Usage accounting
All users belong to an account (usually their PI) and all usage is tracked per user, but limitations can be set by administrators at a few different levels: at the cluster, partition, account, user, or QOS level. User associations with accounts rarely change, so in order to be able to temporarily request additional resources or obtain higher priority for certain projects, users can submit to different SLURM "Quality of Service"s (QOS). By default all users submit jobs to the normal QOS. To submit to a different QOS to obtain a higher priority first discuss with your supervisor/PI, and then contact an administrator to get permission.
Show QOS info and limitations
$ sacctmgr show qos format=name,priority,grptres,mintres,maxtres,maxtrespu,maxjobspu,maxtrespa,maxjobspa
Name Priority GrpTRES MinTRES MaxTRES MaxTRESPU MaxJobsPU MaxTRESPA MaxJobsPA
---------- ---------- ------------- ------------- ------------- ------------- --------- ------------- ---------
normal 0 cpu=1,mem=1G cpu=576
highprio 1 cpu=1,mem=1G cpu=1024
Undergraduate students
Undergraduate students (upto but NOT including master projects) share resources within the students account and only their combined usage is limited. View current limitations with for example:
Job resource usage summary
Running jobs
Use sstat to show the status and live usage accounting information of only running jobs. For batch scripts you need to add .batch to the job ID, for example:
This will print EVERY metric, so it's nice to select only a few most relevant ones, for example:
Useful format variables
| Variable | Description |
|---|---|
| avecpu | Average CPU time of all tasks in job. |
| averss | Average resident set size of all tasks. |
| avevmsize | Average virtual memory of all tasks in a job. |
| jobid | The id of the Job. |
| maxrss | Maximum number of bytes read by all tasks in the job. |
| maxvsize | Maximum number of bytes written by all tasks in the job. |
| ntasks | Number of tasks in a job. |
For all variables see the SLURM documentation
Past jobs
To view the status of past jobs and their usage accounting information use sacct. sacct will return everything accounted for by default which is very inconvenient to view in a terminal window, so the below command will show the most essential information:
$ sacct -o jobid,jobname,start,end,NNodes,NCPUS,ReqMem,CPUTime,AveRSS,MaxRSS --user=$USER --units=G -j 138
JobID JobName Start End NNodes NCPUS ReqMem CPUTime AveRSS MaxRSS
------------ ---------- ------------------- ------------------- -------- ---------- ---------- ---------- ---------- ----------
138 interacti+ 2023-11-21T10:43:48 2023-11-21T10:43:59 1 16 20G 00:02:56
138.interac+ interacti+ 2023-11-21T10:43:48 2023-11-21T10:43:59 1 16 00:02:56 0 0
138.extern extern 2023-11-21T10:43:48 2023-11-21T10:43:59 1 16 00:02:56 0.00G 0.00G
There are a huge number of other options to show, see SLURM docs. If you really want to see everything use sacct --long > file.txt and dump it into a file or else it's too much for the terminal.
Job efficiency summary
Individual jobs
To view the efficiencies of individual jobs use seff, for example:
$ seff 2357
Job ID: 2357
Cluster: biocloud
User/Group: <username>
State: COMPLETED (exit code 0)
Nodes: 1
Cores per node: 96
CPU Utilized: 60-11:06:29
CPU Efficiency: 45.76% of 132-02:48:00 core-walltime
Job Wall-clock time: 1-09:01:45
Memory Utilized: 383.42 GB
Memory Efficiency: 45.11% of 850.00 GB
This information will also be shown in notification emails when jobs finish.
Multiple jobs
Perhaps a more useful way to use sacct is through the reportseff tool (pre-installed), which can be used to calculate the CPU, memory, and time efficiencies of past jobs, so that you can optimize future jobs and ensure resources are utilized to the max (2TM). For example:
$ reportseff -u $(whoami) --format partition,jobid,state,jobname,alloccpus,elapsed,cputime,CPUEff,MemEff,TimeEff -S r,pd,s --since d=4
Partition JobID State JobName AllocCPUS Elapsed CPUTime CPUEff MemEff TimeEff
default-op 306282 COMPLETED midasok 2 00:13:07 00:26:14 4.1% 15.4% 10.9%
general 306290 COMPLETED smk-map2db-sample=barcode46 16 00:01:38 00:26:08 90.6% 18.7% 2.7%
general 306291 COMPLETED smk-map2db-sample=barcode47 16 00:02:14 00:35:44 92.8% 18.4% 3.7%
general 306292 COMPLETED smk-map2db-sample=barcode58 16 00:02:32 00:40:32 80.3% 19.0% 4.2%
general 306293 COMPLETED smk-map2db-sample=barcode34 16 00:02:16 00:36:16 78.1% 18.7% 3.8%
general 306294 COMPLETED smk-map2db-sample=barcode22 16 00:02:38 00:42:08 81.1% 19.0% 4.4%
general 306295 COMPLETED smk-map2db-sample=barcode35 16 00:02:26 00:38:56 79.0% 19.0% 4.1%
general 306296 COMPLETED smk-map2db-sample=barcode82 16 00:01:39 00:26:24 68.9% 17.8% 2.8%
general 306297 COMPLETED smk-map2db-sample=barcode70 16 00:02:04 00:33:04 76.0% 19.5% 3.4%
general 306298 COMPLETED smk-map2db-sample=barcode94 16 00:01:44 00:27:44 70.1% 17.9% 2.9%
general 306331 COMPLETED smk-map2db-sample=barcode59 16 00:04:00 01:04:00 87.2% 19.6% 6.7%
general 306332 COMPLETED smk-map2db-sample=barcode83 16 00:02:13 00:35:28 76.3% 19.0% 3.7%
general 306333 COMPLETED smk-map2db-sample=barcode11 16 00:02:49 00:45:04 81.6% 19.4% 4.7%
general 306334 COMPLETED smk-map2db-sample=barcode23 16 00:03:33 00:56:48 61.6% 19.0% 5.9%
general 306598 COMPLETED smk-mapping_overview-sample=barcode46 1 00:00:09 00:00:09 77.8% 0.0% 1.5%
general 306601 COMPLETED smk-mapping_overview-sample=barcode82 1 00:00:09 00:00:09 77.8% 0.0% 1.5%
general 306625 COMPLETED smk-mapping_overview-sample=barcode94 1 00:00:07 00:00:07 71.4% 0.0% 1.2%
general 306628 COMPLETED smk-concatenate_fastq-sample=barcode71 1 00:00:07 00:00:07 71.4% 0.0% 1.2%
general 306629 COMPLETED smk-concatenate_fastq-sample=barcode70 1 00:00:07 00:00:07 71.4% 0.0% 1.2%
general 306630 COMPLETED smk-concatenate_fastq-sample=barcode34 1 00:00:07 00:00:07 57.1% 0.0% 1.2%
Usage reports
sreport can be used to summarize usage in many different ways, below are some examples.
