Move bind dirs to launch config file, construct bind string on the fl…

…y. Add matplotlib-scalebar
coecms · Nov 27, 2023 · 65db10c · 65db10c
1 parent 455f997
commit 65db10c
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Showing 5 changed files with 14 additions and 3 deletions.
diff --git a/container/container.def b/container/container.def
@@ -32,6 +32,7 @@ Bootstrap: scratch
         mkdir -p ${SINGULARITY_ROOTFS}/system
         mkdir -p ${SINGULARITY_ROOTFS}/usr
         mkdir -p ${SINGULARITY_ROOTFS}/sys/fs/cgroup
+        mkdir -p ${SINGULARITY_ROOTFS}/iointensive
 
         ### Mount points for service sockets
         mkdir -p ${SINGULARITY_ROOTFS}/var/lib/sss
@@ -42,6 +43,7 @@ Bootstrap: scratch
         mkdir -p ${SINGULARITY_ROOTFS}/opt/conda/analysis3-23.01
         mkdir -p ${SINGULARITY_ROOTFS}/opt/conda/analysis3-23.04
         mkdir -p ${SINGULARITY_ROOTFS}/opt/conda/analysis3-23.07
+        mkdir -p ${SINGULARITY_ROOTFS}/opt/conda/analysis3-23.10
 
 %runscript
         /usr/bin/bash -l
diff --git a/scripts/environment.yml b/scripts/environment.yml
@@ -281,5 +281,6 @@ dependencies:
 - icclim>=6.4.0 ### Prevent downgrade
 - py-cordex
 - pdbufr
+- matplotlib-scalebar
 - pip:
   - railroad-diagrams ### Unlisted dependency of pip and pyparsing
diff --git a/scripts/install_config.sh b/scripts/install_config.sh
@@ -22,7 +22,7 @@ export APPS_OWNERS_GROUP=hh5_w
 
 ### Version settings
 export ENVIRONMENT=analysis3
-export VERSION_TO_MODIFY=23.07
+export VERSION_TO_MODIFY=23.10
 export STABLE_VERSION=23.04
 export UNSTABLE_VERSION=23.07
 export FULLENV="${ENVIRONMENT}-${VERSION_TO_MODIFY}"

diff --git a/scripts/launcher.sh b/scripts/launcher.sh
@@ -119,4 +119,10 @@ while IFS= read -r -d: i; do
     overlay_args="${overlay_args}--overlay=${i} "
 done<<<"${CONTAINER_OVERLAY_PATH%:}:"
 
-"$SINGULARITY_BINARY_PATH" -s exec --bind /etc,/half-root,/local,/ram,/run,/system,/usr,/var/lib/sss,/var/run/munge,/sys/fs/cgroup ${overlay_args} "${CONTAINER_PATH}" "${cmd_to_run[@]}"
+bind_str=""
+for bind_dir in "${bind_dirs[@]}"; do
+    [[ -d "${bind_dir}" ]] && bind_str="${bind_str}${bind_dir},"
+done
+bind_str=${bind_str%,}
+
+"$SINGULARITY_BINARY_PATH" -s exec --bind "${bind_str}" "${overlay_args}" "${CONTAINER_PATH}" "${cmd_to_run[@]}"
diff --git a/scripts/launcher_conf.sh b/scripts/launcher_conf.sh
@@ -5,4 +5,6 @@ if [[ "${CONDA_EXE}" ]]; then
     export CONDA_BASE_ENV_PATH="${CONDA_EXE//\/bin\/conda/}"
 else
     export CONDA_BASE_ENV_PATH="__CONDA_BASE__/__APPS_SUBDIR__/__CONDA_INSTALL_BASENAME__"
-fi
+fi
+
+declare -a bind_dirs=( "/etc" "/half-root" "/local" "/ram" "/run" "/system" "/usr" "/var/lib/sss" "/var/run/munge" "/sys/fs/cgroup" "/iointensive" )