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[[Category:Sapelo2]]
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'''This page is being written in preparation for switching the queueing system on Sapelo2 to Slurm, it is not applicable to Sapelo2 yet.'''
= Pending or Running Jobs =


'''This page is application to the Slurm development cluster (SapSlurm)'''
==<code>squeue</code> and <code>sq</code>==


The easiest way to monitor pending or running jobs is with the Slurm <code>squeue</code> command.  Like most Slurm commands, you are able to control the columns displayed in the output of this command (see <code>man squeue</code> for more information).  To save you the trouble of typing a long format string and to make things more convenient, we've created the <code>sq</code> command, which is <code>squeue</code> but pre-formatted and with some additional options for convenience. 


===How to list all user jobs in the queues===
The key thing to remember about <code>squeue</code>/<code>sq</code> is that without any options, it shows ALL currently running and pending jobs on the cluster.  In order to show only your currently running and pending jobs, you will want to use the <code>--me</code> option.


To list all running and pending jobs (by all users), use the command
 
<pre class="gcommand">
The default <code>squeue</code> columns are as follows:
squeue
 
<pre class="gcomment">
JOBID PARTITION    NAME    USER ST      TIME  NODES NODELIST(REASON)
</pre>
</pre>


Sample '''squeue''' output:
Using <code>sq</code> runs the <code>squeue</code> command but provides the following columns:
 
<pre class="gcomment">
<pre class="gcomment">
            JOBID PARTITION     NAME    USER ST       TIME  NODES NODELIST(REASON)
JOBID     NAME            PARTITION       USER      NODES  CPUS   MIN_MEMORY   PRIORITY   TIME            TIME_LIMIT     STATE     NODELIST(REASON)
              274    batch slurmenv ab12345 PD      0:00      1 (Dependency)
              278    interq_p    bash   shtsai  R      0:04      1 c2-4
              277    batch  mpitest   shtsai  R      2:05      2 c2-[11-12]
              276    batch slurmenv   shtsai  R      0:08     1 c1-39
              273    batch slurmenv  ab12345  R      0:44     1 c1-38
</pre>
</pre>


'''Output explained:'''
As you can see, you're able to get much more useful information with <code>sq</code> than with just the default <code>squeue</code> formatting. 


The column entitled '''JOBID''' gives the job id of each job.


The column entitled '''PARTITION''' gives the partition or queue where the job is running. A job in the interq partition is an interactive session (e.g. one that was launched with the '''qlogin''' command).
'''Output Columns Explained'''


The column entitled '''NAME''' gives the name of the job (specified in the job submission script with the --job-name or -J option.
* '''JOBID''': The unique ID of the job (for an array job, it will be of the form "<base_job_id>_<index>").
* '''NAME''': The name of the job.  If not specified in one's submission script, it will default to the name of the submission script (e.g. "sub.sh").
* '''PARTITION''': The partition to which the job was sent (e.g. batch, highmem_p, gpu_p, etc...).
* '''USER''': The user who submitted the job.
* '''NODES''': The number of nodes allocated to the job.
* '''CPUS''': The number of CPU cores allocated to the job.
* '''MIN_MEMORY''': The total amount of memory allocated to the job.
* '''PRIORITY''': The job's priority per Slurm's [https://slurm.schedmd.com/priority_multifactor.html Multifactor Priority Plugin]
* '''TIME''': How much (wall-clock) time has elapsed since the job started, in the format DAYS-HOURS:MINUTES:SECONDS
* '''TIME_LIMIT''': The maximum time given for the job to run, in the format DAYS-HOURS:MINUTES:SECONDS.
* '''STATE''': The job's state (e.g. Running, Pending, etc...)
* '''NODELIST(REASON)''': The name of the node(s) on which the job is running or the reason the job has not started yet, if it is pending.


The column entitled '''USER''' gives the username (MyID) of the user running the job.


The column entitled '''ST''' gives the status of a job, which could be
<code>sq</code> also has a -h/--help option:
* '''R''' : job is running
* '''PD''' : job is pending, waiting for resources to become available or for a job dependency to be satisfied
* '''CG''' : job is being cleared (completed, was deleted, crashed) and is no longer running.


The column entitled '''TIME''' gives the walltime of the job (this is not the CPU time of the job).
<pre class="gcomment">
bc06026@ss-sub3 ~$ sq --help


The column entitled '''NODES''' specifies how many nodes are being used by the job.
Usage: sq [OPTIONS]


The column entitled '''NODELIST(REASON)''' lists the hostnames of the nodes used by running jobs. For pending jobs, this column lists the reason the job is pending. For example '''Dependency''' means the job is waiting for a job dependency to be satisfied.
Descriptions: sq - preformatted wrapper for squeue.  See man squeue for more information.
 
    -j                          Displays squeue output for a given job
    --me                        Displays squeue output for the user executing this command
    -p                          Displays squeue output for a given partition
    -u                          Displays squeue output for a given user
    -T                          Displays submit and start time columns
    -h, --help                  Displays this help output


The command
<pre class="gcommand">
squeue -l
</pre>
</pre>
adds an extra column in the output for the TIME_LIMIT of the jobs.


