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Current version of the intro to the DCC slides.

Introduction to SLURM

Most DCC partitions are lab-owned machines. These can only be used by members of the group. Submitting to a group partition gives “high-priority”.

Submit to partitions with

#SBATCH –p (partition name) --account=(account name)

(in a job script) or

srun –p (partition name) --account=(account name) --pty bash –i

(interactively) In general, the partition name and account name will be the same for most lab-owned machines.

Common DCC Partitions

There are four different DCC partitions to which batch jobs and interactive sessions can be directed by all DCC users:

  • common for jobs that will run on the DCC core nodes (up to 64 GB RAM).
  • gpu-common for jobs that will run on DCC GPU nodes.
  • scavenger for jobs that will run on lab-owned nodes in “low priority” (kill and requeue preemption).
  • scavenger-gpu for GPU jobs that will run on lab-owned nodes in “low priority” (kill and requeue preemption).

Note: These partitions do not require an “–account=” flag. (i.e., they accept jobs from any account.) If a partition is not specified, the default partition is the common partition.

Running an interactive job

Reserve a compute node by typing srun –pty bash -i

tm103@dcc-login-02 ~ $ srun --pty bash -i   
srun: job 186535 queued and waiting for resources   
srun: job 186535 has been allocated resources   
tm103@dcc-core-11 ~ $
tm103@dcc-core-11 ~ $ squeue -u tm103  
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 
186535 common bash tm103 R 0:14 1 dcc-core-11

I now have an interactive session in the common partition on node dcc-core-11

SLURM commands

sbatch – Submit a batch job

#SBATCH – Specify job parameters in a job script

squeue – Show lists of jobs

scancel – Delete one or more batch jobs

sinfo – Show info about machines

scontrol – Show cluster configuration information

Use sbatch (all lower case) to submit text file job scripts, e.g. test.sh

sbatch test.sh

Use #SBATCH (upper case) in your scripts for scheduler directives, e.g.

#SBATCH --mem=1G
#SBATCH ---output=matlab.out

All SLURM directives can be given on the command line instead of the script. slurm.schedmd.com

Slurm memory directives

The default memory request (allocation) is 2 GB RAM. This is a hard limit, always request a little more. To request a total amount of memory for the job, use one of the following: * --mem=<MB> additional memory * --mem=<Gigabyte>G the amount of memory required per node, or * --mem-per-cpu=<MB> the amount of memory per CPU core, for multi-threaded jobs

Note: –mem and –mem-per-cpu are mutually exclusive

Slurm parallel directives

All parallel directives have defaults of 1

-N <number> How many nodes (machines)

-n <number> or --ntasks=<number> How many parallel jobs (“tasks”)

-c <number> or --cpus-per-task=<number>

Use -n and -N for multi-node jobs (e.g. MPI)

Use -c (–cpus-per-task) for multi-threaded jobs

Job script examples

#!/bin/bash  
#SBATCH ---output=test.out
hostname # print hostname

This prints the name of the compute node in the file “test.out”

tm103@dcc-login-02 ~/slurm $ sbatch simple.sh
Submitted batch job 186554tm103@dcc-login-02 ~/slurm $ cat test.out 
dcc-core-14

Long-form commands example

#SBATCH --output=slurm.out
#SBATCH --error=slurm.err  
#SBATCH --mem=100 # 100 MB RAM 
#SBATCH --partition=scavenger# 
hostname 1>&2  #prints hostname to the error file

This job will run in low priority on a lab node in the “scavenger” partition

Short-form commands example.

SLURM short commands don’t use “=“ signs

#!/bin/bash
#SBATCH -o slurm.out
#SBATCH -e slurm.err
#SBATCH --mem=4G # 4 GBs RAM 
#SBATCH –p scavenger
hostname 1>&2  #prints hostname to the error file

R example script

#!/bin/bash
#SBATCH –e slurm.err
#SBATCH --mem=4G # 4 GB RAM 
module load R/3.6.0
R CMD BATCH Rcode.R

This loads the environment module for R/3.6.0 and runs a single R script (“Rcode.R”)

The #SBATCH –mem=4G requests additional RAM

Multi-threaded (multi-core) example

!/bin/bash
#SBATCH –J test 
#SBATCH –o test.out
#SBATCH –c 4
#SBATCH –-mem-per-cpu=500 #(500 MB) 
myApplication –n $SLURM_CPUS_PER_TASK

The value of $SLURM_CPUS_PER_TASK is the number after -c. This example starts a single, multi-threaded job that uses 4 CPU cores and 2 GB (4x500MB) of RAM

OpenMP multicore example

!/bin/bash
#SBATCH –J openmp-test 
#SBATCH –o slurm.out
#SBATCH –c 4
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
myOpenMPapp # will run on 4 CPU cores

This sets $OMP_NUM_THREADS to the value of $SLURM_CPUS_PER_TASK

Slurm job arrays

Slurm job arrays are a mechanism for submitting and managing collections of similar jobs using one job script and one application program.

