1. Getting Started with HPC On Iceberg Michael Griffiths and Deniz Savas Corporate Information and Computing Services The University of Sheffield www.sheffield.ac.uk/wrgrid

2. Introduction to Iceberg –Getting connected –Basic Linux Using the Linux Operating System Remote Visualisation Running Applications and Jobs on Iceberg How to distribute work across the cluster The N8 Facility Getting Help Outline

3. Cluster Grid Computing clusters ( e.g. iceberg ) Enterprise Grid, Campus Grid, Intra-Grid Departmental clusters, servers and PC network Cloud, Utility Grid Access resources over internet on demand Global Grid, Inter-grid White Rose Grid, National Grid Service, Particle Physics Data Grid Types of Grids

4. Iceberg Cluster HEAD NODE1 Iceberg(1) HEAD NODE2 Iceberg(2) Worker node There are 232 worker machines in the cluster There are two head-nodes for the iceberg cluster login qsh,qsub,qrsh All workers share the same user filestore

5. iceberg cluster specifications AMD-based nodes containing; 96 nodes each with 4 cores and 16 GB of memory 31 nodes each with 8 cores and 32 GB of memory TOTAL AMD CORES = 632, TOTAL MEMORY = 2528 GB The 8-core nodes are connected to each other via 16 GBits/sec infiniband for MPI jobs The 4-core nodes are connected via the much slower "1 Gbits/sec" ethernet connections for MPI jobs. Scratch space on each node is 400 GBytes Intel Westmere based nodes all infiniband connected, containing; 103 nodes each with 12 cores and 24 GB of memory ( i.e. 2 * 6-core Intel X5650 ) 4 nodes each with 12 cores and 48 GB of memory 8 Nvidia Tesla Fermi M2070s GPU units for GPU programming TOTAL INTEL CPU CORES = 1152, TOTAL MEMORY = 2400 GB Scratch space on each node is 400 GB Total GPU memory = 48 GB Each GPU unit is capable of about 1TFlop of single precision floating point performance, or 0.5TFlops at double precision. Hence yielding maximum GPU processing power of upto 8 TFlops in total.

6. The Insigneo Nodes Intel Sandybridge based nodes all infiniband connected, containing; 4 nodes each with 16 cores and 256 GB of memory ( i.e. 2 * 8- core Intel E5-2670 ) (racked in 1 Power Edge C6100 chassis) 3 Power Edge R720s each with ▬ 16 cores and 256 GB of memory ( i.e. 2 * 8-core Intel E5-2670 ) ▬ 1 Nvidia Tesla Fermi M2070Qs GPU units for visualisation GPU programming TOTAL INTEL CPU CORES = 224, TOTAL MEMORY = 1792 GB Scratch space on each node is 1 TB Total GPU memory = 24 GB Each GPU unit is capable of about 1TFlop of single precision floating point performance, or 0.5TFlops at double precision.

7. Insigneo Nodes The GPU Nodes are: node097.iceberg.shef.ac.uk node098.iceberg.shef.ac.uk node099.iceberg.shef.ac.uk The Standard Compute Nodes are: node100.iceberg.shef.ac.uk through to….. node107.iceberg.shef.ac.uk

8. Software stack on the worker nodes AMD Opteron/Intel Westmere Redhat 64bit Scientific Linux Portland, GNU,Intel OpenMPI Sun Grid Engine v6 Ganglia

9. Introduction to Linux on Iceberg What are UNIX and Linux? The Shell Getting Connected Basic UNIX/Linux Commands ▬ Working with Directories ▬ Editing files Help! Running Programs Exercise

10. What is UNIX/Linux ? Multi-Tasking O/S Multi-User O/S Available on a range of Computers

11. History of UNIX/Linux?. Unix operating system was developed around 1969 in the Bell Labs Originally written using C Around 1990 Linus Torvalds of Helsinki University started off a freely available academic version of Unix Linux is the Antidote to a microsoft dominated future

12. Which UNIX? SunOSSun Microsystems – now OpenIndiana, OpenSolaris from Oracle IRIXSilicon Graphics HP-UXHewlett Packard LinuxFor IBM PC compatibles There are a number of certification bodies with published standards and test suites to ensure quality of products. Such as; Posix: Portable Operating System Interface ( IEEE standard).

