Issue

• We have a floating issue in the cluster, where multiple tasks/threads seem to be assigned to only a subset of the available cores, leaving the others idle. That may slow down computations drastically and lead to degradation of a whole parallel job run over a number of nodes.

Once we noticed a suspect node during a job operation, we can then observe the issue in more detail running 16 parallel tasks which are summing up to numbers in a loop for a while.

• As cpu scaling is turned on, it's clear that some cores are underused while others are 100% utilized.

# grep MHz /proc/cpuinfo ; top -b -n 1 |grep stress ; ps axur
cpu MHz         : 1200.000
cpu MHz         : 1200.000
cpu MHz         : 2701.000
cpu MHz         : 1200.000
cpu MHz         : 1200.000
cpu MHz         : 1200.000
cpu MHz         : 1200.000
cpu MHz         : 1200.000
cpu MHz         : 1200.000
cpu MHz         : 1200.000
cpu MHz         : 1200.000
cpu MHz         : 2701.000
cpu MHz         : 1200.000
cpu MHz         : 1200.000
cpu MHz         : 1200.000
cpu MHz         : 1200.000
 2986 root      20   0   424  248   88 R 98.7  0.0   0:05.03 stress
 2990 root      20   0   424  248   88 R  7.9  0.0   0:00.34 stress
 2994 root      20   0   424  248   88 R  7.9  0.0   0:00.34 stress
 2987 root      20   0   424  248   88 R  5.9  0.0   0:00.32 stress
 2988 root      20   0   424  244   88 R  5.9  0.0   0:00.33 stress
 2989 root      20   0   424  248   88 R  5.9  0.0   0:00.33 stress
 2991 root      20   0   424  248   88 R  5.9  0.0   0:00.33 stress
 2992 root      20   0   424  248   88 R  5.9  0.0   0:00.33 stress
 2993 root      20   0   424  248   88 R  5.9  0.0   0:00.33 stress
 2995 root      20   0   424  248   88 R  5.9  0.0   0:00.33 stress
 2996 root      20   0   424  248   88 R  5.9  0.0   0:00.33 stress
 2997 root      20   0   424  248   88 R  5.9  0.0   0:00.33 stress
 2998 root      20   0   424  248   88 R  5.9  0.0   0:00.33 stress
 2999 root      20   0   424  248   88 R  5.9  0.0   0:00.32 stress
 3000 root      20   0   424  248   88 R  5.9  0.0   0:00.32 stress
 3001 root      20   0   424  248   88 R  5.9  0.0   0:00.32 stress
USER       PID %CPU %MEM    VSZ   RSS TTY      STAT START   TIME COMMAND
root      2986  101  0.0    424   248 pts/0    R    21:25   0:05 ./stress 50000
root      2987  6.6  0.0    424   248 pts/0    R    21:25   0:00 ./stress 50000
root      2988  6.8  0.0    424   244 pts/0    R    21:25   0:00 ./stress 50000
root      2989  6.6  0.0    424   248 pts/0    R    21:25   0:00 ./stress 50000
root      2990  6.8  0.0    424   248 pts/0    R    21:25   0:00 ./stress 50000
root      2991  6.6  0.0    424   248 pts/0    R    21:25   0:00 ./stress 50000
root      2992  6.6  0.0    424   248 pts/0    R    21:25   0:00 ./stress 50000
root      2993  6.6  0.0    424   248 pts/0    R    21:25   0:00 ./stress 50000
root      2994  6.8  0.0    424   248 pts/0    R    21:25   0:00 ./stress 50000
root      2995  6.6  0.0    424   248 pts/0    R    21:25   0:00 ./stress 50000
root      2996  6.6  0.0    424   248 pts/0    R    21:25   0:00 ./stress 50000
root      2997  6.6  0.0    424   248 pts/0    R    21:25   0:00 ./stress 50000
root      2998  6.8  0.0    424   248 pts/0    R    21:25   0:00 ./stress 50000
root      2999  6.4  0.0    424   248 pts/0    R    21:25   0:00 ./stress 50000
root      3000  6.4  0.0    424   248 pts/0    R    21:25   0:00 ./stress 50000
root      3001  6.4  0.0    424   248 pts/0    R    21:25   0:00 ./stress 50000

• The CPU affinity mask for each process is ffff
• After using 'taskset' to change affinity to explicitly distribute processes across all cores, we get it alright:

