Efficiently transfer large amounts of data to S3
Project description
S3AM, pronounced ˈskrēm, is a fast, parallel, streaming multipart uploader for S3. It efficiently streams content from any URL for which the locally installed libcurl and the remote server support byte range requests, for example file://, ftp:// (many servers) and http:// (some servers).
It is intended to be used with large files, has been tested with 300GB files but imposes no inherent limit on the maximum file size. While it can be used with small files, you will find that it will be slower than other utilities if the file size is below 5MB.
It supports encrypting the uploaded files with SSE-C, where the S3 server performs the actual encryption but the client provides the encryption key. This is more secure that plain SSE because with SSE-C the secret encryption key is not persisted on the server side, it only exists in memory during the request and will be discarded afterwards. Another advantage of SSE-C is that you can make a bucket public and control access via the encryption keys.
S3AM can also copy objects between buckets and within a bucket, and do so without actually transferring any data between client and server. It supports the use of separate SSE-C encryption keys for source and destination of the copy operation so it can be used to efficiently re-encrypt an object.
S3AM uses the PyCurl bindings for libcurl and Python’s multiprocessing module to work around lock contention in the Python interpreter and to avoid potential thread-safety issues with libcurl.
Prerequisites
Python 2.7.x, libcurl and pip.
Installation
sudo pip install git+https://github.com/BD2KGenomics/s3am.git
On OS X systems with a HomeBrew-ed Python, you should omit the sudo. You can find out if yo have a HomeBrew-ed Python by running which python. If that prints /usr/local/bin/python you are most likely using a HomeBrew-ed Python and you should omit sudo. If it prints /usr/bin/python you need to run pip with sudo.
Configuration
Obtain an access and secret key for AWS. Create ~/.boto with the following contents:
[Credentials] aws_access_key_id = PASTE YOUR ACCESS KEY ID HERE aws_secret_access_key = PASTE YOUR SECRET ACCESS KEY HERE
Usage
Run with --help to display usage information:
s3am --help
For example:
s3am upload \
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA12878/sequence_read/ERR001268.filt.fastq.gz \
bd2k-test-data
If an upload was interrupted you can resume it by rerunning the command with the --resume option. To cancel an unfinished upload, run s3am cancel. Note that unfinished multipart uploads incur storage fees.
Optimization
By default S3AM performs one download of a part and one upload of a part on each core but this is very conservative. Since S3AM is mostly IO-bound you should significantly oversubscribe cores, probably by at least 10. On a machine with 8 cores, for example, you should run S3AM with --download-slots 40 --upload-slots 40.
If you run this in EC2, you will likely have more bandwidth to S3 than from the source server. In this case it might help to have more download than upload slots.
The default part size of 5MB is also very conservative. If the source has a high latency, you will want to increase that as it might take a while for the TCP window to grow to an optimal size. If the source is ftp:// there will be several round trips before the actual transfer starts. In either case you should probably increase the part size to at least 50MB.
Caveats
S3AM doesn’t support non-US buckets yet. See #12
S3AM uses at 5M per process for a buffer that hold an upload part. There are as many processes as the sum of the number of download and upload slots, which defaults to twice the number of cores. The reason for the big buffer is that S3 doesn’t support chunked transfer coding and therefore must have the full part when starting the upload of each part. To be precise, it only needs to know its size and MD5. All but the last part have a know size but as S3AM is currently implemented it doesn’t know which part is the last part until it has fully downloaded it. If S3AM knew the size of the source file in advance, it could compute all of that. It could do a FTP ls or an HTTP HEAD request to determine that. But might still need to hack around in boto in order to work around the lack of chunked coding support in S3. Don’t know what to do about MD5 not being known.
S3AM does not implement back-to-back checksumming. An MD5 is computed for every part uploaded to S3 but there is no code in place to compare those with the source side. I think S3 exposes the MD5 of all part MD5’s concatenated. So if we could get libcurl and the sending server to support the Content-MD5 HTTP header we could use that. But that would not be as strong a guarantee as verifying the MD5 over the file in its entirety.
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