13. Linux and GNU Linux is an implementation of Unix Linux/Unix operating system is written in ‘C’ Linux is not part of the GNU project but uses the same licensing agreements Many of the linux utilities and tools are taken from the GNU project. There are many flavours of linux distributions. The mix of the kernel (linux) with the utilities (GNU and other) and the installation procedure determine the flavour. Some of these are; –Fedora –SuSE –Redhat –Debian –Mandrake –Knoppix

14. UNIX Internals (Simplified) Kernel –System Internals Shell –Command Interpreter –Programming language File System Process Management

15. UNIX Shells sh Bourne Shell (Original Shell) (Steven Bourne of AT&T) bash Bourne Again Shell (GNU Improved Bourne Shell) csh C-Shell (C-like Syntax)(Bill Joy of Univ. of California) ksh Korn-Shell (Bourne+some C-shell)(David Korn of AT&T) tcsh Turbo C-Shell (More User Friendly C-Shell). You can switch from one shell to another by just typing the name of the shell. exit return you back to previous shell.

16. Getting an account All staff and research students are entitled to use iceberg For Registration See: http://www.shef.ac.uk/wrgrid/register Staff can have an account by simply emailing ucards-reg@sheffield.ac.uk

17. passwords In normal linux environment the passwd command can be used to change the user passwords. However, because we manage passwords centrally this command will not work on iceberg. If you wish to change your iceberg password you will have to do this via a web interface at the following URL: http://www.shef.ac.uk/cics/password

18. The Insigneo Project To access the insigneo nodes you must send a request to join to –Insigneo Project leader –Prof. D. Lacroix –D.Lacroix@sheffield.ac.ukD.Lacroix@sheffield.ac.uk Prof. Lacroix will e-mail a request to iceberg-admins Iceberg-admins will update the Insigneo project group

19. Access iceberg Remote logging in Terminal access is described at: http://www.shef.ac.uk/wrgrid/using/access Recommended access is via any browser at: www.shef.ac.uk/wrgrid This uses Sun Global Desktop ( All platforms, Graphics-capable) Also possible: Using an X-Windows client ( MS Windows, Graphics-capable) ▬ Exceed 3D ▬ Cygwin Various ssh clients (MS Windows, Terminal-only ) ▬ putty, SSH Note: ssh clients can also be used in combination with Exceed or Cygwin to enable graphics capability. Above web page describes how this can be achieved.

20. Access iceberg from MAC or Linux platforms The web browser method of access ( as for Windows platforms) also works on these platforms. More customary and efficient method of access is by using the ssh command from a command-shell. Example: ssh –X iceberg_username@iceberg.shef.ac.uk Note1: -X parameter is needed to make sure that you can use the graphics or gui capabilities of the software on iceberg. Note2: Depending on the configuration of your workstation you may also have to issue the command : xhost + before the ssh command.

21. Basic X Concepts X Server runs on local machine –PCExceed, Cygwin, Xming –UNIX WorkstationIncluded in OS –Apple MacExodus X Client runs on remote machine –Graphical Application xterm xcalc Modelling and visualisation packages etc.

22. Multiple ssh or xterm shells There are no limits to the number of ssh or xterm windows one can start simultaneously by methods described in the previous slides. You may also start extra xterm windows from the host by simply typing xterm & On iceberg we also have a local command named Xterm that starts up an xterm window with nicer to use parameters. On iceberg we strongly recommend that you use Qsh rather than xterm or Xterm command so as to make use of a free worker node. Qsh will act like Xterm but will make use of a worker node. Typing exit will terminate an xterm or ssh session neatly. This will also close the xterm window but not the ssh window. ssh windows can be closed via the file  exit menu.

