Getting started with Euler Samuel Fux High Performance Computing Group, Scientific IT Services, ETH Zurich ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 1 Outlook . Introduction . Accessing the cluster . Data management . Environment/LMOD modules . Using the batch system . Applications . Getting help ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 2 Outlook . Introduction . Accessing the cluster . Data management . Environment/LMOD modules . Using the batch system . Applications . Getting help ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 3 Intro > What is EULER? . EULER stands for . Erweiterbarer, Umweltfreundlicher, Leistungsfähiger ETH Rechner . It is the 5th central (shared) cluster of ETH . 1999–2007 Asgard ➔ decommissioned . 2004–2008 Hreidar ➔ integrated into Brutus . 2005–2008 Gonzales ➔ integrated into Brutus . 2007–2016 Brutus . 2014–2020+ Euler . It benefits from the 15 years of experience gained with those previous large clusters ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 4 Intro > Shareholder model . Like its predecessors, Euler has been financed (for the most part) by its users . So far, over 100 (!) research groups from almost all departments of ETH have invested in Euler . These so-called “shareholders” receive a share of the cluster’s resources (processors, memory, storage) proportional to their investment . The small share of Euler financed by IT Services is open to all members of ETH . The only requirement is a valid NETHZ account . These “guest users” can use limited resources . If someone needs more computing power, he/she can invest in the cluster and become a shareholder at any time ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 5 Intro > Euler shares by departments Other BIOL 8% 5% BSSE PSI 6% 4% USYS 20% CHAB 27% PHYS 5% ERDW MATH 3% MAVT MATL 4% 14% 4% ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 6 Intro > Performance growth 4500 ] F 4000 T [ ) Leonhard GPU n o i 3500 s i Leonhard CPU c e r 3000 p e Euler CPU l b u 2500 o d ( e 2000 c n a m 1500 r o f r e 1000 p k a e 500 P 0 2014 2015 2016 2017 2018 2019 2020 ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 7 Intro > Euler I (right) & II (left) © 2015 Byrde 2015 © Olivier ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 8 Intro > Euler VI ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 9 Intro > Linux terminal > Bash . Bash is a powerful scripting language, which can directly be used in a Linux terminal and is often combined with Linux commands [sfux@eu-login-01-ng ~]$ for i in *; do if [ -d $i ]; then echo $i; cd $i; du -hs; cd ..; fi; done bin 52K . lib64 36K . scripts 192K . test 324M . testrun 693M . [sfux@eu-login-01-ng ~]$ ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 10 Intro > Linux terminal > Basic commands Command Explanation ls Directory listing cd Change directory pwd Print working directory echo Print to standard output less, cat, more Display content of file to standard output cp, mv Copy/move a file or directory rm Remove a file or directory mkdir Create a directory vi, nano, emacs Command line text editor man Show manual for a command in terminal grep Search for a pattern in a string or file ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 11 Intro > Linux terminal > Basic commands Command Explanation exit Terminate and exit the current terminal sort Sort a file line by line sed String manipulation awk Powerful programming language find Search for files du Show disk space used in a directory tar Create a tar archive with files/directories gzip Compress files/directories top Dynamic real time view of processes in a computer chmod Change permissions of file/directory https://scicomp.ethz.ch/wiki/Linux_command_line ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 12 Intro > Linux permissions . In Linux, access to files and directories is handled via permissions . Read permission (r) - grants permission to read a file or directory . Write permission (w) - grants permission to write a file or directory . Execute permission (x) - grants permission to execute a file or directory . There are 3 permission groups . User (u) - permissions for the user account that owns the file . Group (g) - permissions for the user group that owns the file . Other (o) - permissions for all other users exept the user account and the user group [sfux@eu-login-01-ng ~]$ ls -ltr gurobi.log -rw-r--r-- 1 sfux T0000 330 May 18 13:34 gurobi.log ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 13 Intro > Linux permissions . Permissions can be changed with the chmod command . String representation: chmod ugo+rx filename . Number representation: chmod 750 filename https://scicomp.ethz.ch/wiki/Linux_permissions ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 14 Intro > Paths on Linux . Paths on Windows: C:\Users\Samfux\test . Use backslashes . File and directory names are not case sensitive . Different drives (C:, D:, etc.) . Paths on Linux: /cluster/home/sfux/test . Use forward slashes . Everything is case sensitive . Everything is under the root file system (/), no drives ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 15 Intro > Edit a text file with vi . Vim is a command line text editor that can be started with the command vi. This text editor is useful to edit input files and write scripts directly on the cluster without copying forth and back files . 2 modes (insert mode, command mode) . Type i to switch from command mode to insert mode . Type esc to switch from insert mode to command mode . Insert mode: You can insert text into a text document . Command mode: You can type commands after typing : (colon) and execute it with the enter key . To save a file, type :w . To close a file, type :q . To save and close a file, type :wq https://www.tutorialspoint.com/unix/unix-vi-editor.htm ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 16 Intro > First hands on-exercise in a local shell with MobaXterm . Start MobaXterm on your local computer and click on the button "Local shell". This will open a shell on your local Exercises: 1. Print the current working directory 2. Create a new directory called test 3. Change to the new directory 4. Create a text text file my_first_bash_script.sh with vi with the following content #!/bin/bash echo "Good morning $USER" hostname pwd 5. Change the permission of the file to 755 6. Do a directory listing of the test directory 7. Execute the file that you have created with the command ./my_first_bash_script.sh 8. Use the command grep to search for the word morning in my_first_bash_script.sh file 9. Sort the lines in the text file alphabetically 10. Exit the shell ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 17 Outlook . Introduction . Accessing the cluster . Data management . Environment/LMOD modules . Using the batch system . Applications . Getting help ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 18 Access > Who can use Euler . The only requirement to use Euler is a valid NETHZ account . Members of ETH . Immediate access; no need to fill out an account request form . Use NETHZ credentials to login (via ssh) to [email protected] . New users must accept the cluster’s usage rules upon first login . Euler uses NETHZ database to identify shareholders and guest users, and sets privileges and priorities automatically . External collaborators . Members of other institutions who have a collaboration with a research group at ETH may use Euler for the purpose of said collaboration . Their counterpart (“sponsor”) at ETH must create a NETHZ guest account for them, including e-mail address and VPN service . Once this is done, they can access Euler like members of ETH ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 19 Access > Legal compliance . Euler is subject to ETH’s acceptable use policy for IT resources (Benutzungs- ordnung für Telematik, BOT), in particular: . Euler accounts are strictly personal . Do not share your account (password, ssh keys) with anyone . Do not use someone else’s account, even if they say it’s OK . If you suspect that someone used your account, change your password and contact cluster- [email protected] . Consequences . In case of abuse, the offender’s account may be blocked temporarily or closed . System administrators are obliged by law to investigate abusive or illegal activities and report them to the relevant authorities ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 20 Access > Security . Firewall . Euler access is only possible via secure protocols (ssh, sftp, scp, rsync) . Euler is accessible only inside ETH ➔ use VPN to login from outside . Euler cannot access computers outside ETH ➔ use ETH’s proxy service (http://proxy.ethz.ch:3128) to access external servers . Suspicious clients that repeatedly fail to login are automatically blacklisted . Password . Your account will be temporarily blocked if you enter a wrong password too many times . You can change your NETHZ password at https://password.ethz.ch . Contact your local IT Support Group or the Service Desk if you need help with your NETHZ account (blocked account, forgotten password, etc.) ETH Zürich | Scientific IT Services | HPC Group Samuel Fux | 19.02.2020 | 21 Access > SSH connection . Unix, including Linux and macOS .