Ubuntu update, readme spelling updates

Fixing several spelling errors, a couple updates between ubuntu 20 and 22.

Author: cmcknigh

README.md

@@ -24,3 +24,4 @@ For ROCm installation procedures and validation checks, see:
  - [PETSc in Docker](/petsc-docker/)
  - [PyFR in Docker](/pyfr-docker/)
  - [rocHPL](/rochpl/)
+ - [Specfem3D - Cartesian](/specfem3d/)

gromacs-docker/Dockerfile

@@ -35,8 +35,9 @@ RUN rm /etc/apt/sources.list.d/* \
     libfftw3-dev \
     kmod \
     python3 \
-    libomp-7-dev \
+    libomp-dev \
     rocfft \
+    tar \
   && apt-get clean
 
 # Requires cmake > 3.22 

lammps-docker/Dockerfile

@@ -2,7 +2,7 @@ ARG IMAGE="rocm/dev-ubuntu-20.04:5.3-complete"
 
 FROM ${IMAGE}
 
-ARG LAMMPS_BRANCH="stable_23Jun2022_update3"
+ARG LAMMPS_BRANCH="stable_23Jun2022_update4"
 ARG UCX_BRANCH="v1.13.1"
 ARG OMPI_BRANCH="v4.1.4"
 
@@ -38,7 +38,18 @@ RUN mkdir -p /opt/cmake  \
   && wget --no-check-certificate --quiet -O - https://cmake.org/files/v3.22/cmake-3.22.2-linux-x86_64.tar.gz | tar --strip-components=1 -xz -C /opt/cmake
 
 # Adding rocm/cmake to the PATH
-ENV PATH=/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:/opt/cmake/bin:$PATH
+ENV ROCM_PATH=/opt/rocm \
+    UCX_HOME=/opt/ucx \
+    OMPI_HOME=/opt/ompi
+
+# Adding rocm/cmake to the Environment 
+ENV PATH=$ROCM_PATH/bin:$ROCM_PATH/profiler/bin:$ROCM_PATH/opencl/bin:/opt/cmake/bin:$PATH \
+    LD_LIBRARY_PATH=$ROCM_PATH/lib:$ROCM_PATH/lib64:$ROCM_PATH/llvm/lib:$LD_LIBRARY_PATH \
+    LIBRARY_PATH=$ROCM_PATH/lib:$ROCM_PATH/lib64:$LIBRARY_PATH \
+    C_INCLUDE_PATH=$ROCM_PATH/include:$C_INCLUDE_PATH \
+    CPLUS_INCLUDE_PATH=$ROCM_PATH/include:$CPLUS_INCLUDE_PATH \
+    CPATH=$ROCM_PATH/include:$CPATH \
+    INCLUDE=$ROCM_PATH/include:$INCLUDE
 
 WORKDIR /tmp
 
@@ -51,7 +62,7 @@ RUN cd /tmp/ \
     && ./autogen.sh \
     && mkdir build \
     && cd build \
-    && ../contrib/configure-release --prefix=/opt/ucx \
+    && ../contrib/configure-release --prefix=$UCX_HOME \
           --with-rocm=/opt/rocm --without-knem \
           --without-xpmem  --without-cuda \
           --enable-optimizations  \
@@ -61,7 +72,9 @@ RUN cd /tmp/ \
           --enable-params-check \
           --disable-examples \
     && make -j 8  \
-    && make  install
+    && make  install \
+    && cd /tmp \
+    && rm -rf *  
 
 # Install OpenMPI
 RUN cd /tmp \
@@ -71,7 +84,7 @@ RUN cd /tmp \
     && mkdir build \
     && cd build \
     && ../configure --help \
-    && ../configure --prefix=/opt/ompi --with-ucx=/opt/ucx \
+    && ../configure --prefix=$OMPI_HOME --with-ucx=$UCX_HOME \
           --enable-mca-no-build=btl-uct  \
           --enable-mpi-f90 \
           --enable-mpi-c \
@@ -80,10 +93,20 @@ RUN cd /tmp \
           --enable-mpi-fortran=yes \
           --disable-debug \
     && make -j 8 \
-    && make install
+    && make install \
+    && cd /tmp \
+    && rm -rf *  
+    
 
