From b02680e78655e6727e22bf9a57b3e7b7abbbb200 Mon Sep 17 00:00:00 2001
From: John LaGrone <jlagrone@gmail.com>
Date: Fri, 19 Jan 2024 14:25:05 -0600
Subject: [PATCH 01/16] add index for Amber example

---
 docs/examples/amber/index.md | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 docs/examples/amber/index.md

diff --git a/docs/examples/amber/index.md b/docs/examples/amber/index.md
new file mode 100644
index 00000000..025e92d9
--- /dev/null
+++ b/docs/examples/amber/index.md
@@ -0,0 +1,28 @@
+# Amber
+
+**Amber** is a suite of biomolecular simulation programs.
+
+**Amber homepage**: [ambermd.org/](https://ambermd.org/)
+
+**Official Amber Tutorials**: [ambermd.org/tutorials/](https://ambermd.org/tutorials/)
+
+## Using Amber on the SuperPod
+
+### Example submission script
+
+```{literalinclude} amber_gpu_example.sbatch
+---
+language: bash
+linenos: true
+---
+```
+
+## Using Amber on M3
+
+```{literalinclude} amber_cpu_example.sbatch                 
+---
+language: bash
+linenos: true
+---
+```
+

From f9d2c3aeb3978fce52381bd498d2f54b30b52c2e Mon Sep 17 00:00:00 2001
From: John LaGrone <jlagrone@gmail.com>
Date: Fri, 19 Jan 2024 14:25:45 -0600
Subject: [PATCH 02/16] remove exclusive flag in example

---
 docs/examples/amber/amber_cpu_example.sbatch | 1 -
 1 file changed, 1 deletion(-)

diff --git a/docs/examples/amber/amber_cpu_example.sbatch b/docs/examples/amber/amber_cpu_example.sbatch
index 40cb741e..96ab4d45 100644
--- a/docs/examples/amber/amber_cpu_example.sbatch
+++ b/docs/examples/amber/amber_cpu_example.sbatch
@@ -4,7 +4,6 @@
 #SBATCH -p dev
 #SBATCH -N 1
 #SBATCH --ntasks-per-node=4
-#SBATCH --exclusive
 
 # Amber
 module purge

From 95ce5b7f646b279586ad908bc9aff27e1fd5d56b Mon Sep 17 00:00:00 2001
From: John LaGrone <jlagrone@gmail.com>
Date: Mon, 22 Jan 2024 09:57:06 -0600
Subject: [PATCH 03/16] add links to other docs

---
 docs/examples/amber/index.md | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/docs/examples/amber/index.md b/docs/examples/amber/index.md
index 025e92d9..a703e12b 100644
--- a/docs/examples/amber/index.md
+++ b/docs/examples/amber/index.md
@@ -1,5 +1,11 @@
 # Amber
 
+:::{seealso}
+For examples and tips on submitting jobs, see [our SLURM documentation](../../slurm/slurm.md) and [Best Practices for Jobs](../../slurm/best_practices.md)
+
+For compute resources, see [HPC Queues](../../about/queeues.md)
+:::
+
 **Amber** is a suite of biomolecular simulation programs.
 
 **Amber homepage**: [ambermd.org/](https://ambermd.org/)
@@ -8,6 +14,11 @@
 
 ## Using Amber on the SuperPod
 
+Files used in the example are available: 
+
+  - [on github](https://github.com/SouthernMethodistUniversity/hpc_docs/tree/update_examples/docs/examples/amber)
+  - on the SuperPod at `/hpc/mp/examples/amber/`
+
 ### Example submission script
 
 ```{literalinclude} amber_gpu_example.sbatch
@@ -19,6 +30,13 @@ linenos: true
 
 ## Using Amber on M3
 
+Files used in the example are available:
+
+  - [on github](https://github.com/SouthernMethodistUniversity/hpc_docs/tree/update_examples/docs/examples/amber)
+  - on M3 at `/hpc/m3/examples/amber/` 
+
+### Example submission script
+
 ```{literalinclude} amber_cpu_example.sbatch                 
 ---
 language: bash

From 1e6493044493d3d4c86bda2f2a11485ecc968f34 Mon Sep 17 00:00:00 2001
From: John LaGrone <jlagrone@gmail.com>
Date: Mon, 22 Jan 2024 10:23:50 -0600
Subject: [PATCH 04/16] Start adding labels so links work in admonitions. See
 https://jupyterbook.org/en/stable/content/executable/output-insert.html#content-executable-output-insert

---
 docs/about/queues.md                   | 7 ++++---
 docs/tutorials/slurm/best_practices.md | 1 +
 docs/tutorials/slurm/slurm.md          | 1 +
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/docs/about/queues.md b/docs/about/queues.md
index 568829bb..1e37bbc0 100644
--- a/docs/about/queues.md
+++ b/docs/about/queues.md
@@ -1,11 +1,12 @@
+(about:queues)=
 # Queues
 
 SMU's high-performance computing (HPC) clusters use [SLURM](https://slurm.schedmd.com/)
 to schedule and manage resources.
 
