layout: default
navsection: userguide
navmenu: Tutorials
-title: "Writing a pipeline"
+title: "Writing a Crunch script"
...
-In this tutorial, we will write the "hash" script demonstrated in the first tutorial.
+This tutorial demonstrates how to write a script using Arvados Python SDK. The Arvados SDK supports access to advanced features not available using the @run-command@ wrapper, such as scheduling concurrent tasks across nodes.
-*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' %}
-This tutorial uses *@you@* to denote your username. Replace *@you@* with your user name in all the following examples.
+This tutorial uses @$USER@ to denote your username. Replace @$USER@ with your user name in all the following examples.
-h2. Setting up Git
-
-As discussed in the previous tutorial, all Crunch scripts are managed through the @git@ revision control system.
-
-First, you should do some basic configuration for git (you only need to do this the first time):
-
-<notextile>
-<pre><code>~$ <span class="userinput">git config --global user.name "Your Name"</span>
-~$ <span class="userinput">git config --global user.email <b>you</b>@example.com</span></code></pre>
-</notextile>
-
-On the Arvados Workbench, navigate to "Compute %(rarr)→% Code repositories":https://{{site.arvados_workbench_host}}/repositories . You should see a repository with your user name listed in the *name* column. Next to *name* is the column *push_url*. Copy the *push_url* value associated with your repository. This should look like <notextile><code>git@git.{{ site.arvados_api_host }}:<b>you</b>.git</code></notextile>.
-
-Next, on the Arvados virtual machine, clone your git repository:
-
-<notextile>
-<pre><code>~$ <span class="userinput">git clone git@git.{{ site.arvados_api_host }}:<b>you</b>.git</span>
-Cloning into '<b>you</b>'...</code></pre>
-</notextile>
-
-This will create an git checkout in the directory called *@you@*.
-
-{% include 'notebox_begin' %}
-For more information about using @git@, try
-
-notextile. <pre><code>$ <span class="userinput">man gittutorial</span></code></pre>
-
-or <b>"click here to search Google for git tutorials":http://google.com/#q=git+tutorial</b>
-{% include 'notebox_end' %}
-
-h2. Creating a Crunch script
-
-Start by entering the *@you@* directory created by @git clone@. Next create a subdirectory called @crunch_scripts@ and change to that directory:
+Start by creating a directory called @$USER@ . Next, create a subdirectory called @crunch_scripts@ and change to that directory:
<notextile>
-<pre><code>~$ <span class="userinput">cd <b>you</b></span>
-~/<b>you</b>$ <span class="userinput">mkdir crunch_scripts</span>
-~/<b>you</b>$ <span class="userinput">cd crunch_scripts</span></code></pre>
+<pre><code>~$ <span class="userinput">mkdir -p tutorial/crunch_scripts</span>
+~$ <span class="userinput">cd tutorial/crunch_scripts</span></code></pre>
</notextile>
Next, using @nano@ or your favorite Unix text editor, create a new file called @hash.py@ in the @crunch_scripts@ directory.
-notextile. <pre>~/<b>you</b>/crunch_scripts$ <code class="userinput">nano hash.py</code></pre>
+notextile. <pre>~/tutorial/crunch_scripts$ <code class="userinput">nano hash.py</code></pre>
-Add the following code to compute the md5 hash of each file in a collection:
+Add the following code to compute the MD5 hash of each file in a collection:
<notextile> {% code 'tutorial_hash_script_py' as python %} </notextile>
Make the file executable:
-notextile. <pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">chmod +x hash.py</span></code></pre>
+notextile. <pre><code>~/tutorial/crunch_scripts$ <span class="userinput">chmod +x hash.py</span></code></pre>
-{% include 'notebox_begin' %}
-The steps below describe how to execute the script after committing changes to git. To run a script locally for testing, please see "debugging a crunch script":{{site.baseurl}}/user/topics/tutorial-job-debug.html .
-
-{% include 'notebox_end' %}
-
-Next, add the file to @git@ staging. This tells @git@ that the file should be included on the next commit.
