Amazon Simple Storage Service (S3) is a cloud storage service with some very interesting characteristics for storing
large amounts of data. It has virtually infinite scalability both in terms of storage space and transfer speed.
Bioinformatics pipelines running on EC2 compute instances need fast access to the data stored in S3 but existing tools*
for S3 data transfer do not use the full potential S3 has to offer. (*Evaluated tools were s3cmd and boto (original
and modified versions, Mar 2013))
BiBiS3 is a command line tool that attempts to close this gap by pushing the transfer speeds both from and to S3 to the limits of the underlying hardware. Additionally BiBiS3 in itself is as scalable as Amazon's S3 as it is capable of downloading different chunks of the same data to an arbitrary number of machines simultaneously. The key to maximum speed using S3 is massive, data-agnostic parallelization.
The targets can either be a single machine, a shared Network File System (NFS) between multiple nodes or the filesystems of all the nodes. Directories can be copied recursively while BiBiS3 maintains a stable count of parallel transfer threads regardless of the directory structure.
In another scenario where the parts of a single file are to be evenly distributed across multiple machines, BiBiS3 is performing a split of the data. In case of the FASTQ file format this split is even content-aware and preserves all FASTQ entries. A distributed download can be invoked e.g. via the Oracle Grid Engine (OGE) which is part of BiBiGrid.
Features
- Parallel transfer of multiple chunks of data.
- Recursive transfer of directories with parallelization of multiple files.
- Simultaneous download via a cluster to e.g. a shared NFS where each node only downloads a portion of the data.
Performance On a single AWS instance we have seen download speeds of over to 300 MByte/sec from S3. Using the distributed cluster download mode BiBiS3 downloads show an aggregate throughput of more than 22 GByte/sec on 80 c3.8xlarge instances.
Requirements: Java >= 8, Maven >= 3.3.9
> git clone https://github.com/BiBiServ/bibis3.git
> cd bibis3
> mvn clean packageCredentials File
To get access to buckets that need proper authentication, create a .properties file called
.aws-credentials.properties in your user home directory with the following content:
accessKey=XXXXXXXXXXXXXXXX # your AWS access key
secretKey=XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX # your AWS secret key
Please note: The Access Key and Secret Key are very sensitive information! Please make sure that the configuration file can only be read by you! E.g. use the following command: chmod 600 ~/.aws-credentials.properties
Alternatively the credentials can also be supplied via command-line parameters.
The basic commands follow the behavior of the Unix command cp as closely as possible.
usage: java -jar bibis3-1.7.0.jar -u|d|g|c SRC DEST
--access-key <arg> AWS Access Key.
-c,--clean-up-parts Clean up all unfinished parts of
previous multipart uploads that were
initiated on the specified bucket over
a week ago. BUCKET has to be an S3
URL.
--chunk-size <arg> Multipart chunk size in Bytes.
--create-bucket Create bucket if nonexistent.
-d,--download Download files. SRC has to be an S3
URL.
--debug Debug mode.
--endpoint <arg> Endpoint for client authentication
(default: standard AWS endpoint).
-g,--download-url Download a file with Http GET from
(pre-signed) S3-Http-Url. SRC has to
be an Http-URL with Range support for
Http GET.
--grid-current-node <arg> Identifier of the node that is running
this program (must be 1 >= i <=
grid-nodes.
--grid-download Download only a subset of all chunks.
This is useful for downloading e. g.
to a shared filesystem via different
machines simultaneously.
--grid-download-feature-fastq Download separate parts of a fastq
file to different nodes into different
files and make sure the file splits
conserve the fastq file format.
--grid-download-feature-split Download separate parts of a single
file to different nodes into different
files all with the same name.
(--grid-download required)
--grid-nodes <arg> Number of grid nodes.
-h,--help Help.
-m,--metadata <key> <value> Adds metadata to all uploads. Can be
specified multiple times for
additional metadata.
