I want to mount an AWS s3 bucket on my Docker container which I am using to run some AWS Batch jobs.
I have been researching several ways of going about this but I still lack clarity as to how I can get this to work on AWS Batch which is going to dynamically allocate EC2 instances based on the job definitions.
The following are the ideas I have gathered , but I am unsure of how to put them together:
https://rexray.readthedocs.io/en/v0.9.0/user-guide/docker-plugins/
I could use this plugin to mount S3 bucket as Docker volume , but unsure how to do this on AWS Batch. Should this plugin be a part of the Docker image ?
I could use s3fs-fuse but I was told that I wont be able to install or store any of the files from S3 on EC2 instances on AWS Batch instances, which can then be mounted in docker. - is there a way to do this by including some code in the AMI that will copy files from s3 to instance?
Are there any other ways I can get this to work?
Pardon me if my questions are too basic. I am fairly new to Docker and AWS Batch. Would appreciate any help!
Thanks !
I have personally used s3fs to solve this problem in the past. Using S3 as a mounted filesystem has some caveats which you would be wise to familiarize yourself with (because you are treating something that is not a filesystem like it is a filesystem, a classic leaky abstraction problem), but if your workflow is relatively simple and does not have the possibility for race conditions you should be able to do it with some confidence (especially now that as of Dec 2020 AWS S3 has released read-after-write consistency automatically for all applications).
To answer your other question:
I could use s3fs-fuse but I was told that I wont be able to install or store any of the files from S3 on EC2 instances on AWS Batch instances, which can then be mounted in docker. - is there a way to do this by including some code in the AMI that will copy files from s3 to instance?
If you use s3fs to mount your S3 bucket as a filesystem within docker, you don't need to worry about copying files from S3 to the instance, indeed the whole point of using s3fs is that you can access all your files in S3 from the container without having to move then off of S3.
Say for instance you mount your S3 bucket s3://my-test-bucket to /data in the container. You can then run your program like my-executable --input /data/my-s3-file --output /data/my-s3-output as if the input file was right there on the local filesystem. When its done you can see the output file will be on S3 in s3://my-test-bucket/my-s3-output. This can simply your workflow / cut down on glue code quite a bit.
My dockerfile for my s3fs AWS batch container looks like this:
FROM ubuntu:18.04
RUN apt-get -y update && apt-get -y install curl wget build-essential automake libcurl4-openssl-dev libxml2-dev pkg-config libssl-dev libfuse-dev parallel
RUN wget https://github.com/s3fs-fuse/s3fs-fuse/archive/v1.86.tar.gz && \
tar -xzvf v1.86.tar.gz && \
cd s3fs-fuse-1.86 && \
./autogen.sh && \
./configure --prefix=/usr && \
make && \
make install && \
rm -rf s3fs-fuse-1.86 v1.86.tar.gz
RUN mkdir /data
COPY entrypoint.sh /entrypoint.sh
ENTRYPOINT ["/entrypoint.sh"]
entrypoint.sh is a convenience for always running the s3fs mount before the main program (this breaks the paradigm of one process per docker container but, I don't think its cause for major concern here). It looks like this:
#!/bin/bash
bucket=my-bucket
s3fs ${bucket} /data -o ecs
echo "Mounted ${bucket} to /data"
exec "$#"
Note related answer here: https://stackoverflow.com/a/60556131/1583239
I am assuming you want to read/write to an S3 bucket. You can do this within your containerized code by using a library like boto3. You will also need to provide IAM permissions for the container to access S3.
I'm looking through the documentation of aws cli and I cannot find the way to copy the only files in some directory structure to other bucket with "flattened" structure(I want one directory and all files inside of it).
for example
/a/b/c/1.pg
/a/2.jpg
/a/b/3.jpg
i would want to have in different bucket:
/x/1.jpg
/x/2.jpg
/x/3.jpg
Am I missing something or is it impossible?
Do you have an idea how could I do that?
Assuming that you have aws cli configured on the system and assuming that both the buckets are in the same region.
What you can do is first dowload the s3 bucket to your local machine using:
aws s3 sync s3://originbucket /localdir/
Post this, use a find command to get all the files into one dir
find /localdir/ -type f -exec mv {} /anotherlocaldir/
Finally, you can upload the files to s3 again!
aws s3 sync /anotherlocaldir/ s3://destinationbucket
You don't need to download files locally, as suggested in another answer. Instead, you could write a shell script or something that does the following:
Run ls on s3://bucket1 to get fully-qualified names of all files in it.
For each file, run cp to copy it from current location to s3://bucket2/x/
Here are some examples for your reference:
aws s3 sync /a/b/c/1.pg s3://bucketname/
aws s3 sync /a/2.jpg s3://bucketname/
aws s3 sync /a/b/3.jpg s3://bucketname/
To sync all contents of a dir to S3 bucket:
aws s3 sync /directoryPath/ s3://bucketname/
AWS reference url: http://docs.aws.amazon.com/cli/latest/reference/s3/sync.html
In my amazon EC2 instance, I have a folder named uploads. In this folder I have 1000 images. Now I want to copy all images to my new S3 bucket. How can I do this?
