CINECA M100 SLURM Quick Start Guide - gfiameni/nvdoc-italy GitHub Wiki

$ ssh login.m100.cineca.it -l <your username>

$ srun myApp

This is the simplest way to run a job on a cluster. In this example, the lone srun command defaults to asking for one task on one core on one node of the default queue charging the default account.

Run hostname in an interactive allocation:

$ salloc

salloc: Pending job allocation 3037981
salloc: job 3037981 queued and waiting for resources

blocks here until job runs

salloc: job 3037981 has been allocated resources
salloc: Granted job allocation 3037981
salloc: Waiting for resource configuration
salloc: Nodes login06 are ready for job
manpath: warning: $MANPATH set, ignoring /etc/man_db.conf

$ srun hostname login06

Run it again:

$ srun -n 4 hostname login06 login06 login06 login06

Now exit the job and allocation

$ exit exit salloc: Relinquishing job allocation 3037981 salloc: Job allocation 3037981 has been revoked.

Like srun in the first example, salloc defaults to asking for one node of the default queue charging the default account. Once the job runs and the prompt appears, any further commands are run within the job's allocated resources until exit is invoked. Create a batch job script and submit it

$ cat > myBatch.cmd #!/bin/bash #SBATCH -N 4 #SBATCH -p pdebug #SBATCH -A myAccount #SBATCH -t 30

srun -N 4 -n 32 myApp ^D

This script asks for 4 nodes from the pdebug queue for no more than 30 minutes charging the myAccount account. The srun command launches 32 tasks of myApp across the four nodes.

Now submit the job:

$ sbatch myBatch.cmd Submitted batch job 150104

See the job pending in the queue:

$ squeue JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 150104 pdebug myBatch. me PD 0:00 4 (Priority)

After the job runs, the output will be found in a file named after the job id: slurm-150104.out See only your jobs in the queue

$ squeue -u

See all the jobs in the queue

$ squeue

List queued jobs displaying the fields that are important to you

$ man squeue

and scroll to the output format specifiers listed under the -o option. Then create an environment variable that contains the fields you like to see.

For example, for bash:

$ export SQUEUE_FORMAT="%.7i %.8u %.8a %.9P %.5D %.2t %.19S %.8M %.10l %.10Q"

and for csh:

$ setenv SQUEUE_FORMAT "%.7i %.8u %.8a %.9P %.5D %.2t %.19S %.8M %.10l %.10Q"

Now run squeue:

$ squeue JOBID USER ACCOUNT PARTITION NODES ST START_TIME TIME TIMELIMIT PRIORITY 147445 carol guests pbatch 32 PD N/A 0:00 5:00:00 1005641 147446 henry guests pbatch 32 PD N/A 0:00 5:00:00 1004454 147447 sue guests pbatch 32 PD N/A 0:00 5:00:00 1004296

Display the pending jobs ordered by decreasing priority

$ squeue -t pd -S-p

Display details about a specific job

$ scontrol show job

Display the job script for one of your jobs

$ scontrol -dd show job

Show all the jobs you have run today

$ sacct -X JobID JobName Partition Account AllocCPUS State ExitCode

150096 sh pbatch lc 72 COMPLETED 0:0 150104 myBatch.c+ pdebug lc 288 COMPLETED 0:0 150106 myBatch.c+ pdebug lc 288 COMPLETED 0:0 150109 myBatch.c+ pdebug lc 288 COMPLETED 0:0 150112 libyogrtt+ pdebug lc 72 COMPLETED 0:0 150121 myBatch.c+ pdebug lc 288 COMPLETED 0:0

Show all the job steps that ran within a specific job

$ sacct -j 150065 JobID JobName Partition Account AllocCPUS State ExitCode

150065 myBatch.c+ pdebug lc 72 COMPLETED 0:0 150065.batch batch lc 1 COMPLETED 0:0 150065.0 my_mpi lc 2 COMPLETED 0:0 150065.1 my_mpi lc 2 COMPLETED 0:0 150065.2 my_mpi lc 2 COMPLETED 0:0 150065.3 my_mpi lc 2 COMPLETED 0:0 150065.4 my_mpi lc 2 COMPLETED 0:0

List the charge accounts you are permitted to use (sbatch/salloc/srun -A option)

$ sshare

This command also shows the historical usage your jobs have accrued to each charge account. The fair-share factor is also displayed for you for each of your accounts. This factor will be used in calculating the priority for your current pending jobs and any job you submit. For details, see Multi-factor Priority and Fair-Tree. Display the factors contributing to each pending job's assigned priority

$ sprio -l JOBID USER PRIORITY AGE FAIRSHARE JOBSIZE PARTITION QOS NICE 143104 harriet 1293802 28234 265568 0 0 1000000 0 143105 sam 1293802 28234 265568 0 0 1000000 0

Cancel a job, whether it is pending in the queue or running

$ scancel <job_ID>

Send a signal to a running job

For example, send SIGUSR1:

$ scancel -s USR1 <job_ID>

Display the queues available

$ sinfo

Display details about all the queues (aka partitions)

$ scontrol show partition