===How to list only my jobs in the queues===


To list all your running and pending jobs, use the command
<big><big>'''Examples'''</big></big>
<pre class="gcommand">
 
squeue -u MyID
* See all pending and running jobs: <code>sq</code>
</pre>
* See all of your pending and running jobs: <code>sq --me</code>
where MyID needs to be replaced by your own cluster username (UGA MyID).
* See all pending and running jobs in the highmem_p: <code>sq -p highmem_p</code>
* See all of your pending and running jobs in the batch partition: <code>sq --me -p batch</code>
* See all of your pending and  running jobs including submit time and start time columns: <code>sq --me -T</code> (Note, this will require a wide monitor or small font to display without columns wrapping around)
 
 
<big>'''Example <code>sq</code> output:'''</big>


Sample output (as ran by user shtsai):
<pre class="gcomment">
<pre class="gcomment">
            JOBID PARTITION    NAME    USER ST      TIME NODES NODELIST(REASON)
bc06026@ss-sub3 ~$ sq
              278    interq    bash   shtsai  R      0:04     1 c2-4
JOBID   NAME         PARTITION USER   NODES   CPUS   MIN_MEMORY PRIORITY     TIME   TIME_LIMIT STATE   NODELIST(REASON)
              277    batch mpitest   shtsai  R      2:05     2 c2-[11-12]
4581410   Bowtie2-test batch         zp21982   1   1   12G         6003     2:10:56   10:00:00 RUNNING   c5-4
              276    batch slurmenv   shtsai  R      0:08      1 c1-39
4584815   test-job highmem_p rt12352   1   12   300G         5473     1:51:03   2:00:00 RUNNING   d3-9
4578428   PR6_Cd3 batch         un12354   1   1   40G         5449     4:57:15   1-2:00:00 RUNNING   c4-16
4583491   interact inter_p         ai38821   1   4   2G         5428     1:57:38   12:00:00 RUNNING   d5-21
4580374   BLAST         batch         gh98762   1   1   10G         5397     2:54:41   12:00:00 RUNNING   b1-9
 
...
</pre>
</pre>


===How to list all of my running jobs===
<big>'''Example <code>sq</code> output for an array job:'''</big>
 
<pre class="gcomment">
bc06026@b1-24 workdir$ sq --me
JOBID        NAME            PARTITION        USER      NODES  CPUS  MIN_MEMORY  PRIORITY  TIME            TIME_LIMIT      STATE      NODELIST(REASON)
4711132_4    array-example  batch            bc06026    1      1      1G          5993      0:06            1:00:00        RUNNING    c5-19
4711132_3    array-example  batch            bc06026    1      1      1G          5993      0:06            1:00:00        RUNNING    c5-19
4711132_2    array-example  batch            bc06026    1      1      1G          5993      0:06            1:00:00        RUNNING    c5-19
4711132_1    array-example  batch            bc06026    1      1      1G          5993      0:06            1:00:00        RUNNING    c4-15
4711132_0    array-example  batch            bc06026    1      1      1G          5993      0:06            1:00:00        RUNNING    c4-15


<pre class="gcommand">
squeue -u MyID -t RUNNING
</pre>
</pre>


===How to list all of my pending jobs===


<pre class="gcommand">
----
squeue -u MyID -t PENDING
[[#top|Back to Top]]
</pre>


===How to determine on which node(s) jobs are running===


To see which nodes were assigned to each or your jobs, use the command
== <code>scontrol show job</code> ==
<pre class="gcommand">
squeue
</pre>
The column entitled NODELIST lists the hostnames of the nodes allocated to the jobs.


Another option for viewing information about a pending or running job is <code>scontrol show job ''JOBID''</code>, replacing ''JOBID'' with your job's ID.  This command will display information about a pending or running job with one or more key/value pairs of information about the job per line, one line after another (as opposed to the row/column output of <code>squeue</code> and <code>sq</code>).  This command will return output while the job is pending or running, and only for a few moments after the job has completed.  Using this command with a job that has already finished (more than a few moments ago) will return the output "slurm_load_jobs error: Invalid job id specified".  This just means that the job is too old for <code>scontrol show job</code> to display information about it.


===How to see detailed information about a given job===


To see a long listing with detailed information for a running job (STATE = R), including the initial working directory, the number of cores and memory requested, the job submission and start time, use the command
<big>'''Example <code>scontrol show job</code> output:'''</big>
<pre class="gcommand">
scontrol show job JOBID
</pre>
where JOBID should be replaced by the '''JOBID''' for the job you wish to check (the JOBID is given in the first column
of the '''squeue''' output).


