Monitoring job execution

Output stream redirection

The primary way to monitor job execution is through the stdout and stderr streams. These are redirected to text files specified in the SLURM script.

For this purpose the tail command is particularly useful. To continuously follow the output to a text file use:

tail -f output_987654.txt

To obtain the last X lines of a text file use:

tail -n X output_987654.txt

Replacing X by the desired number of lines.

If the output file gets too long and you wish to read from the begining you may combine the commands cat and less:

cat output_987654.txt | less

Use the Q key to exit less.

Monitoring resource usage

While the output streams may suffice in most cases, certain programmes might not provide much feedback. This could be the case with a programme that rellies on modules that are not verbose. In such situations it is best to monitor resource usage to gauge job execution. Two possible options are described below.

Using sstat

sstat is a SLURM tool that can be used to obtain instantaneous information on resource usage, CPU load, memory, etc. To use it starting by changing your SLURM script so that your programme starts with the srun command (this should be the last line in the script):

srun python3 calc_pi.py

Note down the job number. During execution you can then use sstat, passing the job number with the -j flag:

sstat --format=AveCPU,AveRSS,MaxRSS -P -j 987654

sstat can provide information on many different variables, for more details check the manual.

Using top

Another way it to log the output of the top command. This requires adding an extra command to your SLURM script, again using srun (where "user001" should be replaced by your user name):

srun --overcommit --ntasks=1 top -b -u user001 & python3 calc_pi.py

This will log the output of top to the sdtout stream file specific in the SLURM script every 3 seconds. Using the tail command you will be able to see logs like:

top - 18:09:12 up 53 days, 22:53,  0 users,  load average: 27,04, 27,63, 26,53
Tasks: 1068 total,   4 running, 1064 sleeping,   0 stopped,   0 zombie
%Cpu(s): 41,9 us,  0,2 sy,  0,0 ni, 57,9 id,  0,0 wa,  0,0 hi,  0,0 si,  0,0 st
KiB Mem : 10439453+total, 18650486+free, 43690281+used, 42053763+buff/cache
KiB Swap: 26214400+total, 26214393+free,       52 used. 54182425+avail Mem 

  PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND
29260 user001   20   0   15,6g  15,2g  17392 R  1777  1,5   4014:16 R
29447 user001   20   0  178604  12900   1676 R   1,6  0,0   6:33.17 top
28627 user001   20   0  113184   1520   1260 S   0,0  0,0   0:00.01 slurm_scri+
29253 user001   20   0  245096   4792   1976 S   0,0  0,0   0:00.66 srun
29357 user001   20   0   36124    688     16 S   0,0  0,0   0:00.00 srun