the application:
ingest from kinesis/kafka source
sink to s3
post s3 sink get objectkey/filename and publish to kafka (inform other processes that a file is ready to be examined)
The first 2 steps are simple enough. The 3rd is the tricky one.
From my understanding the S3 object key will be made of the following:
bucket partition (lets assume the defaul here of processing date)
filename. The filename is made up of + + + . It then goes through a series of changes - in-progress, pending and final.
The file will be in a finished state when a checkpoint occurs and all pending files are move to finished.
What I would like is this information as a trigger to kafka publish.
On checkpoint give me a list of all the files(object keys) that have moved to a finished state. These can then be put on a kafka topic.
Is this possible?
Thanks in advance
My funtion is
import boto3
import csv
s3 = boto3.client('s3')
dynamodb = boto3.resource('dynamodb')
def lambda_handler(event, context):
bucket='bucketname'
file_name='filename.csv'
obj = s3.get_object(Bucket=bucket,Key=file_name)
rows = obj['Body'].read()
lines = rows.splitlines()
# print(lines)
reader = csv.reader(lines)
parsed_csv = list(reader)
num_rows = (len(parsed_csv))
table = dynamodb.Table('table_name')
with table.batch_writer() as batch:
for i in range(1,num_rows):
Brand_Name= parsed_csv[i][0]
Assigned_Brand_Name= parsed_csv[i][1]
Brand_URL= parsed_csv[i][2]
Generic_Name= parsed_csv[i][3]
HSN_Code= parsed_csv[i][4]
GST_Rate= parsed_csv[i][5]
Price= parsed_csv[i][6]
Dosage= parsed_csv[i][7]
Package= parsed_csv[i][8]
Size= parsed_csv[i][9]
Size_Unit= parsed_csv[i][10]
Administration_Form= parsed_csv[i][11]
Company= parsed_csv[i][12]
Uses= parsed_csv[i][13]
Side_Effects= parsed_csv[i][14]
How_to_use= parsed_csv[i][15]
How_to_work= parsed_csv[i][16]
FAQs_Downloaded= parsed_csv[i][17]
Alternate_Brands= parsed_csv[i][18]
Prescription_Required= parsed_csv[i][19]
Interactions= parsed_csv[i][20]
batch.put_item(Item={
'Brand Name':Assigned_Brand_Name
'Brand URL':Brand_URL,
'Generic Name':Generic_Name,
'Price':Price,
'Dosage':Dosage,
'Company':Company,
'Uses':Uses,
'Side Effects':Side_Effects,
'How to use':How_to_use,
'How to work':How_to_work,
'FAQs Downloaded?':FAQs_Downloaded,
'Alternate Brands':Alternate_Brands,
'Prescription Required':Prescription_Required,
'Interactions':Interactions
})
Response:
{
"errorMessage": "2020-10-14T11:40:56.792Z ecd63bdb-16bc-4813-afed-cbf3e1fa3625 Task timed out after 3.00 seconds"
}
You haven't specified how many rows there are is your CSV file. "Huge" is pretty subjective so it is possible that your task is timing out due to throttling on the DynamoDB table.
If you are using provisioned capacity on the table you are loading into, make sure you have enough capacity allocated. If you're using on-demand capacity then this might be due to the on-demand partitioning that happens when the table needs to scale up.
Either way, you may want to add some error handling for situations like these and add a delay when you get a timeout, before retrying and resuming.
Something to keep in mind is that writes to Dynamo always take 1 WCU and the maximum capacity a single partition can have is 1000 WCU so as your write throughput increases, the table may undergo multiple splits behind the scenes when you're in on-demand mode. For provisioned mode, you'll have to have allocated enough capacity to begin with, otherwise you'll be limited to writing however many items / second you have allocated write capacity.
I am writing a beam job that is a simple 1:1 ETL from a binary protobuf file stored in GCS into BigQuery. The table schema is quite large, and generated automatically from a representative protobuf.
I am encountering behavior where the BigQuery table is created successfully, but no records are inserted. I have confirmed that records are being generated by the earlier stage, and when I use a normal file sink I can confirm that records are written.
Does anyone know why this is happening?
Logs:
WARNING:root:Inferring Schema...
WARNING:root:Unable to find default credentials to use: The Application Default Credentials are not available. They are available if running in Google Compute Engine. Otherwise, the environment variable GOOGLE_APPLICATION_CREDENTIALS must be defined pointing to a file defining the credentials. See https://developers.google.com/accounts/docs/application-default-credentials for more information.