Sample output of a long job listing ''scontrol show job 11279'':
<pre class="gcomment">
<pre class="gcomment">
JobId=11279 JobName=mpitest
bc06026@b1-24 workdir$ scontrol show job 4707896
   UserId=ab12345(10012) GroupId=abclab(1001) MCS_label=N/A
JobId=4707896 JobName=testjob
   Priority=1 Nice=0 Account=gacrc QOS=normal
   UserId=bc06026(3356) GroupId=gacrc-appadmin(21003) MCS_label=N/A
   Priority=5993 Nice=0 Account=gacrc-instruction QOS=normal
   JobState=RUNNING Reason=None Dependency=(null)
   JobState=RUNNING Reason=None Dependency=(null)
   Requeue=1 Restarts=0 BatchFlag=1 Reboot=0 ExitCode=0:0
   Requeue=1 Restarts=0 BatchFlag=1 Reboot=0 ExitCode=0:0
   RunTime=00:02:24 TimeLimit=02:00:00 TimeMin=N/A
   RunTime=00:00:23 TimeLimit=01:00:00 TimeMin=N/A
   SubmitTime=2018-08-14T12:19:23 EligibleTime=2018-08-14T12:19:23
   SubmitTime=2021-09-17T09:53:30 EligibleTime=2021-09-17T09:53:30
   StartTime=2018-08-14T12:19:23 EndTime=2018-08-14T14:19:23 Deadline=N/A
  AccrueTime=2021-09-17T09:53:30
   PreemptTime=None SuspendTime=None SecsPreSuspend=0
   StartTime=2021-09-17T09:53:30 EndTime=2021-09-17T10:53:30 Deadline=N/A
  LastSchedEval=2018-08-14T12:19:23
   SuspendTime=None SecsPreSuspend=0 LastSchedEval=2021-09-17T09:53:30
   Partition=batch AllocNode:Sid=c2-4:872
   Partition=batch AllocNode:Sid=b1-24:36515
   ReqNodeList=(null) ExcNodeList=(null)
   ReqNodeList=(null) ExcNodeList=(null)
   NodeList=c2-[11-12]
   NodeList=c4-15
   BatchHost=c2-11
   BatchHost=c4-15
   NumNodes=2 NumCPUs=24 NumTasks=24 CPUs/Task=1 ReqB:S:C:T=0:0:*:*
   NumNodes=1 NumCPUs=1 NumTasks=1 CPUs/Task=1 ReqB:S:C:T=0:0:*:*
   TRES=cpu=24,mem=14400M,node=2,billing=24
   TRES=cpu=1,mem=4G,node=1,billing=1
   Socks/Node=* NtasksPerN:B:S:C=12:0:*:* CoreSpec=*
   Socks/Node=* NtasksPerN:B:S:C=0:0:*:* CoreSpec=*
   MinCPUsNode=12 MinMemoryCPU=600M MinTmpDiskNode=0
   MinCPUsNode=1 MinMemoryNode=4G MinTmpDiskNode=0
   Features=(null) DelayBoot=00:00:00
   Features=[Gamma|Beta|Delta|Alpha] DelayBoot=00:00:00
  Gres=(null) Reservation=(null)
   OverSubscribe=OK Contiguous=0 Licenses=(null) Network=(null)
   OverSubscribe=OK Contiguous=0 Licenses=(null) Network=(null)
   Command=/home/ab12345/tests/slurm/mpi/sub.sh
   Command=/scratch/bc06026/workdir/sub.sh
   WorkDir=/home/ab12345/tests/slurm/mpi
   WorkDir=/scratch/bc06026/workdir
   StdErr=/home/ab12345/tests/slurm/mpi/mpitest.o11279
   StdErr=/scratch/bc06026/workdir/testjob_4707896.err
   StdIn=/dev/null
   StdIn=/dev/null
   StdOut=/home/shtsai/tests/slurm/mpi/mpitest.o11279
   StdOut=/scratch/bc06026/workdir/testjob_4707896.out
   Power=
   Power=
  MailUser=bc06026@uga.edu MailType=ALL
  NtasksPerTRES:0
</pre>
</pre>


The long listing of information is not available any more for jobs that are no longer in a running state.
As you can see, there is a little bit more information presented here than is with <code>squeue</code> and <code>sq</code>, such as showing the path to the job's working directory, Slurm job output file path(s), email information, etc...
 
 
----
[[#top|Back to Top]]
 
 
= Finished Jobs =
 
== <code>sacct</code> and <code>sacct-gacrc</code> ==
 
The easiest way to monitor finished jobs is with the Slurm <code>sacct</code> command.  Like most Slurm commands, you are able to control the columns displayed in the output of this command (see <code>man sacct</code> for more information).  To save you the trouble of typing a long format string and to make things more convenient, we've created the <code>sacct-gacrc</code> command, which is <code>sacct</code> but pre-formatted and with some additional options for convenience. 
 
A big difference between <code>squeue</code>/<code>sq</code> and <code>sacct</code>/<code>sacct-gacrc</code> is that by default, <code>sacct</code>/<code>sacct-gacrc</code> without any options only shows you YOUR Jobs.  Another important note about <code>sacct</code>/<code>sacct-gacrc</code> is that by default it will display Slurm job ''steps''.  Unless you're dividing your job into steps with <code>srun</code>, you probably will want <code>sacct</code>/<code>sacct-gacrc</code> to display one line per job (hide job steps, only show job allocation).  To do this, use the <code>-X</code> option.  For more information on Slurm job allocation, please see the Slurm [https://slurm.schedmd.com/job_launch.html documentation].


