saving work on modularized

maouw · Sep 18, 2023 · e6326ae · e6326ae
1 parent d6a27ce
commit e6326ae
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Showing 12 changed files with 1,790 additions and 1,488 deletions.
diff --git a/hyakvnc.sh b/hyakvnc.sh
@@ -0,0 +1,209 @@
+#! /usr/bin/env bash
+
+set -f # Disable pathname expansion.
+#set -o pipefail # Return exit status of the last command in the pipe that failed.
+#set -e          # Exit immediately if a command exits with a non-zero status.
+[ "$DEBUG" == 1 ] && set -x
+
+CLUSTER_ADDRESS=${CLUSTER_ADDRESS:=klone.hyak.uw.edu}
+PORT_ON_CLIENT=${PORT_ON_CLIENT:=5901}
+CURRENT_HOSTNAME=$(hostname)
+
+# List of Klone login node hostnames
+LOGIN_NODE_LIST='klone-login01 klone1.hyak.uw.edu klone2.hyak.uw.edu'
+
+# Slurm configuration variables:
+export SBATCH_ACCOUNT="${SBATCH_ACCOUNT:=escience}"
+export SBATCH_DEBUG="${SBATCH_DEBUG:=0}"
+export SBATCH_GPUS="${SBATCH_GPUS:=0}"
+export SBATCH_PARTITION="${SBATCH_PARTITION:=gpu-a40}"
+export SBATCH_TIMELIMIT="${SBATCH_TIMELIMIT:=1:00:00}"
+export ARG_SBATCH_NTASKS="${ARG_SBATCH_NTASKS:=4}"
+
+# Check if command exists:
+function _command_exists {
+	command -v "$1" >/dev/null
+}
+
+# Check if the current host is a login node:
+function _is_login_node {
+	echo "${LOGIN_NODE_LIST[@]}" | grep -q "${CURRENT_HOSTNAME}"
+}
+
+APPTAINER_INSTANCES_DIR=${APPTAINER_INSTANCES_DIR:=${HOME}/.apptainer/instances}
+
+function _find_vnc_instance_pid_files {
+	# Make sure globstar is enabled
+	shopt -s globstar
+	for f in "$APPTAINER_INSTANCES_DIR"/app/**/*.json; do
+		logOutPath=$(python3 -c'import json, sys;print(json.load(open(sys.argv[1]))["logOutPath"])' "$f" 2>/dev/null)
+		[ -z "$logOutPath" ] && continue
+		[ ! -f "$logOutPath" ] && continue
+
+		vncPidFile=$(sed -E '/Log file is/!d; s/^.*[/]//; s/[.]log$/.pid/' "${logOutPath}")
+		vncPidPath="${HOME}/.vnc/${vncPidFile}"
+		if [ ! -f "$vncPidPath" ]; then
+			echo "Could not find vncPidFile at ${vncPidPath}"
+			continue
+		fi
+		echo $vncPidFile
+	done
+	shopt -u globstar
+}
+
+_log() {
+	_ANSI_BLUE= _ANSI_BOLD= _ANSI_CYAN= _ANSI_GREEN= _ANSI_MAGENTA= _ANSI_RED= _ANSI_RESET= _ANSI_UNDERLINE= _ANSI_YELLOW=
+	[[ "${BASH_SOURCE[0]:-}" != "${0}" ]] && sourced=1 || sourced=0
+	[[ -t 1 ]] && piped=0 || piped=1 # detect if output is piped
+	if [[ $piped -eq 0 ]]; then
+		_ANSI_GREEN="\033[92m"
+		_ANSI_RED="\033[91m"
+		_ANSI_CYAN="\033[36m"
+		_ANSI_YELLOW="\033[93m"
+		_ANSI_MAGENTA="\033[95m"
+		_ANSI_BLUE="\033[94m"
+		_ANSI_RESET="\033[0m"
+		_ANSI_BOLD="\033[1m"
+		_ANSI_UNDERLINE="\033[4m"
+	fi
+	level="${1}"
+	color="${_ANSI_RESET}"
+	shift
+	case "${level}" in
+	INFO)
+		color="${_ANSI_CYAN}"
+		;;
+	WARN)
+		color="${_ANSI_YELLOW}"
+		;;
+	ERROR)
+		color="${_ANSI_RED}"
+		;;
+	esac
+	printf "$(date --rfc-3339=s) ${_ANSI_BOLD}${color}${level}${_ANSI_RESET}: ${color}$* ${_ANSI_RESET}\n"
+}
+
+function list_vnc_pids {
+	for f in $HOME/.vnc/*.pid; do
+		vnchostfull=$(basename ${f%%.pid})
+		vnchost=${vnchostfull%%:*}
+		vncport=${vnchostfull##*:}
+		echo $vnchost $vncport
+	done
+}
+
+function show_connection_string_for_linux_host {
+	echo 'ssh -f -J klone.hyak.uw.edu g3071 -L 5901:localhost:5901 sleep 10; vncviewer localhost:5901'
+	vnchost=$1
+	vncport=$2
