Various updates

Fixes up some steps and scripts
supercontainers · Nov 15, 2024 · 9f5d136 · 9f5d136
1 parent 64f31fd
commit 9f5d136
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/_episodes/41.advanced.md b/_episodes/41.advanced.md
@@ -52,7 +52,7 @@ and we're going to pull an OpenFoam container, which was built on top of MPICH a
 Since this is a large image, we will pull a copy to /tmp for everyone to share.
 
 ```bash
-(cd /tmp && [ -e sc22-openfoam_v2012.sif ] || singularity pull docker://quay.io/pawsey/sc22-openfoam:v2012)
+(cd /tmp && [ -e sc22-openfoam_v2012.sif ] || singularity pull docker://quay.io/pawsey/sc22-openfoam:v2012 && chmod a+r /tmp/sc22-openfoam_v2012.sif)
 ```
 
 OpenFoam comes with a collection of executables, one of which is `simpleFoam`.  We can use the Linux command `ldd` to investigate the libraries that this executable links to.  As `simpleFoam` links to a few tens of libraries, let's specifically look for MPI (`libmpi*`) libraries in the command output:

diff --git a/exercises/openfoam/mpirun_para.sh b/exercises/openfoam/mpirun_para.sh
@@ -13,7 +13,6 @@ export SINGULARITY_BINDPATH="$MPICH_ROOT"
 export SINGULARITYENV_LD_LIBRARY_PATH="$MPICH_LIBS:\$LD_LIBRARY_PATH"
 
 
-
 # pre-processing
 singularity exec $image \
   blockMesh | tee log.blockMesh

diff --git a/exercises/podman-hpc/podman_hpc_setup.sh b/exercises/podman-hpc/podman_hpc_setup.sh
@@ -15,14 +15,15 @@ export PODMANHPC_HOOKS_DIR=/home/training2/.hooks.d
 export PODMANHPC_MODULES_DIR=/home/training2/etc/modules.d
 
 [ -e $PODMANHPC_HOOKS_DIR ] || mkdir $PODMANHPC_HOOKS_DIR
+HT=$(which hook_tool)
 cat << EOF > $PODMANHPC_HOOKS_DIR/02-hook_tool.json
 {
     "version": "1.0.0",
     "hook": {
         "env": [
-	    "HOME=/home/$(id -u -n)"
+	    "HOME=${HOME}"
 	],
-	"path": "/home/$(id -u -n)/.local/bin/hook_tool",
+	"path": "${HT}",
         "args": ["hook_tool"]
     },
     "when": {
@@ -34,9 +35,9 @@ cat << EOF > $PODMANHPC_HOOKS_DIR/02-hook_tool.json
 }
 EOF
 
-[ -e .local/bin/mksquashfs.static ] || (cd .local/bin && wget https://portal.nersc.gov/project/bigdata/mksquashfs.static)
+[ -e ~/.local/bin/mksquashfs.static ] || (cd ~/.local/bin && wget https://portal.nersc.gov/project/bigdata/mksquashfs.static)
 
-chmod a+rx .local/bin/mksquashfs.static
+chmod a+rx ~/.local/bin/mksquashfs.static
 
 export SCRATCH=$HOME