Note that the long listing above does not include the resources utilized by the job.


For your own jobs that are still running or that already completed, you can check how much memory was used, how much CPU time was used, the working directory, etc, please use the command
The default <code>sacct</code> columns are as follows:
<pre class="gcommand">
 
sacct_zh
<pre class="gcomment">
JobID    JobName  Partition    Account  AllocCPUS      State ExitCode
</pre>
</pre>


Sample output of an sacct_zh command:
Using <code>sacct-gacrc</code> runs the <code>sacct</code> command but provides the following columns:
 
<pre class="gcomment">
<pre class="gcomment">
      JobID   JobName      User  Partition       NodeList AllocNodes   NTasks      NCPUS    ReqMem MaxVMSize      State   CPUTime    Elapsed  Timelimit ExitCode             WorkDir
JobID         JobName      User  Partition NNode NCPUS   ReqMem    CPUTime    Elapsed  Timelimit     State ExitCode  NodeList
------------ ---------- --------- ---------- --------------- ---------- -------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- -------- --------------------
275            slurmenv    shtsai      batch          c1-38          1                  2      10Gn            COMPLETED   00:00:00  00:00:00  02:00:00      0:0 /home/shtsai/tests/+
275.batch        batch                                c1-38          1        1          2      10Gn    197240K  COMPLETED  00:00:00  00:00:00                0:0                     
275.extern      extern                                c1-38          1        1          2      10Gn    169800K  COMPLETED  00:00:00  00:00:00                0:0                     
276            slurmenv    shtsai      batch          c1-38          1                  1      10Gn            CANCELLED+  00:03:19  00:03:19  02:00:00      0:0 /home/shtsai/tests/+
276.batch        batch                                c1-38          1        1          1      10Gn    221140K  CANCELLED  00:03:20  00:03:20                0:15                     
276.extern      extern                                c1-38          1        1          1      10Gn    169800K  COMPLETED  00:03:19  00:03:19                0:0                     
277            mpitest    shtsai      batch      c2-[11-12]          2                  24      600Mc            COMPLETED  04:01:12  00:10:03  02:00:00      0:0 /home/shtsai/tests/+
277.batch        batch                                c2-11          1        1        12      600Mc    221268K  COMPLETED  02:00:36  00:10:03                0:0                     
277.extern      extern                          c2-[11-12]          2        2        24      600Mc    169800K  COMPLETED  04:01:12  00:10:03                0:0                     
277.0            orted                                c2-12          1        1          1      600Mc    265640K  COMPLETED  00:00:01  00:00:01                0:0                     
278                bash    shtsai    interq            c2-4          1                  1        2Gn              RUNNING  00:13:37  00:13:37  12:00:00      0:0 /home/shtsai/tests/+
278.extern      extern                                c2-4          1        1          1        2Gn              RUNNING  00:13:37  00:13:37                0:0                     
278.0              bash                                c2-4          1        1          1        2Gn              RUNNING  00:13:37  00:13:37                0:0     
</pre>
</pre>


Note that each job will have several entries in this output, and these correspond to the different steps of the job. In general, non-MPI jobs that are still running will have two entries listed (jobid and jobid.extern), non-MPI jobs that completed or that were cancelled will have 3 entries (jobid, jobid.batch, jobid.extern), and MPI jobs will have an extra entry (jobid.0).
As you can see, you're able to get much more useful information with <code>sacct-gacrc</code> than with just the default <code>sacct</code> formatting. 
 
 
'''Output Columns Explained'''
 
* '''JobID''': The unique ID of the job.
* '''JobName''': The name of the job.  If not specified in one's submission script, it will default to the name of the submission script (e.g. "sub.sh").
* '''User''': The user who submitted the job.
* '''Partition''': The partition to which the job was sent (e.g. batch, highmem_p, gpu_p, etc...).
* '''NNode''': The number of nodes allocated to the job.
* '''NCPUS''': The number of CPU cores allocated to the job.
* '''ReqMem''': The amount of memory allocated to the job.
* '''CPUTime''': Time used (Elapsed time * CPU core count) by a job.
* '''Elapsed''': How much (wall) time has elapsed since the job started, in the format DAYS-HOURS:MINUTES:SECONDS
* '''Timelimit''': The maximum time given for the job to run, in the format DAYS-HOURS:MINUTES:SECONDS.
* '''State''': The job's state (e.g. Running, Pending, etc...).
* '''ExitCode''': The job's exit code.
* '''Nodelist''': The name of the node(s) on which the job is running or ran.
 
 
<code>sacct-gacrc</code> also has a -h/--help option:
 
<pre class="gcomment">
bc06026@ss-sub3 ~$ sacct-gacrc --help
 
Usage: sacct-gacrc [OPTIONS]
 
Description: preformatted wrapper for sacct.  See man sacct for more information.
 
