Cleaning up nn command references

docs/Batch_Computing/Batch_Computing_Guide.md

@@ -122,7 +122,7 @@ You can find more details on its use on the [Slurm Documentation](https://slurm.
 
 ### Checking job efficiency
 
-After a job has completed you can get the basic usage information using `nn_seff <job-id>`.
+After a job has completed you can get the basic usage information using `seff <job-id>`.
 This will return an output as below:
 
 ``` out

docs/Batch_Computing/Checking_resource_usage.md

@@ -3,6 +3,7 @@ created_at: '2022-02-15T01:13:51Z'
 tags:
   - slurm
   - accounting
+status: deprecated
 ---
 
 To check your project's usage of Slurm-managed resources, you can use

docs/Getting_Started/FAQs/Ive_run_out_of_storage_space.md

@@ -11,7 +11,7 @@ There are two tracked resources in the Mahuika filesystem, *disk space* and
 Trying to write to a filesystem over its inode or disk quota will cause
 an error (and probably kill your job).
 
-Current file-count and disk space can be found using `nn_storage_quota`.
+Current file-count and disk space can be found using `storage_quota`.
 
 ```sh
 Quota_Location    AvailableGiB   UsedGiB     Use%
@@ -22,7 +22,7 @@ nobackup_nesi99999      6.833T
 
 !!! note
      There is a delay between making changes to a filesystem and seeing the
-     change in `nn_storage_quota`, immediate file count and disk space can
+     change in `storage_quota`, immediate file count and disk space can
      be found using the commands `du --inodes` and `du -h` respectively.
 
 There are a few ways to deal with file count problems

docs/Interactive_Computing/OnDemand/ood_troubleshooting.md

@@ -37,10 +37,10 @@ To resolve this issue:
     ![NeSI_OnDemand_No_Space_Left_1.png](../../assets/images/NeSI_OnDemand_No_Space_Left_2.png)
 
 2. Log in to your NeSI account through the terminal.
-3. Type into the terminal ```nn_storage_quota```. This will show the amount of space in your `home`, `project`, and `nobackup` directories. You will see that your `home` directory is full.
+3. Type into the terminal ```storage_quota```. This will show the amount of space in your `home`, `project`, and `nobackup` directories. You will see that your `home` directory is full.
 
     ```sh 
-    username@login03:~$ nn_storage_quota 
+    username@login03:~$ storage_quota 
     Quota_Location                          AvailableGiB           UsedGiB Use%
     home_username                                     20                20  100
     ```

docs/Software/Available_Applications/COMSOL.md

@@ -164,7 +164,7 @@ Multithreading will benefit jobs using less than
 
 ## Tmpdir
 
-If you find yourself receiving the error 'Disk quota exceeded', yet `nn_storage_quota` shows plenty of room in your filesystem, you may be running out of tmpdir.
+If you find yourself receiving the error 'Disk quota exceeded', yet `storage_quota` shows plenty of room in your filesystem, you may be running out of tmpdir.
 This can be fixed by using the `--tmpdir` flag in the comsol command line, e.g. `comsol --tmpdir /nesi/nobackup/nesi99991/comsoltmp`, or by exporting `TMPDIR` before running the command, e.g. `export TMPDIR=/nesi/nobackup/nesi99991/comsoltmp`.
 
 You may also want to set this at the Java level with `export _JAVA_OPTIONS=-Djava.io.tmpdir=/nesi/nobackup/nesi99991/comsoltmp`

docs/Software/Available_Applications/Nextflow.md

@@ -302,7 +302,7 @@ Duration    : 11h 16m 47s
 CPU hours   : 319.6
 
 ```bash
-> nn_seff <job-id>
+> seff <job-id>
 Cluster: hpc
 Job ID: 3034402
 State: ['COMPLETED']
@@ -336,7 +336,7 @@ Labeled processes (list below) could submit via slurm array requesting 12 CPUs,
 - `QUALIMAP_RNASEQ`
 
 ```bash
-nn_seff <job-id>
+seff <job-id>
 Cluster: hpc
 Job ID: 3059728
 State: ['OUT_OF_MEMORY']

docs/Software/Available_Applications/OpenFOAM.md

@@ -100,9 +100,9 @@ There are a few ways to mitigate this
         use and I/O load.
 
