Introduction

At ITET the Condor Batch Queueing System has been used for a long time and is still used for running compute-intensive jobs. It uses the free resources on the tardis-PCs of the student rooms and on numerous PCs and compute servers at ITET institutes. Interactive work is privileged over batch computing, so running jobs could be killed by new interactive load or by shutdown/restart of a PC.

The SLURM system installed on the powerful ITET arton compute servers is an alternative to the Condor batch computing system and reserved for staff of the contributing institutes (APS,IBT,IFA,NARI,TIK,WINS). It consists of a master host, where the scheduler resides and the arton compute nodes, where the batch jobs are executed. The compute nodes are powerful servers located in server rooms, they are exclusively reserved for batch processing. Interactive logins are disabled.

SLURM

SLURM (Simple Linux Utility for Resource Management) is a free and open-source job scheduler for Linux and Unix-like kernels, used by many of the world's supercomputers and compute clusters. Slurm's design is very modular with about 100 optional plugins. In 2010, the developers of Slurm founded SchedMD, which maintains the canonical source, provides development, level 3 commercial support and training services and also provide a very good online documentation to Slurm.

gfreudig@trollo:~/Batch$ sinfo 
PARTITION      AVAIL  TIMELIMIT  NODES  STATE NODELIST
cpu.normal.32*    up 1-00:00:00      2   idle arton02,zampano
cpu.normal.64     up 1-00:00:00      1   idle arton09
cpu.normal.256    up 1-00:00:00      1   idle arton09
array.normal      up 1-00:00:00      2   idle arton02,zampano
gpu.normal        up 1-00:00:00      1    mix artongpu01
gfreudig@trollo:~/Batch$ 

SLURM Arton Grid

Hardware

At the moment the computing power of the SLURM Arton Grid is based on the following 11 cpu compute servers and 1 gpu compute server (compute nodes) :

The local disks (/scratch) of arton09, arton10 and arton11 are fast SSD-disks (6 GBit/s) with a size of 720 GByte.

The SLURM job scheduler runs on the linux server itetmaster01.

Software

The artons cpu nodes offer the same software environment as all D-ITET managed Linux clients, gpu nodes have a restricted software (no desktops installed).

Using SLURM

At a basic level, SLURM is very easy to use. The following sections will describe the commands you need to run and manage your batch jobs on the Grid Engine. The commands that will be most useful to you are as follows

• sbatch - submit a job to the batch scheduler

• squeue - examine running and waiting jobs

• sinfo - status compute nodes

• scancel - delete a running job

Setting environment

The above commands only work if the environment variables for SLURM are set. Please add the following two lines to your ~/.bashrc:

export PATH=/usr/pack/slurm-19.05.0-sr/amd64-debian-linux9/bin:$PATH
export SLURM_CONF=/home/sladmitet/slurm/slurm.conf

sbatch -> Submitting a job

sbatch doesn't allow to submit a binary program directly, please wrap the program to run into a surrounding bash script. The sbatch command has the following syntax:

> sbatch [options] job_script [job_script arguments]

The job_script is a standard UNIX shell script. The fixed options for the SLURM Scheduler are placed in the job_script in lines starting with #SBATCH. The UNIX shell interprets these lines as comments and ignores them. Only temporary options should be placed outside the job_script. To test your job-script you can simply run it interactively.

Assume there is a c program primes.c which is compiled to an executable binary named primes with "gcc -o primes primes.c". The program runs 5 seconds and calculates prime numbers. The found prime numbers and a final summary are sent to standard output. A sample job_script primes.sh to perform a batch run of the binary primes on the Arton grid looks like this:

#!/bin/sh
#
#SBATCH  --mail-type=ALL                     # mail configuration: NONE, BEGIN, END, FAIL, REQUEUE, ALL
#SBATCH  --output=log/%j.out                 # where to store the output ( %j is the JOBID )
/bin/echo Running on host: `hostname`
/bin/echo In directory: `pwd`
/bin/echo Starting on: `date`
/bin/echo SLURM_JOB_ID: $SLURM_JOB_ID
#
# binary to execute
./primes
echo finished at: `date`
exit 0;

You can test the script by running it interactively in a terminal:

gfreudig@trollo:~/Batch$ ./primes.sh

If the script runs successfully you can now submit it as a batch job to the SLURM arton grid:

gfreudig@trollo:~/Batch$ sbatch primes.sh 
sbatch: Start executing function slurm_job_submit......
sbatch: Job partition set to : cpu.normal.32 (normal memory)
Submitted batch job 931
gfreudig@trollo:~/Batch$ 

After the job has finished, you will find the output file of the job in the log subdirectory with a name of <JOBID>.out.
The directory for the job output must exist, it is not created automatically!

