Set ENV_LAUNCHER_SCRIPT_PATH and only expose payu commands

environments/payu-dev/build_inner.sh

@@ -1,14 +1,10 @@
 ### Custom install inner
 
 # Fix shebang headers in payu entry points (issue with pip installed packages: https://github.com/ACCESS-NRI/MED-condaenv/issues/78)
-for file in ${CONDA_INSTALLATION_PATH}/envs/${FULLENV}/bin/payu-*; do
+for file in ${CONDA_INSTALLATION_PATH}/envs/${FULLENV}/bin/payu*; do
     # Using payu-* to modify payu-run, payu-collate, payu-sync files
     echo "Adding python header to $file"
     # Substitute the first line of file (e.g. 1s), if it starts with #! (regex ^#!/.*$),
     # with the python executable in the conda environment
     sed -i "1s|^#!/.*$|#!${CONDA_INSTALLATION_PATH}/envs/${FULLENV}/bin/python|" "$file"
-done
-
-# Patch payu shebang header with outer python executable that launches a container when run.
-# This means when payu submits qsub commands (e.g. payu run), it uses this python executable and launches a container on PBS job
-sed -i "1s|^#!/.*$|#!${CONDA_SCRIPT_PATH}/${FULLENV}.d/bin/python|" "${CONDA_INSTALLATION_PATH}/envs/${FULLENV}/bin/payu"
+done

environments/payu-dev/config.sh

@@ -27,4 +27,14 @@ declare -a rpms_to_remove=()
 declare -a replace_from_apps=()
 declare -a outside_commands_to_include=( "pbs_tmrsh" )
 declare -a outside_files_to_copy=()
-declare -a replace_with_external=()
+declare -a replace_with_external=()
+declare -a launcher_commands=(
+    "payu-run"
+    "payu-collate"
+    "payu-sync"
+    "payu"
+    "payu-branch"
+    "payu-checkout"
+    "payu-clone"
+    "payu-profile"
+)

environments/payu/build_inner.sh

@@ -1,16 +0,0 @@
-### Custom install inner to build jupyter lab extensions
-
-# set +u
-# eval "$( ${MAMBA} shell hook --shell bash)"
-# micromamba activate "${CONDA_INSTALLATION_PATH}/envs/${FULLENV}"
-# set -u
-
-# jupyter lab build
-
-# Patch payu shebang header with outer python executable that launches a container when run.
-# This means when payu submits qsub commands (e.g. payu run), it uses this python executable and launches a container on PBS job
-sed -i "1s|^#!/.*$|#!${CONDA_SCRIPT_PATH}/${FULLENV}.d/bin/python|" "${CONDA_INSTALLATION_PATH}/envs/${FULLENV}/bin/payu"
-# Above command follows pattern of "sed -i '1s|pattern|replacement|' filename"
-# which modifies the environment's payu executable in place (-i),
-# and replaces the first line (1s), if it starts with #! (regex ^#!/.*$),
-# with the payu launcher script

environments/payu/config.sh

@@ -27,3 +27,13 @@ declare -a replace_from_apps=()
 declare -a outside_commands_to_include=( "pbs_tmrsh" )
 declare -a outside_files_to_copy=()
 declare -a replace_with_external=()
+declare -a launcher_commands=(
+    "payu-run"
+    "payu-collate"
+    "payu-sync"
+    "payu"
+    "payu-branch"
+    "payu-checkout"
+    "payu-clone"
+    "payu-profile"
+)

modules/common_cmd_v1

@@ -0,0 +1,30 @@
+#%Module1.0
+
+set prefix __CONDA_BASE__/__APPS_SUBDIR__
+set package __CONDA_INSTALL_BASENAME__
+
+# Prevent running this module with a running payu module
+conflict payu
+
+# Name of this module's environment
+lassign [split [module-info name] {/}] module_name module_version
+set condaenv "${module_version}"
+set basedir "$prefix/$package/envs/$condaenv"
+if {![ file exists $basedir ]} {
+    # For modulenames which are $ENVIRONMENT/$VERSION, rather than conda/$ENIRONMENT-$VERSION
+    set condaenv "${module_name}-${module_version}"
+    set basedir "$prefix/$package/envs/$condaenv"
+}
+
+set myscripts [ file normalize __CONDA_BASE__/__SCRIPT_SUBDIR__/$condaenv.d/bin ]
+set overlay_path [ string map {/conda/ /envs/} $basedir ].sqsh
+
+module load singularity
+
+prepend-path CONTAINER_OVERLAY_PATH $overlay_path
+
+# Add launcher script directory to PATH
+prepend-path PATH $myscripts
+
+### Extra env to get other things working
+setenv OMPI_MCA_orte_launch_agent $myscripts/orted