-:::{seealso}
-For examples and tips on SLURM usage, see [our SLURM documentation](../slurm/slurm.md).
-:::
+```{seealso}
+For examples and tips on SLURM usage, see [our SLURM documentation](tutorials:slurm) and [Best Practices](tutorials:slurm:best_practices).
+```
 
 :::{note}
 The efficiency of SLURM and our HPC systems depend on reasonable resource requests.
diff --git a/docs/tutorials/slurm/best_practices.md b/docs/tutorials/slurm/best_practices.md
index d9ace642..cbf7e1d6 100644
--- a/docs/tutorials/slurm/best_practices.md
+++ b/docs/tutorials/slurm/best_practices.md
@@ -1,3 +1,4 @@
+(tutorials:slurm:best_practices)=
 # Best Practices for Jobs
 
 The following are some tips that will help your and everyone elses jobs use HPC resources more efficiently.
diff --git a/docs/tutorials/slurm/slurm.md b/docs/tutorials/slurm/slurm.md
index 67fa7497..9ba4b6c8 100644
--- a/docs/tutorials/slurm/slurm.md
+++ b/docs/tutorials/slurm/slurm.md
@@ -1,3 +1,4 @@
+(tutorials:slurm)=
 # Slurm
 
 ## Submitting Jobs Using Slurm

From ebffbf34c3c3084b32df25f4fe6ddc58898fdd37 Mon Sep 17 00:00:00 2001
From: John LaGrone <jlagrone@gmail.com>
Date: Mon, 22 Jan 2024 10:30:51 -0600
Subject: [PATCH 05/16] remove html divs. They don't appear to have been used /
 unrecognized command from interpreter

---
 docs/tutorials/slurm/slurm.md | 219 ----------------------------------
 1 file changed, 219 deletions(-)

diff --git a/docs/tutorials/slurm/slurm.md b/docs/tutorials/slurm/slurm.md
index 9ba4b6c8..1ee47d77 100644
--- a/docs/tutorials/slurm/slurm.md
+++ b/docs/tutorials/slurm/slurm.md
@@ -46,16 +46,10 @@ jobs:
     [here](https://computing.llnl.gov/linux/slurm/sinfo.html). The usage
     command (with the most-helpful optional arguments in brackets) is
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     $ sinfo [-a] [-l] [-n <nodes>] [-p <partition>] [-s] [-a] [-a] [-a]
     ```
 
-    ```{=html}
-    </div>
-    ```
     where these options are:
 
     -   `-a` or `--all` \-- Display information about all partitions
@@ -72,34 +66,21 @@ jobs:
 
     Examples:
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     $ sinfo --long -p highmem  # long output for all nodes allocated to the "highmem" partition
     $ sinfo -s                 # summarizes output on all nodes on all partitions
     ```
 
-    ```{=html}
-    </div>
-    ```
-
 -   `squeue` \-- views information about jobs located in the SLURM
     scheduling queue. A full list of options is available
     [here](https://computing.llnl.gov/linux/slurm/squeue.html). The
     usage command (with the most-helpful optional arguments in brackets)
     is
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     $ squeue [-a] [-j] [-l] [-p] [--start] [-u]
     ```
 
-    ```{=html}
-    </div>
-    ```
     where these options are:
 
     -   `-a` or `--all` \-- Display information about jobs and job steps
@@ -121,34 +102,22 @@ jobs:
 
     Examples:
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     $ squeue                            # all jobs
     $ squeue -u rkalescky --start       # anticipated start time of jobs
     $ squeue --jobs 12345,12346,12348   # information on only jobs 12345, 12346 and 12348
     ```
 
-    ```{=html}
-    </div>
-    ```
 
 -   `sbatch` \-- submits a batch script to SLURM. A full list of options
     is available
     [here](https://computing.llnl.gov/linux/slurm/sbatch.html). The
     usage command is
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     $ sbatch [options] `<script>` [args]
     ```
 
-    ```{=html}
-    </div>
-    ```
     where `<script>` is a *batch submission script*, and `[args]` are
     any optional arguments that should be supplied to `<script>`. The
     `sbatch` command accepts a multitude of options; these options may
@@ -166,32 +135,19 @@ jobs:
 
     Examples:
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     $ sbatch ./myscript.sh    # submits the batch submission file "myscript.sh" to SLURM
     ```
 
-    ```{=html}
-    </div>
-    ```
-
 -   `srun` \-- runs a parallel or interactive job on the worker nodes. A
     full list of options is available
     [here](https://computing.llnl.gov/linux/slurm/srun.html). The usage
     command (with the most-helpful optional arguments in brackets) is
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     $ srun [-D <path>] [-e <errf>] [--epilog=<executable>] [-o <outf>] [-p <part>] [--pty] [--x11] <executable>
     ```
 
-    ```{=html}
-    </div>
-    ```
     where these options are:
 