-
-notextile. <pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">git add hash.py</span></code></pre>
-
-Next, commit your changes to git. All staged changes are recorded into the local @git@ repository:
-
-<notextile>
-<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">git commit -m"my first script"</span>
-[master (root-commit) 27fd88b] my first script
- 1 file changed, 33 insertions(+)
- create mode 100755 crunch_scripts/hash.py</code></pre>
-</notextile>
-
-Finally, upload your changes to the Arvados server:
+Next, create a submission job record. This describes a specific invocation of your script:
<notextile>
-<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">git push origin master</span>
-Counting objects: 4, done.
-Compressing objects: 100% (2/2), done.
-Writing objects: 100% (4/4), 682 bytes, done.
-Total 4 (delta 0), reused 0 (delta 0)
-To git@git.qr1hi.arvadosapi.com:you.git
- * [new branch] master -> master</code></pre>
+<pre><code>~/tutorial/crunch_scripts$ <span class="userinput">cat >~/the_job <<EOF
+{
+ "repository":"",
+ "script":"hash.py",
+ "script_version":"$HOME/tutorial",
+ "script_parameters":{
+ "input":"c1bad4b39ca5a924e481008009d94e32+210"
+ }
+}
+EOF</span>
+</code></pre>
</notextile>
-h2. Create a pipeline template
-
-Next, create a file that contains the pipeline definition:
+You can now run your script on your local workstation or VM using @arv-crunch-job@:
<notextile>
-<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cd ~</span>
-~$ <span class="userinput">cat >the_pipeline <<EOF
-{
- "name":"My first pipeline",
- "components":{
- "do_hash":{
- "script":"hash.py",
- "script_parameters":{
- "input":{
- "required": true,
- "dataclass": "Collection"
- }
- },
- "repository":"<b>you</b>",
- "script_version":"master"
- }
- }
-}
-EOF
-</span></code></pre>
+<pre><code>~/tutorial/crunch_scripts</span>$ <span class="userinput">arv-crunch-job --job "$(cat ~/the_job)"</span>
+2014-08-06_15:16:22 qr1hi-8i9sb-qyrat80ef927lam 14473 check slurm allocation
+2014-08-06_15:16:22 qr1hi-8i9sb-qyrat80ef927lam 14473 node localhost - 1 slots
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473 start
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473 script hash.py
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473 script_version /home/peter/peter
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473 script_parameters {"input":"c1bad4b39ca5a924e481008009d94e32+210"}
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473 runtime_constraints {"max_tasks_per_node":0}
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473 start level 0
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473 status: 0 done, 0 running, 1 todo
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473 0 job_task qr1hi-ot0gb-lptn85mwkrn9pqo
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473 0 child 14478 started on localhost.1
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473 status: 0 done, 1 running, 0 todo
+2014-08-06_15:16:24 qr1hi-8i9sb-qyrat80ef927lam 14473 0 stderr crunchstat: Running [stdbuf --output=0 --error=0 /home/$USER/tutorial/crunch_scripts/hash.py]
+2014-08-06_15:16:24 qr1hi-8i9sb-qyrat80ef927lam 14473 0 child 14478 on localhost.1 exit 0 signal 0 success=true
+2014-08-06_15:16:24 qr1hi-8i9sb-qyrat80ef927lam 14473 0 success in 1 seconds
+2014-08-06_15:16:24 qr1hi-8i9sb-qyrat80ef927lam 14473 0 output
+2014-08-06_15:16:25 qr1hi-8i9sb-qyrat80ef927lam 14473 wait for last 0 children to finish
+2014-08-06_15:16:25 qr1hi-8i9sb-qyrat80ef927lam 14473 status: 1 done, 0 running, 1 todo
+2014-08-06_15:16:25 qr1hi-8i9sb-qyrat80ef927lam 14473 start level 1
+2014-08-06_15:16:25 qr1hi-8i9sb-qyrat80ef927lam 14473 status: 1 done, 0 running, 1 todo
+2014-08-06_15:16:25 qr1hi-8i9sb-qyrat80ef927lam 14473 1 job_task qr1hi-ot0gb-e3obm0lv6k6p56a
+2014-08-06_15:16:25 qr1hi-8i9sb-qyrat80ef927lam 14473 1 child 14504 started on localhost.1
+2014-08-06_15:16:25 qr1hi-8i9sb-qyrat80ef927lam 14473 status: 1 done, 1 running, 0 todo