+	echo "vncviewer ${vnchost}:${vncport}"
+}
+
+function generate_ssh_command {
+	echo "ssh -f -N -J \"${CLUSTER_HOSTNAME}\" \${HOSTNAME 5901:localhost:5901"
+}
+
+function status {
+	_log ERROR "status task not implemented"
+}
+
+function kill {
+	_log ERROR "kill task not implemented"
+}
+
+function kill-all {
+	_log ERROR "kill-all task not implemented"
+}
+
+function set-passwd {
+	_log ERROR "set-passwd task not implemented"
+}
+
+function repair {
+	_log ERROR "repair task not implemented"
+}
+function build {
+	_log ERROR "build task not implemented"
+}
+
+sbatch -A escience --job-name thing2 -p gpu-a40 -c 1 --mem=1G --time=1:00:00 --wrap "apptainer instance start $(realpath ~/code/apptainer-test/looping/looping.sif) thing2 && while true; do sleep 10; done"
+
+function launch {
+	ARGS_TO_SBATCH=""
+	NTASK_ARGUMENT="--ntasks=${ARG_SBATCH_NTASKS}"
+	for i in "$@"; do
+		case $i in
+		--dry-run)
+			DRY_RUN=1
+			shift
+			;;
+		-n=* | --ntasks=*)
+			NTASK_ARGUMENT="$1"
+			shift # past argument=value
+			;;
+		-c=* | --cpus-per-task=*)
+			NTASK_ARGUMENT="$1"
+			shift # past argument=value
+			;;
+		--sif)
+			shift
+			[ -z "$1" ] && _log ERROR "--sif requires a non-empty option argument" && exit 1
+			SIF_FILE="$1"
+			shift # past argument=value
+			;;
+		*)
+			ARGS_TO_SBATCH="${ARGS_TO_SBATCH} $1"
+			shift
+			;;
+		esac
+	done
+	[ -z "$SIF_FILE" ] && _log ERROR "Requires a --sif argument specifying the path to the container image" && exit 1
+	SIF_PATH=$(realpath "${SIF_FILE}")
+	SIF_BASENAME="$(basename "${SIF_FILE}")"
+	SIF_NAME="${SIF_BASENAME%.*}"
+
+	[ ! -f "$SIF_PATH" ] && _log ERROR "--sif requires a file to be present at ${SIF_FILE}" && exit 1
+
+	ARGS_TO_SBATCH="${NTASK_ARGUMENT} ${ARGS_TO_SBATCH}"
+	ARGS_TO_SBATCH="${ARGS_TO_SBATCH/  /}" # Remove double spaces
+
+	_log INFO "Launching job with sif file ${SIF_FILE} and args ${ARGS_TO_SBATCH}"
+
+	#sbatch -A escience --job-name thing2 -p gpu-a40 -c 1 --mem=1G --time=1:00:00 --wrap "apptainer instance start $(realpath ~/code/apptainer-test/looping/looping.sif) thing2 && while true; do sleep 10; done"
+	COMMAND_TO_RUN=
+	_log INFO "Will run the following command:"
+	echo "${COMMAND_TO_RUN}"
+
+	if [ ! "$DRY_RUN" ]; then
+		! _command_exists sbatch && echo "ERROR: sbatch not found" && exit 1
+		! _is_login_node && echo "ERROR: You must run this from a login node. This is not a login node." && exit 1
+		sbatch ${ARGS_TO_SBATCH} --job-name ${SIF_NAME} --wrap "apptainer instance start ${SIF_PATH} ${SIF_NAME}-\$SLURM_JOBID && while true; do sleep 10; done"
+	else
+		_log INFO "Dry run. Not running sbatch."
+		_log INFO "Would have run sbatch ${ARGS_TO_SBATCH} --job-name ${SIF_NAME} --wrap \"apptainer instance start ${SIF_PATH} ${SIF_NAME}-\$SLURM_JOBID && while true; do sleep 10; done\""
+	fi
+}
+
+function default {
+	echo "Args:" "$@"
+	help
+}
+
+function help {
+	echo "$0 <task> <args>"
+	echo "Tasks:"
+	compgen -A function | grep -v '^_' | cat -n
+}
+
+# Set default action:
+ACTION=default
+
+# If the first argument is a function in this file, set it to the action:
+if [ $# -gt 0 ] && [ $(compgen -A function | grep '^'"$1"'$') ]; then
+	[ "$DEBUG" == 1 ] && echo "Setting action to $1"
+	ACTION="$1"
+	shift
+fi
+
+# Run the action:
+"$ACTION" "$@"