Using resources effectively
OverviewTeaching: 10 min
Exercises: 30 minQuestions
How do we monitor our jobs?
How can I get my jobs scheduled more easily?Objectives
Understand how to look up job statistics and profile code.
Understand job size implications.
We’ve touched on all the skills you need to interact with an HPC cluster: logging in over SSH, loading software modules, submitting parallel jobs, and finding the output. Let’s learn about estimating resource usage and why it might matter.
Estimating required resources using the scheduler
Although we covered requesting resources from the scheduler earlier with the π code, how do we know what type of resources the software will need in the first place, and its demand for each? In general, unless the software documentation or user testimonials provide some idea, we won’t know how much memory or compute time a program will need.
Read the Documentation
Most HPC facilities maintain documentation as a wiki, a website, or a document sent along when you register for an account. Take a look at these resources, and search for the software you plan to use: somebody might have written up guidance for getting the most out of it.
A convenient way of figuring out the resources required for a job to run successfully is
to submit a test job, and then ask the scheduler about its impact using
sacct -u yourUsername. You can use this knowledge to set up the next job with a closer
estimate of its load on the system. A good general rule is to ask the scheduler for 20% to
30% more time and memory than you expect the job to need. This ensures that minor
fluctuations in run time or memory use will not result in your job being cancelled by the
scheduler. Keep in mind that if you ask for too much, your job may not run even though
enough resources are available, because the scheduler will be waiting for other people’s
jobs to finish and free up the resources needed to match what you asked for.
Since we already submitted
pi.py to run on the cluster, we can query the scheduler to
see how long our job took and what resources were used. We will use
sacct -u yourUsername to get statistics about
[[email protected] ~]$ sacct -u yourUsername
JobID JobName Partition Account AllocCPUS State ExitCode ------------ ---------- ---------- ---------- ---------- ---------- -------- 7 file.sh cpubase_b+ def-spons+ 1 COMPLETED 0:0 7.batch batch def-spons+ 1 COMPLETED 0:0 7.extern extern def-spons+ 1 COMPLETED 0:0 8 file.sh cpubase_b+ def-spons+ 1 COMPLETED 0:0 8.batch batch def-spons+ 1 COMPLETED 0:0 8.extern extern def-spons+ 1 COMPLETED 0:0 9 example-j+ cpubase_b+ def-spons+ 1 COMPLETED 0:0 9.batch batch def-spons+ 1 COMPLETED 0:0 9.extern extern def-spons+ 1 COMPLETED 0:0
This shows all the jobs we ran recently (note that there are multiple entries per job). To get info about a specific job, we change command slightly.
[[email protected] ~]$ sacct -u yourUsername -l -j 1965
It will show a lot of info, in fact, every single piece of info collected on your job by
the scheduler. It may be useful to redirect this information to
less to make it easier
to view (use the left and right arrow keys to scroll through fields).
[[email protected] ~]$ sacct -u yourUsername -l -j 1965 | less
Some interesting fields include the following:
- Hostname: Where did your job run?
- MaxRSS: What was the maximum amount of memory used?
- Elapsed: How long did the job take?
- State: What is the job currently doing/what happened to it?
- MaxDiskRead: Amount of data read from disk.
- MaxDiskWrite: Amount of data written to disk.
Measuring the system load from currently running tasks
Typically, clusters allow users to connect directly to compute nodes from the head node. This is useful to check on a running job and see how it’s doing, but is not a recommended practice in general, because it bypasses the resource manager. To reduce the risk of interfering with other users, some clusters will only allow you to connect to nodes on which you have running jobs. Let’s practice by taking a look at what’s running on the login node right now.
Monitor system processes with
The most reliable way to check current system stats is with
top. Some sample output
might look like the following (type
q to exit
[[email protected] ~]$ top
top - 21:00:19 up 3:07, 1 user, load average: 1.06, 1.05, 0.96 Tasks: 311 total, 1 running, 222 sleeping, 0 stopped, 0 zombie %Cpu(s): 7.2 us, 3.2 sy, 0.0 ni, 89.0 id, 0.0 wa, 0.2 hi, 0.2 si, 0.0 st KiB Mem : 16303428 total, 8454704 free, 3194668 used, 4654056 buff/cache KiB Swap: 8220668 total, 8220668 free, 0 used. 11628168 avail Mem PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 1693 jeff 20 0 4270580 346944 171372 S 29.8 2.1 9:31.89 gnome-shell 3140 jeff 20 0 3142044 928972 389716 S 27.5 5.7 13:30.29 Web Content 3057 jeff 20 0 3115900 521368 231288 S 18.9 3.2 10:27.71 firefox 6007 jeff 20 0 813992 112336 75592 S 4.3 0.7 0:28.25 tilix 1742 jeff 20 0 975080 164508 130624 S 2.0 1.0 3:29.83 Xwayland 1 root 20 0 230484 11924 7544 S 0.3 0.1 0:06.08 systemd 68 root 20 0 0 0 0 I 0.3 0.0 0:01.25 kworker/4:1 2913 jeff 20 0 965620 47892 37432 S 0.3 0.3 0:11.76 code 2 root 20 0 0 0 0 S 0.0 0.0 0:00.02 kthreadd
Overview of the most important fields:
PID: What is the numerical id of each process?
USER: Who started the process?
RES: What is the amount of memory currently being used by a process (in bytes)?
%CPU: How much of a CPU is each process using? Values higher than 100 percent indicate that a process is running in parallel.
%MEM: What percent of system memory is a process using?
TIME+: How much CPU time has a process used so far? Processes using 2 CPUs accumulate time at twice the normal rate.
COMMAND: What command was used to launch a process?
htop provides an overlay for
top using curses, producing a better-organized
and “prettier” dashboard in your terminal. Unfortunately, it is not always available. If
this is the case, ask your system administrators to install it for you. Don’t be shy,
they’re here to help!
[[email protected] ~]$ htop
To show all processes from your current session, type
[[email protected] ~]$ ps
PID TTY TIME CMD 15113 pts/5 00:00:00 bash 15218 pts/5 00:00:00 ps
Note that this will only show processes from our current session. To show all processes
you own (regardless of whether they are part of your current session or not), you can use
[[email protected] ~]$ ps ux
USER PID %CPU %MEM VSZ RSS TTY STAT START TIME COMMAND yourUsername 67780 0.0 0.0 149140 1724 pts/81 R+ 13:51 0:00 ps ux yourUsername 73083 0.0 0.0 142392 2136 ? S 12:50 0:00 sshd: [email protected]/81 yourUsername 73087 0.0 0.0 114636 3312 pts/81 Ss 12:50 0:00 -bash
This is useful for identifying which processes are doing what.
The smaller your job, the faster it will schedule.