Similar to condor it is also possible to start an array job. The above job would run 10 times if you added the option #SBATCH --array=0-9 to the job-script. A repeated execution only makes sense if the executed program adapts its behaviour according to the changing array task count number. The array count number can be referenced through the variable $SLURM_ARRAY_TASK_ID. You can pass the value of $SLURM_ARRAY_TASK_ID or some derived parameters to the executable.
Here is a simple example of passing an input filename parameter changing with $SLURM_ARRAY_TASK_ID to the executable:

.
#SBATCH   --array=0-9
#
# binary to execute
<path-to-executable> data$SLURM_ARRAY_TASK_ID.dat

Every run of the program in the array job with a different task-id will produce a separate output file.

The following table shows the most common options available for sbatch to be used in the job_script in lines starting with #SBATCH

The --nodes option should only be used for MPI jobs !

squeue -> Show running/waiting jobs

The squeue command shows the actual list of running and pending jobs in the system. As you can see in the following sample output the default format is quite minimalistic:

gfreudig@trollo:~/Batch$ squeue
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
               951 cpu.norma primes.s gfreudig  R       0:11      1 arton02
               950 cpu.norma primes_4 gfreudig  R       0:36      1 arton02
               949 cpu.norma primes.s fgtest01  R       1:22      1 arton02
               948 gpu.norma primes.s fgtest01  R       1:39      1 artongpu01
gfreudig@trollo:~/Batch$ 

More detailed information can be obtained by issuing the following command:

gfreudig@trollo:~/Batch$ squeue -O jobarrayid:10,state:10,partition:16,reasonlist:18,username:10,tres-alloc:45,timeused:8,command:50
JOBID     STATE     PARTITION       NODELIST(REASON)  USER      TRES_ALLOC                                   TIME    COMMAND                                             
951       RUNNING   cpu.normal.32   arton02           gfreudig  cpu=1,mem=32G,node=1,billing=1               1:20    /home/gfreudig/BTCH/Slurm/jobs/single/primes.sh 600 
950       RUNNING   cpu.normal.32   arton02           gfreudig  cpu=4,mem=8G,node=1,billing=4                1:45    /home/gfreudig/BTCH/Slurm/jobs/multi/primes_4.sh 600
949       RUNNING   cpu.normal.32   arton02           fgtest01  cpu=1,mem=8G,node=1,billing=1                2:31    /home/fgtest01/BTCH/Slurm/jobs/single/primes.sh 600 
948       RUNNING   gpu.normal      artongpu01        fgtest01  cpu=1,mem=8G,node=1,billing=1,gres/gpu=1     2:48    /home/fgtest01/BTCH/Slurm/jobs/single/primes.sh 600 
gfreudig@trollo:~/Batch$ 

Defining an alias in your .bashrc with

alias sq1='squeue -O jobarrayid:10,state:10,partition:16,reasonlist:18,username:10,tres-alloc:45,timeused:8,command:50'

puts the command sq1 at your fingertips.

scancel -> Deleting a job

With scancel you can remove your waiting and running jobs from the scheduler queue by their associated JOBID. The command squeue lists your jobs including their JOBIDs. A job can then be deleted with

> scancel <JOBID>

To operate on an array job you can use the following commands

> scancel <JOBID>          # all jobs (waiting or running) of the array job are deleted
> scancel <JOBID>_n        # the job with task-ID n is deleted
> scancel <JOBID>_[n1-n2]  # the jobs with task-ID in the range n1-n2 are deleted

sinfo -> Show partition configuration

The partition status can be obtained by using the sinfo command. An example listing is shown below.

