Introduction to the ITA computer system

Transcription

1 Introduction to the ITA computer system Tiago M. D. Pereira Slides: Institute of Theoretical Astrophysics

2 Today s lecture in a nutshell 1. Network and users, connecting 2. Compute resources 3. The module system 4. Parallel computing

3 1. Network and Users, Connecting Network accounts used for all users, central home directory Disk quota in MN home directories ($ quota): files, grace, etc. No disk quota for ITA home directories (but don t abuse it...) Access from outside UiO is blocked to all but a few computers: use login.astro.uio.no or login.uio.no to connect

4 Connecting via ssh ssh: secure shell, provides encrypted terminal connection ssh with many options possible Use scp for copying files: scp Password authentication is default. But much easier with keys!

5 ssh continued: keys Alice Bob's Public Key Combine keys 751A696C 24D97009 Alice's Private Key Bob Alice and Bob's shared secret Alice's Public Key Bob's Private Key Combine keys 751A696C 24D97009 Alice and Bob's shared secret

6 ssh continued: keys ssh-keygen In your computer: ~/.ssh/id_rsa.pub ~/.ssh/id_rsa At UiO computers: ~/.ssh/authorized_keys

7 ssh continued: keys In your Unix computer: $ ssh-keygen -t rsa -b 4096 [Choose passphrase, could be empty] Linux only: $ ssh-copy-id -i ~/.ssh/id_rsa.pub user@login.astro.uio.no MacOS or Linux: $ scp ~/.ssh/id_rsa.pub user@login.astro.uio.no:.ssh/mykey $ ssh user@login.astro.uio.no [user@tsih2 ~]$ cd.ssh [user@tsih2 ~]$ cat mykey >> authorized_keys

8 ssh continued: keys For Windows users, recommended approach is to use PuTTY Download: Set up keys:

9 ssh continued: keys So far we ve used a key in your computer to connect to ITA It is also to use keys in ITA s computers to connect to other ITA So you can ssh internally without having to enter your password! $ ssh user@login.astro.uio.no [user@tsih2 ~]$ ssh-keygen -t rsa -b 4096 (...) [user@tsih2 ~]$ ssh-copy-id -i ~/.ssh/id_rsa.pub tsih2

10 ssh continued: proxying Access via login.astro.uio.no, then ssh to your computer Possible to do this automatically via ~/.ssh/config Host beehive* owl* euclid* ForwardX11 yes ProxyCommand ssh -XY -W %h:%p ~]$ chmod 600 ~/.ssh/config In general, you can do several ssh proxies or hops (not needed at ITA)

11 ssh exercises Exercise: connect via ssh to login.astro.uio.no and find out the location of your home directory. Is it at ITA or at MN? Exercise: generate ssh keys in your computer and use them to connect to login.astro.uio.no without entering your password Exercise: set up ssh proxying so you can connect to beehive4.uio.no via login.astro.uio.no

12 ssh continued: X11 forwarding By default ssh is only text terminal. But possible to show graphical programs in your laptop/computer screen (X11 forwarding) $ ssh -XY user@tsih.uio.no [user@tsih ~]$ xeyes X11 forwarding is slow because bitstream sent uncompressed, not usually good enough for movies / dynamic GUIs vnc is a much better option if you want to have remote graphical control of a machine

13 ssh exercises (2) Exercise: connect to login.astro.uio.no and start up xeyes (a graphical programme). Make sure it opens up in your screen! Exercise: from login.astro.uio.no connect to your workstation and start another graphical programme (a browser?).

14 ssh continued: vnc vnc can be used to control the full desktop of a remote computer (can only use it for your own desktop) It is efficient because compression is used Different programmes in different operative systems MacOS: Finder > Go > Connect to server... vnc://hostname.uio.no In general, this will not work out of the box because direct traffic is blocked (see ssh): need ssh tunnel

15 ssh continued: tunnelling Ssh tunnelling is a way to connect to a port in a remote machine using ssh and remaping to a local port Can be used in many different ways and scenarios For vnc server running at hostname.uio.no: $ ssh -fn -L 5091:localhost:5900 hostname.uio.no No terminal Local port Remote port Ideally, with ssh proxy

16 ssh continued: tunnelling

17 ssh continued: tunnelling For jupyter notebook running at hostname.uio.no $ ssh user@hostname.uio.no [user@hostname] $ jupyter notebook --no-browser (...) In a different terminal set up ssh tunnel: $ ssh -fn -L 9999:localhost:8888 hostname.uio.no Finally, run jupyter from your browser: Recommended with %matplotlib inline backend

