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        "author": "Hannes Schmidt",
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        "description": "S3AM, pronounced ``\\\u02c8skr\u0113m\\``, is a fast, parallel, streaming transfer utility\nfor S3. Objects in S3 can be streamed from any URL for which the locally\ninstalled libcurl and the remote server support byte range requests, for\nexample ``file://``, ``ftp://`` (many servers) and ``http://`` (some servers).\nAdditionally, objects in S3 can be downloaded to the local file system. Both\nuploads and downloads can be resumed after interruptions.\n\nS3AM is intended to be used with large files, has been tested with 300GB files\nbut imposes no inherent limit on the maximum file size. While it can be used to\ntransfer small files, you may find that it performs worse than other utilities\nif the file size is below, say, 5MB.\n\nS3AM supports encrypting the uploaded files with SSE-C.\n\nS3AM can also copy objects between buckets and within a bucket, and do so\nwithout actually transferring any data between client and server. It supports\nthe use of separate SSE-C encryption keys for source and destination of the\ncopy operation so it can be used to efficiently re-encrypt an object.\n\nS3AM uses the PyCurl bindings for libcurl and Python's multiprocessing module\nto work around lock contention in the Python interpreter and to avoid potential\nthread-safety issues with libcurl.\n\n\nPrerequisites\n=============\n\nPython 2.7.x, libcurl and pip.\n\nOn Ubuntu the dependencies can be installed with\n\n::\n\n   sudo apt-get install python-dev gcc make libcurl4-openssl-dev libssl-dev\n\n\nInstallation\n============\n\nIt is recommended that you install S3AM into a virtualenv::\n\n   virtualenv ~/s3am && source ~/s3am/bin/activate\n   pip install s3am\n\nIf you would like to install the latest unstable release, you may want to run\n``pip install --pre s3am`` instead.\n\nIf you get ``libcurl link-time ssl backend (nss) is different from compile-time\nssl backend`` the required fix is to prefix the pip installation command with\n``PYCURL_SSL_LIBRARY=nss``, for example ``PYCURL_SSL_LIBRARY=nss pip install\n--pre s3am``.\n\nOptionally, add a symbolic link to the ``s3am`` command such that you don't\nneed to activate the virtualenv before using it::\n\n   mkdir -p ~/bin\n   ln -s ~/s3am/bin/s3am ~/bin\n\nThen append ``~/bin`` to your ``PATH`` environment variable. I would tell you\nexplicitly how to modify ``PATH`` but unfortunately this depends on various\nfactors, e.g. which shell you are using and which operating system. On OS X,\nfor example, you need to edit ``~/.profile`` and append\n\n::\n\n   export PATH=\"$HOME/bin:$PATH\"\n\n\nConfiguration\n=============\n\nObtain an access and secret key for AWS. Create ``~/.aws/credentials`` with the\nfollowing contents::\n\n    [default]\n    aws_access_key_id=PASTE_YOUR_FOO_ACCESS_KEY_ID_HERE\n    aws_secret_access_key=PASTE_YOUR_FOO_SECRET_KEY_ID_HERE\n\nMultiple profiles with credentials for different AWS accounts can coexist in\n``~/.aws/credentials``::\n\n    [foo]\n    aws_access_key_id=PASTE_YOUR_FOO_ACCESS_KEY_ID_HERE\n    aws_secret_access_key=PASTE_YOUR_FOO_SECRET_KEY_ID_HERE\n\n    [bar]\n    aws_access_key_id=PASTE_YOUR_BAR_ACCESS_KEY_ID_HERE\n    aws_secret_access_key=PASTE_YOUR_BAR_SECRET_KEY_ID_HERE\n\nIf you specify multiple profiles in ``~/.aws/credentials`` you can choose an\nactive profile by setting the ``AWS_PROFILE`` environment variable::\n\n    export AWS_PROFILE=foo\n\n.. _access key: http://docs.aws.amazon.com/AWSSimpleQueueService/latest/SQSGettingStartedGuide/AWSCredentials.html\n\n\nUsage\n=====\n\nRun with ``--help`` to display usage information::\n\n   s3am --help\n\nTo upload a file from an FTP server to S3::\n\n   s3am upload \\\n        ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA12878/sequence_read/ERR001268.filt.fastq.gz \\\n        s3://foo-bucket/\n\nCopy the resulting object to another bucket::\n\n   s3am upload \\\n        s3://foo-bucket/ERR001268.filt.fastq.gz \\\n        s3://other-bucket/\n\nDownload the copy to the local file system::\n\n   s3am download \\\n        s3://other-bucket/ERR001268.filt.fastq.gz \\\n        ./\n\nNote how all of the above examples omit the file name from the destination. If\nthe destination ends in a / character, the last path component (aka the 'file\nname') of the source URL will be appended.\n\nIf an upload was interrupted, it can be resumed by running the command again\nwith the ``--resume`` option. To cancel an unfinished upload, run ``s3am\ncancel``. Be aware that incomplete multipart uploads do incur storage fees.