gfreudig@trollo:~/Batch$ sinfo
PARTITION      AVAIL  TIMELIMIT  NODES  STATE NODELIST
cpu.normal.32*    up 1-00:00:00      2   idle arton[01-11]
cpu.normal.64     up 1-00:00:00      1   idle arton[09-11]
cpu.normal.256    up 1-00:00:00      1   idle arton11
array.normal      up 1-00:00:00      2   idle arton[01-08]
gpu.normal        up 1-00:00:00      1   idle artongpu01
gfreudig@trollo:~/Batch$ 

For normal jobs (single, multicore) you can not choose the partition for the job to run in the sbatch command, the partition is selected by the scheduler according to your memory request. Array jobs are put in the array.normal partition, gpu jobs in the gpu.normal partition. The following table shows the job memory limits in different partitions:

Only a job with a --mem request of a maximum of 32 GByte can run in the cpu.normal.32 partition, which contains all 11 artons.

Multicore jobs/ job to core binding

A modern linux kernel is able to bind a process and all its children to a fixed number of cores. By default a job submitted to the SLURM arton grid is bound to to the numbers of requested cores/cpus. The default number of requested cpus is 1, if you have an application which is able to run multithreaded on several cores you must use the --cpus-per-task option in the sbatch command to get a binding to more than one core. To check for processes with core bindings, use the command hwloc-ps -c:

gfreudig@trollo:~/Batch$ ssh arton02 hwloc-ps -c
43369   0x00010001              slurmstepd: [984.batch]
43374   0x00010001              /bin/sh
43385   0x00010001              codebin/primes
gfreudig@trollo:~/Batch$

Job input/output data storage

Temporary data storage of a job used only while the job is running, should be placed in the /scratch directory of the compute nodes. Set the environment variables of the tools you use accordingly. The Matlab MCR_ROOT_CACHE variable is set automatically by the SLURM scheduler.
The file system protection of the /scratch directory allows everybody to create files and directories in it. A cron job runs periodically on the execution hosts to prevent the /scratch directory from filling up and cleans it governed by pre-set policies. Therefore data you place in the /scratch directory of a compute node cannot be assumed to stay there forever.

Small sized input and output data for the jobs is best placed in your home directory. It is available on every compute node through the /home automounter.

If you have problems with the quota limit in your home directory you could transfer data from your home or the /scratch directory of your submit host to the /scratch directories of the arton compute nodes and vice versa. For this purpose interactive logins with personal accounts are allowed on arton01. All /scratch directories of the compute nodes are available on arton01 through the /scratch_net automount system. You can access the /scratch directory of arton<nn> under /scratch_net/arton<nn>. This allows you to transfer data between the /scratch_net directories and your home with normal linux file copy and to the /scratch of your submission host with scp.

Do not log in on arton01 to run compute jobs interactively. Such jobs will be detected by our procguard system and killed.. Other data storage concepts for the arton grid are possible and will be investigated, if the above solution proves not to be sufficient.
In the near future ISG will provide a network attached scratch storage system (Netscratch) which will be accessible on all managed linux clients and compute nodes.

Matlab Distributed Computing Environment (MDCE)

The Matlab Parallel Computing Toolbox (PCT) can be configured with an interface to the SLURM cluster. To work with MDCE please import Slurm.settings in Matlab GUI (Parallel -> Create and manage Clusters -> Import ). You will now see a cluster profile Slurm beside the standard local(default) profile in the profile list. The local profile is for using more workers on one machine while with the Slurm profile up to 32 worker processes distributed over all slurm compute nodes can be used.
Please temporaray reduce the number of workers to 4 in the Slurm profile when performing the profile "Validation" function in the Matlab Cluster Manager.
Don't forget to set the Slurm environment variables before starting matlab !
For the Slurm profile to work you must have a working ssh key pair in ~/.ssh (id_rsa, id_rsa.pub). The Slurm cluster profile can be used with matlab programs in batch mode but it's also possible to use the profile in an interactive matlab session on your client. If you open a Slurm parpool the workers are started automatically in the cluster.
In interactice mode please always close your parpool if you are performing no calculations on the workers.
You can find a sample code for the 3 Matlab PCT methods parfor, spmd, tasks using the local or Slurm cluster profile in PCTRefJobs.tar.gz.