support both cgroup v1 and v2

strike disk I/O because it does not cover network filesystems

examples/plugin_log_task_usage/StressTest.wdl

@@ -1,5 +1,6 @@
 version 1.1
 # MINIWDL__LOG_TASK_USAGE__PERIOD=2 miniwdl run examples/plugin_log_task_usage/StressTest.wdl --dir /tmp --verbose
+# MINIWDL__LOG_TASK_USAGE__PERIOD=2 miniwdl-aws-submit plugin_log_task_usage/StressTest.wdl --verbose --follow
 
 task StressTest {
     input {

examples/plugin_log_task_usage/miniwdl_log_task_usage.py

@@ -7,7 +7,7 @@
 set configuration [log_task_usage] period (or the environment variable
 MINIWDL__LOG_TASK_USAGE__PERIOD) to the desired logging period in seconds.
 
-YMMV because host OS version & configuration may affect availability of the cgroup v2 counters read
+YMMV because host OS version & configuration may affect availability of the cgroup counters read
 from pseudo-files under /sys/fs/cgroup
 """
 
@@ -31,67 +31,58 @@ def main(cfg, logger, run_id, run_dir, task, **recv):
 _logger_sh = r"""
 _miniwdl_log_task_usage() {
     set +ex
-    PERIOD_SECS=${1:-10}  # logging period (default 10s)
-    if [ ! -f /sys/fs/cgroup/cpu.stat ] || [ ! -f /sys/fs/cgroup/io.stat ]; then
-        >&2 echo "miniwdl_log_task_usage unable to report: cgroup v2 counters /sys/fs/cgroup/{cpu,io}.stat not found"
+    local PERIOD_SECS=${1:-10}  # logging period (default 10s)
+
+    # detect whether host provides cgroup v2 or v1, and helper functions to read CPU & memory usage
+    # counters from the appropriate pseudo-files
+    local cgroup_version=""
+    if [ -f /sys/fs/cgroup/cpu.stat ]; then
+        cgroup_version=2
+    elif [ -f /sys/fs/cgroup/cpuacct/cpuacct.stat ]; then
+        cgroup_version=1
+    else
+        >&2 echo "miniwdl_log_task_usage unable to report: cgroup CPU usage counters not found"
         exit 1
     fi
 
-    # CPU usage in microseconds
-    cpu_usecs() {
-        awk '/^usage_usec/ {print $2}' /sys/fs/cgroup/cpu.stat
+    cpu_secs() {
+        local ans
+        if [ $cgroup_version -eq 2 ]; then
+            ans=$(awk '/^usage_usec/ {print $2}' /sys/fs/cgroup/cpu.stat)
+            echo $(( ans / 1000000 ))
+        else
+            ans=$(cut -f2 -d ' ' /sys/fs/cgroup/cpuacct/cpuacct.stat | head -n 1)
+            echo $(( ans / 100 )) # 100 "jiffies" per second
+        fi
     }
 
-    # total block device I/O
-    io_bytes() {
-        awk '{
-            for (i = 1; i <= NF; i++) {
-                if ($i ~ /^rbytes=/) {
-                    rbytes += substr($i, index($i, "=") + 1);
-                }
-                if ($i ~ /^wbytes=/) {
-                    wbytes += substr($i, index($i, "=") + 1);
-                }
-            }
-        }
-        END {
-            print rbytes, wbytes;
-        }' /sys/fs/cgroup/io.stat
+    mem_bytes() {
+        if [ $cgroup_version -eq 2 ]; then
+            awk '$1 == "anon" { print $2 }' /sys/fs/cgroup/memory.stat
+        else
+            awk -F ' ' '$1 == "total_rss" { print $2 }'  /sys/fs/cgroup/memory/memory.stat
+        fi
     }
 
-    T_0=$(date +%s)
-    cpu_usecs_0=$(cpu_usecs)
-    read rbytes0 wbytes0 < <(io_bytes)
-    cpu_usecs_last=$cpu_usecs_0
-    rbytes_last=$rbytes0
-    wbytes_last=$wbytes0
-    t_last=$T_0
-    mem_max_bytes=0
+    local T_0=$(date +%s)
+    local t_last=$T_0
+    local cpu_secs_0=$(cpu_secs)
+    local cpu_secs_last=$cpu_secs_0
 
     while true; do
         sleep "$PERIOD_SECS"
-        t=$(date +%s)
-        wall_secs=$(( t - T_0 ))
+        local t=$(date +%s)
+        local wall_secs=$(( t - T_0 ))
 
-        cpu_usecs_current=$(cpu_usecs)
-        cpu_total_usecs=$(( cpu_usecs_current - cpu_usecs_0 ))
-        cpu_period_usecs=$(( cpu_usecs_current - cpu_usecs_last ))
+        local cpu_secs_current=$(cpu_secs)
+        local cpu_total_secs=$(( cpu_secs_current - cpu_secs_0 ))
+        local cpu_period_secs=$(( cpu_secs_current - cpu_secs_last ))
 
-        read rbytes_current wbytes_current < <(io_bytes)
-        rbytes_total=$(( rbytes_current - rbytes0 ))
-        wbytes_total=$(( wbytes_current - wbytes0 ))
-        rbytes_period=$(( rbytes_current - rbytes_last ))
-        wbytes_period=$(( wbytes_current - wbytes_last ))
+        local mem_bytes_current=$(mem_bytes)
 
-        mem_bytes=$(awk '$1 == "anon" { print $2 }' /sys/fs/cgroup/memory.stat)
-        mem_max_bytes=$(( mem_bytes > mem_max_bytes ? mem_bytes : mem_max_bytes ))
+        >&2 echo "container usage :: cpu_pct: $(( 100 * cpu_period_secs / PERIOD_SECS )), mem_MiB: $(( mem_bytes_current/1048576 )), cpu_total_s: ${cpu_total_secs}, elapsed_s: ${wall_secs}"
 
-        >&2 echo "container usage (last ${PERIOD_SECS}s) :: cpu_pct: $(( 100 * cpu_period_usecs / 1000000 / PERIOD_SECS )), mem_GiB: $(( mem_bytes/1073741824 )), io_read_MiB: $(( rbytes_period/1048576 )), io_write_MiB: $(( wbytes_period/1048576 ))"
-        >&2 echo "container usage (total ${wall_secs}s) :: cpu_s: $(( cpu_total_usecs / 1000000 )), mem_max_GiB: $(( mem_max_bytes/1073741824 )), io_read_GiB: $(( rbytes_total/1073741824 )), io_write_GiB: $(( wbytes_total/1073741824 ))"
-
-        cpu_usecs_last=$cpu_usecs_current
-        rbytes_last=$rbytes_current
-        wbytes_last=$wbytes_current
+        cpu_secs_last=$cpu_secs_current
         t_last=$t
     done
 }