-# Adding OpenMPI and UCX to PATH
-ENV PATH=/opt/ompi/bin:/opt/ucx/bin:$PATH
+# Adding OpenMPI and UCX to Environment
+ENV PATH=$OMPI_HOME/bin:$UCX_HOME/bin:$PATH \
+    LD_LIBRARY_PATH=$OMPI_HOME/lib:$UCX_HOME/lib:$LD_LIBRARY_PATH \
+    LIBRARY_PATH=$OMPI_HOME/lib:$UCX_HOME/lib:$LIBRARY_PATH \
+    C_INCLUDE_PATH=$OMPI_HOME/include:$UCX_HOME/include:$C_INCLUDE_PATH \
+    CPLUS_INCLUDE_PATH=$OMPI_HOME/include:$UCX_HOME/include:$CPLUS_INCLUDE_PATH \
+    CPATH=$OMPI_HOME/include:$UCX_HOME/include:$CPATH \
+    INCLUDE=$OMPI_HOME/include:$UCX_HOME/include:$INCLUDE \
+    PKG_CONFIG_PATH=$OMPI_HOME/lib/pkgconfig:$UCX_HOME/lib/pkgconfig:$PKG_CONFIG_PATH
 
 # Installing LAMMPS
 RUN cd /tmp \
@@ -101,7 +124,7 @@ RUN cd /tmp \
         -DPKG_KSPACE=on \
         -DPKG_RIGID=on \
         -DBUILD_MPI=on \
-        -DCMAKE_INSTALL_PREFIX=../install \
+        -DCMAKE_INSTALL_PREFIX=/opt/lammps \
         -DMPI_CXX_COMPILER=$(which mpicxx) \
         -DCMAKE_BUILD_TYPE=Release \
         -DKokkos_ENABLE_HIP=on \
@@ -112,11 +135,19 @@ RUN cd /tmp \
         -DKokkos_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS=ON \
         -DCMAKE_CXX_FLAGS=-munsafe-fp-atomics \
         ../lammps/cmake \
-   &&   make -j$(nproc) install \
-   &&   cd ..
+    &&   make -j$(nproc) install \
+    && cd /tmp/lammps \  
+    && mv bench /opt/lammps/bench \
+    && mv examples /opt/lammps/examples \
+    && mv potentials /opt/lammps/potentials \
+    && chmod -R a+rwx /opt/lammps \
+    && cd /tmp \
+    && rm -rf *  
 
+WORKDIR /opt/lammps/bench 
 # Adding environment variable for running OMPI as ROOT
 ENV OMPI_ALLOW_RUN_AS_ROOT=1  \
     OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 \
- 
+    PATH=$PATH:/opt/lammps/bin
+
 CMD ["/bin/bash"]

lammps-docker/README.md

@@ -153,7 +153,7 @@ In this section, we provide a couple of examples from the set of [LAMMPS standar
 
 In these examples, the input to the run command is provided via an input file. Other inputs may have additional parameters that can be modified and may change performance. 
 
-Additionaly, we have supplied several arguments such as `cuda/aware on` which modify the behavior of LAMMPS, in this case, forcing enablement of GPU-aware communications. For additional run options, see [Running LAMMPS with the KOKKOS package](https://docs.lammps.org/Speed_kokkos.html#running-lammps-with-the-kokkos-package). 
+Additionally, we have supplied several arguments such as `cuda/aware on` which modify the behavior of LAMMPS, in this case, forcing enablement of GPU-aware communications. For additional run options, see [Running LAMMPS with the KOKKOS package](https://docs.lammps.org/Speed_kokkos.html#running-lammps-with-the-kokkos-package). 
 Note that the use of `neigh full' in the run command triggers the use of full neighbor-lists, as described [here](https://docs.lammps.org/Developer_par_neigh.html).
 