23. Start session on headnode Start an interactive session on a worker Help Start Application on a Worker Web browser method of access: Sun Global Desktop

24. Operating system and utilities Linux Operating System version is- Scientific Linux, which is RedHat Enterprise 5 based Default Shell is- bash Available editors- Graphical Editors: ▬ gedit ( not available on headnode) ▬ emacs ▬ nedit Text editors: ▬ vi ▬ pico ( not available on headnode) ▬ nano

25. Login Environment Default shell is bash ( you can request to change your default shell ). On login into iceberg many environment variables are setup automatically to provide a consistent interface and access to software. Each user has a.bashrc file in their directory to help setup the user environment. Type set to get a list of all the environment variables. Change all variables that are in CAPITALS with extreme care. Modify/enhance your environment by adding commands to the end of your.bashrc file, such as alias commands. (Again do this with care! )

26. Some basic rules Unix is case sensitive. Commands are in lower case. Backspace and/or Del Keys correct typing errors. If the terminal parameters are not correctly set; try Ctrl+H Ctrl+C Aborts a program or command. You can use the arrow keys to recall previous commands, optionally edit and execute them.

27. Key combinations in bash Ctrl+AMove cursor to beginning of line Ctrl+C Stop running program Ctrl+D Ctrl+EMove cursor to end of line Ctrl+HDelete character to the left Ctrl+ZSuspend the program Arrow left/rightMove pointer left/right to insert chars etc. Arrow up/downRecall previous commands so as to edit them andsubmit them by pressing ENTER Tab Tab tab Command or filename completion. Auto-complete the command line (to save typing) If tab does not work tab again to show possibilities

28. Format of Unix commands command [option...] [filename...] eg:ls ls -l tutorial more tutorial

29. List Directory lslist directory ls -llist directory in long format ls -a list all (inc. hidden) files -rw------ l course01 57 Oct 18 11:05 hello.c Number of bytes in file Access Permissions Date and time last modified

30. Directory Structure Home directory of user cs4un1 : /home/cs4un1 usr / (root) home cs4un2cs4un1 When you log in you are positioned in your home directory. The environment variable $HOME is also set to contain this directory name.

31. Working with Directories pwdprint working directory cdchange directory cd move to home directory cd.. move up one level cd mydir move into a subdirectory cd /var/adm move to an absolute directory mkdir directory_namecreate a new directory rmdir directory_namedelete an empty directory

32. Filenames Filenames can comprise of: a-z, A-Z alphabetic characters 0-9 digits.-_+ special characters mon+tue_01.06-03-96 Wildcards when referencing files * any character or sequence of characters ? any single character

33. Displaying contents of a text_file more filename This command will start listing the contents of filename on screen and pause after a screenfull of data. While pausing, use the following characters to control the output. Spacebarnext screenful n Spacebar : next n lines Enternext line b back one screen n b : back n screen’s full qquit ?or h list commands where n is a whole number

34. Displaying contents of a text_file… continued cat [options] filename [filename … ] This command will output the contents of filename[s] to standard-output ( normally screen) without pausing. Following options are useful; -vdisplay non-printing characters -ndisplay with lines numbered on the left tail [-n] filename This command lists the last 10 lines of a text file. If a number is specified (.eg. -20 ) lists the last n (i.e 20) lines

35. Copying files Copy files (optionally directories) cp fromfile tofile Some of the useful options are: -R or –r : Recursive copy ‘fromfile’ is a directory so the entire directory and its contents are copied. e.g. cp –r mydir newdir -p : preserve. Preserves all attributes of the file,such as access rights and creation date. Copy and concatenate files by using cat Cat command concatenates contents of list of files and directs the output to standard output (normally screen). When used with redirection ‘>’ it can be used to join files together. e.g. cat file1 file2 file3 > new_big_file

36. Renaming and deleting files mv :This command will move a file or directory to a new location. It can thus be used to rename files/directories as well as change their locations in the global directory structure. Syntax: mv source destination Example: mv myfile mynewfile mv myfile subdirectory/myfile mv mysubdir mynewsubdir rm : This command will delete a file (optionally a directory if used with –r option). Syntax: rm object_to_delete Example: rm myfile rm –r mydirectory