    -E, --endtime              Display information about jobs up to a date, in the format of yyyy-mm-dd (default: now)
    -j, --jobs                 Display information about a particular job or jobs (comma-separated list if more than one job)
    -r, --partition            Display information about jobs from a particular partition
    -S, --starttime            Display information about jobs starting from a date in the format of yyyy-mm-dd (default: Midnight of today)
    -T                          Display the end time of a particular job or jobs
    -u, --user                  Display information about a particular user's job(s) (default: current user)
    -X, --allocations          Only show one line per job (do not display job steps)
    --debug                    Display the sacct command being executed
    -h, --help                  Display this help output


To see all fields reported by the accounting command for a given job, use the command
<pre class="gcommand">
sacct -l -j JOBID
</pre>
</pre>
where JOBID should be replaced by the '''JOBID''' for the job you wish to check (the JOBID is given in the first column of the '''squeue''' output).




<big><big>'''Examples'''</big></big>
* See information about all of your jobs that started from midnight up to now: <code>sacct-gacrc</code>
* See information about a particular job: <code>sacct-gacrc -j JOBID</code> (replacing JOBID with a particular job ID)
* See information about all of your jobs that started from midnight up to now in the highmem_p: <code>sacct-gacrc -r highmem_p</code>
* See information about your jobs that ran from a particular date up to now: <code>sacct-gacrc -S YYYY-MM-DD</code> (replacing YYYY-MM-DD with a date, e.g. 2021-09-01)
<big>'''Example <code>sacct-gacrc</code> output:'''</big>
<pre class="gcomment">
bc06026@b1-24 ~$ sacct-gacrc -X -S 2021-09-14
      JobID    JobName      User  Partition  NodeList AllocNodes NTask NCPUS  ReqMem  MaxVMSize      State    CPUTime    Elapsed  Timelimit ExitCode
------------ ---------- --------- ---------- ---------- ---------- ----- ----- ------- ---------- ---------- ---------- ---------- ---------- --------
4580375        interact  bc06026  highmem_p    ra4-22          1          1  200Gn            FAILED      00:00:07  00:00:07  12:00:00      1:0
4580382        interact  bc06026  highmem_p      d1-22          1          28  200Gn            COMPLETED    00:03:16  00:00:07  12:00:00      0:0
4584992        interact  bc06026    inter_p      c4-16          1          1    2Gn            COMPLETED    00:00:18  00:00:18  12:00:00      0:0
...
</pre>
Please note that <code>sacct</code> and <code>sacct-gacrc</code> also show jobs in a RUNNING state.


----
----
[[#top|Back to Top]]
[[#top|Back to Top]]


===Monitoring Array Jobs===


To view an array job, use the command
== <code>seff</code> ==


<pre class="gcommand">
<code>seff</code> is a command that can be used to check how efficient a finished job was with the CPU and memory resources it was given.  This is a very useful command as it gives insight into optimizing our job's resources.  It is important to note that <code>seff</code> is only useful after a job has finished.  Using it with a job that is still running will not return an error message, but the CPU and memory usage will be shown as 0.00%, and a warning message will be appended to the bottom of the output that says "WARNING: Efficiency statistics may be misleading for RUNNING jobs.".
squeue -l
</pre>  


Sample output of the '''squeue -l''' command for an array job that has JOBID=81 and that has 10 elements:
<big>'''Example <code>seff</code> output:'''</big>


<pre class="gcomment">
<pre class="gcomment">
Fri Aug  3 16:38:03 2018
bc06026@b1-24 workdir$ seff 4707896
            JOBID PARTITION    NAME    USER    STATE      TIME TIME_LIMI  NODES NODELIST(REASON)
Job ID: 4707896
              81_0    batch arrayjob  shtsai  RUNNING      0:03  10:00:00      1 c2-11
Cluster: tc2
              81_1    batch arrayjob  shtsai  RUNNING      0:03  10:00:00      1 c2-11
User/Group: bc06026/gacrc-appadmin
              81_2    batch arrayjob  shtsai  RUNNING      0:03  10:00:00      1 c2-11
State: COMPLETED (exit code 0)
              81_3    batch arrayjob  shtsai  RUNNING      0:03  10:00:00      1 c2-11
Cores: 1
              81_4    batch arrayjob  shtsai  RUNNING      0:03  10:00:00      1 c2-11
CPU Utilized: 00:09:25
              81_5    batch arrayjob  shtsai  RUNNING      0:03  10:00:00      1 c2-11
CPU Efficiency: 93.08% of 00:10:07 core-walltime
              81_6    batch arrayjob  shtsai  RUNNING      0:03  10:00:00      1 c2-11
Job Wall-clock time: 00:10:07
              81_7    batch arrayjob  shtsai  RUNNING      0:03  10:00:00      1 c2-11
Memory Utilized: 183.43 MB
              81_8    batch arrayjob  shtsai  RUNNING      0:03  10:00:00      1 c2-11
Memory Efficiency: 4.48% of 4.00 GB
              81_9    batch arrayjob  shtsai  RUNNING      0:03  10:00:00      1 c2-11


