Merge pull request #524 from ACCESS-Hive/davide/change-codeblocks

Adjusted codeblocks
ACCESS-NRI · Aug 11, 2023 · 35baa93 · 35baa93
2 parents 9fbfda1 + 18be0aa
commit 35baa93
Show file tree

Hide file tree

Showing 5 changed files with 117 additions and 126 deletions.
diff --git a/docs/css/access-nri.css b/docs/css/access-nri.css
@@ -165,6 +165,15 @@
   --note-bg: rgba(var(--nri-orange-color),.05); /* Note background */
 }
 
+
+/* =============================================================== 
+  Main body grid
+*/
+.md-grid {
+  max-width: 70rem;
+}
+
+
 /* =============================================================== 
   Main headings
 */
@@ -680,7 +689,7 @@ pre:has(code) {
 }
 
 pre>code {
-  white-space: pre-line !important;
+  white-space: pre-wrap !important;
   padding: 0.5em 0.8em !important;
   word-break: break-all !important;
 }

diff --git a/docs/getting_started/index.md b/docs/getting_started/index.md
@@ -196,14 +196,13 @@ To simplify the login and avoid being prompted every time to enter your NCI pass
     </div>
     The following lines should be added to your <code>~/.ssh/config</code> to describe the SSH configuration for <i>Gadi</i> (replace <code>&lt;your-NCI-username&gt;</code> with your NCI <i>username</i>, e.g., <code>ab1234</code>):
     <pre><code>Host gadi
-      &emsp;Hostname gadi.nci.org.au
-      &emsp;User &lt;your-NCI-username&gt;
-      &emsp;ForwardX11 true
-      &emsp;ForwardX11Trusted yes
-      &emsp;IdentityFile ~/.ssh/id_gadi
-      &emsp;AddKeysToAgent yes
-      &emsp;UseKeychain yes
-    </code></pre>
+    Hostname gadi.nci.org.au
+    User &lt;your-NCI-username&gt;
+    ForwardX11 true
+    ForwardX11Trusted yes
+    IdentityFile ~/.ssh/id_gadi
+    AddKeysToAgent yes
+    UseKeychain yes</code></pre>
     <div class="note">
       If you already have an existing <code>~/.ssh/config</code> file which contains configurations for every <code>Host</code> (e.g., by using <code>Host *</code>), make sure you delete any of the keywords present in that SSH configuration from the <i>Gadi</i> configuration above.
       <br>
@@ -244,7 +243,7 @@ For example, if you want to change your default project to `tm70` on <i>Gadi</i>
   <terminal-line data="input">exit</terminal-line>
   <terminal-line>logout</terminal-line>
   <terminal-line>Connection to gadi.nci.org.au closed.</terminal-line>
-  <terminal-line data="input" PS1="<span style='color: #897a36;'>(User PC)$ </span>">ssh gadi</terminal-line>
+  <terminal-line data="input" PS1="&lt;span style='color: #9734bb;'&gt;(User PC)$ &lt;/span&gt;">ssh gadi</terminal-line>
   <terminal-line>###############################################################################</terminal-line>
   <terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;Welcome to the NCI National Facility!&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;#</terminal-line>
   <terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;This service is for authorised clients only. It is a criminal&emsp;&emsp;&emsp;&emsp;&emsp;&nbsp;#</terminal-line>

diff --git a/docs/models/run-a-model/run-access-cm.md b/docs/models/run-a-model/run-access-cm.md
@@ -228,13 +228,12 @@ After the initial tasks are executed, the <i>Cylc</i> GUI will open. You can now
     <div class="note">
         After running the command <code>rose suite-run</code>, if you get an error similar to the following:
         <pre><code><span style="color: orangered">[FAIL]</span> Suite "&lt;suite-ID&gt;" appears to be running:
-            <span style="color: orangered">[FAIL]</span> Contact info from: "/home/565/&lt;$USER&gt;/cylc-run/&lt;suite-ID&gt;/.service/contact"
-            <span style="color: orangered">[FAIL]</span> &emsp;&emsp;CYLC_SUITE_HOST=accessdev.nci.org.au
-            <span style="color: orangered">[FAIL]</span> &emsp;&emsp;CYLC_SUITE_OWNER=&lt;$USER&gt;
-            <span style="color: orangered">[FAIL]</span> &emsp;&emsp;CYLC_SUITE_PORT=&lt;port&gt;
-            <span style="color: orangered">[FAIL]</span> &emsp;&emsp;CYLC_SUITE_PROCESS=&lt;PID&gt; python2 /usr/local/cylc/cylc-7.8.3/bin/cylc-run &lt;suite-ID&gt;
-            <span style="color: orangered">[FAIL]</span> Try "cylc stop '&lt;suite-ID&gt;'" first?
-        </code></pre>
+<span style="color: orangered">[FAIL]</span> Contact info from: "/home/565/&lt;$USER&gt;/cylc-run/&lt;suite-ID&gt;/.service/contact"
+<span style="color: orangered">[FAIL]</span>    CYLC_SUITE_HOST=accessdev.nci.org.au
+<span style="color: orangered">[FAIL]</span>    CYLC_SUITE_OWNER=&lt;$USER&gt;
+<span style="color: orangered">[FAIL]</span>    CYLC_SUITE_PORT=&lt;port&gt;
+<span style="color: orangered">[FAIL]</span>    CYLC_SUITE_PROCESS=&lt;PID&gt; python2 /usr/local/cylc/cylc-7.8.3/bin/cylc-run &lt;suite-ID&gt;
+<span style="color: orangered">[FAIL]</span> Try "cylc stop '&lt;suite-ID&gt;'" first?</code></pre>
         you should run:
         <pre><code>rm /home/565/&lt;$USER&gt;/cylc-run/&lt;suite-ID&gt;/.service/contact</code></pre>
         before running the <code>rose suite-run</code> command again.