# grep MHz /proc/cpuinfo ; top -b -n 1 |grep stress ; ps axur
cpu MHz         : 2701.000
cpu MHz         : 2701.000
cpu MHz         : 2701.000
cpu MHz         : 2701.000
cpu MHz         : 2701.000
cpu MHz         : 2701.000
cpu MHz         : 2701.000
cpu MHz         : 2701.000
cpu MHz         : 2701.000
cpu MHz         : 2701.000
cpu MHz         : 2701.000
cpu MHz         : 2701.000
cpu MHz         : 2701.000
cpu MHz         : 2701.000
cpu MHz         : 2701.000
cpu MHz         : 2701.000
 5185 root      20   0   424  248   88 R 100.0  0.0   0:16.62 stress
 5188 root      20   0   424  244   88 R 100.0  0.0   0:16.60 stress
 5191 root      20   0   424  248   88 R 100.0  0.0   0:16.61 stress
 5192 root      20   0   424  248   88 R 100.0  0.0   0:14.98 stress
 5194 root      20   0   424  248   88 R 100.0  0.0   0:16.61 stress
 5197 root      20   0   424  248   88 R 100.0  0.0   0:14.98 stress
 5198 root      20   0   424  248   88 R 100.0  0.0   0:14.97 stress
 5199 root      20   0   424  244   88 R 100.0  0.0   0:16.61 stress
 5186 root      20   0   424  248   88 R 98.6  0.0   0:16.58 stress
 5187 root      20   0   424  244   88 R 98.6  0.0   0:16.62 stress
 5189 root      20   0   424  252   88 R 98.6  0.0   0:16.58 stress
 5190 root      20   0   424  248   88 R 98.6  0.0   0:14.98 stress
 5193 root      20   0   424  248   88 R 98.6  0.0   0:14.96 stress
 5195 root      20   0   424  248   88 R 98.6  0.0   0:14.97 stress
 5196 root      20   0   424  244   88 R 98.6  0.0   0:14.96 stress
 5200 root      20   0   424  244   88 R 98.6  0.0   0:14.96 stress
USER       PID %CPU %MEM    VSZ   RSS TTY      STAT START   TIME COMMAND
root      5185 92.5  0.0    424   248 pts/0    R    21:43   0:16 ./stress 100000
root      5186 92.2  0.0    424   248 pts/0    R    21:43   0:16 ./stress 100000
root      5187 92.5  0.0    424   244 pts/0    R    21:43   0:16 ./stress 100000
root      5188 92.3  0.0    424   244 pts/0    R    21:43   0:16 ./stress 100000
root      5189 92.2  0.0    424   252 pts/0    R    21:43   0:16 ./stress 100000
root      5190 83.3  0.0    424   248 pts/0    R    21:43   0:15 ./stress 100000
root      5191 92.4  0.0    424   248 pts/0    R    21:43   0:16 ./stress 100000
root      5192 83.3  0.0    424   248 pts/0    R    21:43   0:15 ./stress 100000
root      5193 83.3  0.0    424   248 pts/0    R    21:43   0:15 ./stress 100000
root      5194 92.4  0.0    424   248 pts/0    R    21:43   0:16 ./stress 100000
root      5195 83.3  0.0    424   248 pts/0    R    21:43   0:15 ./stress 100000
root      5196 83.2  0.0    424   244 pts/0    R    21:43   0:14 ./stress 100000
root      5197 83.3  0.0    424   248 pts/0    R    21:43   0:15 ./stress 100000
root      5198 83.3  0.0    424   248 pts/0    R    21:43   0:15 ./stress 100000
root      5199 92.4  0.0    424   244 pts/0    R    21:43   0:16 ./stress 100000
root      5200 83.2  0.0    424   244 pts/0    R    21:43   0:14 ./stress 100000

• The problem is that kernel schedules independent tasks onto the same core leaving others core idle. This is clearly a bug in the kernel behavior as we see it, since it leads to a drastic degradation of performance especially in a parallel environment.
• We used taskset only to show that the cores itself are capable to perform the same tasks at 100% user utilization and time of the task completion would fall significantly. Also the fact is quite eloquent, that this behavior usually goes away as we reboot the node.
• Using taskset is not a real solution as nodes for a task are picked automatically by outside batch scheduler.
• Please confirm if such an issue is a kernel error or it can be somehow be configured so that task a scheduled in the optimal way without manual intervention .