Merge remote-tracking branch 'origin/master' into 1971-show-image-thumbnails

[arvados.git] / doc / user / topics / tutorial-job-debug.html.textile.liquid

diff --git a/doc/user/topics/tutorial-job-debug.html.textile.liquid b/doc/user/topics/tutorial-job-debug.html.textile.liquid
index 0974e51697031449259f89221e4a0dc18e81658c..8d470da140fdd2a08af2da84d618d362522cb0f8 100644 (file)
--- a/doc/user/topics/tutorial-job-debug.html.textile.liquid
+++ b/doc/user/topics/tutorial-job-debug.html.textile.liquid
@@ -12,7 +12,7 @@ This tutorial uses *@you@* to denote your username.  Replace *@you@* with your u
 
 h2. Create a new script
 
-Change to your git directory and create a new script in "crunch_scripts/".
+Change to your git directory and create a new script in @crunch_scripts/@.
 
 <notextile>
 <pre><code>~$ <span class="userinput">cd <b>you</b>/crunch_scripts</span>
@@ -27,17 +27,24 @@ EOF</span>
 
 h2. Using arv-crunch-job to run the job in your VM
 
-Instead of a git commit hash, we provide the path to the directory in the "script_version" parameter.  The script specified in "script" will actually be searched for in the "crunch_scripts/" subdirectory of the directory specified "script_version".  Although we are running the script locally, the script still requires access to the Arvados API server and Keep storage service. The job will be recorded in the Arvados job history, and visible in Workbench.
+Instead of a git commit hash, we provide the path to the directory in the "script_version" parameter.  The script specified in "script" will actually be searched for in the @crunch_scripts/@ subdirectory of the directory specified "script_version".  Although we are running the script locally, the script still requires access to the Arvados API server and Keep storage service. The job will be recorded in the Arvados job history, and visible in Workbench.
 
 <notextile>
 <pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat &gt;~/the_job &lt;&lt;EOF
 {
+ "repository":"",
  "script":"hello-world.py",
- "script_version":"/home/<b>you</b>/<b>you</b>",
+ "script_version":"$HOME/$USER",
  "script_parameters":{}
 }
 EOF</span>
-~/<b>you</b>/crunch_scripts</span>$ <span class="userinput">arv-crunch-job --job "$(cat ~/the_job)"</span>
+</code></pre>
+</notextile>
+
+Your shell should fill in values for @$HOME@ and @$USER@ so that the saved JSON points "script_version" at the directory with your checkout.  Now you can run that job:
+
+<notextile>
+<pre><code>~/<b>you</b>/crunch_scripts</span>$ <span class="userinput">arv-crunch-job --job "$(cat ~/the_job)"</span>
 2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827  check slurm allocation
 2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827  node localhost - 1 slots
 2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827  start
@@ -53,7 +60,7 @@ EOF</span>
 2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827 0 stderr hello world
 2013-12-12_21:36:43 qr1hi-8i9sb-okzukfzkpbrnhst 29827 0 child 29834 on localhost.1 exit 0 signal 0 success=
 2013-12-12_21:36:43 qr1hi-8i9sb-okzukfzkpbrnhst 29827 0 failure (#1, permanent) after 0 seconds
-2013-12-12_21:36:43 qr1hi-8i9sb-okzukfzkpbrnhst 29827 0 output 
+2013-12-12_21:36:43 qr1hi-8i9sb-okzukfzkpbrnhst 29827 0 output
 2013-12-12_21:36:43 qr1hi-8i9sb-okzukfzkpbrnhst 29827  Every node has failed -- giving up on this round
 2013-12-12_21:36:43 qr1hi-8i9sb-okzukfzkpbrnhst 29827  wait for last 0 children to finish
 2013-12-12_21:36:43 qr1hi-8i9sb-okzukfzkpbrnhst 29827  status: 0 done, 0 running, 0 todo
@@ -96,8 +103,9 @@ EOF</span>
 ~/<b>you</b>/crunch_scripts$ <span class="userinput">chmod +x hello-world-fixed.py</span>
 ~/<b>you</b>/crunch_scripts$ <span class="userinput">cat &gt;~/the_job &lt;&lt;EOF
 {
+ "repository":"",
  "script":"hello-world-fixed.py",
- "script_version":"/home/<b>you</b>/<b>you</b>",
+ "script_version":"$HOME/$USER",
  "script_parameters":{}
 }
 EOF</span>
@@ -105,7 +113,7 @@ EOF</span>
 2013-12-12_21:56:59 qr1hi-8i9sb-79260ykfew5trzl 31578  check slurm allocation
 2013-12-12_21:56:59 qr1hi-8i9sb-79260ykfew5trzl 31578  node localhost - 1 slots
 2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578  start
-2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578  script hello-world.py
+2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578  script hello-world-fixed.py
 2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578  script_version /home/<b>you</b>/<b>you</b>
 2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578  script_parameters {}
 2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578  runtime_constraints {"max_tasks_per_node":0}
@@ -122,11 +130,13 @@ EOF</span>
 2013-12-12_21:57:02 qr1hi-8i9sb-79260ykfew5trzl 31578  Freeze not implemented
 2013-12-12_21:57:02 qr1hi-8i9sb-79260ykfew5trzl 31578  collate
 2013-12-12_21:57:02 qr1hi-8i9sb-79260ykfew5trzl 31578  output 576c44d762ba241b0a674aa43152b52a+53
+WARNING:root:API lookup failed for collection 576c44d762ba241b0a674aa43152b52a+53 (<class 'apiclient.errors.HttpError'>: <HttpError 404 when requesting https://qr1hi.arvadosapi.com/arvados/v1/collections/576c44d762ba241b0a674aa43152b52a%2B53?alt=json returned "Not Found">)
 2013-12-12_21:57:03 qr1hi-8i9sb-79260ykfew5trzl 31578  finish
-2013-12-12_21:57:04 qr1hi-8i9sb-79260ykfew5trzl 31578  meta key is 9f937693334d0c9234ccc1f808ee7117+1761
 </code></pre>
 </notextile>
 
+(The WARNING issued near the end of the script may be safely ignored here; it is the Arvados SDK letting you know that it could not find a collection named @576c44d762ba241b0a674aa43152b52a+53@ and that it is going to try looking up a block by that name instead.)
+
 The job succeeded, with output in Keep object @576c44d762ba241b0a674aa43152b52a+53@.  Let's look at our output:
 
 <notextile>