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Introduction to Using the Origin-2000 (hecate) things to know...

Introduction to Using the Origin-2000 (hecate) things to know. Stéphane Ethier CPPG talk series July 6, 1999. Hecate. 64-processor SGI Origin 2000 16 Gbytes of physical memory Shared memory but ... Non-Uniform Memory Architecture (NUMA). Logging in.

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Introduction to Using the Origin-2000 (hecate) things to know...

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  1. Introduction to Using theOrigin-2000 (hecate)things to know... Stéphane Ethier CPPG talk series July 6, 1999

  2. Hecate • 64-processor SGI Origin 2000 • 16 Gbytes of physical memory • Shared memory but ... • Non-Uniform Memory Architecture (NUMA)

  3. Logging in • Always use “secure shell” ssh to connect (works like rlogin but creates encrypted session) % ssh [-l username] hecate.princeton.edu • Answer “yes” if you see: Host key not found from the list of known hosts. Are you sure you want to continue connecting (yes/no)? (it creates an entry in the file ~/.ssh/known_hosts) • Enter your password as you would normally do • To use ssh-agent with RSA authentication, see: http://w3.pppl.gov/info/pppl-unix/ssh_with_RSA_authentication.html

  4. First thing you see Last login: Wed Jun 30 14:56:08 1999 from taurus.pppl.gov You have mail. --------------------------------------------------------------------------------------- Dedicated time 99/06/19 00:01 - 99/06/19 08:00 jps (cs) ---------------------------------------------------------------------------------------- • To view the dedicated time again: % cat /etc/motd • To ask for dedicated time, send a message to sisyfolks@astro.princeton.edu 2 days in advance. You get thewhole machine for yourself but … it is only at night. • Use same format as above

  5. Environment • Default shell: /usr/peyton/bin/tcsh • Default path: /usr/peyton/tex/bin:.:/usr/bsd:/usr/sbin:/usr/bin: /usr/bin/X11:/opt/totalview/bin:/u/${USER}/bin/mipssgiirix6: /u/${USER}/bin/common:/u/${USER}/bin:/usr/peyton/bin: /usr/peyton/bin/X11:/usr/p-ton/bin/X11:/usr/p-ton/bin: /usr/princeton/bin:/usr/princeton/bin/X11 • PPPL users should add to their ~/.cshrc: setenv NCARG_ROOT /usr/pppl setenv GRAPHCAP X11 setenv MANPATH ${MANPATH}:${NCARG_ROOT}/man setenv PATH ${PATH}:${NCARG_ROOT}/bin:/usr/afsws/bin • % ln -s /afs/pppl.gov/u/${USER} /u/${USER}/afs • alias lpr_pppl "/usr/pppl/bin/lpr -Ptheoryne@tern.pppl.gov \!* ” use “lpr_pppl filename” to print at PPPL

  6. To transfer files • “secure copy”: scp % scp filename orion.pppl.gov:code/src % scp username@orion.pppl.gov:tmp/c\*.f ~/code hecate_talk.txt | 7 KB | 7.1 kB/s | ETA: 00:00:00 | 100%  Same restrictions as ssh • NFS mounted filesystem: (user must have same uid and gid to have same permissions) /usr/pppl/work (hecate) /work (PPPL) • AFS (Andrew File System): /afs/pppl.gov/u Use klog to obtain an AFS Token from the Authentication Server (you have to enter your AFS password…) and gain write permission in your AFS directory (you can also use ssh token forwarding, port 1515) see: http://w3.pppl.gov/info/pppl-unix/AFS.html (http://w3.pppl.gov/info/pppl-unix/ssh_with_RSA_authentication.html)