</pre>
</pre>
The key information shown in the output above are the last 6 rows.  We see that the job was allocated 1 CPU core, and that core was doing something for 9 minutes and 25 seconds out of the total 10 minutes and 7 seconds of the job's wall-clock (elapsed) time, (93.08% of the job's wall-clock time).  Generally you want to aim for as much utilization of the resources you request as possible, so perhaps this job could run twice as fast given two cores, if the software/command(s) it used parallelized perfectly.  The memory utilized for the job in the output above is very low.  Four gigabytes of RAM is not much at all in the context of high performance computing, but say for example you requested 100 GB of memory and found that your job was only using ~5% of that memory.  In that case you would definitely want to consider lowering the amount of memory you request for that particular job if ran again in the future.  For more information on job resource tuning, please see [[ Best Practices on Sapelo2 ]] and [[ Job Resource Tuning ]].  Please note that if your job ends abruptly because it ran out of memory, the <code>seff</code> memory utilization values may not reflect that, as a sudden spike in memory usage could cause the job to get killed before <code>seff</code> notices the spike in consumed memory.


----
----
[[#top|Back to Top]]
[[#top|Back to Top]]

Latest revision as of 11:54, 23 July 2024

Pending or Running Jobs

squeue and sq

The easiest way to monitor pending or running jobs is with the Slurm squeue command. Like most Slurm commands, you are able to control the columns displayed in the output of this command (see man squeue for more information). To save you the trouble of typing a long format string and to make things more convenient, we've created the sq command, which is squeue but pre-formatted and with some additional options for convenience.

The key thing to remember about squeue/sq is that without any options, it shows ALL currently running and pending jobs on the cluster. In order to show only your currently running and pending jobs, you will want to use the --me option.


The default squeue columns are as follows: 

JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)

Using sq runs the squeue command but provides the following columns: 

JOBID      NAME            PARTITION        USER       NODES  CPUS   MIN_MEMORY   PRIORITY   TIME            TIME_LIMIT      STATE      NODELIST(REASON)

As you can see, you're able to get much more useful information with sq than with just the default squeue formatting.


Output Columns Explained

  • JOBID: The unique ID of the job (for an array job, it will be of the form "<base_job_id>_<index>").
  • NAME: The name of the job. If not specified in one's submission script, it will default to the name of the submission script (e.g. "sub.sh").
  • PARTITION: The partition to which the job was sent (e.g. batch, highmem_p, gpu_p, etc...).
  • USER: The user who submitted the job.
  • NODES: The number of nodes allocated to the job.
  • CPUS: The number of CPU cores allocated to the job.
  • MIN_MEMORY: The total amount of memory allocated to the job.
  • PRIORITY: The job's priority per Slurm's Multifactor Priority Plugin
  • TIME: How much (wall-clock) time has elapsed since the job started, in the format DAYS-HOURS:MINUTES:SECONDS
  • TIME_LIMIT: The maximum time given for the job to run, in the format DAYS-HOURS:MINUTES:SECONDS.
  • STATE: The job's state (e.g. Running, Pending, etc...)
  • NODELIST(REASON): The name of the node(s) on which the job is running or the reason the job has not started yet, if it is pending.


sq also has a -h/--help option: 

bc06026@ss-sub3 ~$ sq --help

Usage: sq [OPTIONS]

Descriptions: sq - preformatted wrapper for squeue.  See man squeue for more information.

    -j                          Displays squeue output for a given job
    --me                        Displays squeue output for the user executing this command
    -p                          Displays squeue output for a given partition
    -u                          Displays squeue output for a given user
    -T                          Displays submit and start time columns
    -h, --help                  Displays this help output


Examples

  • See all pending and running jobs: sq
  • See all of your pending and running jobs: sq --me
  • See all pending and running jobs in the highmem_p: sq -p highmem_p
  • See all of your pending and running jobs in the batch partition: sq --me -p batch
  • See all of your pending and running jobs including submit time and start time columns: sq --me -T (Note, this will require a wide monitor or small font to display without columns wrapping around)


Example sq output: 

bc06026@ss-sub3 ~$ sq
JOBID	  NAME	        PARTITION	USER	  NODES	  CPUS	  MIN_MEMORY	PRIORITY     TIME	  TIME_LIMIT	STATE	  NODELIST(REASON)
4581410	  Bowtie2-test	batch	        zp21982	  1	  1	  12G	        6003	     2:10:56	  10:00:00	RUNNING	  c5-4
4584815	  test-job	highmem_p	rt12352	  1	  12	  300G	        5473	     1:51:03	  2:00:00	RUNNING	  d3-9
4578428	  PR6_Cd3	batch	        un12354	  1	  1	  40G	        5449	     4:57:15	  1-2:00:00	RUNNING	  c4-16
4583491	  interact	inter_p	        ai38821	  1	  4	  2G	        5428	     1:57:38	  12:00:00	RUNNING	  d5-21
4580374	  BLAST	        batch	        gh98762	  1	  1	  10G	        5397	     2:54:41	  12:00:00	RUNNING	  b1-9

...