     -   `-D <path>` or `--chdir=<path>` \-- have the remote processes
@@ -227,35 +183,22 @@ jobs:
 
     Examples:
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     $ srun -p parallel /bin/program # runs executable /bin/program on "parallel" partition
     $ srun --x11=first --pty emacs  # runs "emacs" and forwards graphics
     $ srun --x11=first --pty $SHELL # runs a the user's current shell and forwards graphics
     ```
 
-    ```{=html}
-    </div>
-    ```
-
 -   `salloc` \-- obtains a SLURM job allocation (a set of nodes),
     executes a command, and then releases the allocation when the
     command is finished. A full list of options is available
     [here](https://computing.llnl.gov/linux/slurm/salloc.html). The
     usage command is
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     $ salloc [options] <command> [command args]
     ```
 
-    ```{=html}
-    </div>
-    ```
     where `<command> [command args]` specifies the command (and any
     arguments) to run. Available options are almost identical to `srun`,
     including:
@@ -279,16 +222,10 @@ jobs:
     usage command (with the most-helpful optional arguments in brackets)
     is
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     $ scancel [-i] [-n <job_name>] [-p <part>] [-t <state>] [-u <uname>] [jobid]
     ```
 
-    ```{=html}
-    </div>
-    ```
     where these options are:
 
     -   `-i` or `--interactive` \-- require response from user for each
@@ -308,19 +245,12 @@ jobs:
 
     Examples:
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     $ scancel 1234  # cancel job number 1234
     $ scancel -u rkalescky  # cancel all jobs owned by user "rkalescky"
     $ scancel -t PENDING -u joe  # cancel all pending jobs owned by user "joe"
     ```
 
-    ```{=html}
-    </div>
-    ```
-
 ### Example: Running Interactive Jobs
 
 In this example, we'll interactively run the Python script
@@ -334,16 +264,10 @@ better your answer*.
 
 While you can run this at the command line:
 
-```{=html}
-<div class="sourceCode">
-```
 ``` bash
 $ python ./pi_monte_carlo.py 50
 ```
 
-```{=html}
-</div>
-```
 as we increase the number of random values to obtain a more accurate
 approximation it can take longer to run, so as "good citizens" we
 should instead run it on dedicated compute nodes instead of the shared
@@ -352,23 +276,14 @@ login nodes.
 Before running this script on a compute node, we need to ensure that
 `myjob.py` has "executable" permissions:
 
-```{=html}
-<div class="sourceCode">
-```
 ``` bash
 $ chmod +x ./pi_monte_carlo.py
 ```
 
-```{=html}
-</div>
-```
 We'll use `srun` to run this script interactively for interval values
 of {50,500,5000,50000}. For each run, we'll direct the output to a
 separate file:
 
-```{=html}
-<div class="sourceCode">
-```
 ``` bash
 $ srun -o run_50.txt ./pi_monte_carlo.py 50
 $ srun -o run_500.txt ./pi_monte_carlo.py 500
@@ -376,23 +291,14 @@ $ srun -o run_5000.txt ./mpi_monte_carlo.py 5000
 $ srun -o run_50000.txt ./pi_monte_carlo.py 50000
 ```
 
-```{=html}
-</div>
-```
 Upon completion you should have the files `run_50.txt`, `run_500.txt`,
 `run_5000.txt` and `run_50000.txt` in your directory. View the results
 to ensure that things ran properly:
 
-```{=html}
-<div class="sourceCode">
-```
 ``` bash
 $ cat run_*
 ```
 
-```{=html}
-</div>
-```
 in the above commands we do not need to directly specify to run on the
 "development" SLURM partition, since that is the default partition.
 
@@ -407,23 +313,14 @@ A batch submission script is just that, a shell script. You are welcome
 to use your preferred shell scripting language; in this tutorial we'll
 use Bash. As a result, the script typically starts with the line
 
-```{=html}
-<div class="sourceCode">
-```
 ``` bash
 #!/bin/bash
 ```
 
-```{=html}
-</div>
-```
 The following lines (before any executable commands) contain the options
 to be supplied to the `sbatch` command. Each of these options must be
 prepended with the text `#SBATCH`, e.g.
 
-```{=html}
-<div class="sourceCode">
-```
 ``` bash
 #!/bin/bash
 #SBATCH -J my_program       # job name to display in squeue
@@ -433,9 +330,6 @@ prepended with the text `#SBATCH`, e.g.
 #SBATCH -t 180              # maximum runtime in minutes
 ```
 