 For convenience, we also added the installed binary path (`install/bin`) to the PATH environment variable (see bare metal build instructions above) so that the lmp binary can be found when running the benchmark examples.
@@ -166,7 +166,7 @@ mpirun --mca pml ucx --mca btl ^vader,tcp,openib,uct -np 8 lmp -k on g 8 -sf kk
 ```
 - Run LJ benchmark on one GPU
 
-The following command runs the LJ benchmark using a x/y/z of size 8/8/8. Note that we have chosen to run a larger problem size than specified in the sample [input file](https://github.com/lammps/lammps/blob/develop/bench/in.lj). The user may wish to experiment with problem sizes and other run otions to achieve optimal performance.
+The following command runs the LJ benchmark using a x/y/z of size 8/8/8. Note that we have chosen to run a larger problem size than specified in the sample [input file](https://github.com/lammps/lammps/blob/develop/bench/in.lj). The user may wish to experiment with problem sizes and other run options to achieve optimal performance.
 
 ```
 mpirun --mca pml ucx --mca btl ^vader,tcp,openib,uct -np 1 lmp -k on g 1 -sf kk -pk kokkos cuda/aware on neigh full -v x 8 -v y 8 -v z 8  -in in.lj -nocite -log log.lammps
@@ -176,7 +176,7 @@ mpirun --mca pml ucx --mca btl ^vader,tcp,openib,uct -np 1 lmp -k on g 1 -sf kk
 
 Your access and use of this application is subject to the terms of the applicable component-level license identified below. To the extent any subcomponent in this container requires an offer for corresponding source code, AMD hereby makes such an offer for corresponding source code form, which will be made available upon request. By accessing and using this application, you are agreeing to fully comply with the terms of this license. If you do not agree to the terms of this license, do not access or use this application.
 
-The application is provided in a container image format that includes the following separate and independent components: Ubuntu (License: Creative Commons CC-BY-SA version 3.0 UK licence), LAMMPS (License: GPL v2.0 or at your option, any later version), CMAKE (License: BSD 3), numpy (License: BSD 3-clause), PANDAS (License: BSD 3 + Restrictions), OpenMPI (License: BSD 3-Clause), OpenUCX (License: BSD 3-Clause), ROCm (License: Custom/MIT/Apache V2.0/UIUC OSL). Additional third-party content in this container may be subject to additional licenses and restrictions. The components are licensed to you directly by the party that owns the content pursuant to the license terms included with such content and is not licensed to you by AMD. ALL THIRD-PARTY CONTENT IS MADE AVAILABLE BY AMD “AS IS” WITHOUT A WARRANTY OF ANY KIND. USE OF SUCH THIRD-PARTY CONTENT IS DONE AT YOUR SOLE DISCRETION AND UNDER NO CIRCUMSTANCES WILL AMD BE LIABLE TO YOU FOR ANY THIRD-PARTY CONTENT. YOU ASSUME ALL RISK AND ARE SOLELY RESPONSIBLE FOR ANY DAMAGES THAT MAY ARISE FROM YOUR USE OF THIRD-PARTY CONTENT.
+The application is provided in a container image format that includes the following separate and independent components: Ubuntu (License: Creative Commons CC-BY-SA version 3.0 UK license), LAMMPS (License: GPL v2.0 or at your option, any later version), CMAKE (License: BSD 3), numpy (License: BSD 3-clause), PANDAS (License: BSD 3 + Restrictions), OpenMPI (License: BSD 3-Clause), OpenUCX (License: BSD 3-Clause), ROCm (License: Custom/MIT/Apache V2.0/UIUC OSL). Additional third-party content in this container may be subject to additional licenses and restrictions. The components are licensed to you directly by the party that owns the content pursuant to the license terms included with such content and is not licensed to you by AMD. ALL THIRD-PARTY CONTENT IS MADE AVAILABLE BY AMD “AS IS” WITHOUT A WARRANTY OF ANY KIND. USE OF SUCH THIRD-PARTY CONTENT IS DONE AT YOUR SOLE DISCRETION AND UNDER NO CIRCUMSTANCES WILL AMD BE LIABLE TO YOU FOR ANY THIRD-PARTY CONTENT. YOU ASSUME ALL RISK AND ARE SOLELY RESPONSIBLE FOR ANY DAMAGES THAT MAY ARISE FROM YOUR USE OF THIRD-PARTY CONTENT.
 