Connecting anonymously.
WARNING:root:Defining Beam Pipeline...
<PATH REDACTED>/venv/lib/python3.7/site-packages/apache_beam/io/gcp/bigquery.py:1145: BeamDeprecationWarning: options is deprecated since First stable release. References to <pipeline>.options will not be supported
experiments = p.options.view_as(DebugOptions).experiments or []
WARNING:root:Running Beam Pipeline...
WARNING:root:extracted {'counters': [MetricResult(key=MetricKey(step=extract_games, metric=MetricName(namespace=__main__.ExtractGameProtobuf, name=extracted_games), labels={}), committed=8, attempted=8)], 'distributions': [], 'gauges': []} games
Pipeline Source:
def main(args):
DEFAULT_REPLAY_IDS_PATH = "./replay_ids.txt"
DEFAULT_BQ_TABLE_OUT = "<PROJECT REDACTED>:<DATASET REDACTED>.games"
# configure logging
logging.basicConfig(level=logging.WARNING)
# set up replay source
replay_source = ETLReplayRemoteSource.default()
# TODO: load the example replay and parse schema
logging.warning("Inferring Schema...")
sample_replay = replay_source.load_replay(DEFAULT_REPLAY_IDS[0])
game_schema = ProtobufToBigQuerySchemaGenerator(
sample_replay.analysis.DESCRIPTOR).schema()
# print("GAME SCHEMA:\n{}".format(game_schema)) # DEBUG
# submit beam job that reads replays into bigquery
def count_ones(word_ones):
(word, ones) = word_ones
return (word, sum(ones))
with beam.Pipeline(options=PipelineOptions()) as p:
logging.warning("Defining Beam Pipeline...")
# replay_ids = p | "create_replay_ids" >> beam.Create(DEFAULT_REPLAY_IDS)
(p | "read_replay_ids" >> beam.io.ReadFromText(DEFAULT_REPLAY_IDS_PATH)
| "extract_games" >> beam.ParDo(ExtractGameProtobuf())
| "write_out_bq" >> WriteToBigQuery(
DEFAULT_BQ_TABLE_OUT,
schema=game_schema,
write_disposition=BigQueryDisposition.WRITE_APPEND,
create_disposition=BigQueryDisposition.CREATE_IF_NEEDED)
)
logging.warning("Running Beam Pipeline...")
result = p.run()
result.wait_until_finish()
n_extracted = result.metrics().query(
MetricsFilter().with_name('extracted_games'))
logging.warning("extracted {} games".format(n_extracted))
My current workflow in BigQuery is as follows:
(1) query data in a public repository (stored in the US), (2) write it to a table in my repository, (3) export a csv to a cloud bucket and (4) download the csv on the server I work on and (5) work with that on the server.
The problem I have now, is that the server I work on is located in EU. Thus, I have to pay quite some fees for transfering data between my US bucket and my EU server. I could now go ahead and locate my bucket in EU, but then I still have the problem that I would transfer data from the US (BigQuery) to EU (bucket). So I could also set my dataset in bq to be located in the EU, but then I cant do any queries anylonger, because the data in the public repository is located in the US, and queries between different locations are not allowed.
Does anyone have an idea of how to approach this?
One way to copy a BigQuery dataset from one region to another is to take advantage of the Storage Data Transfer Service. It doesn't get around the fact that you still have to pay for bucket-to-bucket network traffic, but might save you some CPU time on copying data to a server in the EU.
The flow would be to:
Extract all the BigQuery tables into a bucket in the same region as the tables. (Recommend Avro format for best fidelity in data types and fastest loading speed.)
Run a storage transfer job to copy the extracted files from the starting location bucket to a bucket in the destination location.
Load all the files into a BigQuery dataset located in the destination location.
Python example:
# Copyright 2018 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import datetime
import sys
import time
import googleapiclient.discovery
from google.cloud import bigquery
import json
import pytz
PROJECT_ID = 'swast-scratch' # TODO: set this to your project name
FROM_LOCATION = 'US' # TODO: set this to the BigQuery location
FROM_DATASET = 'workflow_test_us' # TODO: set to BQ dataset name
FROM_BUCKET = 'swast-scratch-us' # TODO: set to bucket name in same location
TO_LOCATION = 'EU' # TODO: set this to the destination BigQuery location
TO_DATASET = 'workflow_test_eu' # TODO: set to destination dataset name
TO_BUCKET = 'swast-scratch-eu' # TODO: set to bucket name in destination loc
# Construct API clients.
bq_client = bigquery.Client(project=PROJECT_ID)
transfer_client = googleapiclient.discovery.build('storagetransfer', 'v1')
def extract_tables():
# Extract all tables in a dataset to a Cloud Storage bucket.
print('Extracting {}:{} to bucket {}'.format(
PROJECT_ID, FROM_DATASET, FROM_BUCKET))
tables = list(bq_client.list_tables(bq_client.dataset(FROM_DATASET)))
extract_jobs = []
for table in tables:
job_config = bigquery.ExtractJobConfig()
job_config.destination_format = bigquery.DestinationFormat.AVRO
extract_job = bq_client.extract_table(
table.reference,
['gs://{}/{}.avro'.format(FROM_BUCKET, table.table_id)],
location=FROM_LOCATION, # Available in 0.32.0 library.
job_config=job_config) # Starts the extract job.
extract_jobs.append(extract_job)
for job in extract_jobs:
job.result()
return tables
def transfer_buckets():
# Transfer files from one region to another using storage transfer service.
print('Transferring bucket {} to {}'.format(FROM_BUCKET, TO_BUCKET))
now = datetime.datetime.now(pytz.utc)
transfer_job = {
'description': '{}-{}-{}_once'.format(
PROJECT_ID, FROM_BUCKET, TO_BUCKET),
'status': 'ENABLED',
'projectId': PROJECT_ID,
'transferSpec': {
'transferOptions': {
'overwriteObjectsAlreadyExistingInSink': True,
},
'gcsDataSource': {
'bucketName': FROM_BUCKET,
},
'gcsDataSink': {
'bucketName': TO_BUCKET,
},
},
# Set start and end date to today (UTC) without a time part to start
# the job immediately.
'schedule': {
'scheduleStartDate': {
'year': now.year,
'month': now.month,
'day': now.day,
},
'scheduleEndDate': {
'year': now.year,
'month': now.month,
'day': now.day,
},
},
}
transfer_job = transfer_client.transferJobs().create(
body=transfer_job).execute()
print('Returned transferJob: {}'.format(
json.dumps(transfer_job, indent=4)))
# Find the operation created for the job.
job_filter = {
'project_id': PROJECT_ID,
'job_names': [transfer_job['name']],
}
# Wait until the operation has started.
response = {}
while ('operations' not in response) or (not response['operations']):
time.sleep(1)
response = transfer_client.transferOperations().list(
name='transferOperations', filter=json.dumps(job_filter)).execute()
operation = response['operations'][0]
print('Returned transferOperation: {}'.format(
json.dumps(operation, indent=4)))
# Wait for the transfer to complete.
print('Waiting ', end='')
while operation['metadata']['status'] == 'IN_PROGRESS':
print('.', end='')
sys.stdout.flush()
time.sleep(5)
operation = transfer_client.transferOperations().get(
name=operation['name']).execute()
print()
print('Finished transferOperation: {}'.format(
json.dumps(operation, indent=4)))
def load_tables(tables):
# Load all tables into the new dataset.
print('Loading tables from bucket {} to {}:{}'.format(
TO_BUCKET, PROJECT_ID, TO_DATASET))
load_jobs = []
for table in tables:
dest_table = bq_client.dataset(TO_DATASET).table(table.table_id)
job_config = bigquery.LoadJobConfig()
job_config.source_format = bigquery.SourceFormat.AVRO
load_job = bq_client.load_table_from_uri(
['gs://{}/{}.avro'.format(TO_BUCKET, table.table_id)],
dest_table,
location=TO_LOCATION, # Available in 0.32.0 library.
job_config=job_config) # Starts the load job.
load_jobs.append(load_job)
for job in load_jobs:
job.result()
# Actually run the script.
tables = extract_tables()
transfer_buckets()
load_tables(tables)
The preceding sample uses google-cloud-bigquery library for BigQuery API and google-api-python-client for Storage Data Transfer API.
Note that this sample does not account for partitioned tables.
No matter what, you have data in the US that you need in the EU, so I think you have two options:
You could continue to pay many smaller fees to move your reduced datasets from the US to the EU as you're doing today.
You could pay the one-off fee to transfer the original public BQ dataset from the US to your own dataset in the EU. From then on, all queries you run stay in the same region, and you have no more trans-continental transfers.
It really depends on how many queries you plan to do. If it's not a lot, then the way you're doing things today seems like it'd be the most efficient. If it's a lot, then moving the data once (paying the up-front fee) might work out cheaper.
