Abel for beginners. Katerina Michalickova The Research Computing Services Group SUF/USIT October 23, 2012

Transcription

1 Abel for beginners Katerina Michalickova The Research Computing Services Group SUF/USIT October 23, 2012

2 Topics The Research Computing Services group Abel Getting access to Abel Windows and Unix Logging in Joining the queue Simple Perl script Shell script Running a simple job Running simple jobs in parallel

3 The Research Computing Services Gruppe for vitenskapelig databehandling The RCS group provides access to IT resources and high performance computing to researches at UiO and to NOTUR users Part of USIT Write to us:

4 The Research Computing Services operation of Abel - a computer cluster Abel user support data storage secure data storage statistical support qualitative methods advanced user support (one on one work with scientists) visualization Bioportal portal to life sciences applications on Abel

5 Abel Large computer cluster Enables parallel computing Science presents multiple problems of parallel nature Sequence database searches Genome assembly and annotation Data sampling and simulations

6 Many computers vs. a useful computer cluster Hardware nodes connected by high-speed network all nodes have an access to a common file system (Fraunhofer global file system) Software Operating system (Rocks flavor of Linux) enables identical mass installations Queuing system enables timely execution of many concurrent processes Read about Abel

7 Nodes Cores Total memory - ~40 TB Total storage - ~400TB # 96 at top500.org Abel in numbers

8 Accessing Abel If you are working or studying at UiO, you can have an Abel account directly from us. If you are Norwegian scientist, you can apply for more resources on Abel through NOTUR Write to us for information: Read about getting access:

9 Logg into Abel If on Windows, download Putty for connecting WinSCP for copying files On Unix systems, open a terminal and type: ssh Y abel.uio.no

10 Logging in - Putty

11 X11 forwarding Enable new windows

12 Logging into Abel Login as: your_uio_user_name Password: your_uio_password

13 You are logged in.

14 File upload/download - WinSCP

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16 File upload/download on command line Unix users can use secure copy or rsync commands Copy myfile.txt from the current directory on your machine to your home area on Abel: scp myfile.txt For large files, use rsync command: rsync -z myfile.tar

17 Software on Abel Available on Abel: Software on Abel is organized in modules. List all software (and version) organized in modules: module avail Load software from a module: module load module_name If you cannot find what you looking for: ask us

18 Your own software You can copy or install own software in your home area Third party software Scripts (Perl, Shell, Php..) Source code (C, Java, Fortran..)

19 Running a simple script Perl script that tells time (and date):

20 Running a script and file permissions Execute the script: perl telltime.pl -rw-r--r-- 1 katerim users 132 Apr 30 15:19 telltime.pl Make script executable: chmod u+x telltime.pl -rwxr--r-- 1 katerim users 132 Apr 30 15:19 telltime.pl Execute the script./myscript.pl

21 Executing a simple script (command line)

22 Executing on Abel Submit a job to the queuing system Software that executes jobs on available resources on the cluster (and much more) SLURM - Simple Linux Utility for Resource Management Communicate with the queuing system using a shell script Read tutorial:

23 Shell scripting Shell script - series of Unix commands written in a plain text file

24 Executing a shell script

25 Project/Account Each user belongs to a project on Abel Each project has set resources Learn about your project(s): Use: projects

26 Job script Your program joins the queue via a job script Job script - shell script with keywords read by the queuing system #SBATCH --xxxx Compulsory keywords: #SBATCH --account #SBATCH --time #SBATCH --mem-per-cpu Setting up a job environment source /cluster/bin/jobsetup For full list of options see:

27 Minimal job script

28 Submitting a job - sbatch Job ID

29 Checking a job - squeue

30 Checking the result of a job

31 Cancelling a job Cancel a single job: scancel job_id Cancel all your jobs: scancel --user=your_uio_user_name

32 Interactive use of Abel - qlogin Send request for a resource Join the queue Work on command line when resource becomes available Example - book one node (or 16 cores) on Abel for your interactive use for 1 hour: qlogin --account=your_project --ntasks-per-node=16 --time=01:00:00 Run source /cluster/bin/jobsetup after receiving allocation For more info, see:

33 Interactive use of Abel - qlogin

34 Strength of cluster computing Large problems (or parts of) can be divided into smaller tasks and executed in parallel Types of parallel applications: Divide input data and execute your program on all subsets (array run) Execute parts of your program in parallel (MPI or OpenMP programming)

35 Executing one program multiple times To run many instances of the same job, use an arrayrun command Special concern organizing input and output files Adapting our example: no input file one output file currenttime.txt

36 TASK_ID variable Variable - a symbolic name associated with a value (e.g. time in our perl script) TASK_ID is an environment variable, it can be accessed by all scripts during the execution of arrayrun 1 st run TASK_ID = 1 2 nd run TASK_ID = 2 N th run TASK_ID = N TASK_ID can be used to organize input and output files Accesing the value of the TASK_ID variable: In shell script : $TASK_ID In perl script: ENV{TASK_ID}

37 Adapted submit script Add TASK_ID to the name of the output file

38 Changes to your Perl script Print out TASK_ID variable

39 How to submit the arrayrun command Arrayrun is a job that starts instances of telltime jobs Arrayrun has to have its own job script that contains the compulsory sbatch values: #SBATCH --account #SBATCH --time #SBATCH --mem-per-cpu source /cluster/bin/jobsetup

40 Arrayrun script

41 Submitting and checking an arrayrun job

42 Cancelling an arrayrun scancel

43 Looking at the results

44 Looking at the results

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46 Troubleshooting Every job produces a log file: slurm-jobid.out Check this file for error messages If you need help, list jobid or paste the slurm file into your Read tutorial:

47 Notur apply for more resources on Abel The Norwegian metacenter for computational science Large part of our funding is provided though Notur You can apply for: Abel compute hours Data storage Advanced user support

48 Thank you.

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50 Basic Unix commands Find an online tutorial or get a book (e.g. O Reilly Unix in a nutshell or Unix for dummies) Following slides illustrate the basics..

51 Finding out where you are: pwd

52 Finding out current directory content: ls

53 Making a new directory: mkdir

54 Moving a file: mv

55 Deleting a file: rm

56 Copying a file: cp

57 Changing a directory: cd

58 Looking at file contents: more (less)

59 Editing a file: emacs

60 Inside emacs

61 Emacs Use emacs to create or edit a text file Move around using the arrow keys Save file: ctrl-x ctrl-s Quit emacs: ctrl-x ctrl-c Search: ctrl-s your_search_string For more functionality, read

62 Basic Unix commands Finding out where we are: pwd Looking at the directory contents: ls -l Make a directory mydir: mkdir mydir Move the file first.txt to mydir: mv first.txt mydir Delete the file first.txt: rm mydir/first.txt Copy the file second.txt to mydir: cp second.txt mydir Change current directory to mydir: cd mydir Edit file second.txt: emacs second.txt Looking at contents of a file: more second.txt Log out: exit (or universal ctrl-d) To read about a command: man command_name