Merge pull request #187 from SouthernMethodistUniversity/update_examples

Update examples

docs/_toc.yml

@@ -8,13 +8,17 @@ parts:
   - file: about.md
     sections:
     - file: about/queues.md
+    - file: about/contact.md
   - file: accounts.md
   - file: access.md
   - file: portal.md
   - file: m3_migration.md
   - 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

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 [[email protected]](mailto:[email protected]?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).
+

docs/about/queues.md

@@ -1,3 +1,4 @@
+(about:queues)=
 # Queues
 
 SMU's high-performance computing (HPC) clusters use [SLURM](https://slurm.schedmd.com/)

docs/examples/amber/amber_cpu_example.sbatch

@@ -1,17 +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 use ../../../modules/m3/applications/
-module load amber
-
-echo $(module list)
-echo $(which mpicc)
+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

docs/examples/amber/index.md

@@ -0,0 +1,57 @@
+# 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/)
+
+:::{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: 
+
+  - [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
+
+The following job script can be submitted using `sbatch amber_gpu_example.sbatch`.
+
+```{literalinclude} amber_gpu_example.sbatch
+---
+language: bash
+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
+
+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
+linenos: true
+---
+```
+

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)

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)

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
+(
+);
+
+
+// ************************************************************************* //

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
+---
+```
+

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

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

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.

docs/tutorials/slurm/slurm.md

@@ -1,3 +1,4 @@
+(tutorials:slurm)=
 # Slurm
 
 ## Submitting Jobs Using Slurm