-```{=html}
-</div>
-```
 Since each of these `sbatch` options begins with the character `#`, they
 are treated as comments by the Bash shell; however `sbatch` parses the
 file to find these and supply them as options for the job.
@@ -464,123 +358,67 @@ list the most useful options for running serial batch jobs.
 -   `-D <dir>` or `--workdir=<dir>` \-- sets the working directory where
     the batch script should be run, e.g.
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     #SBATCH -D /scratch/users/ezekiel/test_run
     ```
 
-    ```{=html}
-    </div>
-    ```
-
 -   `-J <name>` or `--job-name=<name>` \-- sets the job name as output
     by the `squeue` command, e.g.
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     #SBATCH -J test_job
     ```
 
-    ```{=html}
-    </div>
-    ```
-
 -   `-o <fname>` \-- sets the output file name for stdout and stderr (if
     stderr is left unspecified). The default standard output is directed
     to a file of the name `slurm-%j.out`, where `%j` corresponds to the
     job ID number. You can do something similar, e.g.
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     #SBATCH -o output-%j.txt
     ```
 
-    ```{=html}
-    </div>
-    ```
-
 -   `-e <fname>` \-- sets the output file name for stderr only. The
     default is to combine this with stdout. An example similar to `-o`
     above would be
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     #SBATCH -e error-%j.txt
     ```
 
-    ```{=html}
-    </div>
-    ```
-
 -   `-i <fname>` or `--input=<fname>` \-- sets the standard input stream
     for the running job. For example, if an executable program will
     prompt the user for text input, these inputs may be placed in a file
     `inputs.txt` and specified to the script via
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     #SBATCH -i inputs.txt
     ```
 
-    ```{=html}
-    </div>
-    ```
-
 -   `-p <part>` \-- tells SLURM on which partition it should submit the
     job. The options are "interactive", "highmem" or "parallel".
     For example, so submit a batch job to a high-memory node you would
     use
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     #SBATCH -p highmem
     ```
 
-    ```{=html}
-    </div>
-    ```
-
 -   `-t <num>` \-- tells SLURM the maximum runtime to be allowed for the
     job (in minutes). For example, to allow a job to run for up to 3
     hours you would use
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     #SBATCH -t 180
     ```
 
-    ```{=html}
-    </div>
-    ```
-
 -   `--exclusive` \-- tells SLURM that the job can not share nodes with
     other running jobs.
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     #SBATCH --exclusive
     ```
 
-    ```{=html}
-    </div>
-    ```
-
 -   `-s` or `--share` \-- tells SLURM that the job can share nodes with
     other running jobs. This is the opposite of `--exclusive`, whichever
     option is seen last on the command line will be used. This option
@@ -589,31 +427,17 @@ list the most useful options for running serial batch jobs.
     application performance will likely suffer due to competition for
     resources within a node.
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     #SBATCH -s
     ```
 
-    ```{=html}
-    </div>
-    ```
-
 -   `--mail-user <email address>` \-- tells SLURM your email address if
     you'd like to receive job-related email notifications, e.g.
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     #SBATCH --mail-user peruna@smu.edu
     ```
 
-    ```{=html}
-    </div>
-    ```
-
 -   `--mail-type=<flag>` \-- tells SLURM which types of email
     notification messages you wish to receive. Options include:
 
@@ -625,17 +449,10 @@ list the most useful options for running serial batch jobs.
 
     For example,
 
-    ```{=html}
-    <div class="sourceCode">
-    ```
     ``` bash
     #SBATCH --mail-type=all
     ```
 
-    ```{=html}
-    </div>
-    ```
-
 ### Running Batch Jobs
 
 Here we'll look at six ways to run jobs on ManeFrame II using Slurm.
@@ -649,57 +466,36 @@ Here we'll look at six ways to run jobs on ManeFrame II using Slurm.
 
 #### Interactive Session Via `srun`
 
-```{=html}
-<div class="sourceCode">
-```
 ``` bash
 module load python
 srun -p htc --pty $SHELL
 python pi_monte_carlo.py 1000
 ```
 
-```{=html}
-</div>
-```
 This method involves interactively requesting a HTC compute node and
 then running the calculation manually.
 
 #### Single Interactive Job Via `srun`
 
-```{=html}
-<div class="sourceCode">
-```
 ``` bash
 srun -p htc python pi_monte_carlo.py 1000
 ```
 
-```{=html}
-</div>
-```
 This method interactively requests that the calculation be directly run
 on the requested resource.
 
 #### Single-Threaded Batch Job via `sbatch`'s Wrapping Function
 
-```{=html}
-<div class="sourceCode">
-```
 ``` bash
 sbatch -p htc --wrap "sleep 30; time python pi_monte_carlo.py 1000"
 ```
 
-```{=html}
-</div>
-```
 This method submits a batch job by wrapping the command line that you
 wish to run in an `sbatch` script that is then submited for you. This
 method is non-interactive.
 
 #### Single Threaded Batch Job via Batch Script
 
-```{=html}
-<div class="sourceCode">
-```
 ``` bash
 #!/bin/bash
 #SBATCH -J python
@@ -712,17 +508,11 @@ module load python
 time python pi_monte_carlo.py 1000
 ```
 
-```{=html}
-</div>
-```
 This batch script is manually creatd and then submited via
 `sbatch 04_sbatch_htc.sbatch`.
 
