Updates for CP2K and Gromacs to new Format (#29)

Author: cmcknigh

README.md

@@ -5,7 +5,7 @@ Each builds provides parameters to specify different source code branches, relea
 
 ## Single-Node Server Requirements
 | CPUs | GPUs | Operating Systems | ROCm™ Driver | Container Runtimes | 
-| ---- | ---- | ----------------- | ------------ | ------------------ | 
+|---- |---- |----------------- |------------ |------------------ | 
 | X86_64 CPU(s) | AMD Instinct MI200 GPU(s) <br>  AMD Instinct MI100 GPU(s) | Ubuntu 20.04 <br> Ubuntu 22.04 <BR> RHEL8 <br> RHEL9 <br> SLES 15 sp4 | ROCm v5.x compatibility |[Docker Engine](https://docs.docker.com/engine/install/) <br> [Singularity](https://sylabs.io/docs/) |
 
 For ROCm installation procedures and validation checks, see:
@@ -14,21 +14,25 @@ For ROCm installation procedures and validation checks, see:
 * [ROCm Examples](https://github.com/amd/rocm-examples)
 
 ## Applications:
- - [AMD Base Docker Container for GPU-Aware MPI in ROCm applications](/base-gpu-mpi-rocm-docker/)
- - [AMD's Implementation of Gromacs with HIP in Docker](/gromacs-docker/)
- - [Cholla](/cholla)
-   - [Docker](/cholla/docker/)
-   - [Bare Metal](/cholla/baremetal/)
- - [CP2K](/cp2k-docker/)
- - [Grid](/grid/)
-    - [Docker](/grid/docker/)
- - [HPCG in Docker](/hpcg-docker/)
- - [LAMMPS in Docker](/lammps-docker/)
- - [OpenFOAM in Docker](/openfoam-docker/)
- - [OpenMM in Docker](/openmm-docker/)
- - [PETSc in Docker](/petsc-docker/)
- - [PyFR in Docker](/pyfr-docker/)
- - [rocHPL](/rochpl/)
-    - [Docker](/rochpl/docker/)
-    - [Spack](/rochpl/spack/)
- - [Specfem3D - Cartesian](/specfem3d/)
+- [AMD Base Docker Container for GPU-Aware MPI in ROCm applications](/base-gpu-mpi-rocm-docker/)
+- [AMD's Implementation of Gromacs with HIP](/gromacs/)
+  - [Bare Metal](/gromacs/baremetal/)
+  - [Docker](/gromacs/docker/)
+- [Cholla](/cholla)
+  - [Bare Metal](/cholla/baremetal/)
+  - [Docker](/cholla/docker/)
+- [CP2K](/cp2k/)
+  - [Bare Metal](/cp2k/baremetal/)
+  - [Docker](/cp2k/docker/)
+- [Grid](/grid/)
+  - [Docker](/grid/docker/)
+- [HPCG in Docker](/hpcg-docker/)
+- [LAMMPS in Docker](/lammps-docker/)
+- [OpenFOAM in Docker](/openfoam-docker/)
+- [OpenMM in Docker](/openmm-docker/)
+- [PETSc in Docker](/petsc-docker/)
+- [PyFR in Docker](/pyfr-docker/)
+- [rocHPL](/rochpl/)
+  - [Docker](/rochpl/docker/)
+  - [Spack](/rochpl/spack/)
+- [Specfem3D- Cartesian](/specfem3d/)

cholla/README.md

@@ -31,8 +31,8 @@ For ROCm installation procedures and validation checks, see:
 * [ROCm Examples](https://github.com/amd/rocm-examples)
 
 ## Build Recipes
+- [Bare Metal Build](/cholla/baremetal/)
 - [Docker/Singularity Build](/cholla/docker/)
-- [Baremetal Build](/cholla/baremetal/)
 
