1 / 30

Getting acquainted to PDC

Getting acquainted to PDC. Nils Smeds <smeds@pdc.kth.se. Using PDC resources. Acquiring information http://www.pdc.kth.se Guided Tours http://www.pdc.kth.se/support/ AFS Strindberg IBM-SP Helpdesk FAQs Contact information pdc-staff@pdc.kth.se 08-790 7800. http://www.pdc.kth.se/doc.

xue
Télécharger la présentation

Getting acquainted to PDC

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Getting acquainted to PDC Nils Smeds <smeds@pdc.kth.se

  2. Using PDC resources • Acquiring information http://www.pdc.kth.se • Guided Tourshttp://www.pdc.kth.se/support/ • AFS • Strindberg IBM-SP • Helpdesk • FAQs • Contact information • pdc-staff@pdc.kth.se • 08-790 7800

  3. http://www.pdc.kth.se/doc

  4. http://www.pdc.kth.se/support/sp2-tour.html

  5. http://www.pdc.kth.se/compresc/

  6. Your environment as a user • File systems • AFS — Home directories • GPFS — Parallel file system (IBM SP) • HSM — Hierarchical storage management • /scratch — scratch file systems • Modules — handles $PATH, $MANPATH • module add sp2 local • module show local • E-mail — when you leave • Create $HOME/.forward publicly readablehttp://www.pdc.kth.se/support/misc-tour.html#EMAIL

  7. Kerberos commands • kauth — Proves your identity > ./kauth -n nissej@NADA.KTH.SE -l 60 • klist — List your kerberos tokens > ./klist Ticket file: /tmp/tkt58016 Principal: nissej@NADA.KTH.SE Issued Expires Principal Mar 9 12:18:59 Mar 9 13:18:59 krbtgt.NADA.KTH.SE Mar 9 12:19:25 Mar 9 13:18:59 rcmd.r11n07.pdc.kth.se • kdestroy — removes your ticket file > ./klist Ticket file: /tmp/tkt58016 klist: No ticket file (tf_util) • kpasswd — change your passwd

  8. Commands that rely on kerberos • Getting a shell > ./rxtelnet -l username strindberg.pdc.kth.se > ./telnet -l username strindberg.pdc.kth.se • Transferring files > ./ftp strindberg.pdc.kth.se Connected to r11n07-f.pdc.kth.se 220 r11n07.pdc.kth.se FTP server ready. Name (strindberg.pdc.kth.se:smeds): <RET> S:232- //PDC// S:232- //PDC// Welcome to Strindberg, an IBM SP ... S:232 User smeds logged in. ftp> kauth Password for smeds@NADA.KTH.SE: mypassword S:200 Tickets will be destroyed on exit ftp> binary ftp> put filename.dat ftp> get otherfile.dat ftp> quit

  9. AFS commands http://www.pdc.kth.se/support/afs-tour.html • tokens — List your afs tokens – - smeds> kauth smeds@NADA.KTH.SE's Password: mypassword smeds> unlog smeds> tokens Tokens held by the Cache Manager: --End of list-- smeds> afslog smeds> tokens Tokens held by the Cache Manager: (AFS ID 22557) tokens for afs@nada.kth.se [Expires Aug 19 03:38] (AFS ID 22557) tokens for afs@pdc.kth.se [Expires Aug 19 03:38] --End of list-- smeds> • kauth/kdestroy automatically does afslog/unlog

  10. More AFS • fs — Directory access management smeds> fs setacl directorynameusername rl smeds> fs listacl directoryname smeds> fs setacl directorynameusername none smeds> fs setacl directoryname system:anyuser rl smeds> fs help smeds> fs setacl -h • pts — ACL group management smeds> pts mem username smeds> pts creategroup username:bs106 smeds> pts adduser mybuddymygroup smeds> pts examine mygroup smeds> pts adduser -h • Putting it all together smeds> fs setacl MyProject smeds:buddies rl smeds> fs setacl MyProject smeds:REALbuddies rlidwk

  11. HSM usage • Use tar to pack many files into one file which can be saved in HSM smeds> module add hsm smeds> hsmls -l smeds> tar cvf /scratch/MyAnalysis.tar Results-980812/Run1/ smeds> hsmcopyto /scratch/MyAnalysis.tar Res-980812-1.tar • HSM location is kallsup:/hsm/home/u/username/..., see output from hsmmyhome • You may use kerberized rcp to move files to and from this location. • On line help is available: smeds> hsmls -h smeds> hsmcopyfrom -h

