---
layout: default
navsection: userguide
+navmenu: Tutorials
title: "Running a Crunch job"
-navorder: 112
+navorder: 12
---
-h1. Tutorial: Running a crunch job
+h1. Running a crunch job
This tutorial introduces the concepts and use of the Crunch job system using the @arv@ command line tool and Arvados Workbench.
*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html*
-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:
+In "retrieving data using Keep,":tutorial-keep.html we downloaded a file from Keep and did some computation with it (specifically, computing the md5 hash of the complete file). While a straightforward way to accomplish a computational task, 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:
+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.
"script_version": "arvados:master",
"script_parameters":
{
- "input": "33a9f3842b01ea3fdf27cc582f5ea2af"
+ "input": "c1bad4b39ca5a924e481008009d94e32+210"
}
}
EOF
<notextile>
<pre><code>$ <span class="userinput">arv -h job create --job "$(cat the_job)"</span>
{
- "href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-xxxxxxxxxxxxxxx",
+ "href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-1pm1t02dezhupss",
"kind":"arvados#job",
- "etag":"aulvmdxezwxo4zrw15gz1v7x3",
- "uuid":"qr1hi-8i9sb-xxxxxxxxxxxxxxx",
+ "etag":"ax3cn7w9whq2hdh983yxvq09p",
+ "uuid":"qr1hi-8i9sb-1pm1t02dezhupss",
"owner_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
- "created_at":"2013-12-10T17:07:08Z",
+ "created_at":"2013-12-16T20:44:32Z",
"modified_by_client_uuid":"qr1hi-ozdt8-obw7foaks3qjyej",
"modified_by_user_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
- "modified_at":"2013-12-10T17:07:08Z",
- "updated_at":"2013-12-10T17:07:08Z",
+ "modified_at":"2013-12-16T20:44:32Z",
+ "updated_at":"2013-12-16T20:44:33Z",
"submit_id":null,
"priority":null,
"script":"hash",
"script_parameters":{
- "input":"33a9f3842b01ea3fdf27cc582f5ea2af"
+ "input":"c1bad4b39ca5a924e481008009d94e32+210"
},
- "script_version":"d3b10812b443dcf0189c1c432483bf7ac06507fe",
+ "script_version":"d9cd657b733d578ac0d2167dd75967aa4f22e0ac",
"cancelled_at":null,
"cancelled_by_client_uuid":null,
"cancelled_by_user_uuid":null,
"runtime_constraints":{},
"tasks_summary":{},
"dependencies":[
- "33a9f3842b01ea3fdf27cc582f5ea2af"
+ "c1bad4b39ca5a924e481008009d94e32+210"
],
- "log_stream_href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-xxxxxxxxxxxxxxx/log_tail_follow"
+ "log_stream_href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-1pm1t02dezhupss/log_tail_follow"
}
</code></pre>
</notextile>
* @"uuid"@ is the unique identifier for this specific job
* @"script_version"@ is the actual revision of the script used. This is useful if the version was described using the "repository:branch" format.
-h3. Monitor job progress
+h2. Monitor job progress
Go to Workbench, and use the menu to navigate to _Compute %(rarr)→% Jobs_. The job you submitted can be identified by the *uuid* row, which will match the "uuid" field of the JSON object returned when the job was created.
This will print out the last several lines of the log for that job.