 ## Running Cholla Benchmarks
 These examples are using the [Cholla Docker Build](/cholla/docker/), which build the binary file cholla.hydro.cholla-container based on environment variable `CHOLLA_MACHINE` set to `cholla-container` and was build/installed into `/opt/cholla`. 
@@ -45,10 +45,22 @@ You can run the examples using the command syntax below, where `#` is the number
 mpirun -np # cholla.hydro.cholla-container <benchmark-to-run>
 ```
 ### Examples: 
-* 4 GPU 3D sound wave<br>`mpirun -np 4 cholla.hydro.cholla-container /opt/cholla/examples/3D/sound_wave.txt`
-* 8 GPU 3D Sound wave<br>`mpirun -np 8 cholla.hydro.cholla-container /opt/cholla/examples/3D/sound_wave.txt`
-* 4 GPU 3D sod<br> `mpirun -np 4 cholla.hydro.cholla-container /opt/cholla/examples/3D/sod.txt`
-* 8 GPU 3D sod<br> `mpirun -np 8 cholla.hydro.cholla-container /opt/cholla/examples/3D/sod.txt`
+* 4 GPU 3D sound wave
+```
+mpirun -np 4 cholla.hydro.cholla-container /opt/cholla/examples/3D/sound_wave.txt
+```
+* 8 GPU 3D Sound wave
+```
+mpirun -np 8 cholla.hydro.cholla-container /opt/cholla/examples/3D/sound_wave.txt
+```
+* 4 GPU 3D sod<br> 
+```
+mpirun -np 4 cholla.hydro.cholla-container /opt/cholla/examples/3D/sod.txt
+```
+* 8 GPU 3D sod<br> 
+```
+mpirun -np 8 cholla.hydro.cholla-container /opt/cholla/examples/3D/sod.txt
+```
 
 Each MPI rank will bind to a particular unique GPU (1 rank per device) and strong-scale the problem accordingly. Please define `HIP_VISIBLE_DEVICES` to control which particular GPUs are available to Cholla. 
 

cholla/baremetal/README.md

@@ -13,7 +13,7 @@ For ROCm installation procedures and validation checks, see:
 * [AMD Lab Notes ROCm installation notes](https://github.com/amd/amd-lab-notes/tree/release/rocm-installation).
 * [ROCm Examples](https://github.com/amd/rocm-examples)
 
-### System Dependencies
+## System Dependencies
 |Application|Minimum|Recommended|
 |---|---|---|
 |Git|Latest|Latest|
@@ -22,7 +22,7 @@ For ROCm installation procedures and validation checks, see:
 |UCX|1.13.0|1.14.1|
 |HDF5|1.12.1|1.14.1|
 
-### Installing Cholla
+## Installing Cholla
 
 1. Validate the Cluster/System has all of the above applications, with system path, library, and include environments set correctly. If you are unsure, the [Dockerfile](/cholla/docker/Dockerfile) has examples of all useful configurations listed after the `ENV` commands. 
 2. Clone the [Cholla GIT repo](https://github.com/cholla-hydro/cholla.git) into your workspace. 

cholla/docker/README.md

@@ -3,6 +3,10 @@
 ## Overview
 This document provides instructions on how to build Cholla into a Docker container that is portable between environments.
 
+### Build System Requirements
+- Git
+- Docker
+
 ## Inputs
 Possible `build-arg` for the Docker build command  
 
@@ -69,7 +73,7 @@ If you want access to the HDF5 files generated during the run, please add `-v $(
 ```
 docker run --rm -it --device=/dev/kfd --device=/dev/dri --security-opt seccomp=unconfined mycontainer/cholla /bin/bash
 ```
-#### Docker Non-Interactive
+#### Docker Single Command
 ```
 docker run --rm -it --device=/dev/kfd --device=/dev/dri --security-opt seccomp=unconfined mycontainer/cholla <Cholla Command>
 ```
@@ -88,7 +92,7 @@ To launch a Singularity image build locally.
 singularity shell --no-home --writable-tmpfs -pwd /benchmark cholla.sif
 ```
 
-#### Singularity Non-Interactive
+#### Singularity Single Command
 To launch a Singularity image build locally.
 ```
 singularity run --no-home --writable-tmpfs -pwd /benchmark cholla.sif <Cholla Command>
@@ -117,5 +121,3 @@ The information contained herein is for informational purposes only, and is subj
 © 2022-2023 Advanced Micro Devices, Inc. All rights reserved. AMD, the AMD Arrow logo, Instinct, Radeon Instinct, ROCm, and combinations thereof are trademarks of Advanced Micro Devices, Inc.
 
 Docker and the Docker logo are trademarks or registered trademarks of Docker, Inc. in the United States and/or other countries. Docker, Inc. and other parties may also have trademark rights in other terms used herein. Linux® is the registered trademark of Linus Torvalds in the U.S. and other countries.
-
-All other trademarks and copyrights are property of their respective owners and are only mentioned for informative purposes.