  • Add --array or -a option to the job script
  • Each job task will inherit a SLURM_ARRAY_TASK_ID environment variable with a different integer value
  • Each job array can be up 100,000 job tasks on the DCC
  • Job arrays are only supported for batch jobs
  • Job array “tasks” must be independent: slurm.schedmd.com/job_array.html

For example, in a job script, add the line #SBATCH --array=1-30 or, alternatively, #SBATCH -a 1-30 to submit 30 job tasks. The job array indices can also be specified on the command line, e.g.

sbatch -a 1-30 myjob.sh

The index values can be continuous, e.g.

-a 0-31 (32 tasks, numbered from 0,1,2,…,31)

or discontinuous, e.g.

-a 3,5,7-9,12 (6 tasks, numbers 3,5,7,8,9,12)

It can also be a single job task, e.g.

-a 7

The discontinous notation is useful for resubmitting specific job tasks that had previously failed. Each job task is assigned the enviromental variable $SLURM_ARRAY_TASK_ID set to it’s index value.

tm103@dcc-login-02  ~/misc/jobarrays $ cat array-test.sh 
#!/bin/bash
echo $SLURM_ARRAY_TASK_ID
tm103@dcc-login-02  ~/misc/jobarrays $ sbatch -a 1-3 array-test.sh 
Submitted batch job 24845830
tm103@dcc-login-02  ~/misc/jobarrays $ ls slurm-24845830*
slurm-24845830_1.out  slurm-24845830_2.out  slurm-24845830_3.out
tm103@dcc-login-02  ~/misc/jobarrays $ cat slurm-24845830*
1
2
3
tm103@dcc-login-02  ~/misc/jobarrays $

Python job array example

#!/bin/bash
#SBATCH -e slurm_%A_%a.err
#SBATCH -o slurm_%A_%a.out 
#SBATCH --array=1-5000 
python myCode.py

$ cat test.py
import os
taskID=int(os.environ['SLURM_ARRAY_TASK_ID'])
...

Start 5000 Python jobs, each with a different “taskID”, initialized from $SLURM_ARRAY_TASK_ID

Importing Environmental Variables

Python:

numCPUs=int(os.environ['SLURM_CPUS_PER_TASK'])
taskID=int(os.environ['SLURM_ARRAY_TASK_ID'])

R:

numCPUs <- as.integer(Sys.getenv(SLURM_CPUS_PER_TASK)) 
taskID <- as.integer(Sys.getenv(SLURM_ARRAY_TASK_ID))

MATLAB:

numCPUs = str2num(getenv('SLURM_CPUS_PER_TASK'))
taskID = str2num(getenv('SLURM_ARRAY_TASK_ID'))

Processing separate input files

Process an existing file list, e.g. files.txt

#!/bin/bash
readarray -t FILES < files.txt
FILENAME=${FILES[(($SLURM_ARRAY_TASK_ID - 1))]}
myapp $FILENAME

Dynamically generate a file list from “ls”

#!/bin/bash
export FILES=($(ls -1 myfile*))
FILENAME=${FILES[(($SLURM_ARRAY_TASK_ID - 1))]}
myapp $FILENAME

Example: Using the taskID as part of the file name and output directory for the case with input file names of the form input1,input2,…,inputN for -a 1-N, e.g.

#!/bin/bash
#SBATCH -e slurm_%A_%a.err
#SBATCH -o slurm_%A_%a.out      
mkdir out_${SLURM_ARRAY_TASK_ID}     
cd out_${SLURM_ARRAY_TASK_ID}
myapp ../input_${SLURM_ARRAY_TASK_ID}.txt

where output directories out1, out2, … are created for input files input1.txt, input2.txt,…

“Unrolling” for loops example

Original “serial” code (Python)

fibonacci = [0,1,1,2,3,5,8,13,21]
for i in range(len(fibonacci)):
    print(i,fibonacci[i])

