uppmax introduction - github pages
TRANSCRIPT
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Objectives
What is UPPMAX what it provides
Projects at UPPMAX
How to access UPPMAX
Jobs and queuing systems
How to use the resources of UPPMAX
How to use the resources of UPPMAX in a good way!Efficiency!!!
![Page 4: UPPMAX Introduction - GitHub Pages](https://reader034.vdocuments.site/reader034/viewer/2022042723/6267d955d20a1a658c447433/html5/thumbnails/4.jpg)
Objectives
What is UPPMAX what it provides
Projects at UPPMAX
How to access UPPMAX
Jobs and queuing systems
How to use the resources of UPPMAX
How to use the resources of UPPMAX in a good way!Efficiency!!!
![Page 5: UPPMAX Introduction - GitHub Pages](https://reader034.vdocuments.site/reader034/viewer/2022042723/6267d955d20a1a658c447433/html5/thumbnails/5.jpg)
UPPMAX
Uppsala Multidisciplinary Center for Advanced Computational Science
http://www.uppmax.uu.se
computer clusters:● Rackham, 334(600) computers à 20 cores (128GB RAM)● Bianca, 200 nodes à 16 cores (128GB RAM)
(Milou, 208 computers à 16 cores (128GB RAM) 17 with 256, 17 with 512)■
~12 PB fast parallel storage
Bioinformatics software
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UPPMAX
The basic structure of supercomputer cluster
Login nodes
node = computer
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UPPMAX
The basic structure of supercomputer
Login nodes
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UPPMAX
The basic structure of supercomputer
Login nodes
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UPPMAX
UPPMAX provides
Compute and Storage
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Objectives
What is UPPMAX what it provides
Projects at UPPMAX
How to access UPPMAX
Jobs and queuing systems
How to use the resources of UPPMAX
How to use the resources of UPPMAX in a good way!Efficiency!!!
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Projects
UPPMAX provides its resources via
projects
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Projects
your project
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Projects
Resources:
compute storage(core-hours/month) (GB/TB)
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Projects
two separate projects: SNIC project:
cluster Rackham2000 core-hours/month128 GB
Uppstore project:storage system CREX
1 - 100 TB
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Projects
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Projects
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Objectives
What is UPPMAX what it provides
Projects at UPPMAX
How to access UPPMAX
Jobs and queuing systems
How to use the resources of UPPMAX
How to use the resources of UPPMAX in a good way!Efficiency!!!
![Page 18: UPPMAX Introduction - GitHub Pages](https://reader034.vdocuments.site/reader034/viewer/2022042723/6267d955d20a1a658c447433/html5/thumbnails/18.jpg)
How to access UPPMAX
SSH to a cluster
ssh -Y your_username@cluster_name.uppmax.uu.se
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How to access UPPMAX
SSH to Rackham
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SSH
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SSH
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How to use UPPMAX
Login nodes use them to access UPPMAXnever use them to run jobsdon’t even use them to do “quick stuff”
Calculation nodesdo your work here - testing and running
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How to use UPPMAX
Calculation nodesnot accessible directlySLURM (queueing system) gives you access
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Objectives
What is UPPMAX what it provides
Projects at UPPMAX
How to access UPPMAX
Jobs and queuing systems
How to use the resources of UPPMAX
How to use the resources of UPPMAX in a good way!Efficiency!!!
![Page 25: UPPMAX Introduction - GitHub Pages](https://reader034.vdocuments.site/reader034/viewer/2022042723/6267d955d20a1a658c447433/html5/thumbnails/25.jpg)
Job
Job (computing)From Wikipedia, the free encyclopedia
For other uses, see Job (Unix) and Job stream.
In computing, a job is a unit of work or unit of execution (that performs said work). A component of a job (as a unit of work) is called a task or a step (if sequential, as in a
job stream). As a unit of execution, a job may be concretely identified with a single process, which may in turn have subprocesses (child processes; the process
corresponding to the job being the parent process) which perform the tasks or steps that comprise the work of the job; or with a process group; or with an abstract
reference to a process or process group, as in Unix job control.