 #### Single Multi-Threaded Job via Batch Script
 
-```{=html}
-<div class="sourceCode">
-```
 ``` bash
 #!/bin/bash
 #SBATCH -J pi
@@ -737,17 +527,11 @@ module load python
 time python pi_monte_carlo_shared.py 10000000 ${SLURM_NTASKS}
 ```
 
-```{=html}
-</div>
-```
 This batch script runs a parallel version of the Monte Carlo *π*
 approximation script on two cores.
 
 #### Array of Single Threaded Jobs via Batch Script
 
-```{=html}
-<div class="sourceCode">
-```
 ``` bash
 #!/bin/bash
 #SBATCH -J pi_array
@@ -761,8 +545,5 @@ module load python
 time python pi_monte_carlo.py $((10**${SLURM_ARRAY_JOB_ID}))
 ```
 
-```{=html}
-</div>
-```
 This batch script submits a job that will perform an array of jobs in
 parallel as allowed by the queue system.

From e413702eb4f559cee27df2d6d95148e01b5f2d6e Mon Sep 17 00:00:00 2001
From: John LaGrone <jlagrone@gmail.com>
Date: Mon, 22 Jan 2024 12:21:25 -0600
Subject: [PATCH 06/16] add a contact page

---
 docs/about/contact.md | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 docs/about/contact.md

diff --git a/docs/about/contact.md b/docs/about/contact.md
new file mode 100644
index 00000000..ae9e9137
--- /dev/null
+++ b/docs/about/contact.md
@@ -0,0 +1,17 @@
+(about:contact)=
+# Contact
+
+We can be contacted using SMU's Help Desk. 
+
+Tickets can be directly created using the [STABLE ticketing system](https://www.smu.edu/OIT/services/STABLE).
+
+You can also email [help@smu.edu](mailto:help@smu.edu?subject=[HPC]). Please be sure to include `[HPC]` in the subject for more expedient routing.
+
+# GitHub
+
+:::{important}
+Time critical and emergency issues should **always** go through SMU's Help Desk.
+:::
+
+We also actively use GitHub. You are welcome to open issues and/or create pull requests [our github page](https://github.com/SouthernMethodistUniversity/hpc_docs).
+

From ba3bdbc79dc9a2289f17c14b3c1822fff51bcac5 Mon Sep 17 00:00:00 2001
From: John LaGrone <jlagrone@gmail.com>
Date: Mon, 22 Jan 2024 12:21:54 -0600
Subject: [PATCH 07/16] add a chemistry landing page

---
 docs/examples/chemistry.md | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 docs/examples/chemistry.md

diff --git a/docs/examples/chemistry.md b/docs/examples/chemistry.md
new file mode 100644
index 00000000..1468969d
--- /dev/null
+++ b/docs/examples/chemistry.md
@@ -0,0 +1,13 @@
+(examples:chemistry)=
+# Chemistry
+
+We have examples of submitting jobs using the following 
+software packages.
+
+If you would like examples for other software packages,
+please [contact us.](about:contact).
+
+You can also submit issues and/or pull requests for updates or additions at
+[our github page](https://github.com/SouthernMethodistUniversity/hpc_docs)
+
+- [Amber](amber/index.md)
\ No newline at end of file

From f7ab70d6d7d362be0f0d3d4ef8295fdfa5fbbbff Mon Sep 17 00:00:00 2001
From: John LaGrone <jlagrone@gmail.com>
Date: Mon, 22 Jan 2024 12:22:37 -0600
Subject: [PATCH 08/16] update TOC

---
 docs/_toc.yml        | 4 ++++
 docs/about/queues.md | 4 ++--
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/docs/_toc.yml b/docs/_toc.yml
index fb9eb9a6..7161934a 100644
--- a/docs/_toc.yml
+++ b/docs/_toc.yml
@@ -8,6 +8,7 @@ parts:
   - file: about.md
     sections:
     - file: about/queues.md
+    - file: about/contact.md
   - file: accounts.md
   - file: access.md
   - file: portal.md
@@ -15,6 +16,9 @@ parts:
   - file: mp_update.md
 - caption: Applications
   chapters:
+  - file: examples/chemistry.md
+    sections: 
+    - file: examples/amber/index.md
   - file: examples/conda/README.md
   - file: examples/torch/README.md
 - caption: Tutorials
diff --git a/docs/about/queues.md b/docs/about/queues.md
index 1e37bbc0..2a543ac9 100644
--- a/docs/about/queues.md
+++ b/docs/about/queues.md
@@ -4,9 +4,9 @@
 SMU's high-performance computing (HPC) clusters use [SLURM](https://slurm.schedmd.com/)
 to schedule and manage resources.
 
-```{seealso}
+:::{seealso}
 For examples and tips on SLURM usage, see [our SLURM documentation](tutorials:slurm) and [Best Practices](tutorials:slurm:best_practices).
-```
+:::
 
 :::{note}
 The efficiency of SLURM and our HPC systems depend on reasonable resource requests.