Account usage by user
$ sreport cluster AccountUtilizationByUser format=account%8,login%23,used%10 -t hourper start="now-1week"
--------------------------------------------------------------------------------
Cluster/Account/User Utilization 2024-03-13T12:00:00 - 2024-03-19T23:59:59 (561600 secs)
Usage reported in CPU Hours/Percentage of Total
--------------------------------------------------------------------------------
Account Login Used
-------- ----------------------- ------------------
root 154251(63.71%)
root <username> 37176(15.35%)
jln 3988(1.65%)
jln <username> 2010(0.83%)
jln <username> 0(0.00%)
jln <username> 1978(0.82%)
kln 7(0.00%)
kln <username> 7(0.00%)
ma 13460(5.56%)
ma <username> 6152(2.54%)
ma <username> 2504(1.03%)
ma <username> 3710(1.53%)
ma <username> 963(0.40%)
ma <username> 131(0.05%)
md 52921(21.86%)
md <username> 18690(7.72%)
md <username> 22443(9.27%)
md <username> 11788(4.87%)
mms 17036(7.04%)
mms <username> 600(0.25%)
mms <username> 16436(6.79%)
phn 6799(2.81%)
phn <username> 114(0.05%)
phn <username> 31(0.01%)
phn <username> 6654(2.75%)
phn <username> 0(0.00%)
sss 22081(9.12%)
sss <username> 22081(9.12%)
students 638(0.26%)
students <username> 638(0.26%)
User usage by account
$ sreport cluster UserUtilizationByAccount format=login%23,account%8,used%10 -t hourper start="now-1week"
--------------------------------------------------------------------------------
Cluster/User/Account Utilization 2024-03-13T12:00:00 - 2024-03-19T23:59:59 (561600 secs)
Usage reported in CPU Hours/Percentage of Total
--------------------------------------------------------------------------------
Login Account Used
----------------------- -------- ------------------
<username> root 37176(15.35%)
<username> md 22443(9.27%)
<username> sss 22081(9.12%)
<username> md 18690(7.72%)
<username> mms 16436(6.79%)
<username> md 11788(4.87%)
<username> phn 6654(2.75%)
<username> ma 6152(2.54%)
<username> ma 3710(1.53%)
<username> ma 2504(1.03%)
<username> jln 2010(0.83%)
<username> jln 1978(0.82%)
<username> ma 963(0.40%)
<username> students 638(0.26%)
<username> mms 600(0.25%)
<username> compute+ 145(0.06%)
<username> ma 131(0.05%)
<username> phn 114(0.05%)
<username> phn 31(0.01%)
<username> kln 7(0.00%)
<username> phn 0(0.00%)
<username> jln 0(0.00%)
Top users
$ sreport user top topcount=20 format=login%21,account%8,used%10 start="now-1week" -t hourper
--------------------------------------------------------------------------------
Top 20 Users 2024-03-13T11:00:00 - 2024-03-19T23:59:59 (565200 secs)
Usage reported in CPU Hours/Percentage of Total
--------------------------------------------------------------------------------
Login Account Used
--------------------- -------- ------------------
<username> root 37176(15.26%)
<username> md 22698(9.32%)
<username> sss 22082(9.06%)
<username> md 18850(7.74%)
<username> mms 16436(6.75%)
<username> md 12038(4.94%)
<username> phn 6654(2.73%)
<username> ma 6167(2.53%)
<username> ma 3780(1.55%)
<username> ma 2504(1.03%)
<username> jln 2383(0.98%)
<username> jln 1978(0.81%)
<username> ma 963(0.40%)
<username> students 648(0.27%)
<username> mms 600(0.25%)
<username> kt 146(0.06%)
<username> ma 133(0.05%)
<username> phn 114(0.05%)
<username> kln 98(0.04%)
<username> phn 31(0.01%)