diff --git a/docs/models/run-a-model/run-access-esm.md b/docs/models/run-a-model/run-access-esm.md
@@ -20,8 +20,7 @@ Before running {{ model }}, you need to fulfil general requirements outlined in
         <br>
         After obtaining <i>hh5</i> project membership, load the <code>conda/analysis3</code> environment to automatically retrieve <i>payu</i> as follows:
         <pre><code>module use /g/data/hh5/public/modules
-            module load conda/analysis3
-        </code></pre> 
+module load conda/analysis3</code></pre> 
         To check that <i>payu</i> is available, run:
         <pre><code>payu --version</code></pre>
         <terminal-window>
@@ -102,9 +101,8 @@ This file, which controls the general model configuration, contains several part
         <b>PBS resources</b>
         <br>
         <pre><code>jobname: pre-industrial
-            queue: normal
-            walltime: 20:00:00
-        </code></pre>
+queue: normal
+walltime: 20:00:00</code></pre>
         These lines can be edited to change the settings for the PBS scheduler.
         <br>
         For example, to run {{ model }} under the <code>tm70</code> project (ACCESS-NRI), add the following line:
@@ -117,8 +115,7 @@ This file, which controls the general model configuration, contains several part
         <b>Link to the laboratory directory</b>
         <br>
         <pre><code># note: if laboratory is relative path, it is relative to /scratch/$PROJECT/$USER
-            laboratory: access-esm
-        </code></pre>
+laboratory: access-esm</code></pre>
         These lines set the laboratory directory path, which is relative to <code>/scratch/$PROJECT/$USER</code>. Absolute paths can also be specified.
     </li>
     <li>
@@ -131,32 +128,31 @@ This file, which controls the general model configuration, contains several part
         <b>Submodels</b>
         <br>
         <pre><code>submodels:
-            &nbsp;&nbsp;- name: atmosphere
-            &nbsp;&nbsp;&nbsp;&nbsp;model: um
-            &nbsp;&nbsp;&nbsp;&nbsp;ncpus: 192
-            &nbsp;&nbsp;&nbsp;&nbsp;exe: /g/data/access/payu/access-esm/bin/coe/um7.3x
-            &nbsp;&nbsp;&nbsp;&nbsp;input:
-            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;- /g/data/access/payu/access-esm/input/pre-industrial/atmosphere
-            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;- /g/data/access/payu/access-esm/input/pre-industrial/start_dump<br>
-            &nbsp;&nbsp;- name: ocean
-            &nbsp;&nbsp;&nbsp;&nbsp;model: mom
-            &nbsp;&nbsp;&nbsp;&nbsp;ncpus: 180
-            &nbsp;&nbsp;&nbsp;&nbsp;exe: /g/data/access/payu/access-esm/bin/coe/mom5xx
-            &nbsp;&nbsp;&nbsp;&nbsp;input:
-            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;- /g/data/access/payu/access-esm/input/pre-industrial/ocean/common
-            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;- /g/data/access/payu/access-esm/input/pre-industrial/ocean/pre-industrial<br>
-            &nbsp;&nbsp;- name: ice
-            &nbsp;&nbsp;&nbsp;&nbsp;model: cice
-            &nbsp;&nbsp;&nbsp;&nbsp;ncpus: 12
-            &nbsp;&nbsp;&nbsp;&nbsp;exe: /g/data/access/payu/access-esm/bin/coe/cicexx
-            &nbsp;&nbsp;&nbsp;&nbsp;input:
-            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;- /g/data/access/payu/access-esm/input/pre-industrial/ice<br>
-            &nbsp;&nbsp;- name: coupler
-            &nbsp;&nbsp;&nbsp;&nbsp;model: oasis
-            &nbsp;&nbsp;&nbsp;&nbsp;ncpus: 0
-            &nbsp;&nbsp;&nbsp;&nbsp;input:
-            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;- /g/data/access/payu/access-esm/input/pre-industrial/coupler
-        </code></pre>
+    - name: atmosphere
+      model: um
+      ncpus: 192
+      exe: /g/data/access/payu/access-esm/bin/coe/um7.3x
+      input:
+        - /g/data/access/payu/access-esm/input/pre-industrial/atmosphere
+        - /g/data/access/payu/access-esm/input/pre-industrial/start_dump<br>
+    - name: ocean
+      model: mom
+      ncpus: 180
+      exe: /g/data/access/payu/access-esm/bin/coe/mom5xx