+2014-08-06_15:16:26 qr1hi-8i9sb-qyrat80ef927lam 14473 1 stderr crunchstat: Running [stdbuf --output=0 --error=0 /home/$USER/tutorial/crunch_scripts/hash.py]
+2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 1 child 14504 on localhost.1 exit 0 signal 0 success=true
+2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 1 success in 10 seconds
+2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 1 output 50cafdb29cc21dd6eaec85ba9e0c6134+56+Aef0f991b80fa0b75f802e58e70b207aa184d24ff@53f4bbd3
+2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 wait for last 0 children to finish
+2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 status: 2 done, 0 running, 0 todo
+2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 Freeze not implemented
+2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 collate
+2014-08-06_15:16:36 qr1hi-8i9sb-qyrat80ef927lam 14473 output d6338df28d6b8e5d14929833b417e20e+107+Adf1ce81222b6992ce5d33d8bfb28a6b5a1497898@53f4bbd4
+2014-08-06_15:16:37 qr1hi-8i9sb-qyrat80ef927lam 14473 finish
+2014-08-06_15:16:38 qr1hi-8i9sb-qyrat80ef927lam 14473 log manifest is 7fe8cf1d45d438a3ca3ac4a184b7aff4+83
+</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_pipeline@ redirects standard output to a file called @the_pipeline@
-* @"name"@ is a human-readable name for the pipeline
-* @"components"@ is a set of scripts that make up the pipeline
-* The component is listed with a human-readable name (@"do_hash"@ in this example)
-* @"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"@.
-* @"repository"@ is the git repository to search for the script version. You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)→% Code repositories":https://{{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 (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.
-* @"script_parameters"@ describes the parameters for the script. In this example, there is one parameter called @input@ which is @required@ and is a @Collection@.
-
-Now, use @arv pipeline_template create@ tell Arvados about your pipeline template:
+Although the job runs locally, the output of the job has been saved to Keep, the Arvados file store. The "output" line (third from the bottom) provides the "Keep locator":{{site.baseurl}}/user/tutorials/tutorial-keep-get.html to which the script's output has been saved. Copy the output identifier and use @arv-ls@ to list the contents of your output collection, and @arv-get@ to download it to the current directory:
<notextile>
-<pre><code>~$ <span class="userinput">arv pipeline_template create --pipeline-template "$(cat the_pipeline)"</span>
+<pre><code>~/tutorial/crunch_scripts$ <span class="userinput">arv-ls d6338df28d6b8e5d14929833b417e20e+107+Adf1ce81222b6992ce5d33d8bfb28a6b5a1497898@53f4bbd4</span>
+./md5sum.txt
+~/tutorial/crunch_scripts$ <span class="userinput">arv-get d6338df28d6b8e5d14929833b417e20e+107+Adf1ce81222b6992ce5d33d8bfb28a6b5a1497898@53f4bbd4/ .</span>
+~/tutorial/crunch_scripts$ <span class="userinput">cat md5sum.txt</span>
+44b8ae3fde7a8a88d2f7ebd237625b4f c1bad4b39ca5a924e481008009d94e32+210/./var-GS000016015-ASM.tsv.bz2
</code></pre>
</notextile>
-Your new pipeline template will appear on the "Workbench %(rarr)→% Compute %(rarr)→% Pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_instances page. You can run the "pipeline using workbench":tutorial-pipeline-workbench.html
+Running locally is convenient for development and debugging, as it permits a fast iterative development cycle. Your job run is also recorded by Arvados, and will appear in the *Recent jobs and pipelines* panel on the "Workbench Dashboard":https://{{site.arvados_workbench_host}}. This provides limited provenance, by recording the input parameters, the execution log, and the output. However, running locally does not allow you to scale out to multiple nodes, and does not store the complete system snapshot required to achieve reproducibility; to do that you need to "submit a job to the Arvados cluster":{{site.baseurl}}/user/tutorials/tutorial-submit-job.html.
projects / arvados.git / blobdiff