From 0ae9badcbf6a0ceeac4409ae695b5973553019db Mon Sep 17 00:00:00 2001
From: Jo Basevi <johanna.basevi@anu.edu.au>
Date: Wed, 18 Mar 2026 09:55:15 +1100
Subject: [PATCH] Use new apptainer singularity install to avoid transient
 errors

---
 modules/common_v3              |  2 +-
 scripts/install_config.sh      |  2 +-
 scripts/launcher.sh            | 10 +++++-----
 scripts/launcher_conf.sh       |  2 +-
 scripts/overrides/functions.sh |  2 +-
 5 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/modules/common_v3 b/modules/common_v3
index 8d41354..6a75ed5 100644
--- a/modules/common_v3
+++ b/modules/common_v3
@@ -21,7 +21,7 @@ set overlay_path [ string map {/conda/ /envs/} $basedir ].sqsh
 
 set launcher $myscripts/launcher.sh
 
-module load singularity
+module load apptainer
 
 prepend-path CONTAINER_OVERLAY_PATH $overlay_path
 prepend-path SINGULARITYENV_PREPEND_PATH $basedir/condabin
diff --git a/scripts/install_config.sh b/scripts/install_config.sh
index cd505df..5d4de2f 100644
--- a/scripts/install_config.sh
+++ b/scripts/install_config.sh
@@ -57,7 +57,7 @@ fi
 export TEST_OUT_FILE=test_results.xml
 export PYTHONNOUSERSITE=true
 export CONTAINER_PATH="${SCRIPT_DIR}"/../container/base.sif
-export SINGULARITY_BINARY_PATH="/opt/singularity/bin/singularity"
+export SINGULARITY_BINARY_PATH="/opt/nci/apptainer/bin/singularity"
 
 declare -a bind_dirs=( "/etc" "/half-root" "/local" "/ram" "/run" "/system" "/usr" "/var/lib/sss" "/var/lib/rpm" "/var/run/munge" "/sys/fs/cgroup" "/iointensive" )
 
diff --git a/scripts/launcher.sh b/scripts/launcher.sh
index 06b65a4..bba6432 100755
--- a/scripts/launcher.sh
+++ b/scripts/launcher.sh
@@ -78,7 +78,7 @@ done
 $debug "PROG_ARGS =" "${PROG_ARGS[@]}"
 
 if ! [[ "${SINGULARITY_BINARY_PATH}" ]]; then
-    module load singularity
+    module load apptainer
     export SINGULARITY_BINARY_PATH=$( type -p singularity )
 fi
 
@@ -114,10 +114,10 @@ $debug "CONTAINER_OVERLAY_PATH after override check = " ${CONTAINER_OVERLAY_PATH
 
 export CONDA_BASE="${CONDA_BASE_ENV_PATH}/envs/${myenv}"
 
-if ! [[ -x "${SINGULARITY_BINARY_PATH}" ]]; then
-    ### Short circuit detection
+if [[ $(awk '/NoNewPrivs/ {print $2}' /proc/self/status) -ne 0 ]]; then
+    ### Short circuit detection - check process status (0 if running out outside a container)
     ### In some cases (e.g. mpi processes launched from orterun), launcher will be invoked from
-    ### within the container. The tell-tale sign for this is if /opt/singularity is missing.
+    ### within the container. 
     ### The only way this can happen is if we've tried to run something that has come
     ### from the bin directory in scripts/env.d/bin/ - the only place these can come from is the
     ### bin directory of the active conda env, so just reset the path to that but keep the 
@@ -144,7 +144,7 @@ declare -a singularity_default_path=( '/usr/local/sbin' '/usr/local/bin' '/usr/s
 
 while IFS= read -r -d: i; do
     in_array "${singularity_default_path[@]}" "${i}" && continue
-    [[ "${i}" == "/opt/singularity/bin" ]] && continue
+    [[ "${i}" == "/opt/nci/apptainer/bin" ]] && continue
     [[ "${i}" == "${wrapper_bin}" ]] && continue
     SINGULARITYENV_PREPEND_PATH="${SINGULARITYENV_PREPEND_PATH}:${i}"
 done<<<"${PATH%:}:"
diff --git a/scripts/launcher_conf.sh b/scripts/launcher_conf.sh
index 34dbcb8..e2abd0a 100644
--- a/scripts/launcher_conf.sh
+++ b/scripts/launcher_conf.sh
@@ -1,5 +1,5 @@
 ### Subject to change
-export SINGULARITY_BINARY_PATH="/opt/singularity/bin/singularity"
+export SINGULARITY_BINARY_PATH="/opt/nci/apptainer/bin/singularity"
 export CONTAINER_PATH="__CONDA_BASE__/__APPS_SUBDIR__/__CONDA_INSTALL_BASENAME__/etc/base.sif"
 
 export CONDA_BASE_ENV_PATH="__CONDA_BASE__/__APPS_SUBDIR__/__CONDA_INSTALL_BASENAME__"
diff --git a/scripts/overrides/functions.sh b/scripts/overrides/functions.sh
index 28fa911..73ef91f 100755
--- a/scripts/overrides/functions.sh
+++ b/scripts/overrides/functions.sh
@@ -11,4 +11,4 @@ function findreal {
 }
 
 ### Subject to change
-export SINGULARITY_BINARY_PATH=/opt/singularity/bin/singularity
\ No newline at end of file
+export SINGULARITY_BINARY_PATH=/opt/nci/apptainer/bin/singularity
\ No newline at end of file