Merge remote-tracking branch 'origin/main' into zihua/testing

Dockerfile

@@ -122,7 +122,7 @@ RUN git clone --recursive --depth 1 --single-branch --branch v2.2.7 https://gith
     && cmake .. -DCMAKE_INSTALL_PREFIX=/home/tools -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_BUILD_TYPE=Release -DSCOREC_CXX_FLAGS="-Wno-error=array-bounds" \
     && make -j$(nproc) && make install
 
-RUN git clone --recursive https://github.com/SeisSol/PUMGen.git \
+RUN git clone --recursive --branch v1.0.1 https://github.com/SeisSol/PUMGen.git \
     && cd PUMGen \
     && mkdir build && cd build \
     && cmake .. -DCMAKE_INSTALL_PREFIX=/home/tools -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_BUILD_TYPE=Release \

README.md

@@ -7,15 +7,21 @@ The Docker container contains an interactive learning environment (Jupyter) whic
 ## Installation
 
 Please install [Docker](https://docs.docker.com/engine/install/), launch the Docker Desktop and then run
+
+(i) For Frontera and all Intel/AMD machines: 
+ -  use label: hps-2024-frontera
+
+(ii) Macs with M1/M2/M3 ARM  CPUs: 
+  - use label: hps-2024-remote-arm
 ```bash
-docker pull seissol/training
+docker pull seissol/training:{label}
 ```
 
 ## Training
 
 After installation, run
 ```bash
-docker run -p 53155:53155 seissol/training
+docker run -p 53155:53155 seissol/training:{label}
 ```
 or run the [start.sh](start.sh) script.
 

source_modules.sh

@@ -0,0 +1,48 @@
+#!/bin/sh
+
+# source this file to load the modules to run the paraview and jupyter notebook in frontera VNC 
+
+echo "TACC: unloading xalt"
+module unload xalt
+
+echo "MNMN: install python libraries"
+ml gcc/9
+ml swr/21.2.5 qt5/5.14.2 oneapi_rk/2021.4.0
+ml paraview/5.11
+module load python3/3.9.2
+
+
+export PATH="$PATH:$HOME/.local"
+# pip install --user obspy cartopy
+
+# urllib compatibility
+pip uninstall -y urllib3
+pip install --user 'urllib3<2.0'
+pip install --user vtk pyvista
+pip install --user --update gmsh
+pip install --user scipy matplotlib pyproj
+
+cp /work2/10000/jwjeremy/share/libgmsh.so.4.11.1  ~/.local/lib/libgmsh.so.4.11
+
+echo "MNMN: load appatainer module"
+module load tacc-apptainer
+
+#
+SHARED_PATH="/your/path/to/container/"
+SIF_NAME="training_latest.sif"
+
+if [ ! -f $SIF_NAME ]; then
+    if [ ! -f $SHARED_PATH/$SIF_NAME ]; then
+        # load the image if no image exists in the shared directory
+        echo "MNMN: pull the appatainer image"
+        apptainer pull -F docker://seissol/training:hps-2024-frontera
+    else
+        # create symlink to the shared directory
+        echo "MNMN: create symlink to the shared directory"
+        ln -s $SHARED_PATH/$SIF_NAME $SIF_NAME
+    fi
+fi
+
+
+echo "To run jupyter notebook:"
+echo "swr -p 1 jupyter notebook"

tpv13/tpv13.ipynb

@@ -288,7 +288,7 @@
    "source": [
     "You can also visualize the SeisSol output in Paraview on your local machine. For that, you have to copy the files from your Docker container. \n",
     "\n",
-    "Do you remember the name of your container? Type the following command in the terminal of your local machine and replace my_docker by the name of your container and my_output by the output file you want to copy: \n",
+    "The following commands allow you to copy the simulation output from docker to the native filesystem of your machine. Type the commands in the terminal of your local machine: \n",
     "\n"
    ]
   },
@@ -298,7 +298,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "docker cp my_docker:/home/training/tpv13/my_output ."
+    "# Execute on your local machine, not within this notebook!", 
+    "\n",
+    "export my_docker=$(docker ps --format \"{{.Names}}\")",
+    "\n",
+    "docker cp ${my_docker}:/home/training/tpv13/output ."
    ]
   },
   {