37. Working with files To copy a file: cp my_file my_new_file To move ( or rename ) a file : mv my_file my_new_file To delete a file : rm my_file To list the contents of a file : less file_name To make a new directory( i.e. folder) : mkdir new_directory To copy a file into another directory: cp my_file other_directory To move a file into another directory: mv my_file other_directory To copy a directory to another location: cp –R directory other_directory To remove a directory and all its contents!!!: rm –R directory ( use with care ) Wildcards : * means matching any sequence of characters. For example: cp *.dat my_directory

38. Searching in files grep string file This command finds and prints out the lines in the file(s) containing the specified string string = word or phrase file = file or list of files (wild_card can be used) Note: We strongly advise that the string is quoted. Examples: grep ‘Green Man’ england.dat grep ‘Zodiac’ t*.dat grep ‘Zone[a-z]’ security.fil

39. Transferring files to/from iceberg Summary of file transfer methods as well as links to downloadable tools for file transfers to iceberg are published at: http://www.sheffield.ac.uk/wrgrid/using/access Command line tools such as scp, sftp and gftp are available on most platforms. Can not use ftp ( non-secure ) to iceberg. Graphical tools that transfer files by dragging and dropping files between windows are available winscp, coreftp, filezilla, cyberduck

40. Pitfalls when transferring files ftp is not allowed to by iceberg. Only sftp is accepted. Do not use spaces ‘ ’ in filenames. Linux do not like it. Secure file transfer programs ‘sftp’ classify all files to be transferred as either ASCII_TEXT or BINARY. All SFTP clients attempt to detect the type of a file automatically before a transfer starts but also provide advanced options to manually declare the type of the file to be transferred. Wrong classification can cause problems particularly when transfers take place between different operating systems such as between Linux and Windows. If you are transferring ASCII_TEXT files to/from windows/Linux, to check that transfers worked correctly while on iceberg, type; cat –v journal_file If you see a ^M at the end of each line you are in trouble !!! CURE: dos2unix wrong_file on iceberg

41. Your filestore Three areas of filestore always available on iceberg These areas are available from all headnode and worker nodes. 1. home directory: /home/username 5 GBytes allocations Permanent, secure, backed up area ( deleted files can be recovered ) 2. data directory /data/username 50 GBytes of ollocation Not backed but mirrored on another server 3. /fastdata area /fastdata Much faster access from MPI jobs No storage limits but no backup, or mirroring Files older than 90 days gets deleted automatically Always make a directory under /fastdata and work there.

42. Scratch area ( only available during a job) Located at /scratch Used as temporary data storage on the current compute node alone. File I/O to /scratch is faster than to NFS mounted /home and /data areas File I/O to small files is faster than to /fastdata but … for large files /fastdata is faster than /scratch Data not visible to other worker nodes and expected to exist only during the duration of the job. HOW TO USE SCRATCH: Create a directory using your username under /scratch on a worker and work from that directory Example: mkdir /scratch/$USER cp mydata /scratch/$USER cd /scratch/$USER ( then run your program )

43. Storage allocations Storage allocations for each area are as follows: –On /home 5 GBytes –On /data 50 GBytes –No limits on /fastdata Check your usage and allocation often to avoid exceeding the quota by typing quota If you exceed your quota, you get frozen and the only way out of it is by reducing your filestorage usage by deleting unwanted files via the RM command ( note this is in CAPITALS ). Requesting more storage: Email iceberg-admins@sheffield.ac.uk to request for more storage. Excepting the /scratch areas on worker nodes, the view of the filestore is the same on every worker.

44. Running Tasks and Remote Visualisation on Iceberg (Established by Insigneo Group)

45. Running tasks on iceberg Two iceberg headnodes are gateways to the cluster of worker nodes. Headnodes’ main purpose is to allow access to the worker nodes but NOT to run cpu intensive programs. All cpu intensive computations must be performed on the worker nodes. This is achieved by; ▬ qsh command for interactive jobs and ▬ qsub command for batch jobs. Once you log into iceberg, taking advantage of the power of a worker-node for interactive work is done simply by typing qsh and working in the new shell window that is opened. The next set of slides assume that you are already working on one of the worker nodes (qsh session).

