[biomade-users] BioMade HPC Core "smap" command has been removed

Tue Feb 8 11:42:48 EST 2022

To BioMade users that have been utilizing the "smap" command to view the 
Slurm queue. The "smap" command has been removed on the lastest Slurm 
software that was deploy during last weeks biomade.sr.unh.edu shutdown. I 
have already received two email wondering what happened to "smap" so I 
thought it made sense to send out a general message to all of the BioMade 
HPC Core users.
The Slurm team removed "smap" because they felt it was redundant with the 
"squeue" command.
See email message below with an example of the both the default "squeue" 
command, as well as the output of an alias that RCC added via the "unhrcc" 
module that provides a bit more useful information. These commands can be 
adjusted to more or less information. If you come up with a variation that 
you feel is useful, let me know and I can add another alias for it.,
Robert E. Anderson
Associate Director
Univ of NH Research Computing Center
-------- Original Message --------
Subject: Re: [biomade-users] BioMadee HPC Core is back online
Date: Fri Feb 04 2022 12:24:36 GMT-0500 (Eastern Standard Time)
 From: "Robert E. Anderson" <rea at sr.unh.edu>
To: "Nikolai Matukhno" <nikolai.matukhno at unh.edu>
CC: "rccops at sr.unh.edu" <rccops at sr.unh.edu>
Thanks for the heads up, but apparently the "smap" command has been removed 
from slurm because it was considered to be just a special case of squeue.
https://slurm.schedmd.com/SLUG19/Slurm_20.02_and_Beyond.pdf
What was it that you used in smap? Perhaps an alias for squeue could 
provide that same information. I have already created one alias that I find 
useful. Here's an example of the default squeue output, loading the 
"unhrcc" module and using the squeue2 command. All followed by the actual 
alias for squeue2 (and sacct2):
[rea at login02 ~]$ squeue -a 
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 
1528022_[252-1349% general TestPara kv1033 PD 0:00 1 (JobArrayTaskLimit) 
1528222_[110-1349% general TestPara kv1033 PD 0:00 1 (JobArrayTaskLimit) 
1528022_251 general TestPara kv1033 R 0:49 1 node19 
1528022_250 general TestPara kv1033 R 1:31 1 node19 
1528022_249 general TestPara kv1033 R 1:34 1 node19 
1528022_248 general TestPara kv1033 R 1:50 1 node19 
1528022_247 general TestPara kv1033 R 2:14 1 node19 
1528022_229 general TestPara kv1033 R 18:25 1 node19 
1528022_220 general TestPara kv1033 R 25:36 1 node19 
1528022_202 general TestPara kv1033 R 44:25 1 node19 
1528022_193 general TestPara kv1033 R 53:16 1 node19 
1528022_184 general TestPara kv1033 R 57:04 1 node19 
1528221 general newParam kv1033 R 50:26 1 node21 
1528222_109 general TestPara kv1033 R 0:20 1 node19 
1528222_106 general TestPara kv1033 R 10:53 1 node19 
1528222_105 general TestPara kv1033 R 11:40 1 node19 
1528222_103 general TestPara kv1033 R 12:25 1 node19 
1528222_94 general TestPara kv1033 R 17:46 1 node19 
1528222_76 general TestPara kv1033 R 30:33 1 node19 
1528222_67 general TestPara kv1033 R 33:16 1 node19 
1528222_49 general TestPara kv1033 R 37:56 1 node19 
1528222_22 general TestPara kv1033 R 44:05 1 node19 
1528222_13 general TestPara kv1033 R 46:30 1 node19 
1528012 thrust3 k89a1 sp1564 R 13:21:30 1 node10 
1528020 thrust3 k89a2 sp1564 R 2:59:49 1 node18 
[rea at login02 ~]$ module load unhrcc 
[rea at login02 ~]$ squeue2 -a 
Fri Feb 4 12:19:18 EST 2022 
JOBID PARTITIO SUBMIT_TIME USER GROUP TIME START_TIME TIME_LEFT i 