 ## Notices and Attribution
 

openfoam-docker/scripts/bench-hpc-motorbike.sh

@@ -13,7 +13,7 @@ function setup()
 {
     # setting the env
     MAXGPUS=10
-    if [[ ${NGPUS} -le 0 ]] ||  [[ ${NGPUS} > ${MAXGPUS} ]]; then  
+    if [[ ${NGPUS} -le 0 ]] ||  [[ ${NGPUS} -gt ${MAXGPUS} ]]; then  
         # ERR condition
         echo " ERROR: This script is designed to run with a maximum of ${MAXGPUS} GPUs."
         echo "        Either change your current selection of NGPUs: ${NGPUS} or modify the 'MAXGPUS' count in the script!  "

openfoam-docker/scripts/bench-lid-driven-cavity.sh

@@ -12,7 +12,7 @@ function setup()
 {
     # setting the env
     MAXGPUS=10
-    if [[ ${NGPUS} -le 0 ]] ||  [[ ${NGPUS} > ${MAXGPUS} ]]; then  
+    if [[ ${NGPUS} -le 0 ]] ||  [[ ${NGPUS} -gt ${MAXGPUS} ]]; then  
         # ERR condition
         echo " ERROR: This script is designed to run with a maximum of ${MAXGPUS} GPUs."
         echo "        Either change your current selection of NGPUs: ${NGPUS} or modify the 'MAXGPUS' count in the script!  "

petsc-docker/Dockerfile

@@ -34,7 +34,7 @@ RUN apt-get update \
     kmod \
     python3 \
     python3-distutils \
-    libomp-7-dev \
+    libomp-dev \
     dos2unix \
     libopenblas-dev \
     libnuma-dev \

pyfr-docker/README.md

@@ -125,19 +125,19 @@ The script extracts, then converts the mesh to a PyFR mesh first, for multiple G
 As a convenience, this is performed in the benchmark script which can be run using one to eight GPUs.  
 **1 GPU**
 ```
-/examples/tgv/run_tgv 1
+/examples/naca0021/run_naca0021 1
 ```
 **2 GPU**
 ```
-/examples/tgv/run_tgv 2
+/examples/naca0021/run_naca0021 2
 ```
 **4 GPU**
 ```
-/examples/tgv/run_tgv 4
+/examples/naca0021/run_naca0021 4
 ```
 **8 GPU**
 ```
-/examples/tgv/run_tgv 8
+/examples/naca0021/run_naca0021 8
 ```
 
 #### PyFR Test Cases

pyfr-docker/examples/bsf/run_bsf

@@ -1,5 +1,5 @@
 #!/bin/bash
 
 echo "Running BSF benchmark"
-cd /examples/dfs
+cd /examples/bsf
 mpirun -np 1 pyfr -v run -b hip -p mesh.pyfrm inistep.ini

pyfr-docker/examples/naca0021/run_naca0021

@@ -1,12 +1,7 @@
 #!/bin/bash
 
-cd /examples/naca0021
-unzip -u naca0021_p3_1c.msh.zip
-mkdir ../$1gpu-naca0021
-cd ../$1gpu-naca0021
-cp ../naca0021-input-set/naca0021_p3_1c.msh .
-cp ../naca0021-input-set/p3_warmup.ini .
-cp ../naca0021-input-set/3d_naca.ini .
+cd /examples/naca0021/
+unzip -u /examples/naca0021/naca0021_p3_1c.msh.zip -d .
 
 pyfr import naca0021_p3_1c.msh naca0021_p3_1c.pyfrm
 if [[ -z "$1" ]]; then