---
layout: default
navsection: userguide
title: "Tutorial: Introduction to Keep and your first Crunch job"
navorder: 11
---
h1. Tutorial: Introduction to Keep and your first crunch job
This tutorial introduces the concepts and use of the Arvados Keep storage and Crunch job system using the @arv@ command line tool and Arvados Workbench.
*This tutorial assumes that you are logged into an Arvados VM instance, as described in "accessing arvados over ssh.":ssh-access.html#login*
h2. Checking your environment
Check that you are able to access the Arvados API server using the following command:
bc. $ arv user current
If you receive the message @ARVADOS_API_HOST and ARVADOS_API_TOKEN need to be defined as environment variables@, follow the instructions for "getting an API token,":api-tokens.html then return to this document.
When @arv user current@ is able to access the API server, it will print out the unique identifier associated with your account. Here is an example (you will receive a different identifier):
bc. qr1hi-xioed-9z2p3pn12yqdaem
This unique identifier represents your identity in the Arvados system and is similar to the concept of a pointer or a foreign key. You may de-reference (get the contents of) any identifier returned by the "arv" command using the @-h@ command line option. For example:
bc. $ arv -h user current
{
"href":"https://qr1hi.arvadosapi.com/arvados/v1/users/qr1hi-xioed-9z2p3pn12yqdaem",
"kind":"arvados#user",
"etag":"8u0xwb9f3otb2xx9hto4wyo03",
"uuid":"qr1hi-tpzed-92d3kxnimy3d4e8",
"owner_uuid":"qr1hi-tpqed-23iddeohxta2r59",
"created_at":"2013-12-02T17:05:47Z",
"modified_by_client_uuid":"qr1hi-xxfg8-owxa2oa2s33jyej",
"modified_by_user_uuid":"qr1hi-tpqed-23iddeohxta2r59",
"modified_at":"2013-12-02T17:07:08Z",
"updated_at":"2013-12-05T19:51:08Z",
"email":"you@example.com",
"full_name":"Example User",
"first_name":"Example",
"last_name":"User",
"identity_url":"https://www.google.com/accounts/o8/id?id=AItOawnhlZr-pQ_Ic2f2W22XaO02oL3avJ322k1",
"is_active": true,
"is_admin": false,
"prefs":{}
}
h2. Managing data in Arvados using Keep
The Arvados distributed file system is called *Keep*. Keep is a content-addressable file system. This means that files are managed using special unique identifiers derived from the _contents_ of the file, rather than human-assigned file names (specifically, the md5 hash). This has a number of advantages:
* Files can be stored and replicated across a cluster of servers without requiring a central name server.
* Systematic validation of data integrity by both server and client because the checksum is built into the identifier.
* Minimizes data duplication (two files with the same contents will result in the same identifier, and will not be stored twice.)
* Avoids data race conditions (an identifier always points to the same data.)
In Keep, information is stored in *data blocks*. Data blocks are normally between 1 byte and 64 megabytes in size. If a file exceeds the maximum size of a single data block, the file will be split across multiple data blocks until the entire file can be stored. These data blocks may be stored and replicated across multiple disks, servers, or clusters. Each data block has its own identifier for the contents of that specific data block.
In order to reassemble the file, Keep stores a *collection* data block which lists in sequence the data blocks that make up the original file. A collection data block may store the information for multiple files, including a directory structure.
In this example we will use @33a9f3842b01ea3fdf27cc582f5ea2af@ which is already available on {{ site.arvados_api_host }}. First let us examine the contents of this collection using @arv keep get@:
bc. $ arv keep get 33a9f3842b01ea3fdf27cc582f5ea2af
. 204e43b8a1185621ca55a94839582e6f+67108864+K@qr1hi b9677abbac956bd3e86b1deb28dfac03+67108864+K@qr1hi fc15aff2a762b13f521baf042140acec+67108864+K@qr1hi 323d2a3ce20370c4ca1d3462a344f8fd+25885655+K@qr1hi 0:227212247:var-GS000016015-ASM.tsv.bz2
@arv keep get@ fetches the contents of the locator @33a9f3842b01ea3fdf27cc582f5ea2af@. This is a locator for a collection data block, so it fetches the contents of the collection. In this example, this collection consists of a single file @var-GS000016015-ASM.tsv.bz2@ which is 227212247 bytes long, and is stored using four sequential data blocks, 204e43b8a1185621ca55a94839582e6f+67108864+K@qr1hi, b9677abbac956bd3e86b1deb28dfac03+67108864+K@qr1hi, fc15aff2a762b13f521baf042140acec+67108864+K@qr1hi, 323d2a3ce20370c4ca1d3462a344f8fd+25885655+K@qr1hi.
Let's use @arv keep get@ to download the first datablock:
bc. $ arv keep get 204e43b8a1185621ca55a94839582e6f+67108864+K@qr1hi > block1
Let's look at the size and compute the md5 hash of @block1@:
bc. $ ls -l block1
-rw-r--r-- 1 you group 67108864 Dec 9 20:14 block1
$ md5sum block1
204e43b8a1185621ca55a94839582e6f block1
Notice that the block identifer 204e43b8a1185621ca55a94839582e6f+67108864+K@qr1hi consists of:
* the md5 hash @204e43b8a1185621ca55a94839582e6f@
* a size hint @67108864@
* a location hint K@qr1hi
In fact, _only_ the md5 hash is required to find the block.
Next, let's use @arv keep get@ to download and reassemble @var-GS000016015-ASM.tsv.bz2@ using the following command:
bc. $ arv keep get 33a9f3842b01ea3fdf27cc582f5ea2af/var-GS000016015-ASM.tsv.bz2 .
This downloads the file @var-GS000016015-ASM.tsv.bz2@ described by collection @33a9f3842b01ea3fdf27cc582f5ea2af@ from Keep and places it into the local directory. Now that we have the file, we can compute the md5 hash of the complete file:
bc. $ md5sum var-GS000016015-ASM.tsv.bz2
44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
h2. Submitting your first job
In the previous section, we downloaded a file from Keep and computed the md5 hash of the complete file. While straightforward, there are several obvious drawbacks to this approach:
* Large files require significant time to download.
* Very large files may exceed the scratch space of the local disk.
* We are only able to use the local CPU to process the file.
The Arvados "crunch" framework is designed to support processing very large data batches (gigabytes to terabytes) efficiently, and provides the following benefits:
* Increase concurrency by running tasks asynchronously, using many CPUs and network interfaces at once (especially beneficial for CPU-bound and I/O-bound tasks respectively).
* Track inputs, outputs, and settings so you can verify that the inputs, settings, and sequence of programs you used to arrive at an output is really what you think it was.
* Ensure that your programs and workflows are repeatable with different versions of your code, OS updates, etc.
* Interrupt and resume long-running jobs consisting of many short tasks.
* Maintain timing statistics automatically, so they're there when you want them.
For your first job, you will run the "hash" crunch script using the Arvados system. The "hash" script computes the md5 hash of each file in a collection.
Crunch jobs are described using JSON objects. For example:
bc. $ read -d $'\000' the_job <