How to run a job on a Cluster?
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1 How to run a job on a Cluster? Cluster Training Workshop Dr Samuel Kortas Computational Scientist KAUST Supercomputing Laboratory Samuel.kortas@kaust.edu.sa 17 October 2017
2 Outline 1. Resources available 2. Why Scheduling? 3. How to specify, submit, and monitor a job 4. SLURM interesting or advanced features comprehensive examples in the application talk!
3 1. Resources available 2. Why Scheduling? Outline 3. How to specify, submit, and monitor a job 4. SLURM interesting or advanced features comprehensive examples in the application talk!
4 Cluster's Resources Available resources Intel Nodes GPU Nodes AMD Nodes
5 Cluster's Resources Tightly connected nodes Different CPU Generation Intel Nodes GPU Nodes AMD Nodes Large memory Nodes Local disk space Different Generation
6 Outline 1. Resources available 2. Why Scheduling? 3. How to specify, submit, and monitor a job 4. SLURM interesting or advanced features comprehensive examples in the application talk!
7 Why scheduling?...to optimize shared resource use. Available Resources 5 nodes T I M E 20 min CFD Workflow node job Deep Learning Workflow 1 GPU job Biology Workflow s 1 core job On Shaheen 2 and Dragon : SLURM Same principle with PBS, LoadLeveler, Sun GridEngine.
8 Why scheduling?...to optimize shared resource use. Available Resources 5 nodes T I M E 20 min CFD Workflow node job Deep Learning Workflow 1 GPU job Biology Workflow s 1 core job On Shaheen 2 and Dragon : SLURM Same principle with PBS, LoadLeveler, Sun GridEngine.
9 Why scheduling?...to optimize shared resource use. Available Resources Current > time 20 min The scheduling plan is recomputed every n minutes. T I M E
10 Why scheduling?...to optimize shared resource use. Available Resources Current > time 20 min Your > Job 60 min T I M E
11 Why scheduling?...to optimize shared resource use. Available Resources Current > time 20 min Your > Job 60 min T I M E
12 Why scheduling?...to optimize shared resource use. Available Resources Current > time 20 min Your > Actual Job 15 min T I M E
13 Why scheduling?...to optimize shared resource use. Available Resources Current > time 20 min Your > Actual Job 15 min T I M E A better estimation of your real need will schedule your job earlier on the cluster duration time, type of nodes, memory, type of disks required make a change!
14 Outline 1. Resources available 2. Why Scheduling? 3. How to specify, submit, and monitor a job 4. SLURM interesting or advanced features comprehensive examples in the application talk!
15 Cluster as a whole environment... Intel Nodes GPU Nodes AMD Nodes /home CPUs, GPUs, Storage, Network, Compilers, Applications...
16 You need to be there! Submit from here Intel Nodes GPU Nodes AMD Nodes /home
17 First, log in! ssh -X ssh -X Intel Nodes GPU Nodes AMD Nodes ssh -X
18 Each type of login node has di?erent environment ssh -X Intel, GNU compilers, Applications running on Intel Former /legacy stack Noor, SMC ssh -X Nvidia tools, GPU compilers, CUDA, application GPU tuned Intel Nodes GPU Nodes AMD Nodes ssh -X AMD, GNU compilers, Applications running on AMD Former /cbrc stack Dragon
19 ...but AMD should be compatible with Intel ssh -X Intel, GNU compilers, Applications running on Intel and AMD /legacy and /cbrc stack ssh -X Nvidia tools, GPU compilers, CUDA, application GPU tuned Intel Nodes GPU Nodes AMD Nodes ssh -X AMD, GNU compilers, Applications running on AMD and Intel /cbrc and /legacy stack
20 An enhanced choice of Resource...and some compiling subtilities. 1. You can submit any kind of job from any login node (see constraint option) 2. When compiling, chose the right kind of node Compiling on ilogin or alogin will NEVER run eeciently on a GPU. 3. SpeciFc tuning for AMD or Intel may beneft some codes. Remember to have them scheduled on the good target.