First Option sm3cmd
Use s3cmd
s3cmd get s3://AWS_S3_Bucket/dir/file
Take a look at this s3cmd documentation
if you are on linux, run this on the command line:
sudo apt-get install s3cmd
or Centos, Fedore.
yum install s3cmd
Example of usage:
s3cmd put my.file s3://pactsRamun/folderExample/fileExample
Second Option
Using Cli from amazon
Update
Like #tedder42 said in the comments, instead of using cp, use sync.
Take a look at the following syntax:
aws s3 sync <source> <target> [--options]
Example:
aws s3 sync . s3://my-bucket/MyFolder
More information and examples available at Managing Objects Using High-Level s3 Commands with the AWS Command Line Interface
aws s3 sync your-dir-name s3://your-s3-bucket-name/folder-name
Important: This will copy each item in your named directory into the s3 bucket folder you selected. This will not copy your directory as a whole.
Or, you can use the following command for one selected file.
aws s3 sync your-dir-name/file-name s3://your-s3-bucket-name/folder-name/file-name
Or you can use a wild character to select all. Note that this will copy your directory as a whole and also generate metadata and save them to your s3 bucket folder.
aws s3 sync . s3://your-s3-bucket-name/folder-name
To copy from EC2 to S3 use the below code in the Command line of EC2.
First, you have to give "IAM Role with full s3 Access" to your EC2 instance.
aws s3 cp Your_Ec2_Folder s3://Your_S3_bucket/Your_folder --recursive
Also note on aws cli syncing with s3 it is multithreaded and uploads multiple parts of a file at one time. The number of threads however, is not configurable at this time.
aws s3 mv /home/inbound/ s3://test/ --recursive --region us-west-2
This can be done very simply. Follow the following steps:
Open the AWS EC2 on console.
Select the instance and navigate to actions.
Select instances settings and select Attach/Replace IAM Role
When this is done, connect to the AWS instance and the rest will be done via the following CLI commands:
aws s3 cp filelocation/filename s3://bucketname
Hence you don't need to install or do any extra efforts.
Please note... the file location refers to the local address. And the bucketname is the name of your bucket.
Also note: This is possible if your instance and S3 bucket are in the same account.
Cheers.
We do have a dryrun feature available for testing.
To begin with I would assign ec2-instance a role to be able read
write to S3
SSH into the instance and perform the following
vi tmp1.txt
aws s3 mv ./ s3://bucketname-bucketurl.com/ --dryrun
If this works then all you have to do is either create a script to
upload all files with specific from this folder to s3 bucket
I have done the wrritten the following command in my script to move
files older than 2 minutes from current directory to bucket/folder
cd dir; ls . -rt | xargs -I FILES find FILES -maxdepth 1 -name
'*.txt' -mmin +2 -exec aws s3 mv '{}' s3://bucketurl.com
I noticed that there does not seem to be an option to download an entire s3 bucket from the AWS Management Console.
Is there an easy way to grab everything in one of my buckets? I was thinking about making the root folder public, using wget to grab it all, and then making it private again but I don't know if there's an easier way.
AWS CLI
See the "AWS CLI Command Reference" for more information.
AWS recently released their Command Line Tools, which work much like boto and can be installed using
sudo easy_install awscli
or
sudo pip install awscli
Once installed, you can then simply run:
aws s3 sync s3://<source_bucket> <local_destination>
For example:
aws s3 sync s3://mybucket .
will download all the objects in mybucket to the current directory.
And will output:
download: s3://mybucket/test.txt to test.txt
download: s3://mybucket/test2.txt to test2.txt
This will download all of your files using a one-way sync. It will not delete any existing files in your current directory unless you specify --delete, and it won't change or delete any files on S3.
You can also do S3 bucket to S3 bucket, or local to S3 bucket sync.
Check out the documentation and other examples.
Whereas the above example is how to download a full bucket, you can also download a folder recursively by performing
aws s3 cp s3://BUCKETNAME/PATH/TO/FOLDER LocalFolderName --recursive
This will instruct the CLI to download all files and folder keys recursively within the PATH/TO/FOLDER directory within the BUCKETNAME bucket.
You can use s3cmd to download your bucket:
s3cmd --configure
s3cmd sync s3://bucketnamehere/folder /destination/folder
There is another tool you can use called rclone. This is a code sample in the Rclone documentation:
rclone sync /home/local/directory remote:bucket
I've used a few different methods to copy Amazon S3 data to a local machine, including s3cmd, and by far the easiest is Cyberduck.