NODELIST(R 
152802 general 2022-02-04T09:53 kv1033 thrust2 0:00 N/A 1:00:00 i 
(JobArrayT 
152822 general 2022-02-04T11:30 kv1033 thrust2 0:00 N/A 1:00:00 i 
(JobArrayT 
152838 general 2022-02-04T09:53 kv1033 thrust2 0:06 2022-02-04T12:19 59:54 
i node19 
152838 general 2022-02-04T09:53 kv1033 thrust2 1:03 2022-02-04T12:18 58:57 
i node19 
152838 general 2022-02-04T09:53 kv1033 thrust2 1:48 2022-02-04T12:17 58:12 
i node19 
152838 general 2022-02-04T09:53 kv1033 thrust2 2:04 2022-02-04T12:17 57:56 
i node19 
152838 general 2022-02-04T09:53 kv1033 thrust2 2:28 2022-02-04T12:16 57:32 
i node19 
152834 general 2022-02-04T09:53 kv1033 thrust2 18:39 2022-02-04T12:00 41:21 
i node19 
152832 general 2022-02-04T09:53 kv1033 thrust2 25:50 2022-02-04T11:53 34:10 
i node19 
152824 general 2022-02-04T09:53 kv1033 thrust2 44:39 2022-02-04T11:34 15:21 
i node19 
152821 general 2022-02-04T09:53 kv1033 thrust2 53:30 2022-02-04T11:25 6:30 
i node19 
152820 general 2022-02-04T09:53 kv1033 thrust2 57:18 2022-02-04T11:22 2:42 
i node19 
152822 general 2022-02-04T11:28 kv1033 thrust2 50:40 2022-02-04T11:28 9:20 
i node21 
152838 general 2022-02-04T11:30 kv1033 thrust2 0:34 2022-02-04T12:18 59:26 
i node19 
152837 general 2022-02-04T11:30 kv1033 thrust2 11:07 2022-02-04T12:08 48:53 
i node19 
152836 general 2022-02-04T11:30 kv1033 thrust2 11:54 2022-02-04T12:07 48:06 
i node19 
152836 general 2022-02-04T11:30 kv1033 thrust2 12:39 2022-02-04T12:06 47:21 
i node19 
152835 general 2022-02-04T11:30 kv1033 thrust2 18:00 2022-02-04T12:01 42:00 
i node19 
152831 general 2022-02-04T11:30 kv1033 thrust2 30:47 2022-02-04T11:48 29:13 
i node19 
152830 general 2022-02-04T11:30 kv1033 thrust2 33:30 2022-02-04T11:45 26:30 
i node19 
152828 general 2022-02-04T11:30 kv1033 thrust2 38:10 2022-02-04T11:41 21:50 
i node19 
152825 general 2022-02-04T11:30 kv1033 thrust2 44:19 2022-02-04T11:34 15:41 
i node19 
152823 general 2022-02-04T11:30 kv1033 thrust2 46:44 2022-02-04T11:32 13:16 
i node19 
152801 thrust3 2022-02-03T22:57 sp1564 thrust3 13:21:44 2022-02-03T22:57 
59-10:38:16 i node10 
152802 thrust3 2022-02-04T09:19 sp1564 thrust3 3:00:03 2022-02-04T09:19 
59-20:59:57 i node18
[rea at login02 ~]$ alias 
alias sacct2='date ; sacct --format 
jobid,partition,user,jobname,state,end,elapsed' 
alias squeue2='date ; squeue -o "%6A %8P %16V %10u %10g %8M %16S %14Li 
%10R"'
Robert E. Anderson
Associate Director
Univ of NH Research Computing Center
Nikolai Matukhno wrote:
Hi Robert,
I logged into my account in BioMade and tried to run a simple Slurm command 
"smap" and it says "smap: command not found". But if I use "sinfo" and 
"squeue" - it works just fine. Am I missing here something? I usually use 
smap before submitting any job to make sure I can add my job with a 
specified number of CPUs and RAM.
Any help is appreciated.
Thank you,
Nikolai
 From: biomade-users <biomade-users-bounces at lists.sr.unh.edu> on behalf of 
Robert E. Anderson <rea at sr.unh.edu>
Sent: Thursday, February 3, 2022 12:04 PM
To: biomade-users at lists.sr.unh.edu <biomade-users at lists.sr.unh.edu>
Subject: [biomade-users] BioMadee HPC Core is back online 

RCC has completed the BIOS, OS Patches, and new hardware installs on the 
BioMade HPC Core. 
You may login and run jobs at this time.
If you discover anything that is not working correctly please let us know.
Thanks.
Robert E. Anderson
Associate Director
Univ of NH Research Computing Center
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