v01

scripts/batch/list-jobs.sh

@@ -0,0 +1,139 @@
+#!/usr/bin/env bash
+##
+## BSD 3-Clause License
+##
+## This file is part of the Basalt project.
+## https://gitlab.com/VladyslavUsenko/basalt.git
+##
+## Copyright (c) 2019-2021, Vladyslav Usenko and Nikolaus Demmel.
+## All rights reserved.
+##
+
+#
+# Usage:
+#    list-jobs.sh DIRNAME [DIRNAME ...] [-s|--short] [-o|--only STATUS]
+#
+# Lists all batch jobs found in DIRNAME. If the optional argument
+# STATUS is passed, only lists jobs with that status. Multiple
+# statuses can be passed in a space-separated string.
+#
+# Possible status arguments: queued, running, completed, failed, unknown
+# You can also use 'active' as a synonym for 'queued running unknown'
+
+# exit on error
+set -o errexit -o pipefail
+
+
+# we need GNU getopt...
+GETOPT=getopt
+if [[ "$OSTYPE" == "darwin"* ]]; then
+    if [ -f /usr/local/opt/gnu-getopt/bin/getopt ]; then
+        GETOPT="/usr/local/opt/gnu-getopt/bin/getopt"
+    fi
+fi
+
+# option parsing, see: https://stackoverflow.com/a/29754866/1813258
+usage() { echo "Usage: `basename $0` DIRNAME [DIRNAME ...] [-s|--short] [-o|--only STATUS]" ; exit 1; }
+
+# -allow a command to fail with !’s side effect on errexit
+# -use return value from ${PIPESTATUS[0]}, because ! hosed $?
+! "$GETOPT" --test > /dev/null
+if [[ ${PIPESTATUS[0]} -ne 4 ]]; then
+    echo 'I’m sorry, `getopt --test` failed in this environment.'
+    exit 1
+fi
+
+OPTIONS=hsjo:
+LONGOPTS=help,short,jobids,only:
+
+# -regarding ! and PIPESTATUS see above
+# -temporarily store output to be able to check for errors
+# -activate quoting/enhanced mode (e.g. by writing out “--options”)
+# -pass arguments only via   -- "$@"   to separate them correctly
+! PARSED=$("$GETOPT" --options=$OPTIONS --longoptions=$LONGOPTS --name "`basename $0`" -- "$@")
+if [[ ${PIPESTATUS[0]} -ne 0 ]]; then
+    # e.g. return value is 1
+    #  then getopt has complained about wrong arguments to stdout
+    usage
+fi
+# read getopt’s output this way to handle the quoting right:
+eval set -- "$PARSED"
+
+SHORT=n
+ONLY=""
+JOBIDS=n
+# now enjoy the options in order and nicely split until we see --
+while true; do
+    case "$1" in
+        -h|--help) usage ;;
+        -s|--short) SHORT=y; shift ;;
+        -j|--jobids) JOBIDS=y; shift ;;
+        -o|--only) ONLY="$2"; shift 2 ;;
+        --) shift; break ;;
+        *) echo "Programming error"; exit 3 ;;
+    esac
+done
+
+# handle non-option arguments --> directories
+if [[ $# -lt 1 ]]; then
+    echo "Error: Pass at least one folder"
+    usage
+fi
+DIRS=("$@")
+
+# status aliases:
+ONLY="${ONLY/active/queued running unknown}"
+ONLY="${ONLY/notcompleted/queued running failed unknown}"
+
+contains() {
+    [[ $1 =~ (^| )$2($| ) ]] && return 0 || return 1
+}
+
+display() {
+    if [ -z "$ONLY" ] || contains "$ONLY" $2; then
+        if [ $SHORT = y ]; then
+            echo "$1"
+        else
+            echo -n "$1 : $2"
+            if [ -n "$3" ]; then
+                echo -n " - $3"
+            fi
+            echo ""
+        fi
+    fi
+}
+
+for d in "${DIRS[@]}"; do
+    for f in `find "$d" -name status.log | sort`; do
+        DIR=`dirname "$f"`
+
+        # ignore backup folder from "rerun" scripts
+        if [[ `basename $DIR` = results-backup* ]]; then
+            continue
+        fi
+
+        if ! grep Started "$f" > /dev/null; then
+            display "$DIR" unknown "not started"
+            continue
+        fi
+
+        # job has started:
+
+        if grep Completed "$f" > /dev/null ; then
+            display "$DIR" completed ""
+            continue
+        fi
+
+        # job has started, but not completed (cleanly)
+
+        # check signs of termination
+        if [ -f "$DIR"/output.log ] && grep "Command terminated by signal" "$DIR"/output.log > /dev/null; then
+            display "$DIR" failed killed "`grep -oP 'Command terminated by \Ksignal .+' "$DIR"/output.log`"
+            continue
+        fi
+
+        # might be running or aborted
+        display "$DIR" unknown started
+
+    done
+done