All you need to do is enter your Amazon credentials and use the simple interface to download, upload, sync any of your buckets, folders or files.
You've many options to do that, but the best one is using the AWS CLI.
Here's a walk-through:
Download and install AWS CLI in your machine:
Install the AWS CLI using the MSI Installer (Windows).
Install the AWS CLI using the Bundled Installer for Linux, OS X, or Unix.
Configure AWS CLI:
Make sure you input valid access and secret keys, which you received when you created the account.
Sync the S3 bucket using:
aws s3 sync s3://yourbucket /local/path
In the above command, replace the following fields:
yourbucket >> your S3 bucket that you want to download.
/local/path >> path in your local system where you want to download all the files.
To download using AWS S3 CLI:
aws s3 cp s3://WholeBucket LocalFolder --recursive
aws s3 cp s3://Bucket/Folder LocalFolder --recursive
To download using code, use the AWS SDK.
To download using GUI, use Cyberduck.
The answer by #Layke is good, but if you have a ton of data and don't want to wait forever, you should read "AWS CLI S3 Configuration".
The following commands will tell the AWS CLI to use 1,000 threads to execute jobs (each a small file or one part of a multipart copy) and look ahead 100,000 jobs:
aws configure set default.s3.max_concurrent_requests 1000
aws configure set default.s3.max_queue_size 100000
After running these, you can use the simple sync command:
aws s3 sync s3://source-bucket/source-path s3://destination-bucket/destination-path
or
aws s3 sync s3://source-bucket/source-path c:\my\local\data\path
On a system with CPU 4 cores and 16GB RAM, for cases like mine (3-50GB files) the sync/copy speed went from about 9.5MiB/s to 700+MiB/s, a speed increase of 70x over the default configuration.
100% works for me, i have download all files from aws s3 backet.
Install AWS CLI. Select your operating system and follow the steps here: Installing or updating the latest version of the AWS CLI
Check AWS version: aws --version
Run config command: aws configure
aws s3 cp s3://yourbucketname your\local\path --recursive
Eg (Windows OS): aws s3 cp s3://yourbucketname C:\aws-s3-backup\project-name --recursive
Check out this link: How to download an entire bucket from S3 to local folder
If you use Visual Studio, download "AWS Toolkit for Visual Studio".
After installed, go to Visual Studio - AWS Explorer - S3 - Your bucket - Double click
In the window you will be able to select all files. Right click and download files.
For Windows, S3 Browser is the easiest way I have found. It is excellent software, and it is free for non-commercial use.
Use this command with the AWS CLI:
aws s3 cp s3://bucketname . --recursive
Another option that could help some OS X users is Transmit.
It's an FTP program that also lets you connect to your S3 files. And, it has an option to mount any FTP or S3 storage as a folder in the Finder, but it's only for a limited time.
I've done a bit of development for S3 and I have not found a simple way to download a whole bucket.
If you want to code in Java the jets3t lib is easy to use to create a list of buckets and iterate over that list to download them.
First, get a public private key set from the AWS management consule so you can create an S3service object:
AWSCredentials awsCredentials = new AWSCredentials(YourAccessKey, YourAwsSecretKey);
s3Service = new RestS3Service(awsCredentials);
Then, get an array of your buckets objects:
S3Object[] objects = s3Service.listObjects(YourBucketNameString);
Finally, iterate over that array to download the objects one at a time with:
S3Object obj = s3Service.getObject(bucket, fileName);
file = obj.getDataInputStream();
I put the connection code in a threadsafe singleton. The necessary try/catch syntax has been omitted for obvious reasons.
If you'd rather code in Python you could use Boto instead.
After looking around BucketExplorer, "Downloading the whole bucket" may do what you want.
AWS SDK API is only the best option for uploading entire folder and repository to AWS S3 and to download entire AWS S3 bucket locally.
To upload whole folder to AWS S3: aws s3 sync . s3://BucketName
To download whole AWS S3 bucket locally: aws s3 sync s3://BucketName .
You can also assign path like BucketName/Path for particular folder in AWS S3 bucket to download.
If you only want to download the bucket from AWS, first install the AWS CLI in your machine. In terminal change the directory to where you want to download the files and run this command.
aws s3 sync s3://bucket-name .
If you also want to sync the both local and s3 directories (in case you added some files in local folder), run this command:
aws s3 sync . s3://bucket-name
You can do this with MinIO Client as follows: mc cp -r https://s3-us-west-2.amazonaws.com/bucketName/ localdir
MinIO also supports sessions, resumable downloads, uploads and many more. MinIO supports Linux, OS X and Windows operating systems. It is written in Golang and released under Apache Version 2.0.
AWS CLI is the best option to download an entire S3 bucket locally.
Install AWS CLI.
Configure AWS CLI for using default security credentials and default AWS Region.
