deploy: 2a4cb7a

Author: jrlagrone

_sources/examples/chemistry.md

@@ -10,4 +10,5 @@ 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)
+- [Amber](amber/index.md)
+- [Gaussian](gaussian/index.md)

_sources/examples/gaussian/index.md

@@ -0,0 +1,84 @@
+# Gaussian
+
+:::{important}
+Access to Gaussian requires permission. Please open a help ticket by emailing
+[help@smu.edu with
+"[HPC]"](mailto:help@smu.edu?subject=[HPC]%20Gaussian%20Access%20Request)
+in the subject line.
+:::
+
+**Gaussian** Gaussian series of electronic structure programs, used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide.
+
+**Gaussian homepage**: [gaussian.com/](https://gaussian.com/)
+
+**Official Gaussian Manual**: [gaussian.com/man/](https://gaussian.com/man/)
+
+:::{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 Gaussian on the SuperPod
+
+Files used in the example are available:
+
+  - [on github](https://github.com/SouthernMethodistUniversity/hpc_docs/tree/main/docs/examples/gaussian)
+  - on the SuperPod at `/hpc/mp/examples/gaussian/`
+
+### Example submission script
+
+The following job script can be submitted using `sbatch gaussian_gpu_example.sbatch`.
+
+```{literalinclude} gaussian_gpu_example.sbatch
+---
+language: bash
+linenos: true
+---
+``` -->
+
+## Using Gaussian on M3
+
+Files used in the example are available:
+
+  - [on github](https://github.com/SouthernMethodistUniversity/hpc_docs/tree/main/docs/examples/gaussian)
+  - on M3 at `/hpc/m3/examples/gaussian/` 
+
+### Example submission script
+
+The following job script can be submitted using `sbatch guassian_cpu_example.sbatch`.
+
+This example will run in about 10 seconds and use less that `1GB` of memory.
+In general, more complicated simulations will take much longer and should typically
+use more cores and memory. 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.
+
+This uses the `dev`
+queue which has a 2 hour time limit.
+In general, the `dev` queue should only be used for testing code and running interactive
+sessions.
+Most normal jobs should be submitted to the standard queues such as `standard-s` where
+longer runtimes are allowed.
+
+This example also writes output to `$SCRATCH`. 
+`$SCRATCH` is a high performance file system designed to be used for temporary
+job files and data.
+After a job has finished running, any data you need to keep should be moved to
+a project directory or your $HOME directory.
+**Files in `SCRATCH` are subject to a 60 day purge policy where files older than 60 days
+may be automatically deleted without warning.**
+
+:::{note}
+This job script will not run without modification. In particular, you must change
+the account from `peruna_project_0001` to the account name for an allocation you
+have access to.
+:::
+
+```{literalinclude} gaussian_cpu_example.sbatch                 
+---
+language: bash
+linenos: true
+---
+```
+

examples/chemistry.html

@@ -414,6 +414,7 @@ <h1>Chemistry</h1>
 <a class="reference external" href="https://github.com/SouthernMethodistUniversity/hpc_docs">our github page</a></p>
 <ul class="simple">
 <li><p><a class="reference internal" href="amber/index.html"><span class="doc std std-doc">Amber</span></a></p></li>
+<li><p><a class="reference internal" href="gaussian/index.html"><span class="doc std std-doc">Gaussian</span></a></p></li>
 </ul>
 <div class="toctree-wrapper compound">
 </div>