  12. Strindberg usage • http://www.pdc.kth.se/cgi-bin/strindberg-usage.pl

  13. Node types • http://www.pdc.kth.se/compresc/hardware/ • Batch nodes (T) • 160 MHz (640 MFlop/s), 256MB RAM, 2 GB /scratch • Batch nodes with more memory (W,Z) • 160 MHz (640 MFlop/s), 512/1024 MB RAM, 2 GB /scratch • 4-way SMP nodes (M) • 4332 MHz (4664 MFlop/s), 512 MB RAM, 4 GB /scratch • 8-way SMP nodes (N,H) • 8222 MHz (8888 Mflop/s), 4/16 GB RAM • Serial nodes (G, S) • One 135MHz wide node w. 2 GB RAM, some 67MHz nodes

  14. Login node(s) • The node of the SP that you are connected to after./rxtelnet -l name strindberg.pdc.kth.se./rxtelnet -l name august.pdc.kth.se./rxtelnet -l name nf01r01.pdc.kth.se • Interactive nodes • Nodes that are shared among several users. Used for eg debugging and compiling. spattach -i -p# • These nodes must be used with IP communication:export MP_EUILIB=ip • Dedicated (or batch) nodes • Nodes used for production codes and/or longer pre/post-jobsspsubmit -p# -t time -c CAC scriptfilespattach -p# -t time -c CAC

  15. rxtelnet strindberg.pdc.kth.se (New window) klist kauth cd workdir mpcc -g -o myprog myprog.c spattach -i -p5 (wait) ./myprog ./myprog -procs 3 ./myprog -procs 3 -stdoutmode ordered -labelio yes A full interactive example

  16. Interacting with the EASY scheduler smeds> spsubmit -h spsubmit [-h][-inWvCb][-c cac][-I#][-s#][[-p# -t#][-j#][-M] file[args]] -h: help -p processors: number of processors. (Example: -p2W) -t minutes: number of minutes (Wall-clock) -j Job Type: available job types mpi, task, pvm3... -c CAC: optional, submit for accounting group cac. -I InitialDir: optional, default current working directory. -b: optional, hold job until all jobs completed -i: optional, use IP instead of UserSpace. -v: optional, verbose. -C: optional, commit before submit. -s Filename: optional, save EASY generated script [...] program: executable or script. args: optional arguments to program. User smeds can specify: staff free ta.smeds

  17. spsubmit examples • Submitting an MPI program smeds> spsubmit -p 4T -t 30 -j mpi ./mympiprog • Saving the generated script for later re-use smeds> spsubmit -p 4T -t 30 -j mpi -s myscript.esy ./mympiprog • To have a mix of nodes and start on a Z-node smeds> spsubmit -p 1Z8T -t 30 -j mpi ./mympiprog "arg1 'arg2 here'" • Redirecting STDOUT for your program smeds> spsubmit -p 4T -t 30 -j mpi ./mympiprog "> job.out" • Submitting an MPI program smeds> spsubmit -p 4T -t 30 -j mpi ./mympiprog

  18. The batch script file #!/bin/bash #------ Customizable part ------ # (Use submitting directory as working directory) cd $SP_INITIALDIR OUT=MyProgram.out #------ End customizable part ------ #------ Generic part ------ PROGRAM="MyProgram" ; PROGRAMDIR="$HOME/Public/MyProgramDir" export MP_HOSTFILE=$SP_HOSTFILE export MP_PROCS=$SP_PROCS export MP_EUILIB=us ; export MP_EUIDEVICE=css0 export MP_INFOLEVEL=0 export MP_CSS_INTERRUPT="yes” export TMPDIR=/scratch echo "Executing $PROGRAM in directory `pwd` at `date`" poe ${PROGRAMDIR}/${PROGRAM} > $OUT echo "Program finished `date`"

  19. http://wwww.pdc.kth.se/info/qwatch/ • A snapshot from different queues at PDC • Updated at regular intervals • It is generated from the same information you get using the command spq smeds> spq -a smeds> spq -r smeds> spq -u smeds