Maybe Google has some magical way to make this better, but as far as I can tell, you're dealing with lots of data on one side of the Atlantic that you need on the other side, and moving it across that wire costs money.
I am running Spark in standalone mode on 2 machines which have these configs
500gb memory, 4 cores, 7.5 RAM
250gb memory, 8 cores, 15 RAM
I have created a master and a slave on 8core machine, giving 7 cores to worker. I have created another slave on 4core machine with 3 worker cores. The UI shows 13.7 and 6.5 G usable RAM for 8core and 4core respectively.
Now on this I have to process an aggregate of user ratings over a period of 15 days. I am trying to do this using Pyspark
This data is stored in hourwise files in day-wise directories in an s3 bucket, every file must be around 100MB eg
s3://some_bucket/2015-04/2015-04-09/data_files_hour1
I am reading the files like this
a = sc.textFile(files, 15).coalesce(7*sc.defaultParallelism) #to restrict partitions
where files is a string of this form 's3://some_bucket/2015-04/2015-04-09/*,s3://some_bucket/2015-04/2015-04-09/*'
Then I do a series of maps and filters and persist the result
a.persist(StorageLevel.MEMORY_ONLY_SER)
Then I need to do a reduceByKey to get an aggregate score over the span of days.
b = a.reduceByKey(lambda x, y: x+y).map(aggregate)
b.persist(StorageLevel.MEMORY_ONLY_SER)
Then I need to make a redis call for the actual terms for the items the user has rated, so I call mapPartitions like this
final_scores = b.mapPartitions(get_tags)
get_tags function creates a redis connection each time of invocation and calls redis and yield a (user, item, rate) tuple
(The redis hash is stored in the 4core)
I have tweaked the settings for SparkConf to be at
conf = (SparkConf().setAppName(APP_NAME).setMaster(master)
.set("spark.executor.memory", "5g")
.set("spark.akka.timeout", "10000")
.set("spark.akka.frameSize", "1000")
.set("spark.task.cpus", "5")
.set("spark.cores.max", "10")
.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
.set("spark.kryoserializer.buffer.max.mb", "10")
.set("spark.shuffle.consolidateFiles", "True")
.set("spark.files.fetchTimeout", "500")
.set("spark.task.maxFailures", "5"))
I run the job with driver-memory of 2g in client mode, since cluster mode doesn't seem to be supported here.
The above process takes a long time for 2 days' of data (around 2.5hours) and completely gives up on 14 days'.
What needs to improve here?
Is this infrastructure insufficient in terms of RAM and cores (This is offline and can take hours, but it has got to finish in 5 hours or so)
Should I increase/decrease the number of partitions?
Redis could be slowing the system, but the number of keys is just too huge to make a one time call.
I am not sure where the task is failing, in reading the files or in reducing.
Should I not use Python given better Spark APIs in Scala, will that help with efficiency as well?
This is the exception trace
Lost task 4.1 in stage 0.0 (TID 11, <node>): java.net.SocketTimeoutException: Read timed out
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.read(SocketInputStream.java:152)
at java.net.SocketInputStream.read(SocketInputStream.java:122)
at sun.security.ssl.InputRecord.readFully(InputRecord.java:442)
at sun.security.ssl.InputRecord.readV3Record(InputRecord.java:554)
at sun.security.ssl.InputRecord.read(InputRecord.java:509)
at sun.security.ssl.SSLSocketImpl.readRecord(SSLSocketImpl.java:934)
at sun.security.ssl.SSLSocketImpl.readDataRecord(SSLSocketImpl.java:891)
at sun.security.ssl.AppInputStream.read(AppInputStream.java:102)
at org.apache.http.impl.io.AbstractSessionInputBuffer.read(AbstractSessionInputBuffer.java:198)
at org.apache.http.impl.io.ContentLengthInputStream.read(ContentLengthInputStream.java:178)
at org.apache.http.impl.io.ContentLengthInputStream.read(ContentLengthInputStream.java:200)
at org.apache.http.impl.io.ContentLengthInputStream.close(ContentLengthInputStream.java:103)
at org.apache.http.conn.BasicManagedEntity.streamClosed(BasicManagedEntity.java:164)
at org.apache.http.conn.EofSensorInputStream.checkClose(EofSensorInputStream.java:227)
