updated Dockerfile and docker-image.md

docs/docker-image.md

@@ -36,35 +36,30 @@ To run the SiMLInt Docker image follow these steps:
 1. "Pure" BOUT++ Simulation: Run the following command:
 
     ```shell
-    docker run -v $SIMLINT_HOME/files/containerised-runs:/sim -v $SIMLINT_HOME/files/6-simulation:/6-sim \
-    ghcr.io/epcced/simlint:latest \
-    sh -c \
-    "cp /6-sim/BOUT.inp /sim/data/BOUT.inp && cp /sim/BOUT.restart.0.nc /sim/data/BOUT.restart.0.nc \
-    && mpirun -np 1 bout-hw"
+    cp $SIMLINT_HOME/files/6-simulation/BOUT.inp $SIMLINT_HOME/files/containerised-runs/data; \
+    cp $SIMLINT_HOME/files/containerised-runs/BOUT.restart.0.nc $SIMLINT_HOME/files/containerised-runs/data; \
+    docker run -v $SIMLINT_HOME/files/containerised-runs:/sim -u $(id -u):$(id -g) ghcr.io/epcced/simlint:latest mpirun -np 1 bout-hw nout=10
     ```
 
 2. Ground-truth simulation:
 
     ```shell
-    docker run -v $SIMLINT_HOME/files/containerised-runs:/sim -v $SIMLINT_HOME/files/6-simulation:/6-sim \
-    ghcr.io/epcced/simlint:latest \
-    sh -c \
-    "cp /6-sim/BOUT.inp /sim/data/BOUT.inp && cp /sim/BOUT.restart.0.nc /sim/data/BOUT.restart.0.nc \
-    && mpirun -np 1 gt-hw"
+    cp $SIMLINT_HOME/files/6-simulation/BOUT.inp $SIMLINT_HOME/files/containerised-runs/data; \
+    cp $SIMLINT_HOME/files/containerised-runs/BOUT.restart.0.nc $SIMLINT_HOME/files/containerised-runs/data; \
+    docker run -v $SIMLINT_HOME/files/containerised-runs:/sim -u $(id -u):$(id -g) ghcr.io/epcced/simlint:latest mpirun -np 1 gt-hw nout=10
     ```
 
     For these first two commands, the OpenMPI command `mpirun -n 1`, which instructs BOUT++ to use one processor only due to the format of the example input data, can be instructed to use *N* processors `mpirun -n N`, however appropriately decomposed input data must be provided.
 
 3. Inference runs:
 
     ```shell
-    docker run -v $SIMLINT_HOME/files/containerised-runs:/sim -v $SIMLINT_HOME/files/models:/models -v $SIMLINT_HOME/files/6-simulation:/6-sim \
-    ghcr.io/epcced/simlint:latest \
-    sh -c \
-    "cp /6-sim/BOUT.inp /sim/data/BOUT.inp && cp /sim/BOUT.restart.0.nc /sim/data/BOUT.restart.0.nc \
-    && python /start_db.py /models/model-hw-20240427-164026-vort.pb /models/model-hw-20240427-210530-dens.pb \
+    cp $SIMLINT_HOME/files/6-simulation/BOUT.inp $SIMLINT_HOME/files/containerised-runs/data && \
+    cp $SIMLINT_HOME/files/containerised-runs/BOUT.restart.0.nc $SIMLINT_HOME/files/containerised-runs/data && \
+    docker run -v $SIMLINT_HOME/files/containerised-runs:/sim -v $SIMLINT_HOME/files/models:/models -u $(id -u):$(id -g) ghcr.io/epcced/simlint:latest sh -c \
+    "python /start_db.py /models/model-hw-20240427-164026-vort.pb /models/model-hw-20240427-210530-dens.pb \
     && export SSDB=127.0.0.1:6899 \
-    && mpirun -np 1 smartsim-hw"
+    && mpirun -np 1 smartsim-hw nout=10"
     ```
 
 That's it! You have successfully built the SiMLInt Docker image and run it with a volume. Feel free to explore and modify the code inside the container as needed.

files/container/Dockerfile

@@ -98,13 +98,14 @@ RUN $conda init && . $bashrc && conda activate boutsmartsim \
     && chmod 777 /simlint-bin/smartsim-hw
 
 COPY files/container/entrypoint.sh /entrypoint.sh
+COPY files/6-simulation/start_db.py /start_db.py
 
-RUN mkdir /sim && chmod -R 777 /sim
+RUN mkdir -p /sim/data && chmod -R 777 /sim
 RUN chmod -R 777 /miniconda3
 
-RUN useradd -ms /bin/bash simlint
+# RUN useradd -ms /bin/bash simlint
 
-USER simlint
+# USER simlint
 
 WORKDIR /sim
 

files/container/entrypoint.sh

@@ -13,4 +13,4 @@ conda activate "${_CONDA_DEFAULT_ENV}"
 export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
 export PATH=/simlint-bin:$PATH
 
-$@
+echo $@

files/containerised-runs/data/BOUT.inp

@@ -0,0 +1,49 @@
+#
+# Hasegawa-Wakatani training data
+#
+
+timestep = 1.0   # Output timestep
+nout = 100      # Number of output steps
+
+MYG = 0  # No need for Y communications
+
+periodicX = true  # Domain is periodic in X
+
+[mesh]
+
+nx = 260  # Note 4 guard cells in X
+ny = 1
+nz = 256  # Periodic, so no guard cells in Z
+
+dx = 0.025
+dy = 1.0
+dz = 0.025
+
+[hw]
+
+alpha = 1.0    # Adiabaticity (~ conductivity)
+kappa = 2.0    # Density gradient drive
+Dvort = 0.005   # Vorticity diffusion
+Dn = 0.005   # Density diffusion
+
+modified = true
+
+bracket = 2  # 0 = std, 1 = simple, 2 = arakawa
+
+[solver]
+type = rk4
+adaptive = false
+timestep = 0.0065
+
+[all]
+#scale = 0.0
+bndry_all = dirichlet_o2
+
+[n]
+#bndry_all = neumann_o2
+
+[vort]
+#bndry_all = dirichlet_o2
+
+#scale = 0.1  # Fluctuation amplitude
+#function = mixmode(2*pi*x) * mixmode(z) # Fluctuation function