+      input:
+        - /g/data/access/payu/access-esm/input/pre-industrial/ocean/common
+        - /g/data/access/payu/access-esm/input/pre-industrial/ocean/pre-industrial<br>
+    - name: ice
+      model: cice
+      ncpus: 12
+      exe: /g/data/access/payu/access-esm/bin/coe/cicexx
+      input:
+        - /g/data/access/payu/access-esm/input/pre-industrial/ice<br>
+    - name: coupler
+      model: oasis
+      ncpus: 0
+      input:
+        - /g/data/access/payu/access-esm/input/pre-industrial/coupler</code></pre>
         {{ model }} is a coupled model deploying multiple submodels (i.e. model components).
         This section specifies the submodels and configuration options required to execute the model correctly.
         <br>
@@ -166,10 +162,9 @@ This file, which controls the general model configuration, contains several part
         <b>Collate</b>
         <br>
         <pre><code>collate:
-            &nbsp;&nbsp;exe: /g/data/access/payu/access-esm/bin/mppnccombine
-            &nbsp;&nbsp;restart: true
-            &nbsp;&nbsp;mem: 4GB
-        </code></pre>
+    exe: /g/data/access/payu/access-esm/bin/mppnccombine
+    restart: true
+    mem: 4GB</code></pre>
         The <code>collate</code> process combines a number of smaller files, which contain different parts of the model grid, into target output files. Restart files are typically tiled in the same way and will also be combined together if the <code>restart</code> option is set to <code>true</code>.
     </li>
     <li>
@@ -182,15 +177,14 @@ This file, which controls the general model configuration, contains several part
         <b>Start date and internal run length</b>
         <br>
         <pre><code>calendar:
-            &nbsp;&nbsp;start:
-            &nbsp;&nbsp;&nbsp;&nbsp;year: 101
-            &nbsp;&nbsp;&nbsp;&nbsp;month: 1
-            &nbsp;&nbsp;&nbsp;&nbsp;days: 1<br>
-            &nbsp;&nbsp;runtime:
-            &nbsp;&nbsp;&nbsp;&nbsp;years: 1
-            &nbsp;&nbsp;&nbsp;&nbsp;months: 0
-            &nbsp;&nbsp;&nbsp;&nbsp;days: 0
-        </code></pre>
+    start:
+        year: 101
+        month: 1
+        days: 1<br>
+    runtime:
+        years: 1
+        months: 0
+        days: 0</code></pre>
         This section specifies the start date and internal run length.
         <div class="note">
             The internal run length (controlled by <code>runtime</code>) can be different from the total run length. Also, while <code>runtime</code> can be reduced, it should not be increased to more than 1 year to avoid errors. For more information about the difference between internal run and total run lengths, or how to run the model for more than 1 year, refer to the section <a href="#run-configuration-for-multiple-years">Run configuration for multiple years</a>.
@@ -302,9 +296,8 @@ Now some practical examples:
         <br>
         To have a total run length of 3 months and 10 days in a single submission, set the <code>runtime</code> as follows:
         <pre><code>years: 0
-            months: 3
-            days: 10
-        </code></pre>
+months: 3
+days: 10</code></pre>
         Set <code>runspersub</code> to <code>1</code> (or any value > 1) and run the configuration without option <code>-n</code> (or with <code>-n</code> set to <code>1</code>):
         <pre><code>payu run -f</code></pre>
     </li>
@@ -313,9 +306,8 @@ Now some practical examples:
         <br>
         To have a total run length of 1 year and 4 months (16 months), you need to split it into multiple internal runs. For example, 4 internal runs of 4 months each. In this case, set the <code>runtime</code> as follows:
         <pre><code>years: 0
-            months: 4
-            days: 0
-        </code></pre>
+months: 4
+days: 0</code></pre>
         Since the internal run length is set to 4 months, set <code>runspersub</code> to <code>1</code> to resubmit your jobs every 4 months (i.e. every internal run). Then, run the configuration with <code>-n</code> set to <code>4</code>:
         <pre><code>payu run -f -n 4</code></pre>
     </li>