21 Steps to run a job 1. Listing available resource : sinfo 2. Acquiring resources asking SLURM to make available what you need : salloc, batch 3. Waiting for the resource to be scheduled : squeue, and monitor your job 4. Gathering information on resource: scontrol 5. Using the resource : srun 6. Releasing the resource : scancel 7. Tracking my resource use : sacct
22 Listing Resources : sinfo Job limit in size and duration Current status & names of the nodes Among all the nodes 23 are available, 466 are allocated 60 are drained For now, There is only one unique partition : batch, with a 5 day limit
23 How to select resources? Features, tag, characterizing each node
24 Some available feature... Previously: dragon, vcc, kcc, snapdragon Target: Intel, amd, gpu, P100,tesla_k40m, cpu_amd_6376, cpu_intel_e5_2670_v2 Memory: largemem Local disk space: local_[200g,400g,500g,1t,2t,7t] Other(?): zram, sata, blade, ibid304 To select the desired resource: srun/salloc/sbatch --constraint=intel,local_200g + --memory=xxxx --cpus=yyy --gres=xxx.
25 3 ways to use available Resources test develop run srun salloc sbatch One elementary task Interactive work, several tasks Batch mode, job file Like launching a single job on your workstation but waiting for the resource Booking some resource and work on it immediately Queue a larger job, wait for result
26 Running a simple task srun Waiting for the resource to be given once granted, job is starting If no output <filename>, output sent to current terminal. Resource are immediately released after job completion or expiration of duration requested.
27 Acquiring interactive resources : salloc Waiting for the resource to be given Now you can run! $ prog1.exe will run on the login node $ srun ntasks. prog2.exe will run on the given nodes. Release resources via exit or CTRL-D or...
28 Queueing a request sbatch sbatch job.sh Sequential runs Only execute on the Frst node given concurrent runs on all the nodes File job.sh #!/bin/bash #SBATCH --job-name=my_job #SBATCH --output=out.txt #SBATCH --error=err.txt #SBATCH nodes=12 #SBATCH --ntasks-per-node=20 #SBATCH --time=hh:mm:ss (or dd-hh:mm) #SBATCH --constraint=intel,. #SBATCH --exclusive echo helllo cd WORKING_DIR srun n 240 a.out.
29 Sharing or not sharing? sbatch/salloc/srun... --exclusive job.sh You will be the only one using the nodes You may wait more to have them Performance will be better and reproducible?? sbatch/salloc/srun... job.sh You may have to share your node with others You will wait less Performance may vary, depending on others...
30 Monitoring resources : squeue squeue : lists all jobs queued (can be long ) squeue u <my_login> (only my jobs, much faster) squeue l (queue displayed in more detailed format) squeue --start (display expected starting time) squeue -i60 -u <my_login> reports currently active jobs every 60 seconds
31 Monitoring resources : scontrol show job scontrol show job jobid
32 Managing already allocated resources scancel <job_id> kills a given job scancel --user=<login> --state=pending kills all pending jobs of the user <login> scancel --name=<job_name> kills all jobs of the user <login> with a given name sacct Report information about previous jobs: exit code, requested resources, steps...
33 Job.sh Slurm Control parameters Script Command Slurm counts in threads: 1 Slurm CPU is a Thread
34 Job.sh Name of the job in the queue Output file name for the job Error file name for the job Requested number of tasks Requested ellapse time constraints Slurm counts in threads: 1 Slurm CPU is a Thread
35 Job.sh Slurm counts in threads: 1 Slurm CPU is a Thread
36 Job.out dbn504-r Slurm counts in threads: 1 Slurm CPU is a Thread
37 Job.err
38 Outline 1. Resources available 2. Why Scheduling? 3. How to specify, submit, and monitor a job 4. SLURM interesting or advanced features comprehensive examples in the application talk!
39 SLURM s interesting features Job arrays Job dependency on job state transition Interactive job with salloc (no direct ssh!!!) Fine tuning of process on resources Reservation (with the help of sysadmin) Flexible scheduling : the job will run with the set of parameters with which it can start soonest sbatch nodes= sbatch time=10:00:00 time-min=4:00:00...
40 Environment Variables
41 Launching thousands of jobs Submit and manage collection of similar jobs easily To submit 50,000 element job array: sbatch array= N1 -i my_in_%a -o my_out_%a job.sh %a in Fle name mapped to array task ID ( ) Default standard output: slurm-<job_id>_<task_id>.out Only supported for batch jobs
42 squeue and scancel commands plus some scontrol options can operate on entire job array or select task IDs squeue -r option prints each task ID separately
43 That s all Folks! Questions? samuel.kortas@kaust.edu.sa help@cluster.kaust.edu.sa
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