Specifying Memory for Jobs on Quest

Quest and Kellogg Linux Cluster Downtime, June 8th-14th, 2024.

Quest, including the Quest Analytics Nodes, the Genomics Compute Cluster (GCC), the Kellogg Linux Cluster (KLC), and Quest OnDemand, will be unavailable for scheduled maintenance starting at 7 A.M. on Saturday, June 8, and ending approximately at 5 P.M. on Friday, June 14. During the maintenance window, you will not be able to login to Quest, Quest Analytics Nodes, the GCC, KLC, or Quest OnDemand submit new jobs, run jobs, or access files stored on Quest in any way including Globus. For details on this maintenance, please see the Status of University IT Services page.

This document outlines how to modify job submission scripts to request the correct amount of memory for jobs on Quest.

Why should I reserve memory (RAM) in my submission script?
Jobs need access to memory on the compute nodes to run successfully. If your job does not explicitly reserve memory in its submission script, it will be given 3.25 GB of memory for each core reserved. This default amount of memory may not be enough for your job, and jobs that do not reserve enough memory fail.

How can I tell if my job needs more memory to run successfully?
Use the sacct -X command to see information about your recent jobs, for example:

$ sacct -X
       JobID    JobName  Partition    Account  AllocCPUS      State ExitCode 
------------ ---------- ---------- ---------- ---------- ---------- -------- 
1273539      lammps-te+      short     p1234          40  COMPLETED      0:0 
1273543      vasp-open+      short     p1234          40 OUT_OF_ME+    0:125

The "State" field is the status of your job when it finished. Jobs with a "COMPLETED" state have run without system errors. Jobs with an "OUT_OF_ME+" state have run out of memory and failed. "OUT_OF_ME+" jobs need to request more memory in their job submission scripts to complete successfully.

If the job you're investigating is not recent enough to be listed bysacct -X, add date fields to the command to see jobs between specific start and end dates. For example, to see all jobs between September 15, 2019 and September 16, 2019:

$ sacct -X --starttime 091519 --endtime 091619

Specify the date using MMDDYY. More information on sacct is available here.



My job ran out of memory and failed, now what?

First, determine how much memory your job needs following the steps outlined below. Once you know how much memory your job needs, edit your job submission script to reserve that amount of memory + 10% for your job.

How much memory does my job need?
To determine out how much memory your job uses on a compute node:
1) create a test job by editing your job's submission script to reserve all of the memory of the node it runs on
2) run your test job
3) confirm your test job has completed successfully
4) use seff to see how much memory your job actually used.

1) Create a test job
To profile your job's memory usage, create a test job by modifying your job's submission script to include the lines:

#SBATCH --mem=0
#SBATCH --nodes=1

Setting --mem=0 reserves all of the memory on the node for your job; if you already have a --mem= directive in your job submission script, comment it out. Now your job will not run out of memory unless your job needs more memory than is on the node.

Setting --nodes=1 reserves a single node for your job. For jobs that run on multiple nodes such as MPI-based programs, request the number of nodes that your job runs on. Be sure to specify a value for #SBATCH --nodes= or the cores your job submission script reserves could end up on as many nodes as cores requested. Be aware that by setting --mem=0, you will be reserving all the memory on each of those nodes that your cores are reserved on.

2) Run your test job
Submit your test job to the cluster with the sbatch command. For interactive jobs, use srun or salloc. More information on submitting jobs to Quest is available here.

3) Did your test job complete successfully?
When your job has stopped running use the sacct -X command to confirm your job finished with state "COMPLETED". If your test job finishes with an "OUT_OF_ME+" state, confirm that you are submitting the modified job submission script that requests all of the memory on the node. If the "OUT_OF_ME+" errors persist, your job may require more memory than is available on the compute node it ran on. In this case, please email quest-help@northwestern.edu for assistance.

4) How much memory did your job actually use?
To see how much memory it used run the command: seff <test_job_id_number>. This returns output similar to:

Job ID: 767731
Cluster: quest
User/Group: abc123/abc123
State: COMPLETED (exit code 0)
Cores: 1
CPU Utilized: 00:10:00
CPU Efficiency: 100.00% of 00:10:00 core-walltime
Job Wall-clock time: 00:10:00
Memory Utilized: 60.00 GB
Memory Efficiency: 50.00% of 120.00 GB

Check the job State reported in the 4th line. If it is "COMPLETED (exit code 0)", look at the last two lines. "Memory Utilized" is the amount of memory your job used, in this case 60Gb.

If the job State is FAILED or CANCELLED, the Memory Efficiency percentage reported by seff will be extremely inaccurate. The seff command only works on jobs that have COMPLETED successfully.

How much memory should I reserve in my job script?
It's a good idea to reserve slightly more memory than your job utilized since the same job may require slightly different amounts of memory depending on variations in data it processes in each run of the job. To correctly reserve memory for this job, edit your test job submission script to modify the #SBATCH --mem= directive to reserve 10% more than 60Gb in the job submission script:

#SBATCH --mem=66G

For jobs that use MPI, remove the #SBATCH --mem= directive from your job submission script. Now specify the amount of memory you'd like to reserve per core instead. For example, if your job uses 100Gb of memory total and runs on 10 cores, reserve 10Gb plus a safety factor per cpu:

#SBATCH --mem-per-cpu=11G



If it doesn't matter how many nodes your cores are distributed on you may remove the #SBATCH --nodes= directive as well.

Be careful not to reserve significant amounts of memory beyond what your job requires as your job's wait time will increase and reserving excessive memory also wastes shared resources that could be used by other researchers.

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Article ID: 1809
Thu 5/12/22 12:39 PM
Wed 5/1/24 9:14 AM