  20. http://www.pdc.kth.se/sp/sptetris/

  21. Scheduling limits smeds> spq -h Usage: spq [-h] [-l] [-L] [-r] [-q] … ... smeds> spq -l NICKNAME SATURATE CAC NJOB Wall Total - - weekend - r1149 1 16h - - weekend saturate tf109 3 169h40 - - night saturate gw11 4 48h40 - - day - gw11 1 3h30 . . . smeds> spq -L INTERVAL NICKNAME MAXNJOB MAXWALLTIME [15h,60h] weekend - - - 30h [4h,15h] night - - - 16h [1h,4h] day - - - 16h . . . [0m01s,2h] Nshort - - 4 -

  22. The concept of CACs • Computer cycle "accounts" smeds> cac members smeds CAC groups smeds is a member of: ta.smeds staff summer-2000 free smeds> cac -h smeds> spjobsummary -c summer-2000 usr jid req npe treq tstart r-cpu ucpu smeds ###### 1G2Z2T 5 0h30 yyhhmm 2h30 1h49 mike ###### 4T 4 0h15 yyhhmm 1h 0h56 . . . smeds> cac -h smeds> spjobsummary -u smeds -f 200003 -l smeds> spjobsummary -h smeds> spsummary -h

  23. Compilers (IBM SP) • cc, mpcc • IBM C-compiler, mpcc adds special flags for compiling MPI parallel programs. Include file search path, tags binary to be parallel etc. • xlC, mpCC • IBM C++-compiler. Not fully ANSI compliant. • xlf, mpxlf, xlf90, mpxlf90, f90 • Fortran, Fortran90/95 compilers • Reentrant code generation (thread safety) • xlc_r, xlf_r, mpxlf90_r … • OpenMP directives only available in Fortran currently

  24. Code optimization • -O2 -O3 • Code restructure. Code in-lining. Level 3 may cause arithmetic reorganization. • -qhot • Higher order transformations of generated code. Uses cache size information. Occasionally slows code down. • -qipa, -O4, -O5 • Interprocedure analysis. Mainly code inlining across file boundaries. -O4 => -O3 -qhot -qipa -qtune=arch -qcache=arch • -qsmp=omp, -qsmp=auto, -qreport=smplist • All of the above. Long compile time. Needs thorough checking of results

  25. The lab session • The object of the exercise is to get familiar to the PDC environment by a hands on experience • The lab session has three parts • Install a kerberos travel kit • The workstation is a Sun Solaris 2.6 workstation • Install a travel kit and verify that you can use that to log in to the SP • Experiment with file systems and storage media • Try AFS, tokens and ACLs • Use the HSM data migration system • Run a Fortran90 program on the IBM SP2 • Serial and parallel - interactive and batch • Play, experiment, think and ask!

  26. Topics that can not be covered in this talk • Compiler options • Optimization options, linker options, file name convention options • Programming tools • Tracing, Sampling, Debugging, F90 conversion • See http://www.pdc.kth.se/compresc/software • Totalview, Foresys, Vampir, Dimemas • Running parallel programs on other computers • Running MPICH in the NADA computer lab rooms

  27. Totalview and “How to trick the OS” • Have the program read from the keyboard as early in the program flow as possible after MPI_Init() • Start the process and attach to the running poe process module add totalview ./myprog & (Start your program) totalview -no_stop_all & (Or start totalview in other window) • "Show all unattached processes" • Attach to the poe process, the debugger locates all MPI processes • Select one of the MPI-processes (not the poe process) • Set break-points later in the program flow if you want • In one of the MPI-process windows say "Go group <G> " • Give the program the input it is waiting for

  28. MPICH - 1.2.0 Argonne National Laboratories Reference MPI implementation module add workshop/5.0 module add mpich/1.2 mpicc -o myprog-sun myprog.c mpirun -np 4 -machinefile LOCAL ./myprog-sun The machinefile is reused up to the number of processes requested by -np Further information on MPI at KTH:http://www.nada.kth.se/datorer/unix/ Running MPI programs on SUNs (locally) LOCAL red01.nada.kth.se red01.nada.kth.se

  29. Running on several hosts You may need to set up AFS tokens on the remote hosts kauth -h red02.nada.kth.se -l 30kauth -h red03.nada.kth.se -l 30kauth -h red04.nada.kth.se -l 30kauth (For your local rights) mpirun -np 4 -machinefile RED ./myprog-sun mpirun -np 6 -nolocal -machinefile RED ./myprog-sun The remote processes are started of by a kerberos rsh to the remote host. Modern kerberos rsh has a call to the command afslog in them. The remote ticket must be there in advance Running MPI programs on SUNs (remote) RED red02.nada.kth.se red03.nada.kth.se red04.nada.kth.se

  30. The End

More Related