SLURM
SLURM is the batch job scheduling system for the SLAC batch compute systems. Generic documentation about SLURM can be found in this Quick Start User Guide.
S3DF Computing Facility
LCLS specific information about the S3DF facility is here: Running at S3DF.
General S3DF documentation is here: https://s3df.slac.stanford.edu
Some hardware details about the S3DF can be found here, although note that 8 of the milano cluster node cores are reserved for the filesystem so only 120 (out of 128) can be used on each node for batch processing: https://s3df.slac.stanford.edu/public/doc/#/batch-compute?id=clusters-amp-repos
Partitions
The partition/queue information can be provided by the sinfo command.
sinfo
LCLS users typically use the "milano" queue at s3df:
sinfo
[cpo@sdfiana002 ~]$ sinfo PARTITION AVAIL TIMELIMIT NODES STATE NODELIST roma* up 10-00:00:0 1 comp sdfrome004 roma* up 10-00:00:0 16 drng@ sdfrome[006-018,041-043] roma* up 10-00:00:0 1 down$ sdfrome003 roma* up 10-00:00:0 1 drain$ sdfrome037 roma* up 10-00:00:0 1 drain sdfrome005 roma* up 10-00:00:0 21 mix sdfrome[019-036,038-040] milano up 10-00:00:0 1 inval sdfmilan221 milano up 10-00:00:0 14 drng@ sdfmilan[036-038,120-121,126,129,204-205,212,229-232] milano up 10-00:00:0 4 drain$ sdfmilan[009,041,049,112] milano up 10-00:00:0 1 drain sdfmilan032 milano up 10-00:00:0 12 resv sdfmilan[001-005,029-030,052,057,117-119] milano up 10-00:00:0 102 mix sdfmilan[006-008,010-019,021-028,031,033-035,039-040,042-048,050-051,053-056,058-072,101-111,113-116,122-125,127-128,130-131,201-203,206-211,213-220,222-228] milano up 10-00:00:0 1 idle sdfmilan020 ampere up 10-00:00:0 1 drng@ sdfampere010 ampere up 10-00:00:0 1 drng sdfampere011 ampere up 10-00:00:0 3 drain sdfampere[005,008,023] ampere up 10-00:00:0 18 mix sdfampere[001-004,006-007,009,012-022] [cpo@sdfiana002 ~]$
The "*" following the roma queue name indicates that it is a default queue for submission.
Job Submission
sbatch
The following is a simple submission script of a parallel psana batch job run with mpi. It can be submitted with the command "sbatch submit.sh". The commands specified in the script file will be ran on the first available compute node that fits the resources requested. There are two ideas: "nodes" and "tasks per node". A "node" is a physical computer box (with a host-name, for example) but each box/node typically has multiple-cpu-cores. Typically the tasks-per-node parameter is set to utilize all the cores on each node.
NOTE: when running interactively the "mpirun" command takes a "-n" argument with a number of cores. However, when running with slurm no "-n" is needed, as slurm infers it from the "--nodes" and "--ntasks-per-node" values.
> cat submit.sh #!/bin/bash #SBATCH --partition=milano #SBATCH --nodes=2 #SBATCH --ntasks-per-node=120 #SBATCH --output=%j.log # -u flushes print statements which can otherwise be hidden if mpi hangs mpirun python -u -m mpi4py.run my_psana_script.py
One can also do this same command from the command line using the "--wrap" option for sbatch:
sbatch -p milano --nodes 2 --ntasks-per-node 3 --wrap="mpirun python -u -m mpi4py.run my_psana_script.py"
srun
In principle the slurm "srun" command can also be used to launch parallel jobs, however the current S3DF "srun" version only supports an older "pmi2" protocol, which is incompatible the mpi packages from conda that LCLS uses which use the newer "pmix" protocol. srun should be avoided for parallel jobs at S3DF (see output of "srun --mpi=list").
Monitoring/Status
squeue
To check that jobs that exist on the system use the squeue command:
squeue
[cpo@sdfiana002 ~]$ squeue -u ytl
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
30703603 ampere,ro out ytl PD 0:00 1 (launch failed requeued held)
30703602 ampere,ro out ytl PD 0:00 1 (launch failed requeued held)
30701730 ampere,ro out ytl PD 0:00 1 (launch failed requeued held)
30700739 ampere,ro out ytl PD 0:00 1 (launch failed requeued held)
30700738 ampere,ro out ytl PD 0:00 1 (launch failed requeued held)
30699545 ampere,ro out ytl PD 0:00 1 (launch failed requeued held)
30704838 milano out ytl CG 4:07 1 sdfmilan221
[cpo@sdfiana002 ~]$
The ST (job state) field shows that most jobs are pending (PD) and one is completing (CG).
sacct
Get information about status of finished jobs
sacct
[cpo@sdfiana002 ~]$ sacct -u ytl JobID JobName Partition Account AllocCPUS State ExitCode ------------ ---------- ---------- ---------- ---------- ---------- -------- 30682524 out milano shared:de+ 112 PREEMPTED 0:0 30682524.ba+ batch shared:de+ 112 CANCELLED 0:15 30682524.ex+ extern shared:de+ 112 COMPLETED 0:0 30682525 out milano shared:de+ 112 PREEMPTED 0:0 30682525.ba+ batch shared:de+ 112 CANCELLED 0:15 30682525.ex+ extern shared:de+ 112 COMPLETED 0:0
Misc Slurm commands
scontrol is used to view or modify Slurm configuration including: job, job step, node, partition, reservation, and overall system configuration. Most of the commands can only be executed by user root or an Administrator.
- Detail job information:
scontrol show jobid -dd <jobID> - Show reservation:
scontrol show res
sacctmgr is used to deal with accounts, associations and users.
Format can be modified at will or removed to see all (can be hard to read, especially on smaller windows):
- Show what account a user is associated with:
sacctmgr show associations Users=<user_names> format=cluster,account,partition,QOS - Show priorities for an account:
sacctmgr list associations -p accounts=<accounts> - Show priority coefficients:
sacctmgr show qos format=name,priority,usagefactor
Others
- Show priority level for a job:
sprio -j <jobID>
Overview
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