title: "Running a Crunch job on the command line"
...
-This tutorial introduces the concepts and use of the Crunch job system using the @arv@ command line tool and Arvados Workbench.
+This tutorial introduces how to run individual Crunch jobs using the @arv@ command line tool.
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
+{% include 'tutorial_expectations' %}
-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:
-* 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.
+You will create a job to run the "hash" Crunch script. The "hash" script computes the MD5 hash of each file in a collection.
h2. Jobs
-A "job" is a single run of a specific version of a crunch script with a specific input.
+Crunch pipelines consist of one or more jobs. A "job" is a single run of a specific version of a Crunch script with a specific input. You can also run jobs individually.
-A request to run a crunch job are is described using a JSON object. For example:
+A request to run a Crunch job are is described using a JSON object. For example:
<notextile>
-<pre><code>~$ <span class="userinput">cat >the_job <<EOF
+<pre><code>~$ <span class="userinput">cat >~/the_job <<EOF
{
"script": "hash",
- "script_version": "arvados:master",
- "script_parameters":
- {
+ "repository": "arvados",
+ "script_version": "master",
+ "script_parameters": {
"input": "c1bad4b39ca5a924e481008009d94e32+210"
- }
+ },
+ "no_reuse": "true"
}
EOF
</code></pre>
</notextile>
-* @cat@ is a standard Unix utility that simply copies standard input to standard output
-* @<<EOF@ tells the shell to direct the following lines into the standard input for @cat@ up until it sees the line @EOF@
-* @>the_job@ redirects standard output to a file called @the_job@
-* @"script"@ specifies the name of the script to run. The script is searched for in the "crunch_scripts/" subdirectory of the @git@ checkout specified by @"script_version"@.
-* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit @git@ revision hash, or in the form "repository:branch" (in which case it will take the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run. You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)→% Code repositories":http://{{site.arvados_workbench_host}}/repositiories .
-* @"script_parameters"@ are provided to the script. In this case, the input is the locator for the collection that we inspected in the previous section.
+* @cat@ is a standard Unix utility that writes a sequence of input to standard output.
+* @<<EOF@ tells the shell to direct the following lines into the standard input for @cat@ up until it sees the line @EOF@.
+* @>~/the_job@ redirects standard output to a file called @~/the_job@.
+* @"repository"@ is the name of a Git repository to search for the script version. You can access a list of available git repositories on the Arvados Workbench under "*Code repositories*":{{site.arvados_workbench_host}}/repositories.
+* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit Git revision hash, a tag, or a branch. Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run.
+* @"script"@ specifies the name of the script to run. The script must be given relative to the @crunch_scripts/@ subdirectory of the Git repository.
+* @"script_parameters"@ are provided to the script. In this case, the input is the PGP data Collection that we "put in Keep earlier":{{site.baseurl}}/user/tutorials/tutorial-keep.html.
+* Setting the @"no_reuse"@ flag tells Crunch not to reuse work from past jobs. This helps ensure that you can watch a new Job process for the rest of this tutorial, without reusing output from a past run that you made, or somebody else marked as public. (If you want to experiment, after the first run below finishes, feel free to edit this job to remove the @"no_reuse"@ line and resubmit it. See what happens!)
Use @arv job create@ to actually submit the job. It should print out a JSON object which describes the newly created job:
<notextile>
-<pre><code>~$ <span class="userinput">arv job create --job "$(cat the_job)"</span>
+<pre><code>~$ <span class="userinput">arv job create --job "$(cat ~/the_job)"</span>
{
"href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-1pm1t02dezhupss",
"kind":"arvados#job",
"is_locked_by_uuid":null,
"log":null,
"runtime_constraints":{},
- "tasks_summary":{},
- "dependencies":[
- "c1bad4b39ca5a924e481008009d94e32+210"
- ],
- "log_stream_href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-1pm1t02dezhupss/log_tail_follow"
+ "tasks_summary":{}
}
</code></pre>
</notextile>
The job is now queued and will start running as soon as it reaches the front of the queue. Fields to pay attention to include:
- * @"uuid"@ is the unique identifier for this specific job
+ * @"uuid"@ is the unique identifier for this specific job.
* @"script_version"@ is the actual revision of the script used. This is useful if the version was described using the "repository:branch" format.
h2. Monitor job progress
-Go to the "Workbench dashboard":http://{{site.arvados_workbench_host}}. Your job should be at the top of the "Recent jobs" table. This table refreshes automatically. When the job has completed successfully, it will show <span class="label label-success">finished</span> in the *Status* column.
-
-On the command line, you can access log messages while the job runs using @arv job log_tail_follow@:
-
-notextile. <pre><code>~$ <span class="userinput">arv job log_tail_follow --uuid qr1hi-8i9sb-xxxxxxxxxxxxxxx</span></code></pre>
-
-This will print out the last several lines of the log for that job.