From ad18192b4df59a01900fbc30ee65177e5118fbd3 Mon Sep 17 00:00:00 2001
From: John LaGrone <jlagrone@gmail.com>
Date: Mon, 22 Jan 2024 12:54:14 -0600
Subject: [PATCH 09/16] add more flags and comments to job script

---
 docs/examples/amber/amber_cpu_example.sbatch | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/docs/examples/amber/amber_cpu_example.sbatch b/docs/examples/amber/amber_cpu_example.sbatch
index 96ab4d45..0f56e8f9 100644
--- a/docs/examples/amber/amber_cpu_example.sbatch
+++ b/docs/examples/amber/amber_cpu_example.sbatch
@@ -1,13 +1,16 @@
 #!/bin/bash
-#SBATCH -J example
-#SBATCH -o example_%j.out
-#SBATCH -p dev
-#SBATCH -N 1
-#SBATCH --ntasks-per-node=4
+#SBATCH -J amber_example          # Job name, display in queue
+#SBATCH -o amber_example_%j.out   # output file, %j is the job id
+#SBATCH -p dev                    # partition to use
+#SBATCH -N 1                      # number of nodes
+#SBATCH -c 1                      # number of cpu cores per task
+#SBATCH --ntasks-per-node=4       # number of tasks per node
+#SBATCH --mem=1G                  # memory per node
+#SBATCH -t 0-00:03:00             # run time, days-HH:MM:SS
 
 # Amber
 module purge
-module load amber
+module load amber/22
 
 # Program Command
 srun sander.MPI -O -o stdout -i alanine_md.in -c alanine_md.rst -p alanine_md.prmtop -r alanine_md_new.rst -x alanine_md_new.mdcrd

From ef6dc3371bff71844f2e7d59fdf556b6fc5ad0d5 Mon Sep 17 00:00:00 2001
From: John LaGrone <jlagrone@gmail.com>
Date: Mon, 22 Jan 2024 13:03:44 -0600
Subject: [PATCH 10/16] add some comments to M3 example

---
 docs/examples/amber/index.md | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/docs/examples/amber/index.md b/docs/examples/amber/index.md
index a703e12b..dbe4041d 100644
--- a/docs/examples/amber/index.md
+++ b/docs/examples/amber/index.md
@@ -21,6 +21,8 @@ Files used in the example are available:
 
 ### Example submission script
 
+The following job script can be submitted using `sbatch amber_gpu_example.sbatch`.
+
 ```{literalinclude} amber_gpu_example.sbatch
 ---
 language: bash
@@ -37,6 +39,15 @@ Files used in the example are available:
 
 ### Example submission script
 
+The following job script can be submitted using `sbatch amber_cpu_example.sbatch`.
+
+This example should run in approximately 90 seconds and use about 600 MB of memory when using 4 cores. Therefore, we request 1 GB of memory and 3 minutes of run time to give
+ourselves some room for error. 
+
+Note, we know this from running the job. 
+It is always a good idea to review the resources your jobs use
+and adjust future jobs to more accurately request resources.
+
 ```{literalinclude} amber_cpu_example.sbatch                 
 ---
 language: bash

From 78933afec04f2217a2dc95213d8ad64e01f5094f Mon Sep 17 00:00:00 2001
From: John LaGrone <jlagrone@gmail.com>
Date: Mon, 22 Jan 2024 14:55:51 -0600
Subject: [PATCH 11/16] fix links

---
 docs/examples/amber/index.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/examples/amber/index.md b/docs/examples/amber/index.md
index dbe4041d..2c87e5b2 100644
--- a/docs/examples/amber/index.md
+++ b/docs/examples/amber/index.md
@@ -1,9 +1,9 @@
 # Amber
 
 :::{seealso}
-For examples and tips on submitting jobs, see [our SLURM documentation](../../slurm/slurm.md) and [Best Practices for Jobs](../../slurm/best_practices.md)
+For examples and tips on submitting jobs, see [our SLURM documentation](tutorials:slurm) and [Best Practices for Jobs](tutorials:slurm:best_practices)
 
-For compute resources, see [HPC Queues](../../about/queeues.md)
+For compute resources, see [HPC Queues](about:queues)
 :::
 
 **Amber** is a suite of biomolecular simulation programs.

From 130eba627034cee1e73f0459975b87158ca174b1 Mon Sep 17 00:00:00 2001
From: John LaGrone <jlagrone@gmail.com>
Date: Mon, 22 Jan 2024 14:58:37 -0600
Subject: [PATCH 12/16] remove M2 reference

---
 docs/policies/policies.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/policies/policies.md b/docs/policies/policies.md
index 64ea1936..cb1b801a 100644
--- a/docs/policies/policies.md
+++ b/docs/policies/policies.md
@@ -2,7 +2,7 @@
 
 ## Account and Account Password Sharing Policy
 
-No two individuals should share the same ManeFrame II account, nor
+No two individuals should share the same HPC account, nor
 should two individuals share the password of the same account. Each
 individual is entitled to have their own account hence please request
 one.