Example sq output for an array job: 

bc06026@b1-24 workdir$ sq --me
JOBID         NAME            PARTITION        USER       NODES  CPUS   MIN_MEMORY   PRIORITY   TIME            TIME_LIMIT      STATE      NODELIST(REASON)
4711132_4     array-example   batch            bc06026    1      1      1G           5993       0:06            1:00:00         RUNNING    c5-19
4711132_3     array-example   batch            bc06026    1      1      1G           5993       0:06            1:00:00         RUNNING    c5-19
4711132_2     array-example   batch            bc06026    1      1      1G           5993       0:06            1:00:00         RUNNING    c5-19
4711132_1     array-example   batch            bc06026    1      1      1G           5993       0:06            1:00:00         RUNNING    c4-15
4711132_0     array-example   batch            bc06026    1      1      1G           5993       0:06            1:00:00         RUNNING    c4-15


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scontrol show job

Another option for viewing information about a pending or running job is scontrol show job JOBID, replacing JOBID with your job's ID. This command will display information about a pending or running job with one or more key/value pairs of information about the job per line, one line after another (as opposed to the row/column output of squeue and sq). This command will return output while the job is pending or running, and only for a few moments after the job has completed. Using this command with a job that has already finished (more than a few moments ago) will return the output "slurm_load_jobs error: Invalid job id specified". This just means that the job is too old for scontrol show job to display information about it.


Example scontrol show job output: 

bc06026@b1-24 workdir$ scontrol show job 4707896
JobId=4707896 JobName=testjob
   UserId=bc06026(3356) GroupId=gacrc-appadmin(21003) MCS_label=N/A
   Priority=5993 Nice=0 Account=gacrc-instruction QOS=normal
   JobState=RUNNING Reason=None Dependency=(null)
   Requeue=1 Restarts=0 BatchFlag=1 Reboot=0 ExitCode=0:0
   RunTime=00:00:23 TimeLimit=01:00:00 TimeMin=N/A
   SubmitTime=2021-09-17T09:53:30 EligibleTime=2021-09-17T09:53:30
   AccrueTime=2021-09-17T09:53:30
   StartTime=2021-09-17T09:53:30 EndTime=2021-09-17T10:53:30 Deadline=N/A
   SuspendTime=None SecsPreSuspend=0 LastSchedEval=2021-09-17T09:53:30
   Partition=batch AllocNode:Sid=b1-24:36515
   ReqNodeList=(null) ExcNodeList=(null)
   NodeList=c4-15
   BatchHost=c4-15
   NumNodes=1 NumCPUs=1 NumTasks=1 CPUs/Task=1 ReqB:S:C:T=0:0:*:*
   TRES=cpu=1,mem=4G,node=1,billing=1
   Socks/Node=* NtasksPerN:B:S:C=0:0:*:* CoreSpec=*
   MinCPUsNode=1 MinMemoryNode=4G MinTmpDiskNode=0
   Features=[Gamma|Beta|Delta|Alpha] DelayBoot=00:00:00
   OverSubscribe=OK Contiguous=0 Licenses=(null) Network=(null)
   Command=/scratch/bc06026/workdir/sub.sh
   WorkDir=/scratch/bc06026/workdir
   StdErr=/scratch/bc06026/workdir/testjob_4707896.err
   StdIn=/dev/null
   StdOut=/scratch/bc06026/workdir/testjob_4707896.out
   Power=
   MailUser=bc06026@uga.edu MailType=ALL
   NtasksPerTRES:0

As you can see, there is a little bit more information presented here than is with squeue and sq, such as showing the path to the job's working directory, Slurm job output file path(s), email information, etc...


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Finished Jobs

sacct and sacct-gacrc

The easiest way to monitor finished jobs is with the Slurm sacct command. Like most Slurm commands, you are able to control the columns displayed in the output of this command (see man sacct for more information). To save you the trouble of typing a long format string and to make things more convenient, we've created the sacct-gacrc command, which is sacct but pre-formatted and with some additional options for convenience.

A big difference between squeue/sq and sacct/sacct-gacrc is that by default, sacct/sacct-gacrc without any options only shows you YOUR Jobs. Another important note about sacct/sacct-gacrc is that by default it will display Slurm job steps. Unless you're dividing your job into steps with srun, you probably will want sacct/sacct-gacrc to display one line per job (hide job steps, only show job allocation). To do this, use the -X option. For more information on Slurm job allocation, please see the Slurm documentation.


The default sacct columns are as follows: 

JobID    JobName  Partition    Account  AllocCPUS      State ExitCode

Using sacct-gacrc runs the sacct command but provides the following columns: 

JobID         JobName      User  Partition NNode NCPUS   ReqMem    CPUTime    Elapsed  Timelimit      State ExitCode   NodeList

As you can see, you're able to get much more useful information with sacct-gacrc than with just the default sacct formatting.