18 ssh exercises (3) Exercise: connect to beehive4 and start jupyter (may need to $ module load python first). Now set up an ssh tunnel so you can connect to jupyter via your own browser

19 Shell profile scripts When you open up a terminal (or ssh) into Unix machines, initialisation scripts load useful things into the environment Tcsh: /etc/csh.cshrc /etc/csh.login (login shells only) ~/.tcshrc ~/.cshrc (if.tcshrc is not found) ~/.history ~/.login (login shells only) ~/.cshdirs Bash login shell: /etc/profile ~/.bash_profile ~/.bash_login (if no.bash_profile) Bash non-login shell: /etc/bashrc ~/.bashrc

20 Login vs non-login shells Do you have a login or non-login shell: shopt (look for login_shell) Login shells are run when you first connect to a machine Non-login shells are run when you run a new shell from the shell or when you run a non-interactive ssh command (e.g scp, tunnelling) All shells in MacOS are login shells Different profiles can separate initialisation scripts for both scenarios All tcsh/csh scripts also run ~/.tshrc, use #!/bin/csh -f to avoid

21 Shell profile scripts, continued Modify your.tcsh /.bashrc to suit your needs, but don t screw up! Can use ifs inside to separate operative systems / computers unamestr=`uname` if [ "$unamestr" == 'Linux' ]; then echo "This is Linux!" elif [ "$unamestr" == 'Darwin' ]; then echo "This is a Mac!" if [ $HOSTNAME == beehive4.uio.no]; then echo "From beehive4!"

22 Shell profile scripts exercises Exercise: is your current shell login or non-login? Can you get a shell of a different kind? Exercise: modify the bash script below to tcsh to print something when connecting to beehive4 (login shell only): if [ $HOSTNAME == beehive4.uio.no]; then echo "From beehive4!"

23 2. Compute Resources Check out web page for most up-to-date information: Institute has workstations (Linux, Mac) or thin clients (Linux), but also compute nodes (powerful machines with no desktop) Machines for general use have names starting with beehive beehive.uio.no, beehive2.uio.no,..., beehive23.uio.no All beehive machines have 20 cores, 128 GB RAM, infiniband. Load more info:

24 Compute Resources, continued Machines are shared between all users at the Institute, be considerate and follow etiquette: Choose machine with low load at Do NOT use all cores in all machines at once Run top when connecting to a machine to double-check usage Avoid using more processes than cores If some user taking up a lot, notify her/him if you need to run stuff Check top to find out about your CPU and memory usage

25 Compute Resources, continued Additional clusters available for some groups: ask supervisor! Some beehive nodes are special, e.g. beehive32-gpu, beehive33-gpu: 2x NVIDIA K20 (2496 CUDA cores, 5 GB memory) Large memory (~768 GB) beehive nodes coming soon

26 Compute Resources, exercises Exercise: which beehive node is getting more used right now? Which user is running more things?

27 3. The Module System Most Linux machines at the Institute have the Unix module system module allows loading complex initialisation shell scripts for different software packages Typical commands are: $ module avail show available modules $ module load <name> load a module $ module list show loaded modules

28 The Module System, continue Each typically sets the $PATH, $LD_LIBRARY_PATH, or other important variables Used in most supercomputers, and also at ITA s clusters You can write and use your own module files: $ module load use.own, save modules in ~/privatemodules At ITA, use module for Intel compilers (Intel_parallel_studio) and python (python/3.6 or python/2.7)

29 The module system exercises Exercise: login to beehive4 and load module hdf5. What happens? What modules to you have loaded at the end? Exercise: login to beehive4 and start python. Check version number. Now load python 3.6 module, and recheck python version

30 4. Parallel computing The compute clusters at ITA are made for parallel computing Two major paradigms: OpenMP (shared memory) and MPI (message passing interface, combine different machines) For compiled languages and MPI, recommended to use the Intel compilers (Intel_parallel_studio module), mpiifort, mpiicc In Python, possible to use mpi4py from the system packages (python module)

31 Parallel computing, continued With OpenMP, you can only run on one beehive machine (maximum 20 cores) With MPI, you can run in several beehive machines at the same time (hundreds of cores)

32 Parallel computing, exercises Exercise: check the Institute s IT help web pages and find the page on Setting up MPI in compute clusters. Compile and run the Fortran example on a beehive machine (5 cores) Exercise: following the instructions in the same page, run a Python test script with mpi4py using beehive4 and beehive5 at the same time

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