-h3. Inspect the job output
+h2. Inspect the job output
You can access the job output under the *output* column of the _Compute %(rarr)→% Jobs_ page. Alternately, you can use @arv job get@ to access a JSON object describing the output:
<notextile>
<pre><code>$ <span class="userinput">arv -h job get --uuid qr1hi-8i9sb-xxxxxxxxxxxxxxx</span>
{
- "href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-zs6d9pxkr0vk175",
+ "href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-1pm1t02dezhupss",
"kind":"arvados#job",
- "etag":"eoe99lw7rnqxo7j29fh53hz",
- "uuid":"qr1hi-8i9sb-zs6d9pxkr0vk175",
+ "etag":"1bk98tdj0qipjy0rvrj03ta5r",
+ "uuid":"qr1hi-8i9sb-1pm1t02dezhupss",
"owner_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
- "created_at":"2013-12-10T17:23:26Z",
+ "created_at":"2013-12-16T20:44:32Z",
"modified_by_client_uuid":null,
"modified_by_user_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
- "modified_at":"2013-12-10T17:23:45Z",
- "updated_at":"2013-12-10T17:23:45Z",
+ "modified_at":"2013-12-16T20:44:55Z",
+ "updated_at":"2013-12-16T20:44:55Z",
"submit_id":null,
"priority":null,
"script":"hash",
"script_parameters":{
- "input":"33a9f3842b01ea3fdf27cc582f5ea2af"
+ "input":"c1bad4b39ca5a924e481008009d94e32+210"
},
- "script_version":"0a8c7c6fce7a9667ee42c1984a845100f51906a2",
+ "script_version":"d9cd657b733d578ac0d2167dd75967aa4f22e0ac",
"cancelled_at":null,
"cancelled_by_client_uuid":null,
"cancelled_by_user_uuid":null,
- "started_at":"2013-12-10T17:23:29Z",
- "finished_at":"2013-12-10T17:23:44Z",
- "output":"880b55fb4470b148a447ff38cacdd952+54+K@qr1hi",
+ "started_at":"2013-12-16T20:44:36Z",
+ "finished_at":"2013-12-16T20:44:53Z",
+ "output":"880b55fb4470b148a447ff38cacdd952+54",
"success":true,
"running":false,
"is_locked_by_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
- "log":"f760f3dd3105103e058a043310f7e72b+3028+K@qr1hi",
+ "log":"2afdc6c8b67372ffd22d8ce89d35411f+91",
"runtime_constraints":{},
"tasks_summary":{
"done":2,
"todo":0
},
"dependencies":[
- "33a9f3842b01ea3fdf27cc582f5ea2af"
+ "c1bad4b39ca5a924e481008009d94e32+210"
],
"log_stream_href":null
}
</code></pre>
</notextile>
-* @"output"@ is the unique identifier for this specific job's output. This is a Keep collection. Because the output of Arvados jobs should be deterministic, the known expected output is <code>880b55fb4470b148a447ff38cacdd952+54+K@qr1hi</code>.
+* @"output"@ is the unique identifier for this specific job's output. This is a Keep collection. Because the output of Arvados jobs should be deterministic, the known expected output is <code>880b55fb4470b148a447ff38cacdd952+54</code>.
Now you can list the files in the collection:
<notextile>
-<pre><code>$ <span class="userinput">arv keep get 880b55fb4470b148a447ff38cacdd952+54+K@qr1hi</span>
+<pre><code>$ <span class="userinput">arv keep get 880b55fb4470b148a447ff38cacdd952+54</span>
. 78b268d1e03d87f8270bdee9d5d427c5+61 0:61:md5sum.txt
</code></pre>
</notextile>
-This collection consists of the md5sum.txt file. Use @arv keep get@ to show the contents of the md5sum.txt file:
+This collection consists of the @md5sum.txt@ file. Use @arv keep get@ to show the contents of the @md5sum.txt@ file:
<notextile>
-<pre><code>$ <span class="userinput">arv keep get 880b55fb4470b148a447ff38cacdd952+54+K@qr1hi/md5sum.txt</span>
+<pre><code>$ <span class="userinput">arv keep get 880b55fb4470b148a447ff38cacdd952+54/md5sum.txt</span>
44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
</code></pre>
</notextile>
This md5 hash matches the md5 hash which we computed earlier.
+h2. The job log
+
+When the job completes, you can access the job log. The keep identifier listed in the @"log"@ field from @arv job get@ specifies a collection. You can list the files in the collection:
+
+<notextile>
+<pre><code>$ <span class="userinput">arv keep ls xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx+91</span>
+qr1hi-8i9sb-xxxxxxxxxxxxxxx.log.txt
+</code></pre>
+</notextile>
+
+The log collection consists of one log file named with the job id. You can access it using @arv keep get@:
+
+<notextile>
+<pre><code>$ <span class="userinput">arv keep get xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx+91/qr1hi-8i9sb-xxxxxxxxxxxxxxx.log.txt</span>
+2013-12-16_20:44:35 qr1hi-8i9sb-1pm1t02dezhupss 7575 check slurm allocation
+2013-12-16_20:44:35 qr1hi-8i9sb-1pm1t02dezhupss 7575 node compute13 - 8 slots
+2013-12-16_20:44:36 qr1hi-8i9sb-1pm1t02dezhupss 7575 start
+2013-12-16_20:44:36 qr1hi-8i9sb-1pm1t02dezhupss 7575 Install revision d9cd657b733d578ac0d2167dd75967aa4f22e0ac
+2013-12-16_20:44:37 qr1hi-8i9sb-1pm1t02dezhupss 7575 Clean-work-dir exited 0
+2013-12-16_20:44:37 qr1hi-8i9sb-1pm1t02dezhupss 7575 Install exited 0
+2013-12-16_20:44:37 qr1hi-8i9sb-1pm1t02dezhupss 7575 script hash
+2013-12-16_20:44:37 qr1hi-8i9sb-1pm1t02dezhupss 7575 script_version d9cd657b733d578ac0d2167dd75967aa4f22e0ac
+2013-12-16_20:44:37 qr1hi-8i9sb-1pm1t02dezhupss 7575 script_parameters {"input":"c1bad4b39ca5a924e481008009d94e32+210"}
+2013-12-16_20:44:37 qr1hi-8i9sb-1pm1t02dezhupss 7575 runtime_constraints {"max_tasks_per_node":0}
+2013-12-16_20:44:37 qr1hi-8i9sb-1pm1t02dezhupss 7575 start level 0
+2013-12-16_20:44:37 qr1hi-8i9sb-1pm1t02dezhupss 7575 status: 0 done, 0 running, 1 todo
+2013-12-16_20:44:38 qr1hi-8i9sb-1pm1t02dezhupss 7575 0 job_task qr1hi-ot0gb-23c1k3kwrf8da62
+2013-12-16_20:44:38 qr1hi-8i9sb-1pm1t02dezhupss 7575 0 child 7681 started on compute13.1
+
+2013-12-16_20:44:38 qr1hi-8i9sb-1pm1t02dezhupss 7575 status: 0 done, 1 running, 0 todo
+2013-12-16_20:44:39 qr1hi-8i9sb-1pm1t02dezhupss 7575 0 child 7681 on compute13.1 exit 0 signal 0 success=true
+2013-12-16_20:44:39 qr1hi-8i9sb-1pm1t02dezhupss 7575 0 success in 1 seconds
+2013-12-16_20:44:39 qr1hi-8i9sb-1pm1t02dezhupss 7575 0 output
+2013-12-16_20:44:39 qr1hi-8i9sb-1pm1t02dezhupss 7575 wait for last 0 children to finish
+2013-12-16_20:44:39 qr1hi-8i9sb-1pm1t02dezhupss 7575 status: 1 done, 0 running, 1 todo
+2013-12-16_20:44:39 qr1hi-8i9sb-1pm1t02dezhupss 7575 start level 1
+2013-12-16_20:44:39 qr1hi-8i9sb-1pm1t02dezhupss 7575 status: 1 done, 0 running, 1 todo
+2013-12-16_20:44:39 qr1hi-8i9sb-1pm1t02dezhupss 7575 1 job_task qr1hi-ot0gb-iwr0o3unqothg28
+2013-12-16_20:44:39 qr1hi-8i9sb-1pm1t02dezhupss 7575 1 child 7716 started on compute13.1
+2013-12-16_20:44:39 qr1hi-8i9sb-1pm1t02dezhupss 7575 status: 1 done, 1 running, 0 todo
+2013-12-16_20:44:52 qr1hi-8i9sb-1pm1t02dezhupss 7575 1 child 7716 on compute13.1 exit 0 signal 0 success=true
+2013-12-16_20:44:52 qr1hi-8i9sb-1pm1t02dezhupss 7575 1 success in 13 seconds
+2013-12-16_20:44:52 qr1hi-8i9sb-1pm1t02dezhupss 7575 1 output 880b55fb4470b148a447ff38cacdd952+54
+2013-12-16_20:44:52 qr1hi-8i9sb-1pm1t02dezhupss 7575 wait for last 0 children to finish
+2013-12-16_20:44:52 qr1hi-8i9sb-1pm1t02dezhupss 7575 status: 2 done, 0 running, 0 todo
+2013-12-16_20:44:52 qr1hi-8i9sb-1pm1t02dezhupss 7575 release job allocation
+2013-12-16_20:44:52 qr1hi-8i9sb-1pm1t02dezhupss 7575 Freeze not implemented
+2013-12-16_20:44:52 qr1hi-8i9sb-1pm1t02dezhupss 7575 collate
+2013-12-16_20:44:53 qr1hi-8i9sb-1pm1t02dezhupss 7575 output 880b55fb4470b148a447ff38cacdd952+54
+2013-12-16_20:44:53 qr1hi-8i9sb-1pm1t02dezhupss 7575 finish
+</code></pre>
+</notextile>
+
This concludes the first tutorial. In the next tutorial, we will "write a script to compute the hash.":tutorial-firstscript.html
projects / arvados.git / blobdiff