Output Columns Explained

  • JobID: The unique ID of the job.
  • JobName: The name of the job. If not specified in one's submission script, it will default to the name of the submission script (e.g. "sub.sh").
  • User: The user who submitted the job.
  • Partition: The partition to which the job was sent (e.g. batch, highmem_p, gpu_p, etc...).
  • NNode: The number of nodes allocated to the job.
  • NCPUS: The number of CPU cores allocated to the job.
  • ReqMem: The amount of memory allocated to the job.
  • CPUTime: Time used (Elapsed time * CPU core count) by a job.
  • Elapsed: How much (wall) time has elapsed since the job started, in the format DAYS-HOURS:MINUTES:SECONDS
  • Timelimit: The maximum time given for the job to run, in the format DAYS-HOURS:MINUTES:SECONDS.
  • State: The job's state (e.g. Running, Pending, etc...).
  • ExitCode: The job's exit code.
  • Nodelist: The name of the node(s) on which the job is running or ran.


sacct-gacrc also has a -h/--help option: 

bc06026@ss-sub3 ~$ sacct-gacrc --help

Usage: sacct-gacrc [OPTIONS]

Description: preformatted wrapper for sacct.  See man sacct for more information. 

    -E, --endtime               Display information about jobs up to a date, in the format of yyyy-mm-dd (default: now)
    -j, --jobs                  Display information about a particular job or jobs (comma-separated list if more than one job)
    -r, --partition             Display information about jobs from a particular partition
    -S, --starttime             Display information about jobs starting from a date in the format of yyyy-mm-dd (default: Midnight of today)
    -T                          Display the end time of a particular job or jobs
    -u, --user                  Display information about a particular user's job(s) (default: current user)
    -X, --allocations           Only show one line per job (do not display job steps)
    --debug                     Display the sacct command being executed
    -h, --help                  Display this help output


Examples

  • See information about all of your jobs that started from midnight up to now: sacct-gacrc
  • See information about a particular job: sacct-gacrc -j JOBID (replacing JOBID with a particular job ID)
  • See information about all of your jobs that started from midnight up to now in the highmem_p: sacct-gacrc -r highmem_p
  • See information about your jobs that ran from a particular date up to now: sacct-gacrc -S YYYY-MM-DD (replacing YYYY-MM-DD with a date, e.g. 2021-09-01)


Example sacct-gacrc output: 

bc06026@b1-24 ~$ sacct-gacrc -X -S 2021-09-14
       JobID    JobName      User  Partition   NodeList AllocNodes NTask NCPUS  ReqMem  MaxVMSize      State    CPUTime    Elapsed  Timelimit ExitCode 
------------ ---------- --------- ---------- ---------- ---------- ----- ----- ------- ---------- ---------- ---------- ---------- ---------- -------- 
4580375        interact   bc06026  highmem_p     ra4-22          1           1   200Gn            FAILED       00:00:07   00:00:07   12:00:00      1:0 
4580382        interact   bc06026  highmem_p      d1-22          1          28   200Gn            COMPLETED    00:03:16   00:00:07   12:00:00      0:0 
4584992        interact   bc06026    inter_p      c4-16          1           1     2Gn            COMPLETED    00:00:18   00:00:18   12:00:00      0:0 

...

Please note that sacct and sacct-gacrc also show jobs in a RUNNING state.

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seff

seff is a command that can be used to check how efficient a finished job was with the CPU and memory resources it was given. This is a very useful command as it gives insight into optimizing our job's resources. It is important to note that seff is only useful after a job has finished. Using it with a job that is still running will not return an error message, but the CPU and memory usage will be shown as 0.00%, and a warning message will be appended to the bottom of the output that says "WARNING: Efficiency statistics may be misleading for RUNNING jobs.".

Example seff output: 

bc06026@b1-24 workdir$ seff 4707896
Job ID: 4707896
Cluster: tc2
User/Group: bc06026/gacrc-appadmin
State: COMPLETED (exit code 0)
Cores: 1
CPU Utilized: 00:09:25
CPU Efficiency: 93.08% of 00:10:07 core-walltime
Job Wall-clock time: 00:10:07
Memory Utilized: 183.43 MB
Memory Efficiency: 4.48% of 4.00 GB

The key information shown in the output above are the last 6 rows. We see that the job was allocated 1 CPU core, and that core was doing something for 9 minutes and 25 seconds out of the total 10 minutes and 7 seconds of the job's wall-clock (elapsed) time, (93.08% of the job's wall-clock time). Generally you want to aim for as much utilization of the resources you request as possible, so perhaps this job could run twice as fast given two cores, if the software/command(s) it used parallelized perfectly. The memory utilized for the job in the output above is very low. Four gigabytes of RAM is not much at all in the context of high performance computing, but say for example you requested 100 GB of memory and found that your job was only using ~5% of that memory. In that case you would definitely want to consider lowering the amount of memory you request for that particular job if ran again in the future. For more information on job resource tuning, please see Best Practices on Sapelo2 and Job Resource Tuning . Please note that if your job ends abruptly because it ran out of memory, the seff memory utilization values may not reflect that, as a sudden spike in memory usage could cause the job to get killed before seff notices the spike in consumed memory.


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