Environment updates

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
-    # Using payu-* to modify payu-run, payu-collate, payu-sync files
+for file in ${CONDA_INSTALLATION_PATH}/envs/${FULLENV}/bin/payu*; do
+    # Using payu* to modify payu, 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/environment.yml

@@ -17,4 +17,5 @@ dependencies:
   - xarray
   - mule
   - um2nc
-  - accessnri::yamanifest
+  - accessnri::yamanifest
+  - netcdf4=*=nompi_*

modules/common_v3

@@ -40,8 +40,3 @@ if { [ file exists $mydir/.$module_version ] } {
     puts stderr "ERROR! Environment spec is missing!"
     exit 1
 }
-
-### Extra env to get other things working
-setenv OMPI_MCA_orte_launch_agent $myscripts/orted
-setenv MAMBA_ROOT_PREFIX $prefix/$package
-setenv CONDA_EXE $prefix/$package/bin/micromamba

scripts/build.sh

@@ -120,7 +120,7 @@ function inner() {
     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}"/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}

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"