From 4fd80ece8f3e88d476f35680bbd0cd12471446c7 Mon Sep 17 00:00:00 2001
From: John LaGrone <jlagrone@gmail.com>
Date: Mon, 22 Jan 2024 15:37:01 -0600
Subject: [PATCH 13/16] move seealso

---
 docs/examples/amber/index.md | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/docs/examples/amber/index.md b/docs/examples/amber/index.md
index 2c87e5b2..6357f2a5 100644
--- a/docs/examples/amber/index.md
+++ b/docs/examples/amber/index.md
@@ -1,17 +1,17 @@
 # Amber
 
-:::{seealso}
-For examples and tips on submitting jobs, see [our SLURM documentation](tutorials:slurm) and [Best Practices for Jobs](tutorials:slurm:best_practices)
-
-For compute resources, see [HPC Queues](about:queues)
-:::
-
 **Amber** is a suite of biomolecular simulation programs.
 
 **Amber homepage**: [ambermd.org/](https://ambermd.org/)
 
 **Official Amber Tutorials**: [ambermd.org/tutorials/](https://ambermd.org/tutorials/)
 
+:::{seealso}
+For examples and tips on submitting jobs, see [our SLURM documentation](tutorials:slurm) and [Best Practices for Jobs](tutorials:slurm:best_practices)
+
+For compute resources, see [HPC Queues](about:queues)
+:::
+
 ## Using Amber on the SuperPod
 
 Files used in the example are available: 

From a7ef65c7aad51acafcc6df22d595ef80ed40bf8d Mon Sep 17 00:00:00 2001
From: John LaGrone <jlagrone@gmail.com>
Date: Mon, 22 Jan 2024 15:38:57 -0600
Subject: [PATCH 14/16] fix path for cpp example