+Go to "*Recent jobs*":{{site.arvados_workbench_host}}/jobs in Workbench. Your job should be near the top of the table. This table refreshes automatically. When the job has completed successfully, it will show <span class="label label-success">finished</span> in the *Status* column.
h2. Inspect the job output
-On the "Workbench dashboard":http://{{site.arvados_workbench_host}}, look for the *Output* column of the *Recent jobs* table. Click on the link under *Output* for your job to go to the files page with the job output. The files page lists all the files that were output by the job. Click on the link under the *files* column to view a file, or click on the download icon <span class="glyphicon glyphicon-download-alt"></span> to download the output file.
+On the "Workbench Dashboard":{{site.arvados_workbench_host}}, look for the *Output* column of the *Recent jobs* table. Click on the link under *Output* for your job to go to the files page with the job output. The files page lists all the files that were output by the job. Click on the link under the *file* column to view a file, or click on the download button <span class="glyphicon glyphicon-download-alt"></span> to download the output file.
On the command line, you can use @arv job get@ to access a JSON object describing the output:
"cancelled_by_user_uuid":null,
"started_at":"2013-12-16T20:44:36Z",
"finished_at":"2013-12-16T20:44:53Z",
- "output":"880b55fb4470b148a447ff38cacdd952+54",
+ "output":"dd755dbc8d49a67f4fe7dc843e4f10a6+54",
"success":true,
"running":false,
"is_locked_by_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
"running":0,
"failed":0,
"todo":0
- },
- "dependencies":[
- "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</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>dd755dbc8d49a67f4fe7dc843e4f10a6+54</code>.
Now you can list the files in the collection:
<notextile>
-<pre><code>~$ <span class="userinput">arv keep ls 880b55fb4470b148a447ff38cacdd952+54</span>
-md5sum.txt
+<pre><code>~$ <span class="userinput">arv keep ls dd755dbc8d49a67f4fe7dc843e4f10a6+54</span>
+./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:
<notextile>
-<pre><code>~$ <span class="userinput">arv keep get 880b55fb4470b148a447ff38cacdd952+54/md5sum.txt</span>
-44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
+<pre><code>~$ <span class="userinput">arv keep get dd755dbc8d49a67f4fe7dc843e4f10a6+54/md5sum.txt</span>
+44b8ae3fde7a8a88d2f7ebd237625b4f ./var-GS000016015-ASM.tsv.bz2
</code></pre>
</notextile>
-This md5 hash matches the md5 hash which we computed earlier.
+This MD5 hash matches the MD5 hash which we "computed earlier":{{site.baseurl}}/user/tutorials/tutorial-keep.html.
h2. The job log
-When the job completes, you can access the job log. On the workbench dashboard, this is the link under the *Log* column of the *Recent jobs* table.
+When the job completes, you can access the job log. On the Workbench, visit "*Recent jobs*":{{site.arvados_workbench_host}}/jobs %(rarr)→% your job's UUID under the *uuid* column %(rarr)→% the collection link on the *log* row.
-On the command line, the keep identifier listed in the @"log"@ field from @arv job get@ specifies a collection. You can list the files in the collection:
+On the command line, 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
+./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@:
+The log collection consists of one log file named with the job's UUID. 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
+2013-12-16_20:44:35 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 check slurm allocation
+2013-12-16_20:44:35 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 node compute13 - 8 slots
+2013-12-16_20:44:36 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 start
+2013-12-16_20:44:36 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 Install revision d9cd657b733d578ac0d2167dd75967aa4f22e0ac
+2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 Clean-work-dir exited 0
+2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 Install exited 0
+2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 script hash
+2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 script_version d9cd657b733d578ac0d2167dd75967aa4f22e0ac
+2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 script_parameters {"input":"c1bad4b39ca5a924e481008009d94e32+210"}
+2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 runtime_constraints {"max_tasks_per_node":0}
+2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 start level 0
+2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 status: 0 done, 0 running, 1 todo
+2013-12-16_20:44:38 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 0 job_task qr1hi-ot0gb-23c1k3kwrf8da62
+2013-12-16_20:44:38 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 0 child 7681 started on compute13.1
+2013-12-16_20:44:38 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 status: 0 done, 1 running, 0 todo
+2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 0 child 7681 on compute13.1 exit 0 signal 0 success=true
+2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 0 success in 1 seconds
+2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 0 output
+2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 wait for last 0 children to finish
+2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 status: 1 done, 0 running, 1 todo
+2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 start level 1
+2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 status: 1 done, 0 running, 1 todo
+2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 1 job_task qr1hi-ot0gb-iwr0o3unqothg28
+2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 1 child 7716 started on compute13.1
+2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 status: 1 done, 1 running, 0 todo
+2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 1 child 7716 on compute13.1 exit 0 signal 0 success=true
+2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 1 success in 13 seconds
+2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 1 output dd755dbc8d49a67f4fe7dc843e4f10a6+54
+2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 wait for last 0 children to finish
+2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 status: 2 done, 0 running, 0 todo
+2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 release job allocation
+2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 Freeze not implemented
+2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 collate
+2013-12-16_20:44:53 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 output dd755dbc8d49a67f4fe7dc843e4f10a6+54+K@qr1hi
+2013-12-16_20:44:53 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 finish
</code></pre>
</notextile>
-
-<hr>
-
-This concludes the first tutorial. In the next tutorial, we will "write a crunch job script.":tutorial-firstscript.html
projects / arvados.git / blobdiff