reviewed and fixed page (#41)

* reviewed and fixed page

* change lexers

* small changes

* Move proselint conf into seperate file, add more rule exceptions.

---------

Co-authored-by: cal <[email protected]>

.markdownlint.json

@@ -1,5 +1,6 @@
 {
   "MD013": false,
   "MD033": false,
-  "MD038": false
+  "MD038": false,
+  "MD041": false
 }

.proselint.json

@@ -0,0 +1,6 @@
+{
+    "checks":{
+    "hyperbole.misc": false,
+    "typography.exclamation": false,
+    "typography.symbols": false
+}}

checks/run_proselint.py

@@ -6,18 +6,21 @@
 
 import sys
 import proselint
-from proselint import config
-
+from proselint import config, tools
 
 
 files = sys.argv[1:]
 
 ret_code = 0
-proselint.config.default["checks"]["hyperbole.misc"] = False
+
+# Load defaults from config.
+config_custom = tools.load_options(config_file_path=".proselint.json", conf_default=config.default)
+
+print(config_custom)
 
 for file in files:
     with open(file, "r", encoding="utf8") as f:
-        for notice in proselint.tools.lint(f.read(), config=config.default):
+        for notice in proselint.tools.lint(f.read(), config=config_custom):
             if (notice[7] == "error"):
                 ret_code = 1
             print(f"::{notice[7]} file={file},line={notice[2]},col={notice[3]},endLine={notice[2]+notice[6]},title={notice[0]}::'{notice[1]}'")

docs/Getting_Started/Next_Steps/Finding_Job_Efficiency.md

@@ -4,22 +4,12 @@ hidden: false
 position: 5
 tags:
 - slurm
-title: Finding Job Efficiency
 vote_count: 8
 vote_sum: 8
 zendesk_article_id: 360000903776
 zendesk_section_id: 360000189716
 ---
 
-
-
-[//]: <> (REMOVE ME IF PAGE VALIDATED)
-[//]: <> (vvvvvvvvvvvvvvvvvvvv)
-!!! warning
-    This page has been automatically migrated and may contain formatting errors.
-[//]: <> (^^^^^^^^^^^^^^^^^^^^)
-[//]: <> (REMOVE ME IF PAGE VALIDATED)
-
 ## On Job Completion
 
 It is good practice to have a look at the resources your job used on
@@ -29,13 +19,13 @@ future.
 Once your job has finished check the relevant details using the tools:
 `nn_seff` or `sacct` For example:  
 
-**nn\_seff**
+### Using `nn_seff`
 
-``` sl
+```bash
 nn_seff 30479534
 ```
 
-``` sl
+```txt
 Job ID: 1936245
 Cluster: mahuika
 User/Group: user/group
@@ -48,30 +38,25 @@ CPU Efficiency: 98.55% 00:01:08 of 00:01:09 core-walltime
 Mem Efficiency: 10.84% 111.00 MB of 1.00 GB
 ```
 
-Notice that the CPU efficiency was high but the memory efficiency was
-very low and consideration should be given to reducing memory requests
-for similar jobs.  If in doubt, please contact <[email protected]> for
-guidance.
-
-
+Notice that the CPU efficiency was high but the memory efficiency was low and consideration should be given to reducing memory requests
+for similar jobs.  If in doubt, please contact [[email protected]](mailto:[email protected]) for guidance.
 
-**sacct**
+### Using `sacct`
 
-``` sl
+```bash
 sacct --format="JobID,JobName,Elapsed,AveCPU,MinCPU,TotalCPU,Alloc,NTask,MaxRSS,State" -j <jobid>
 ```
-!!! prerequisite Tip
+
+!!! tip
      *If you want to make this your default* `sacct` *setting, run;*
-     ``` sl
+     ```bash
      echo 'export SACCT_FORMAT="JobID,JobName,Elapsed,AveCPU,MinCPU,TotalCPU,Alloc%2,NTask%2,MaxRSS,State"' >> ~/.bash_profile
      source ~/.bash_profile
      ```
 
-------------------------------------------------------------------------
-
 Below is an output for reference:
 
-``` sl
+```txt
        JobID    JobName    Elapsed     AveCPU     MinCPU   TotalCPU  AllocCPUS   NTasks     MaxRSS      State
 ------------ ---------- ---------- ---------- ---------- ---------- ---------- -------- ---------- ----------
 3007056      rfm_ANSYS+   00:27:07                         03:35:55         16                      COMPLETED
@@ -82,9 +67,7 @@ Below is an output for reference:
 *All of the adjustments below still allow for a degree of variation.
 There may be factors you have not accounted for.*
 
-------------------------------------------------------------------------
-
-### **Walltime**
+#### Walltime
 
 From the `Elapsed` field we may want to update our next run to have a
 more appropriate walltime.
@@ -93,7 +76,7 @@ more appropriate walltime.
 #SBATCH --time=00:40:00
 ```
 