at org.apache.http.conn.EofSensorInputStream.close(EofSensorInputStream.java:174)
at org.apache.http.util.EntityUtils.consume(EntityUtils.java:88)
at org.jets3t.service.impl.rest.httpclient.HttpMethodReleaseInputStream.releaseConnection(HttpMethodReleaseInputStream.java:102)
at org.jets3t.service.impl.rest.httpclient.HttpMethodReleaseInputStream.close(HttpMethodReleaseInputStream.java:194)
at org.apache.hadoop.fs.s3native.NativeS3FileSystem$NativeS3FsInputStream.seek(NativeS3FileSystem.java:152)
at org.apache.hadoop.fs.BufferedFSInputStream.seek(BufferedFSInputStream.java:89)
at org.apache.hadoop.fs.FSDataInputStream.seek(FSDataInputStream.java:63)
at org.apache.hadoop.mapred.LineRecordReader.<init>(LineRecordReader.java:126)
at org.apache.hadoop.mapred.TextInputFormat.getRecordReader(TextInputFormat.java:67)
at org.apache.spark.rdd.HadoopRDD$$anon$1.<init>(HadoopRDD.scala:236)
at org.apache.spark.rdd.HadoopRDD.compute(HadoopRDD.scala:212)
at org.apache.spark.rdd.HadoopRDD.compute(HadoopRDD.scala:101)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:277)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:244)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:35)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:277)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:244)
at org.apache.spark.rdd.CoalescedRDD$$anonfun$compute$1.apply(CoalescedRDD.scala:93)
at org.apache.spark.rdd.CoalescedRDD$$anonfun$compute$1.apply(CoalescedRDD.scala:92)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
at scala.collection.Iterator$class.foreach(Iterator.scala:727)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
at org.apache.spark.api.python.PythonRDD$.writeIteratorToStream(PythonRDD.scala:405)
at org.apache.spark.api.python.PythonRDD$WriterThread$$anonfun$run$1.apply(PythonRDD.scala:243)
at org.apache.spark.util.Utils$.logUncaughtExceptions(Utils.scala:1617)
at org.apache.spark.api.python.PythonRDD$WriterThread.run(PythonRDD.scala:205)
I could really use some help, thanks in advance
Here is what my main code looks like
def main(sc):
f=get_files()
a=sc.textFile(f, 15)
.coalesce(7*sc.defaultParallelism)
.map(lambda line: line.split(","))
.filter(len(line)>0)
.map(lambda line: (line[18], line[2], line[13], line[15])).map(scoring)
.map(lambda line: ((line[0], line[1]), line[2])).persist(StorageLevel.MEMORY_ONLY_SER)
b=a.reduceByKey(lambda x, y: x+y).map(aggregate)
b.persist(StorageLevel.MEMORY_ONLY_SER)
c=taggings.mapPartitions(get_tags)
c.saveAsTextFile("f")
a.unpersist()
b.unpersist()
The get_tags function is
def get_tags(partition):
rh = redis.Redis(host=settings['REDIS_HOST'], port=settings['REDIS_PORT'], db=0)
for element in partition:
user = element[0]
song = element[1]
rating = element[2]
tags = rh.hget(settings['REDIS_HASH'], song)
if tags:
tags = json.loads(tags)
else:
tags = scrape(song, rh)
if tags:
for tag in tags:
yield (user, tag, rating)
The get_files function is as:
def get_files():
paths = get_path_from_dates(DAYS)
base_path = 's3n://acc_key:sec_key#bucket/'
files = list()
for path in paths:
fle = base_path+path+'/file_format.*'
files.append(fle)
return ','.join(files)
The get_path_from_dates(DAYS) is
def get_path_from_dates(last):
days = list()
t = 0
while t <= last:
d = today - timedelta(days=t)
path = d.strftime('%Y-%m')+'/'+d.strftime('%Y-%m-%d')
days.append(path)
t += 1
return days
As a small optimization, I have created two separate tasks, one to read from s3 and get additive sum, second to read transformations from redis. The first tasks has high number of partitions since there are around 2300 files to read. The second one has much lesser number of partitions to prevent redis connection latency, and there is only one file to read which is on the EC2 cluster itself. This is only partial, still looking for suggestions to improve ...
I was in a similar usecase: doing coalesce on a RDD with 300,000+ partitions. The difference is that I was using s3a(SocketTimeoutException from S3AFileSystem.waitAysncCopy). Finally the issue was resolved by setting a larger fs.s3a.connection.timeout(Hadoop's core-site.xml). Hopefully you can get a clue.