46. Where on the cluster ? Most of the application packages, compilers and software libraries are only available on the worker_nodes. Iceberg headnodes are suitable for only light-weight jobs such as editing files. If you are on one of the headnodes, you will need to type qsh to get an interactive session to the worker nodes. How do you know where you are ? The command prompt will contain your userid@hostname Example: ch1abc@node-056 $ ▬ If you are on one of the headnodes, hostname will be iceberg1 or iceberg2 ▬ If you are on an amd-based worker-node, it will be amd-nodenn where nn is the number of the amd-node. ▬ If you are on an intel-based worker-node it will be node-nnn where nnn is the number of the intel node. You can always type echo $HOSTNAME to find out the name of the machine you are currently using.

47. Running programs on iceberg Iceberg is the gateway to the cluster of worker nodes and the only one where direct logging in is allowed. Iceberg’s main purpose is to allow access to the worker nodes but NOT to run cpu intensive programs. All cpu intensive computations must be performed on the worker nodes. This is achieved by the qsh command for the interactive jobs and qsub command for the batch jobs. Once you log into iceberg, taking advantage of the power of a worker node for interactive work is done simply by typing qsh and working in the new shell window that is opened. This what appears to be a trivial task has would in fact have queried all the worker nodes for you and started a session on the least loaded worker in the cluster. The next set of slides assume that you are already working on one of the worker nodes (qsh session).

48. Starting An Interactive Job On the Insigneo Nodes Use Qsh, qsh or qrsh Specify the insigneo project and the insigneo q –Qsh –P insigneo –q insigneo.q See next session on Sun Grid Engine

49. Running programs Two modes of operation foreground and background –ForegroundInteract with program via keyboard/screen –BackgroundNo connection with keyboard/screen Submit to backbround by Appending ‘&’ EG: myprog >& myfile & The symbols ‘>&’ redirect output and any errors to the file myfile Although the above method of running jobs on the background is feasible, the prio we recommend that you submit your background into the batch queue via the qsub command.

50. Redirection Most unix commands are not aware of the source of their input or the destination of their output. They simply read/write from/to stdin/stdout. The shell takes care of these issues. Standard Input (default=>keyboard) Standard Output (default=>screen) Redirection symbols,>> can be used to specify files as the source/destination of the read/write operations to override the above defaults.

51. Redirection continued … Most unix commands are not aware of the source of their input or the destination of their output. They simply read/write from/to stdin/stdout. The shell takes care of these issues. To redirect the output to a file use the ‘ > ‘ symbol. Example: ls -l > dirlist The ‘ > ‘ symbol should be used with care as it may over-write an existing file. ‘>>’ symbol can be used instead if the output should be appended to the end of an existing file rather than over-writing it. Example: ls -l >> logfile If nothing is directed to a file then a zero size file is created, or if the file already existed then the contents of the file is removed Example: > afile The file /dev/null is a special symbol to indicate a ‘black-hole’ Example : ls –l > /dev/null

52. Redirection continued … If any program expects any of it’s input from the standard-input-channel, i.e. the keyboard, it can also read the same information from a file by redirection. To read input from a file use the ‘ < ‘ symbol. Example: write cs1xyz < message.fil Here any text input {write} program expects from the keyboard will be simply read from a file named message.fil. Each end-of-line will be treated as an on the keyboard.

53. Piping Feeding the output of one command into the input of another command The symbol ‘|’ is called a pipe command | command eg: ls -al | more ls -la | grep Nov

54. Examples of re-direction and piping ls –l | grep ‘Jun’ ls –l | grep `Jun` > june_files ls –l | grep `Jun` | cut –c 57-80 > june_files cut –c 1-10 < test_files aspell –l report.txt grep fluent < news.dat grep fluent < news.dat | cut –c 1-72 (grep fluent < news.dat ) | cut –c 1-72 (grep fluent fluent.news

55. Foreground Program Control Kill a programCtrl C Stop a programCtrl Z Note a stopped program still exists in the system and hence can be re-started.