To download the entire S3 bucket use command
aws s3 sync s3://yourbucketname localpath
Reference to AWS CLI for different AWS services: AWS Command Line Interface
To add another GUI option, we use WinSCP's S3 functionality. It's very easy to connect, only requiring your access key and secret key in the UI. You can then browse and download whatever files you require from any accessible buckets, including recursive downloads of nested folders.
Since it can be a challenge to clear new software through security and WinSCP is fairly prevalent, it can be really beneficial to just use it rather than try to install a more specialized utility.
If you use Firefox with S3Fox, that DOES let you select all files (shift-select first and last) and right-click and download all.
I've done it with 500+ files without any problem.
When in Windows, my preferred GUI tool for this is CloudBerry Explorer Freeware for
Amazon S3. It has a fairly polished file explorer and FTP-like interface.
You can use sync to download whole S3 bucket. For example, to download whole bucket named bucket1 on current directory.
aws s3 sync s3://bucket1 .
If you have only files there (no subdirectories) a quick solution is to select all the files (click on the first, Shift+click on the last) and hit Enter or right click and select Open. For most of the data files this will download them straight to your computer.
Try this command:
aws s3 sync yourBucketnameDirectory yourLocalDirectory
For example, if your bucket name is myBucket and local directory is c:\local, then:
aws s3 sync s3://myBucket c:\local
For more informations about awscli check this
aws cli installation
It's always better to use awscli for downloading / uploading files to s3. Sync will help you to resume without any hassle.
aws s3 sync s3://bucketname/ .
aws s3 sync s3://<source_bucket> <local_destination>
is a great answer, but it won't work if the objects are in storage class Glacier Flexible Retrieval, even if the the files have been restored. In that case you need to add the flag --force-glacier-transfer .
Here is a summary of what you have to do to copy an entire bucket:
1. Create a user that can operate with AWS s3 bucket
Follow this official article: Configuration basics
Don't forget to:
tick "programmatic access" in order to have the possibility to deal with with AWS via CLI.
add the right IAM policy to your user to allow him to interact with the s3 bucket
2. Download, install and configure AWS CLI
See this link allowing to configure it: https://docs.aws.amazon.com/cli/latest/userguide/cli-configure-quickstart.html
You can use the following command in order to add the keys you got when you created your user:
$ aws configure
AWS Access Key ID [None]: <your_access_key>
AWS Secret Access Key [None]: <your_secret_key>
Default region name [None]: us-west-2
Default output format [None]: json
3. Use the following command to download content
You can a recursive cp commande, but aws sync command is f:
aws s3 sync s3://your_bucket /local/path
To see what would be the dowloaded files before really do the download, you can use the --dryrun option.
To improve speed, you can adjust s3 max_concurrent_requests and max_queue_size properties. See: http://docs.aws.amazon.com/cli/latest/topic/s3-config.html
You can exclude/include some files using --exclude and --include options. See: https://docs.aws.amazon.com/cli/latest/reference/s3/
For example, the below command will show all the .png file presents in the bucket. Replay the command without --dryrun to make the resulting files be downloaded.
aws s3 sync s3://your_bucket /local/path --recursive --exclude "*" --include "*.png" --dryrun
Windows User need to download S3EXPLORER from this link which also has installation instructions :- http://s3browser.com/download.aspx
Then provide you AWS credentials like secretkey, accesskey and region to the s3explorer, this link contains configuration instruction for s3explorer:Copy Paste Link in brower: s3browser.com/s3browser-first-run.aspx
Now your all s3 buckets would be visible on left panel of s3explorer.
Simply select the bucket, and click on Buckets menu on top left corner, then select Download all files to option from the menu. Below is the screenshot for the same:
Bucket Selection Screen
Then browse a folder to download the bucket at a particular place
Click on OK and your download would begin.
aws sync is the perfect solution. It does not do a two way.. it is a one way from source to destination. Also, if you have lots of items in bucket it will be a good idea to create s3 endpoint first so that download happens faster (because download does not happen via internet but via intranet) and no charges
As #layke said, it is the best practice to download the file from the S3 cli it is a safe and secure. But in some cases, people need to use wget to download the file and here is the solution
aws s3 presign s3://<your_bucket_name/>
This will presign will get you temporary public URL which you can use to download content from S3 using the presign_url, in your case using wget or any other download client.
You just need to pass --recursive & --include "*" in the aws s3 cp command as follows: aws --region "${BUCKET_REGION}" s3 cp s3://${BUCKET}${BUCKET_PATH}/ ${LOCAL_PATH}/tmp --recursive --include "*" 2>&1
In addition to the suggestions for aws s3 sync, I would also recommend looking at s5cmd.
In my experience I found this to be substantially faster than the AWS CLI for multiple downloads or large downloads.
s5cmd supports wildcards so something like this would work:
s5cmd cp s3://bucket-name/* ./folder