---
 docs/tutorials/cpp/session_4.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/tutorials/cpp/session_4.md b/docs/tutorials/cpp/session_4.md
index 76647026..95528b28 100644
--- a/docs/tutorials/cpp/session_4.md
+++ b/docs/tutorials/cpp/session_4.md
@@ -47,7 +47,7 @@ linenos: true
 ---
 ```
 
-```{literalinclude} ../../examples/cpp/classes/inheritance_test.hpp
+```{literalinclude} ../../examples/cpp/classes/inheritance_test.cpp
 ---
 language: c++
 linenos: true

From 65fe63fe1ed595d35c9ef7134e476d76330b50ee Mon Sep 17 00:00:00 2001
From: John LaGrone <jlagrone@gmail.com>
Date: Fri, 19 Jul 2024 09:00:16 -0500
Subject: [PATCH 15/16] add openfoam example

---
 docs/examples/openfoam/decomposeParDict       | 65 +++++++++++++++++++
 docs/examples/openfoam/index.md               | 44 +++++++++++++
 docs/examples/openfoam/openfoam.sh            |  7 --
 .../openfoam/openfoam_cpu_example.sbatch      | 31 +++++++++
 4 files changed, 140 insertions(+), 7 deletions(-)
 create mode 100644 docs/examples/openfoam/decomposeParDict
 create mode 100644 docs/examples/openfoam/index.md
 delete mode 100644 docs/examples/openfoam/openfoam.sh
 create mode 100644 docs/examples/openfoam/openfoam_cpu_example.sbatch

diff --git a/docs/examples/openfoam/decomposeParDict b/docs/examples/openfoam/decomposeParDict
new file mode 100644
index 00000000..0b20cd18
--- /dev/null
+++ b/docs/examples/openfoam/decomposeParDict
@@ -0,0 +1,65 @@
+/*---------------------------------------------------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  1.3                                   |
+|   \\  /    A nd           | Web:      http://www.openfoam.org               |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+    version         2.0;
+    format          ascii;
+
+    root            "";
+    case            "";
+    instance        "";
+    local           "";
+
+    class           dictionary;
+    object          decomposeParDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+
+numberOfSubdomains 4;
+
+method          simple;
+
+simpleCoeffs
+{
+    n               (1 4 1);
+    delta           0.001;
+}
+
+hierarchicalCoeffs
+{
+    n               (1 1 1);
+    delta           0.001;
+    order           xyz;
+}
+
+metisCoeffs
+{
+    processorWeights
+    (
+        1
+        1
+        1
+    );
+}
+
+manualCoeffs
+{
+    dataFile        "";
+}
+
+distributed     no;
+
+roots
+(
+);
+
+
+// ************************************************************************* //
\ No newline at end of file
diff --git a/docs/examples/openfoam/index.md b/docs/examples/openfoam/index.md
new file mode 100644
index 00000000..01820b8e
--- /dev/null
+++ b/docs/examples/openfoam/index.md
@@ -0,0 +1,44 @@
+# OpenFoam (.com)
+
+**OpenFoam** is an open source Computation Fluid Dynamics Package.
+
+**OpenFoam homepage**: [openfoam.com/](https://www.openfoam.com/)
+
+**Official OpenFoam Tutorials**: [openfoam.com/documentation/tutorial-guide](https://www.openfoam.com/documentation/tutorial-guide)
+
+
+:::{seealso}
+For examples and tips on submitting jobs, see [our SLURM documentation](tutorials:slurm) and [Best Practices for Jobs](tutorials:slurm:best_practices)
+
+For compute resources, see [HPC Queues](about:queues)
+:::
+
+
+## Using OpenFoam on M3
+
+Files used in the example are available:
+
+  - [on github](https://github.com/SouthernMethodistUniversity/hpc_docs/tree/update_examples/docs/examples/openfoam)
+  - on M3 at `/hpc/m3/examples/openfoam/` 
+
+### Example submission script
+
+The following job script can be submitted using `sbatch openfoam_example.sbatch`.
+
+It requires a `decomposeParDict` to run, (see e.g. [running in paralell](https://doc.cfd.direct/openfoam/user-guide-v12/running-applications-parallel)). An example file is included in the files mentioned above
+
+This example should run in approximately 10 seconds and use about 600 MB of memory when using 4 tasks. 
+Therefore, we request 1 GB of memory and 3 minutes of run time to give
+ourselves some room for error. 
+
+Note, we know this from running the job. 
+It is always a good idea to review the resources your jobs use
+and adjust future jobs to more accurately request resources.
+
+```{literalinclude} openfoam_cpu_example.sbatch
+---
+language: bash
+linenos: true
+---
+```
+
diff --git a/docs/examples/openfoam/openfoam.sh b/docs/examples/openfoam/openfoam.sh
deleted file mode 100644
index 6a514060..00000000
--- a/docs/examples/openfoam/openfoam.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-module purge
-export HPCX_HOME=/hpc/applications/hpc-x/hpcx-v2.0.0-gcc-MLNX_OFED_LINUX-4.2-1.0.0.0-redhat7.3-x86_64
-module use $HPCX_HOME/modulefiles
-module load gcc-4.8.5
-module load hpcx scotch/6.0.4-ztlbfxi qt/5.9.1-bxmsbfc cmake/3.8.1-ncxngnb
-source /hpc/applications/openfoam/OpenFOAM-5.0/etc/bashrc
-
diff --git a/docs/examples/openfoam/openfoam_cpu_example.sbatch b/docs/examples/openfoam/openfoam_cpu_example.sbatch
new file mode 100644
index 00000000..e96d3100
--- /dev/null
+++ b/docs/examples/openfoam/openfoam_cpu_example.sbatch
@@ -0,0 +1,31 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=4
+#SBATCH --mem=10G
+#SBATCH --job-name=OpenFOAM
+#SBATCH --output=output_OpenFOAM_%j.out
+#SBATCH --time=00:05:00
+#SBATCH -p dev
+
+# load openfoam
+module purge
+module load gcc/11.2.0
+module load openfoam/2312-5z7e7ot
+module load openmpi/4.1.6-vfi4iwj
+
+# make a test directory in scratch with the Job id
+# NOTE: $SCRATCH has a 60 day purge policy
+mkdir -p ${SCRATCH}/openfoam/test_run_${SLURM_JOB_ID}/
+cd ${SCRATCH}/openfoam/test_run_${SLURM_JOB_ID}/
+
+# copy example from official tutorial
+cp -r $FOAM_TUTORIALS/incompressible/simpleFoam/pitzDaily .
+chmod 700 -R pitzDaily && cd pitzDaily
+
+# copy our decomposeParDict into the $SCRATCH job folder
+cp ${SLURM_SUBMIT_DIR}/decomposeParDict system/decomposeParDict
+
+# run the example
+srun blockMesh
+srun decomposePar
+srun simpleFoam -parallel
\ No newline at end of file

From 8505354793b47331faaebe5fbb93205b49156130 Mon Sep 17 00:00:00 2001
From: John LaGrone <jlagrone@gmail.com>
Date: Fri, 19 Jul 2024 09:03:02 -0500
Subject: [PATCH 16/16] add landing page for fluids examples

---
 docs/examples/fluid_dynamics.md | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 docs/examples/fluid_dynamics.md

diff --git a/docs/examples/fluid_dynamics.md b/docs/examples/fluid_dynamics.md
new file mode 100644
index 00000000..de96dcdd
--- /dev/null
+++ b/docs/examples/fluid_dynamics.md
@@ -0,0 +1,13 @@
+(examples:fluids)=
+# Fluid Dynamics
+
+We have examples of submitting jobs using the following 
+software packages.
+
+If you would like examples for other software packages,
+please [contact us.](about:contact).
+
+You can also submit issues and/or pull requests for updates or additions at
+[our github page](https://github.com/SouthernMethodistUniversity/hpc_docs)
+
+- [OpenFOAM (.com)](openfoam/index.md)
\ No newline at end of file