 - **Monitor Filesystem**  
-    The command `nn_storage_quota` should be used to track filesystem
+    The command `storage_quota` should be used to track filesystem
     usage. There is a delay between making changes to a filesystem and
-    seeing it on `nn_storage_quota`.
+    seeing it on `storage_quota`.
 
     ```sh
     Filesystem         Available      Used     Use%     Inodes     IUsed     IUse%

docs/Software/Profiling_and_Debugging/Finding_Job_Efficiency.md

@@ -12,12 +12,12 @@ completion, this way you can improve your job specifications in the
 future.
 
 Once your job has finished check the relevant details using the tools:
-`nn_seff` or `sacct` For example:  
+`seff` or `sacct` For example:  
 
-### Using `nn_seff`
+### Using `seff`
 
 ```bash
-nn_seff 30479534
+seff 30479534
 ```
 
 ```txt
@@ -36,7 +36,7 @@ Mem Efficiency: 10.84% 111.00 MB of 1.00 GB
 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.
 
-_nn_seff_ is based on the same numbers as are shown by _sacct_.
+_seff_ is based on the same numbers as are shown by _sacct_.
 
 ### Using `sacct`
 

docs/Storage/Filesystems_and_Quotas.md

@@ -10,10 +10,10 @@ You may query your actual usage and disk allocations using the following
 command:
 
 ```sh
- nn_storage_quota
+ storage_quota
 ```
 
-The values for `nn_storage_quota` are updated approximately every hour
+The values for `storage_quota` are updated approximately every hour
 and cached between updates.
 
 ![neSI\_filetree.svg](../assets/images/NeSI_File_Systems_and_Quotas.png)

docs/Tutorials/Introduction_To_HPC/Bash_Shell.md

@@ -85,7 +85,7 @@ When your space is locked you will need to move or remove data.
 Also note that none of the nobackup space is being used, a smart idea would be to move data from `project` to `nobackup`.  
 
 !!! note
-    `nn_storage_quota` uses cached data, and so will not immediately show changes to storage use.  
+    `storage_quota` uses cached data, and so will not immediately show changes to storage use.  
 
 For more details on our persistent and nobackup storage systems, including data retention and the nobackup auto-delete schedule,
 please see our [Filesystem and Quota](../../Storage/Filesystems_and_Quotas.md) documentation.

docs/Tutorials/Introduction_To_HPC/Resources.md

@@ -179,10 +179,10 @@ _48 seconds_ used out of _15 minutes_ requested give a time efficiency of about
 
     b. Memory efficiency is `( 14 / 32 ) x 100` or around **43%**.
 
-For convenience, Mahuika has provided the command `nn_seff <jobid>` to calculate **S**lurm **Eff**iciency (all Mahuika commands start with `nn_`, for **N**eSI **N**IWA).
+For convenience, Mahuika has provided the command `seff <jobid>` to calculate **S**lurm **Eff**iciency.
 
 ```sh
- nn_seff <jobid>
+ seff <jobid>
 ```
 
 ```out

docs/Tutorials/Introduction_To_HPC/Scaling.md

@@ -43,9 +43,9 @@ It is worth noting that Amdahl's law assumes all other elements of scaling are h
     seconds will not have it's memory use recorded.
     Submit the job with `sbatch --acctg-freq 1 example_job.sl`.
     4. Watch the job with `squeue --me` or `watch squeue --me`.
-    5. On completion of job, use `nn_seff <job-id>`.
+    5. On completion of job, use `seff <job-id>`.
     6. Record the jobs "Elapsed", "TotalCPU", and "Memory" values in the spreadsheet.
-    (Hint: They are the first numbers after the percentage efficiency in output of `nn_seff`).
+    (Hint: They are the first numbers after the percentage efficiency in output of `seff`).
     Make sure you have entered the values in the correct format and there is a tick next to each entry.
     ![Correctly entered data in spreadsheet](../../assets/images/correct-spreadsheet-entry.png)