\n\n\nTroubleshooting\n===============\n\nIf you get ``error: [Errno 104] Connection reset by peer`` you may be running\nS3AM with too many upload slots or with too low a part size. Note that by\ndefault, S3AM uses a conservatively small part size but allocates one upload\nslot per core. For example, running s3am on a 32-core EC2 instance and using\nthe default part size of 5 MiB can result in more than 100 requests per second,\nwhich will trigger a request rate limiter on the S3 side that could lead to\nthis particular error. Consider passing either ``--part-size=256MB`` or\n``--upload-slots=8``. The former is recommended as the latter will negatively\nimpact your throughput.\n\n\nOptimization\n============\n\nBy default S3AM concurrently transfers one part per core. This is a very\nconservative setting. Since S3AM is mostly IO-bound you should significantly\noversubscribe cores, probably by a factor of at least 10. On a machine with 8\ncores, for example, you should run S3AM with ``--download-slots 40\n--upload-slots 40``.\n\nIf you run S3AM on EC2, you will likely have more bandwidth to S3 than from the\nsource server. In this case it might help to have more download than upload\nslots.\n\nThe default part size of 5MB is also very conservative. If the source has a\nhigh latency, you will want to increase that as it might take a while for the\nTCP window to grow to an optimal size. If the source is ``ftp://`` there will\nbe significantly more round-trips before the actual transfer starts than with\n``http://`` or ``http://``. In either case you should probably increase the\npart size to at least 50MB.\n\n\nBuilding\n========\n\nClone the repository, create a virtualenv, activate it and run `make develop`::\n\n    git clone https://github.com/BD2KGenomics/s3am.git\n    cd s3am\n    virtualenv venv\n    venv/bin/activate\n    make develop\n\n\nEncryption\n==========\n\nWith SSE-C, the S3 server performs the actual encryption but the client\nprovides the encryption key. This is more secure than plain SSE because with\nSSE-C the secret encryption key is not persisted on the server, it only exists\nthere in memory for the duration of a request and is discarded afterwards.\nSSE-C also lets you make a bucket public and control access via the\ndistribution of encryption keys.\n\n\nScripting\n=========\n\nYou can enable resumption and keep trying a few times::\n\n    for i in 1 2 3; do s3am upload --resume $src $dst && break; done\n    s3am cancel $dst\n\nThere are situations after which resumption is futile and care must be taken\nnot to get into an infinite loop that would likely cost an infinite amount of\nmoney. S3AM exits with status code 2 on obvious user errors but there may be\nother failures like auth problems where user intervention is required. There is\nno reliable way to classify errors into resumable and non-resumable ones so\nS3AM doesn't even try. Running ``s3am cancel`` is a best effort to avoid\nleaving unfinished uploads. If ``s3am upload`` was successful for a given\nobject, running ``s3am cancel`` on that object does nothing.\n\nAlternatively, you can force S3AM to eradicate previous, unsuccessful attempts,\ncreating a clean slate and preventing them from corrupting the current attempt.\nThis comes at the expense of wasting resources by discarding the progress made\nin those previous attempts::\n\n   for i in 1 2 3; s3am upload --force $src $dst && break; done\n   s3am cancel $dst\n   \nThe --force and --resume options are mutually exclusive, but both provide a\ncertain degree of idempotence. While ``--resume`` refuses to function if it\ndetects *multiple* unfinished uploads for a given S3 object, ``--force`` is not\nso easily dissuaded. Hence the name.\n\nIn a Toil script I would either use the ``--resume`` option with a hand-coded\nloop or the ``--force`` option while relying on Toil's built-in job retry\nmechanism.\n\n\nCaveats\n=======\n\nS3AM doesn't support non-US buckets yet. See issue #12.\n\nS3AM uses a buffer per upload and download slot. The buffer will hold an entire\npart. This means that the lower bound of S3AM's memory footprint is\n(download_slots + upload_slots) * part_size. The buffer is needed because S3\ndoesn't support chunked transfer coding.\n\nS3AM does not implement back-to-back checksumming. An MD5 is computed for every\npart uploaded to S3 but there is no code in place to compare the MD5 with the\nsource side. I think S3 exposes the MD5 of all part MD5's concatenated. So if\nwe could get libcurl and the sending server to support the Content-MD5 HTTP\nheader we could use that. But that would not be as strong a guarantee as\nverifying the MD5 over the file in its entirety.\n",
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