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Job
Read/open files
Do something with the data
Print/save output
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Job
Read/open files
Do something with the data
Print/save output
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Job
Standard way of running jobs
job
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Parallel computing
Job
jobs
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Queue System
More users than nodesNeed for a queue
nodes - hundredsusers - thousands
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Queue System
More users than nodesNeed for a queue
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Queue System
More users than nodesNeed for a queue
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Queue System
More users than nodesNeed for a queue
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SLURM
queue systemworkload managerjob queuebatch queuejob scheduler
SLURM (Simple Linux Utility for Resource Management)free and open source
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Objectives
What is UPPMAX what it provides
Projects at UPPMAX
How to access UPPMAX
Jobs and queuing systems
How to use the resources of UPPMAX
How to use the resources of UPPMAX in a good way!Efficiency!!!
![Page 36: UPPMAX Introduction - GitHub Pages](https://reader034.vdocuments.site/reader034/viewer/2022042723/6267d955d20a1a658c447433/html5/thumbnails/36.jpg)
SLURM
1) Ask for resource and run jobs manuallymainly for testing and small jobs
2)Write a script and submit it to SLURMdo the real job
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SLURM
1) Ask for resource and run jobs manually
submit a request for resources
ssh to a calculation node
run programs
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SLURM
1) Ask for resource and run jobs manuallysubmit a request for resources
salloc -A b2015245 -p core -n 1 -t 00:05:00
salloc - commandmandatory job parameters:-A - project ID (who “pays”)-p - node or core (the type of resource)-n - number of nodes/cores-t - time
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SLURM-A project ID
you have to be a member
-p 1 node = 16 cores1 hour walltime = 16 core-hours
-n number of cores (default value = 1)-N number of nodes
-t format - hh:mm:ssdefault value= 7-00:00:00
jobs killed when time limit reaches - always overestimate ~ 50%
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SLURM
Information about your jobs squeue -u <user>
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SLURM
SSH to a calculation node (from a login node)
ssh -Y <node_name>
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SLURM
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SLURM
You can run programs now!
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SLURM
2)Write a script and submit it to SLURM
put all commands in a text file - script
tell SLURM to run the script (use the same job parameters)
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SLURM
2)Write a script and submit it to SLURM
put all commands in a text file - script
job parameters
tasks to be done
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SLURM
2)Write a script and submit it to SLURM
put all commands in a text file - script
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2)Write a script and submit it to SLURM
tell SLURM to run the script (use the same job parameters)
sbatch test.sbatch
SLURM
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2)Write a script and submit it to SLURM
tell SLURM to run the script (use the same job parameters)
sbatch test.sbatch
sbatch - commandtest.sbatch - name of the script file
SLURM
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2)Write a script and submit it to SLURM
tell SLURM to run the script (use the same job parameters)
sbatch -A b2015245 -p core -n 1 -t 00:05:00 test.sbatch
SLURM
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SLURM OutputPrints to a file instead of terminal
slurm-<job id>.out
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Squeue
Shows information about your jobs squeue -u <user>
jobinfo -u <user>
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Queue System
SLURM user guidego to http://www.uppmax.uu.se/click Support (left-hand side menu)click User Guidesclick Slurm user guide
or just google “uppmax slurm user guide”
link: http://www.uppmax.uu.se/support/user-guides/slurm-user-guide/
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UPPMAX Software
100+ programs installed
Managed by a 'module system'Installed, but hiddenManually loaded before use
■
module avail - Lists all available modulesmodule load <module name> - Loads the modulemodule unload <module name> - Unloads the modulemodule list - Lists loaded modulesmodule spider <word> - Searches all modules after 'word'
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UPPMAX Commands
uquota
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UPPMAX Commands
projinfo
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UPPMAX Commands
projplot -A <proj-id> (-h for more options)
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Objectives
What is UPPMAX what it provides
Projects at UPPMAX
How to access UPPMAX
Jobs and queuing systems
How to use the resources of UPPMAX
How to use the resources of UPPMAX in a good way!Efficiency!!!
![Page 59: UPPMAX Introduction - GitHub Pages](https://reader034.vdocuments.site/reader034/viewer/2022042723/6267d955d20a1a658c447433/html5/thumbnails/59.jpg)
UPPMAX Commands
Plot efficiencyjobstats -p -A <projid>
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UPPMAX
SummaryAll jobs are run on nodes through queue systemA job script usually consists of
Job settings (-A, -p, -n, -t)Modules to be loadedBash code to perform actions
Run a program, or multiple programs
More info on UPPMAX homepagehttp://www.uppmax.uu.se/milou-user-guide