scripts/build.sh

@@ -119,16 +119,24 @@ function inner() {
         copy_if_changed "${override}" "${CONDA_SCRIPT_PATH}"/overrides/"${override##*/}"
     done
     mkdir -p "${CONDA_MODULE_PATH}"
-    copy_and_replace "${SCRIPT_DIR}"/../modules/common_v3 "${CONDA_MODULE_PATH}"/.common_v3       CONDA_BASE APPS_SUBDIR CONDA_INSTALL_BASENAME SCRIPT_SUBDIR
-    copy_and_replace "${SCRIPT_DIR}"/launcher_conf.sh     "${CONDA_SCRIPT_PATH}"/launcher_conf.sh CONDA_BASE APPS_SUBDIR CONDA_INSTALL_BASENAME
+    copy_and_replace "${SCRIPT_DIR}"/../modules/"${COMMON_MODULEFILE}" "${CONDA_MODULE_PATH}"/."${COMMON_MODULEFILE}" CONDA_BASE APPS_SUBDIR CONDA_INSTALL_BASENAME SCRIPT_SUBDIR
+    copy_and_replace "${SCRIPT_DIR}"/launcher_conf.sh     "${CONDA_SCRIPT_PATH}"/launcher_conf.sh CONDA_BASE APPS_SUBDIR CONDA_INSTALL_BASENAME CONDA_SCRIPT_PATH FULLENV
 
     ### Create symlink tree
     mkdir -p "${CONDA_SCRIPT_PATH}"/"${FULLENV}".d/{bin,overrides}
     cp "${CONDA_SCRIPT_PATH}"/{launcher.sh,launcher_conf.sh} "${CONDA_SCRIPT_PATH}"/"${FULLENV}".d/bin
     pushd "${CONDA_SCRIPT_PATH}"/"${FULLENV}".d/bin
-    for i in $( ls "${ENV_INSTALLATION_PATH}"/bin ); do
-        ln -s launcher.sh $i
-    done
+    if [ "${#launcher_commands[@]}" -gt 0 ]; then
+        # Only create launcher symlinks for the specified commands
+        for cmd in "${launcher_commands[@]}"; do
+            ln -s launcher.sh $cmd
+        done
+    else
+        # Create a launcher symlinks for each executable in the bin directory
+        for i in $( ls "${ENV_INSTALLATION_PATH}"/bin ); do
+            ln -s launcher.sh $i
+        done
+    fi
 
     ### Add in the outside commands
     for i in "${outside_commands_to_include[@]}"; do
@@ -225,7 +233,7 @@ fi
 
 
 if [[ "${DO_UPDATE}" == "--install" ]]; then
-    ln -s .common_v3 "${CONDA_OUTER_BASE}"/"${MODULE_SUBDIR}"/"${MODULE_NAME}"/"${MODULE_VERSION}"
+    ln -s ."${COMMON_MODULEFILE}" "${CONDA_OUTER_BASE}"/"${MODULE_SUBDIR}"/"${MODULE_NAME}"/"${MODULE_VERSION}"
 fi
 
 pushd "${CONDA_TEMP_PATH}"

scripts/install_config.sh

@@ -37,6 +37,9 @@ export CONDA_INSTALL_BASENAME="base_conda" #TODO: Eventually replace with conda
 # so payu modules are named payu/$MODULE_VERSION (e.g. payu/1.1.5)
 export MODULE_NAME="conda"
 
+# Common modulefile to use for conda environments
+export COMMON_MODULEFILE="common_cmd_v1"
+
 ### Derived locations - extra '.' for arcane rsync magic
 export CONDA_SCRIPT_PATH="${CONDA_BASE}"/./"${SCRIPT_SUBDIR}"
 export CONDA_MODULE_PATH="${CONDA_BASE}"/./"${MODULE_SUBDIR}"/"${MODULE_NAME}"

scripts/launcher_conf.sh

@@ -1,10 +1,11 @@
 ### Subject to change
 export SINGULARITY_BINARY_PATH="/opt/singularity/bin/singularity"
 export CONTAINER_PATH="__CONDA_BASE__/__APPS_SUBDIR__/__CONDA_INSTALL_BASENAME__/etc/base.sif"
-if [[ "${CONDA_EXE}" ]]; then
-    export CONDA_BASE_ENV_PATH="${CONDA_EXE//\/bin\/micromamba/}"
-else
-    export CONDA_BASE_ENV_PATH="__CONDA_BASE__/__APPS_SUBDIR__/__CONDA_INSTALL_BASENAME__"
-fi
+
+export CONDA_BASE_ENV_PATH="__CONDA_BASE__/__APPS_SUBDIR__/__CONDA_INSTALL_BASENAME__"
 
 declare -a bind_dirs=( "/etc" "/half-root" "/local" "/ram" "/run" "/system" "/usr" "/var/lib/sss" "/var/run/munge" "/sys/fs/cgroup" "/iointensive" )
+
+# Set up the environment launcher script path - useful for scripts, such as payu,
+# to know how launch the container directly
+export ENV_LAUNCHER_SCRIPT_PATH="__CONDA_SCRIPT_PATH__/__FULLENV__.d/bin/launcher.sh"