+++ /dev/null
----
-layout: default
-navsection: userguide
-navmenu: Tutorials
-title: "Writing a Crunch script"
-...
-
-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 parallel tasks across nodes.
-
-{% include 'tutorial_expectations' %}
-
-This tutorial uses @$USER@ to denote your username. Replace @$USER@ with your user name in all the following examples.
-
-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">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>~/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:
-
-<notextile> {% code 'tutorial_hash_script_py' as python %} </notextile>
-
-Make the file executable:
-
-notextile. <pre><code>~/tutorial/crunch_scripts$ <span class="userinput">chmod +x hash.py</span></code></pre>
-
-Next, create a submission job record. This describes a specific invocation of your script:
-
-<notextile>
-<pre><code>~/tutorial/crunch_scripts$ <span class="userinput">cat >~/the_job <<EOF
-{
- "repository":"",
- "script":"hash.py",
- "script_version":"$HOME/tutorial",
- "script_parameters":{
- "input":"c1bad4b39ca5a924e481008009d94e32+210"
- }
-}
-EOF</span>
-</code></pre>
-</notextile>
-
-You can now run your script on your local workstation or VM using @arv-crunch-job@:
-
-<notextile>
-<pre><code>~/tutorial/crunch_scripts</span>$ <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/$USER/tutorial/crunch_scripts/hash.py]
-2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 1 child 14504 on localhost.1 exit 0 signal 0 success=true
-2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 1 success in 10 seconds
-2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 1 output 50cafdb29cc21dd6eaec85ba9e0c6134+56+Aef0f991b80fa0b75f802e58e70b207aa184d24ff@53f4bbd3
-2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 wait for last 0 children to finish
-2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 status: 2 done, 0 running, 0 todo
-2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 Freeze not implemented
-2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 collate
-2014-08-06_15:16:36 qr1hi-8i9sb-qyrat80ef927lam 14473 output d6338df28d6b8e5d14929833b417e20e+107+Adf1ce81222b6992ce5d33d8bfb28a6b5a1497898@53f4bbd4
-2014-08-06_15:16:37 qr1hi-8i9sb-qyrat80ef927lam 14473 finish
-2014-08-06_15:16:38 qr1hi-8i9sb-qyrat80ef927lam 14473 log manifest is 7fe8cf1d45d438a3ca3ac4a184b7aff4+83
-</code></pre>
-</notextile>
-
-Although the job runs locally, the output of the job has been saved to Keep, the Arvados file store. The "output" line (third from the bottom) provides the "Keep locator":/user/topics/tutorial-keep-get.html to which the script's output has been saved. Copy the output identifier and use @arv-ls@ to list the contents of your output collection, and @arv-get@ to download it to the current directory:
-
-<notextile>
-<pre><code>~/tutorial/crunch_scripts$ <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>
-
-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 show up 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 reproducibilty; to that you need to "submit a job to the Arvados cluster":/user/tutorials/tutorial-submit-job.html
projects / arvados.git / blobdiff