add slurm profiling figures to Runtime data

Author: DininduSenanayake

docs/1-runtime-info.md

@@ -0,0 +1,27 @@
+# Runtime data
+
+
+
+![image](./images/runtime_vs_cpu1.png)
+
+<center><small> Runtime for  one sample across varying number of CPUs: This is for the second phase of the workflow which creates the .db files from .apxims files (`08-snakemake/Snakefile_2`) </small></center>
+
+## Runtime behaviour
+
+??? hourglass "4cpu"
+    ![image](./images/4c.png)
+
+??? hourglass "8cpu"
+    ![image](./images/8c.png)
+
+??? hourglass "12cpu"
+    ![image](./images/12c.png)
+
+??? hourglass "16cpu"
+    ![image](./images/16c.png)
+
+??? hourglass "20cpu"
+    ![image](./images/20c.png)
+
+??? hourglass "24cpu"
+    ![image](./images/24c.png)

docs/images/12c.png

@@ -128,7 +128,9 @@ Deploy APSIM (Agricultural Production Systems sIMulator - https://www.apsim.info
 
     1. Cloned the latest version of the repo (https://github.com/nesi/APSIM-HPC.git)
     2. `03-generate-config-files/generate_apsim_configs.R` , `08-snakemake/Snakefile_1` and `08-snakemake/Snakefile_2` were updated with names of the template files,etc. 
-    3. Filenames and directory structure **were/was not** altered. 
+    3. Filenames and directory structure of the **cloned repo** **were/was not** altered.
+        - submission script relies on the relative paths and names as it is within the Github repo.
+        - If you are to change paths or names, make sure to review `submit.sh` and amend to reflect the changes.  
 
 
 !!! rocket "Launch it with the command `source submit.sh`"

docs/images/16c.png

@@ -1178,4 +1178,22 @@
   background-color: rgb(25,25,112);
   -webkit-mask-image: var(--md-admonition-icon--rocket);
           mask-image: var(--md-admonition-icon--rocket);
+}
+
+:root {
+  --md-admonition-icon--hourglass: url('data:image/svg+xml;charset=utf-8,<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><!--!Font Awesome Free 6.6.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free Copyright 2024 Fonticons, Inc.--><path d="M32 0C14.3 0 0 14.3 0 32S14.3 64 32 64l0 11c0 42.4 16.9 83.1 46.9 113.1L146.7 256 78.9 323.9C48.9 353.9 32 394.6 32 437l0 11c-17.7 0-32 14.3-32 32s14.3 32 32 32l32 0 256 0 32 0c17.7 0 32-14.3 32-32s-14.3-32-32-32l0-11c0-42.4-16.9-83.1-46.9-113.1L237.3 256l67.9-67.9c30-30 46.9-70.7 46.9-113.1l0-11c17.7 0 32-14.3 32-32s-14.3-32-32-32L320 0 64 0 32 0zM96 75l0-11 192 0 0 11c0 19-5.6 37.4-16 53L112 128c-10.3-15.6-16-34-16-53zm16 309c3.5-5.3 7.6-10.3 12.1-14.9L192 301.3l67.9 67.9c4.6 4.6 8.6 9.6 12.1 14.9L112 384z"/></svg>')
+}
+.md-typeset .admonition.hourglass,
+.md-typeset details.hourglass {
+  border-color: rgb(243, 198, 49);
+}
+.md-typeset .hourglass > .admonition-title,
+.md-typeset .hourglass > summary {
+  background-color: rgba(243, 147, 22, 0.562);
+}
+.md-typeset .hourglass > .admonition-title::before,
+.md-typeset .hourglass > summary::before {
+  background-color: rgb(25,25,112);
+  -webkit-mask-image: var(--md-admonition-icon--hourglass);
+          mask-image: var(--md-admonition-icon--hourglass);
 }