56. Program control within current shell jobsLists jobs (programs) bg %job_idPlace a job in the background fg %job_idReturn a job to the foreground stop %job_idStop a job kill %job_idKill a job Process_id can be used in place of %job_id for more definitive way of identification. jobs [1] + Runningtime.sh > out stop %1 [1] + Stopped (signal)time.sh > out bg %1 [1] + time.sh > out & kill %1 Terminated

57. Program control using ‘ps’ and ‘kill’ psReport process status ps -f -u username UID PID PPID C STIME TTY TIME CMD username 24816 24585 0 16:23:04 pts/50 0:00 sleep 2 username 20169 19956 0 16:05:45 pts/50 0:01 -csh username 24585 20169 0 16:35:07 pts/50 0:00 /bin/sh time.sh killTerminate process –Find its process ID (PID) using the ps command –Kill the process using the kill command kill 24585 –Sometimes kill on its own does not work so try kill -KILL 24585 or kill -9 pid

58. Repeating Previous Commands Operation –history List previous commands –!!re-run last command –!n re-run the nth command –!str last command starting with str eg:!vi Setup –Add the following to your.cshrc file –set history=40

59. Remote Visualisation Undertake visualisation using thin clients accessing remote high quality visualisation hardware Remote visualisation removes the need to transfer data and allows researchers to visualise data sets on remote visualisation servers attached to the high performance computer and its storage facility

60. VirtualGL VirtualGL is an open source package which gives any UNIX or Linux remote display software the ability to run 3D applications with full hardware accelerations. VirtualGL can also be used in conjunction with remote display software such as VNC to provide 3D hardware accelerated rendering for OpenGL applications. VirtualGL is very useful in providing remote display to thin clients which lack the 3D hardware acceleration.

61. VirtualGL: Client-Server

62. Client Access to Visualisation Cluster VirtualGL Client Iceberg – Campus Compute Cloud VirtualGL Server (NVIDIA GPU)

63. Testing Remote Visualisation on Iceberg Using NVIDIA Fermi M2070Q Graphical Processing Unit Iceberg clients access –TigerVNC –Through sheffield application portal, Sun Global Desktop (SGD)

64. Remote Visualisation Using SGD Star a browser and goto –https://myapps.shef.ac.ukhttps://myapps.shef.ac.uk –login to Sun Global Desktop Under Iceberg Applications start the Remote visualisation session This opens a shell with instructions to either –Open a browser and enter the address http://iceberg.shef.ac.uk:XXXX –Start Tiger VNCViewer on your desktop Use the address iceberg.shef.ac.uk:XXXX XXXX is a port address provided on the iceberg terminal When requested use your usual iceberg user credentials

66. Remote Desktop Through VNC

67. Remote Visualisation Using Tiger VNC and the Putty SHH Client Login in to iceberg using putty At the prompt type qsh-vis This opens a shell with instructions to either –Open a browser and enter the address http://iceberg.shef.ac.uk:XXXX –Start Tiger VNCViewer on your desktop Use the address iceberg.shef.ac.uk:XXXX XXXX is a port address provided on the iceberg terminal When requested use your usual iceberg user credentials

68. Links for Software Downloads Putty http://www.chiark.greenend.org.uk/~sgtatham/putty/ WinSCP http://winscp.net/eng/download.php TigerVNC http://sourceforge.net/projects/tigervnc/ http://sourceforge.net/apps/mediawiki/tigervnc/index.php?title= Main_Page

69. Manual Pages and Info system Man: Manual pages : Give text-based help on usage. Manual pages are grouped into sections (1,2,3,4..). There is usually one manual page per command which is located in one of the directories defined by the MANPATH environment variable. To access the Manual page for a command just type; man command To get a list of manual pages that contain a ‘word’ type; man – k topic Info : Similar to man but can scroll with cursor keys and link to other information.

70. Further Help Getting started with iceberg –http://www.shef.ac.uk/wrgrid/iceberg http://www.shef.ac.uk/wrgrid/using/introlinux http://www.shef.ac.uk/wrgrid/using/introbash GNU/Linux Command-Line Tools Summary –http://en.tldp.org/LDP/GNU-Linux-Tools-Summary/html/index.html Bash Guide for Beginners –http://tldp.org/LDP/Bash-Beginners-Guide/html/index.html Advanced Bash-Scripting Guide –http://en.tldp.org/LDP/abs/html/index.html The Linux Documentation Project –http://en.tldp.org/