[ARVADOS] created: fdbef7b63085492ddbc9201726508d63d0c8bf8f
git at public.curoverse.com
git at public.curoverse.com
Tue Mar 11 13:38:32 EDT 2014
at fdbef7b63085492ddbc9201726508d63d0c8bf8f (commit)
commit fdbef7b63085492ddbc9201726508d63d0c8bf8f
Author: Brett Smith <brett at curoverse.com>
Date: Tue Mar 11 12:33:55 2014 -0400
doc: Bold `you` in tutorial-parallel's job spec.
diff --git a/doc/user/topics/tutorial-parallel.html.textile.liquid b/doc/user/topics/tutorial-parallel.html.textile.liquid
index cf83900..21d9841 100644
--- a/doc/user/topics/tutorial-parallel.html.textile.liquid
+++ b/doc/user/topics/tutorial-parallel.html.textile.liquid
@@ -40,7 +40,7 @@ You should now be able to run your new script using Crunch, with "script" referr
<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat >~/the_job <<EOF
{
"script": "parallel-hash.py",
- "script_version": "you:master",
+ "script_version": "<b>you</b>:master",
"script_parameters":
{
"input": "887cd41e9c613463eab2f0d885c6dd96+83"
commit 4638e5fd00707c755c685bf601f92d27038703f3
Author: Brett Smith <brett at curoverse.com>
Date: Tue Mar 11 11:43:40 2014 -0400
doc: Fix hello-world-fixed.py name in job-debug.
diff --git a/doc/user/topics/tutorial-job-debug.html.textile.liquid b/doc/user/topics/tutorial-job-debug.html.textile.liquid
index 14ceb9b..0974e51 100644
--- a/doc/user/topics/tutorial-job-debug.html.textile.liquid
+++ b/doc/user/topics/tutorial-job-debug.html.textile.liquid
@@ -71,7 +71,7 @@ bc. 2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827 0 stderr hello world
The script's output is captured in the log, which is useful for print statement debugging. However, although this script returned a status code of 0 (success), the job failed. Why? For a job to complete successfully scripts must explicitly add their output to Keep, and then tell Arvados about it. Here is a second try:
<notextile>
-<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat >hello-world.py <<EOF
+<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat >hello-world-fixed.py <<EOF
#!/usr/bin/env python
import arvados
commit 15dd4bd9a033b3ca45774994a84fe1bfa2226655
Author: Brett Smith <brett at curoverse.com>
Date: Tue Mar 11 11:31:09 2014 -0400
doc: Consistent style for `you` in job-debug.
diff --git a/doc/user/topics/tutorial-job-debug.html.textile.liquid b/doc/user/topics/tutorial-job-debug.html.textile.liquid
index f07a7da..14ceb9b 100644
--- a/doc/user/topics/tutorial-job-debug.html.textile.liquid
+++ b/doc/user/topics/tutorial-job-debug.html.textile.liquid
@@ -8,7 +8,7 @@ To test changes to a script by running a job, the change must be pushed into @gi
*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*
-This tutorial uses _you_ to denote your username. Replace _you_ with your user name in all the following examples.
+This tutorial uses *@you@* to denote your username. Replace *@you@* with your user name in all the following examples.
h2. Create a new script
@@ -33,7 +33,7 @@ Instead of a git commit hash, we provide the path to the directory in the "scrip
<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat >~/the_job <<EOF
{
"script":"hello-world.py",
- "script_version":"/home/you/you",
+ "script_version":"/home/<b>you</b>/<b>you</b>",
"script_parameters":{}
}
EOF</span>
@@ -42,7 +42,7 @@ EOF</span>
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
2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827 script hello-world.py
-2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827 script_version /home/you/you
+2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827 script_version /home/<b>you</b>/<b>you</b>
2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827 script_parameters {}
2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827 runtime_constraints {"max_tasks_per_node":0}
2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827 start level 0
@@ -97,7 +97,7 @@ EOF</span>
~/<b>you</b>/crunch_scripts$ <span class="userinput">cat >~/the_job <<EOF
{
"script":"hello-world-fixed.py",
- "script_version":"/home/you/you",
+ "script_version":"/home/<b>you</b>/<b>you</b>",
"script_parameters":{}
}
EOF</span>
@@ -106,7 +106,7 @@ EOF</span>
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_version /home/you/you
+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}
2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578 start level 0
commit 55d96c71c561e51e8a00974caf60123698fc0647
Author: Brett Smith <brett at curoverse.com>
Date: Tue Mar 11 11:24:07 2014 -0400
doc: Update job1's expected output.