-q,--quiet Disable all log messages.
-r,--recursive Enable recursive transfer of a
directory.
--reduced-redundancy Set the storage class for uploads to
Reduced Redundancy instead of
Standard.
--region <arg> S3 region. For AWS has to be one of:
ap-south-1, eu-west-3, eu-west-2,
eu-west-1, ap-northeast-2,
ap-northeast-1, ca-central-1,
sa-east-1, cn-north-1, us-gov-west-1,
ap-southeast-1, ap-southeast-2,
eu-central-1, us-east-1, us-east-2,
us-west-1, cn-northwest-1, us-west-2
(default: us-east-1).
--secret-key <arg> AWS Secret Key.
--session-token <arg> AWS Session Token.
--streaming-download Run single threaded download and send
special progress info to STDOUT.
-t,--threads <arg> Number of parallel threads to use
(default: 50).
--trace Extended debug mode.
-u,--upload Upload files. DEST has to be an S3
URL.
--upload-list-stdin Take list of files to upload from
STDIN. In this case the SRC argument
has to be omitted.
-v,--version Version.
S3 URLs have to be in the form of: 's3://<bucket>/<key>', e.g.
's3://mybucket/mydatafolder/data.txt'. When using recursive transfer (-r)
the trailing slash of the directory is mandatory, e.g.
's3://mybucket/mydatafolder/'.Upload of a single file from the local directory to S3:
java -jar bibis3.jar -u myfile.tgz s3://mybucket/somedir/Download of a single file from S3 to the current directory:
java -jar bibis3.jar -d s3://mybucket/somedir/myfile.tgz .Download of a directory from S3 to a local directory called 'mydir' using 20 threads:
java -jar bibis3.jar -t 20 -r -d s3://mybucket/somedir/ mydirAttention should be paid to the trailing slash of the S3 URL which in addition to the -r option is required
for the recursive transfer of a directory.
Example shell script for the simultaneous download of all the contents of an S3 directory via a cluster:
simultaneous-download.sh:
#!/bin/bash
java -jar bibis3.jar \
--access-key "XXXXXXX" \
--secret-key "XXXXXXXXXXXX" \
--region eu-west-1 \
--grid-download \
--grid-nodes "$1" \
--grid-current-node "$SGE_TASK_ID" \
-d s3://mybucket/mydir/ targetdirwhich could be run within an SGE/OGE with 5 nodes (4 cores each) as follows:
qsub -pe multislot 4 -t 1-5 simultaneous-download.sh 5The parameter -pe multislot 4 ensures that the array job ist equally distributed among the nodes (leading to only
one task per node).
The targetdir is usually located inside a shared filesystem (e.g. NFS). However, if --grid-download-feature-split
is enabled, then the targetdir has to be local for each node.
Grid Download Feature Flags can be used in addition to --grid-download. When supplying one of these flags, the
file parts are saved to different files on different machines. Additionally these flags can be used to force a specific
split position for individual file types. Grid Download Feature Flags cannot be combined. Only the last one
supplied will be in effect.
Split:
--grid-download-feature-split
Splits arbitrarily.
FASTQ:
--grid-download-feature-fastq
Preserves FASTQ entries as well as paired-ends/mate-pairs for files using Illumina sequence identifiers.
The Amazon S3 documentation says:
"Once you initiate a multipart upload, Amazon S3 retains all the parts until you either complete or abort the upload. Throughout its lifetime, you are billed for all storage, bandwidth, and requests for this multipart upload and its associated parts."
When an upload encounters a fatal error, the upload gets neither completed nor aborted. Already uploaded multipart chunks remain in S3 but are invisible to the user. Therefore, it is recommended to clean up interrupted multipart uploads periodically.
Clean up the remainings of interrupted multipart uploads for the bucket 'mybucket' that were initiated more than 7 days ago:
java -jar bibis3.jar -c s3://mybucket/
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