-### **Memory**
+#### Memory
 
 The `MaxRSS` field shows the maximum memory used by each of the job
 steps, so in this case 13 GB. For our next run we may want to set:
@@ -102,7 +85,7 @@ steps, so in this case 13 GB. For our next run we may want to set:
 #SBATCH --mem=15G
 ```
 
-### **CPU's**
+#### CPUs
 
 `TotalCPU` is the number of computation hours, in the best case scenario
 the computation hours would be equal to `Elapsed` x `AllocCPUS`.
@@ -116,8 +99,6 @@ however bear in mind there are other factors that affect CPU efficiency.
 #SBATCH --cpus-per-task=10
 ```
 
-
-
 Note: When using sacct to determine the amount of memory your job used -
 in order to reduce memory wastage - please keep in mind that Slurm
 reports the figure as RSS (Resident Set Size) when in fact the metric
@@ -153,19 +134,20 @@ If 'nodelist' is not one of the fields in the output of your `sacct` or
 `squeue` commands you can find the node a job is running on using the
 command; `squeue -h -o %N -j <jobid>` The node will look something like
 `wbn123` on Mahuika or `nid00123` on Māui
-!!! prerequisite Note
+
+!!! note
      If your job is using MPI it may be running on multiple nodes
 
-### htop 
+### Using `htop`
 
-``` sl
+```bash
 ssh -t wbn175 htop -u $USER
 ```
 
 If it is your first time connecting to that particular node, you may be
 prompted:
 
-``` sl
+```txt
 The authenticity of host can't be established 
 Are you sure you want to continue connecting (yes/no)?
 ```
@@ -185,15 +167,16 @@ Processes in green can be ignored
 
 **S** - State, what the thread is currently doing.
 
--   R - Running
--   S - Sleeping, waiting on another thread to finish.
--   D - Sleeping
--   Any other letter - Something has gone wrong!
+- R - Running
+- S - Sleeping, waiting on another thread to finish.
+- D - Sleeping
+- Any other letter - Something has gone wrong!
 
 **CPU%** - Percentage CPU utilisation.
 
-**MEM% **Percentage Memory utilisation.
-!!! prerequisite Warning
+**MEM%** - Percentage Memory utilisation.
+
+!!! warning
      If the job finishes, or is killed you will be kicked off the node. If
      htop freezes, type `reset` to clear your terminal.
 
@@ -204,21 +187,18 @@ time* the CPUs are in use. This is not enough to get a picture of
 overall job efficiency, as required CPU time *may vary by number of
 CPU*s.
 
-The only way to get the full context, is to compare walltime performance
-between jobs at different scale. See [Job
-Scaling](../../Getting_Started/Next_Steps/Job_Scaling_Ascertaining_job_dimensions.md)
-for more details.
+The only way to get the full context, is to compare walltime performance between jobs at different scale. See [Job Scaling](../../Getting_Started/Next_Steps/Job_Scaling_Ascertaining_job_dimensions.md) for more details.
 
 ### Example
 
 ![qdyn\_eff.png](../../assets/images/Finding_Job_Efficiency_0.png)
 
 From the above plot of CPU efficiency, you might decide a 5% reduction
-of CPU efficiency is acceptable and scale your job up to 18 CPU cores . 
+of CPU efficiency is acceptable and scale your job up to 18 CPU cores .
 
 ![qdyn\_walltime.png](../../assets/images/Finding_Job_Efficiency_1.png)
 
 However, when looking at a plot of walltime it becomes apparent that
 performance gains per CPU added drop significantly after 4 CPUs, and in
 fact absolute performance losses (negative returns) are seen after 8
-CPUs.
+CPUs.