Job array version

import os
i=int(os.environ['SLURM_ARRAY_TASK_ID'])
fibonacci = [0,1,1,2,3,5,8,13,21]
#for i in range(len(fibonacci)):
    print(i,fibonacci[i])

where the for loop is commented-out and each job task is doing a single “iteration”

tm103@dcc-login-02  ~/misc/jobarrays $ cat fib-array.sh 
#!/bin/bash
#SBATCH -e slurm.err
module load Python/2.7.11
python fibonacci.py
tm103@dcc-login-02  ~/misc/jobarrays $ sbatch –a 1-8 fib-array.sh 
Submitted batch job 24856052
tm103@dcc-login-02  ~/misc/jobarrays $ ls slurm-24856052_*
slurm-24856052_1.out  slurm-24856052_3.out  slurm-24856052_5.out  slurm-24856052_7.out
slurm-24856052_2.out  slurm-24856052_4.out  slurm-24856052_6.out  slurm-24856052_8.out
tm103@dcc-login-02  ~/misc/jobarrays $ cat slurm-24856052*
(1, 1)
(2, 1)
(3, 2)
(4, 3)
(5, 5)
(6, 8)
(7, 13)
(8, 21)
tm103@dcc-login-02  ~/misc/jobarrays $

Running MPI jobs

Supported MPI versions are Intel MPI and OpenMPI

Compiling with OpenMPI

tm103@dcc-login-02  ~ $ module load OpenMPI/4.0.5-rhel8
OpenMPI 4.0.5-rhel8
tm103@dcc-login-03  ~ $ mpicc -o openhello hello.c
tm103@dcc-login-02  ~ $ ls -l openhello 
-rwxr-xr-x. 1 tm103 scsc 9184 Sep  1 16:08 openhello`

OpenMPI job script

#!/bin/bash
#SBATCH -o openhello.out
#SBATCH -e slurm.err
#SBATCH -n 20
module load OpenMPI/4.0.5-rhel8
mpirun -n $SLURM_NTASKS openhello

OpenMPI example output

tm103@dcc-login-02 ~/misc/slurm/openmpi $ cat openhello.out  
dcc-core-01, rank 0 out of 20 processors  
dcc-core-01, rank 1 out of 20 processors  
dcc-core-01, rank 2 out of 20 processors  
dcc-core-01, rank 3 out of 20 processors  
dcc-core-01, rank 4 out of 20 processors   
dcc-core-03, rank 13 out of 20 processors 
dcc-core-03, rank 14 out of 20 processors 
dcc-core-03, rank 10 out of 20 processors 
dcc-core-03, rank 11 out of 20 processors 
dcc-core-03, rank 12 out of 20 processors 
dcc-core-02, rank 8 out of 20 processors 
dcc-core-02, rank 9 out of 20 processors 
dcc-core-02, rank 5 out of 20 processors

GPU jobs

To run a GPU batch job, add the job script lines

#SBATCH -p gpu --gres=gpu:1 
#SBATCH -c 6

To get an interactive GPU node session, type the command line srun -p gpu-common --gres=gpu:1 --pty bash –i tm103@dcc-clogin-02 ~ $ srun -p gpu-common --gres=gpu:1 --pty bash -i tm103@dcc-gpu-01 ~ $ /usr/local/cuda-7.5/samples/1_Utilities/deviceQuery/deviceQuery ... Detected 1 CUDA Capable device(s)

Device 0: "Tesla K80"
    CUDA Driver Version / Runtime Version          7.5 / 7.5
    CUDA Capability Major/Minor version number:    3.7
    Total amount of global memory:                 11520 MBytes (12079136768 bytes)
    (13) Multiprocessors, (192) CUDA Cores/MP:     2496 CUDA Cores

Job dependencies

Submit a job that waits for another job to finish.

$ sbatch dep1.q
Submitted batch job 666898

Make a note of the assigned job ID of dep1

$ sbatch --dependency=afterok:666898 dep2.q
Job dep2 will not start until dep1 finishes

Job dependencies with arrays

Wait for specific job array elements

sbatch --depend=after:123_4 my.job sbatch --depend=afterok:123_4:123_8 my.job2

Wait for entire job array to complete

sbatch --depend=afterany:123 my.job

Wait for entire job array to complete successfully

sbatch --depend=afterok:123 my.job

Wait for entire job array to complete and at least one task fails

sbatch --depend=afternotok:123 my.job

More information: hcc-docs.unl.edu/display/HCCDOC/Job+Dependencies

Additional Resources

http://schedmd.com

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