Pete changed this script so that the output filename has a leading
`./`. This commit updates the tutorial to match.
diff --git a/doc/user/topics/tutorial-job1.html.textile.liquid b/doc/user/topics/tutorial-job1.html.textile.liquid
index c4db2db..0e90d9e 100644
--- a/doc/user/topics/tutorial-job1.html.textile.liquid
+++ b/doc/user/topics/tutorial-job1.html.textile.liquid
@@ -125,7 +125,7 @@ On the command line, you can use @arv job get@ to access a JSON object describin
"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",
@@ -145,12 +145,12 @@ On the command line, you can use @arv job get@ to access a JSON object describin
</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>
+<pre><code>~$ <span class="userinput">arv keep ls dd755dbc8d49a67f4fe7dc843e4f10a6+54</span>
md5sum.txt
</code></pre>
</notextile>
@@ -158,8 +158,8 @@ md5sum.txt
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>
@@ -209,13 +209,13 @@ The log collection consists of one log file named with the job id. You can acce
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 1 output dd755dbc8d49a67f4fe7dc843e4f10a6+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 output dd755dbc8d49a67f4fe7dc843e4f10a6+54+K at qr1hi
2013-12-16_20:44:53 qr1hi-8i9sb-1pm1t02dezhupss 7575 finish
</code></pre>
</notextile>
commit a0bcef395615dc00d3b14d6f33a802e789d571e4
Author: Brett Smith <brett at curoverse.com>
Date: Tue Mar 11 12:05:50 2014 -0400
doc: Highlight `you` in the first script job spec.
diff --git a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
index 5d0a4da..2e48833 100644
--- a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
@@ -110,7 +110,7 @@ Next, create a file that contains the pipeline definition:
"dataclass": "Collection"
}
},
- "script_version":"you:master"
+ "script_version":"<b>you</b>:master"
}
}
}
commit c592425e9ce54bee52f825c1ec1d2caa665ba308
Author: Brett Smith <brett at curoverse.com>
Date: Tue Mar 11 11:10:44 2014 -0400
doc: Suggest setting User in .ssh/config.
diff --git a/doc/user/getting_started/ssh-access.html.textile.liquid b/doc/user/getting_started/ssh-access.html.textile.liquid
index ddaf192..e4a2b9c 100644
--- a/doc/user/getting_started/ssh-access.html.textile.liquid
+++ b/doc/user/getting_started/ssh-access.html.textile.liquid
@@ -180,6 +180,7 @@ Since the above command line is cumbersome, it can be greatly simplfied by addin
<notextile>
<pre><code class="userinput">Host *.arvados
ProxyCommand ssh -a -x -p2222 turnout at switchyard.{{ site.arvados_api_host }} $SSH_PROXY_FLAGS %h
+ User <b>you</b>
ForwardAgent yes
ForwardX11 no
</code></pre>
@@ -187,7 +188,7 @@ Since the above command line is cumbersome, it can be greatly simplfied by addin
This will recognize any host ending in ".arvados" and automatically apply the proxy, user and forwarding settings from the configuration file, allowing you to log in with a much simpler command:
-notextile. <pre><code>$ <span class="userinput">ssh <b>you at shell</b>.arvados</span></code></pre>
+notextile. <pre><code>$ <span class="userinput">ssh <b>shell</b>.arvados</span></code></pre>
h2(#windowsvm). Logging in using PuTTY (Windows)
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