added --init-commands option to put a line into job script

galyleo.sh

@@ -42,7 +42,7 @@
 # future, may include a Makefile with a PREFIX option to install
 # correctly and set this variable. e.g., https://github.com/oyvinev/log.sh
 
-declare -xr GALYLEO_INSTALL_DIR="${PWD}"
+declare -xr GALYLEO_INSTALL_DIR="/home/kenneth/info/elba/galyleo"
 
 # Declare a global environment variable to set the galyleo cache
 # directory, which will hold all output files generated by galyleo.
@@ -106,6 +106,7 @@ fi
 #   -s | --sif <singularity_image_file>
 #   -B | --bind <singularity_bind_mounts>
 #      | --nv
+#      | --init-commands <init_commands>
 #      | --conda-init <conda_init>
 #      | --conda-env <conda_env>
 #      | --conda-yml <conda_yml>
@@ -152,6 +153,9 @@ function galyleo_launch() {
   # Declare input variables associated with environment modules.
   local env_modules=''
 
+  # Declare input variables associated with init script.
+  local init_commands=''
+
   # Declare input variables associated with Singularity containers.
   local singularity_image_file=''
   local singularity_bind_mounts=''
@@ -263,6 +267,10 @@ function galyleo_launch() {
         singularity_gpu_type='rocm'
         shift 1
         ;;
+      --init-commands )
+        init_commands="${2}"
+        shift 2
+        ;;
       --conda-init )
         conda_init="${2}"
         shift 2
@@ -326,6 +334,7 @@ function galyleo_launch() {
   slog output -m "    -s | --sif               : ${singularity_image_file}"
   slog output -m "    -B | --bind              : ${singularity_bind_mounts}"
   slog output -m "       | --nv                : ${singularity_gpu_type}"
+  slog output -m "       | --init-commands       : ${init_commands}"
   slog output -m "       | --conda-init        : ${conda_init}"
   slog output -m "       | --conda-env         : ${conda_env}"
   slog output -m "       | --conda-yml         : ${conda_yml}"
@@ -398,6 +407,16 @@ function galyleo_launch() {
       done
     fi
 
+    # Check if init line specified by the user, if any, is
+    # available and can be run successfully. If not, then halt the launch.
+    if [[ -n "${init_commands}" ]]; then
+      sh -c "${init_commands}"
+      if [[ $? -ne 0 ]]; then
+        slog error -m "init-commands failed: ${init_commands}"
+        return 1
+      fi
+    fi
+
     # Check if the conda environment specified by the user, if any, can be
     # initialized and activated successfully. If not, then halt the launch.
     if [[ -n "${conda_env}" ]] && [[ -z "${conda_yml}" ]]; then
@@ -446,7 +465,8 @@ function galyleo_launch() {
       fi
     else
       if [[ -z "${conda_yml}" ]]; then
-        jupyter "${jupyter_interface}" --version > /dev/null
+        #jupyter "${jupyter_interface}" --version > /dev/null
+        which jupyter
         if [[ "${?}" -ne 0 ]]; then
           slog error -m "No jupyter executable was found within the software environment."
           return 1
@@ -468,15 +488,18 @@ function galyleo_launch() {
     slog error -m "Unable to connect to the Satellite reverse proxy service: ${http_status_code}"
     return 1
   fi
+  #: # don't run, just testing
 
   # Extract the reverse proxy connection token and export it as a
   # read-only environment variable.
   declare -xr REVERSE_PROXY_TOKEN="$(echo ${http_response} | awk 'NF>1{printf $((NF-1))}' -)"
+  #: # don't run, just testing
 
   # Generate an authentication token to be used for first-time 
   # connections to the Jupyter notebook server and export it as a 
   # read-only environment variable.
   declare -xr JUPYTER_TOKEN="$(openssl rand -hex 16)"
+  #: # don't run, just testing
 
   # Change present working directory to GALYLEO_CACHE_DIR. Generate and
   # store all Jupyter launch scripts and standard output files in the
@@ -499,6 +522,7 @@ function galyleo_launch() {
 
   # Generate a Jupyter launch script.
   slog output -m 'Generating Jupyter launch script ...'
+  echo ${GALYLEO_SCHEDULER}
   if [[ ! -f "${job_name}.sh" ]]; then
 
     slog append -f "${job_name}.sh" -m '#!/usr/bin/env sh'
@@ -624,6 +648,11 @@ function galyleo_launch() {
       done
     fi
 
+    # Run user init commands.
+    if [[ -n "${init_commands}" ]]; then
+      slog append -f "${job_name}.sh" -m  "${init_commands}"
+    fi
+
     # Activate a pre-installed conda environment specified by the user.
     if [[ -n "${conda_env}" ]] && [[ -z "${conda_yml}" ]]; then
       if [[ -n "${conda_init}" ]]; then
@@ -741,6 +770,9 @@ function galyleo_launch() {
   # Submit Jupyter launch script to scheduler.
   if [[ "${GALYLEO_SCHEDULER}" == 'slurm' ]]; then
     job_id="$(sbatch ${job_name}.sh | grep -o '[[:digit:]]*')"
+    #cat ${job_name}.sh
+    #job_id=0 # don't run, just testing
+    #: # don't run, just testing
     if [[ "${?}" -ne 0 ]]; then
       slog error -m 'Failed job submission to Slurm.'
       http_response="$(curl -s https://manage.${GALYLEO_REVERSE_PROXY_FQDN}/destroytoken.cgi?token=${REVERSE_PROXY_TOKEN})"
@@ -764,6 +796,7 @@ function galyleo_launch() {
   # Associate batch job id to the connection token from the reverse proxy service.
   http_response="$(curl -s https://manage.${GALYLEO_REVERSE_PROXY_FQDN}/linktoken.cgi?token=${REVERSE_PROXY_TOKEN}\&jobid=${job_id})"
   slog output -m "${http_response}"
+  #: # don't run, just testing
 
   # Always print to standard output the URL where the Jupyter notebook 
   # server may be accessed by the user.
@@ -974,6 +1007,7 @@ function galyleo_help() {
   slog output -m "    -B | --bind         : ${singularity_bind_mounts}"
   slog output -m "       | --nv           : ${singularity_gpu_type}"
   slog output -m "    -e | --env-modules  : ${env_modules}"
+  slog output -m "       | --init-commands  : ${init_commands}"
   slog output -m "       | --conda-init   : ${conda_init}"
   slog output -m "       | --conda-env    : ${conda_env}"
   slog output -m "       | --conda-yml    : ${conda_yml}"