  7. Scratch disks • Use the scratch disks to run jobs with large output files • You have to ask for a directory. You cannot create it yourself. Nice but … NO BACKUPS! hecate[33]% df -kl Filesystem Type kbytes use avail %use Mounted on /dev/root xfs 4188256 2776528 1411728 67 / /dev/xlv/xlv11 xfs 17775472 2051364 15724108 12 /scr11 /dev/xlv/xlv8 xfs 8884712 8822820 61892 100 /scr5 /dev/xlv/xlv5 xfs 8880616 8742460 138156 99 /scr2 /dev/xlv/xlv10 xfs 17775472 5967228 11808244 34 /scr10 /dev/xlv/xlv3 xfs 4788712 1893716 2894996 40 /export/home /dev/dsk/dks4d1s0 xfs 4175968 2138104 2037864 52 /original /dev/xlv/xlv6 xfs 8884712 7091596 1793116 80 /scr3 /dev/xlv/xlv7 xfs 8884712 8166236 718476 92 /scr4 /dev/xlv/xlv4 xfs 8880616 7754328 1126288 88 /scr1 /dev/xlv/xlv9 xfs 35550816 17554000 17996816 50 /scr9 /dev/dsk/dks4d2s7 xfs 8884712 7071876 1812836 80 /scr8 /dev/xlv/xlv1 xfs 71105632 62363740 8741892 88 /scr6 /dev/xlv/xlv0 xfs 106672736 104936992 1735744 99 /scr0 /dev/xlv/xlv2 xfs 142231648 64785880 77445768 46 /scr7

  8. Compilers • MIPSpro 7.2.1 f90, f77, cc, CC • To see the compilers default options: • % f90 -show_defaults • % cat /etc/compiler.defaults ( -DEFAULT:abi=n32:isa=mips4:proc=r10k) • To access the MIPSpro 7.3 compilers (beta version): % source /opt/modules/modules/init/tcsh % module load modules % module load MIPSpro.73 % module list (to see which modules are loaded) Currently Loaded Modulefiles: 1) modules 2) MIPSpro.73 • To return to MIPSpro 7.2.1 (check with % f90 -version) % module unload MIPSpro.73 % module load MIPSpro.721

  9. Do I need -64 ??? • When you compile with -n32, the chip executes in 64-bit mode and the software restricts addresses to 32 bits • Compile with -n32 when you want: • To generate smaller executables than for -64 • Executables to have fewer data cache misses and less memory paging than for -64 • Compile with -64 if your program: • Requires more than 2 gigabytes of address space • Will overflow a 32-bit long integer (for C) C Type -n32 -64 Fortran Type ------ ------- ------ -------------- char 8 8 character short int 16 16 integer*2 int 32 32 integer long int 32 64 none long long int 64 64 integer*8 pointer 32 64 pointer float 32 32 real double 64 64 real*8 long double 64 128 real*16

  10. Directory search for “ld” linker • Default search order: • -n32  /usr/lib32, /lib32 • -64  /usr/lib64, /lib64 • -o32  /usr/lib, /lib • That is as far as it goes… you have to know if you are using -n32 or -64 for some libraries.

  11. Libraries of interest • Mathematical libraries: • NAG • link with “-lnag” • use “naghelp” on hecate or at PPPL • SCSL (SGI/Cray Scientific Library) • SGI’s own optimized BLAS, LAPACK, etc • man scsl • man name_of_individual_routine • I/O format library: • NETCDF • Graphic library: • NCAR Graphics

  12. Debuggers • Compile program with -g for all debuggers • dbx comes with the system so always latest version (see man dbx) • cvd WorkShop pro debugger (SGI-style graphics) (see http://techpubs.sgi.com/library  Books  Developer  Developer Magic: Debugger User’s Guide) • totalview Beta version only (GUI oriented) (see /opt/totalview/docs/User_Guide.pdf (or .ps) on hecate) • All of them can more or less debug multi-process programs

  13. Linking multi-language programs • Compile object files from the source files of each language separately by using the -c option • % cc -c more.c rest.c • % f77 -c main.f • Use the compiler associated with the language of the main program to link the objects: • % f77 main.o more.o rest.o

  14. Running a job... • To run a 1-cpu job on a fix processor: % runon cpu# command • To run a multi-processor job on chosen processors: % dplace -place pfile [-mustrun] command • Where pfile contains something like: #physical placement_file for 2 specific memories and 4 threads memories 2 in topology physical near \ /hw/module/3/slot/n1/node \ /hw/module/3/slot/n2/node threads 4 distribute threads across memories

  15. Multi-processor jobs • MPI programs (link with -lmpi): % setenv MPI_DSM_OFF % mpirun -np nproc dplace - place pfile -mustrun a.out < /dev/null & • OpenMP or automatically parallelized code (link with -lmp): % setenv MP_SET_NUMTHREADS nproc % dplace -place pfile a.out >& stdout.out &

  16. Monitoring system activity: top • % top or % top -U username IRIX64 hecate 6.5 IP27 load averages: 47.97 48.17 44.95 10:24:21 165 processes: 111 sleeping, 1 zombie, 53 running 64 CPUs: 18.3% idle, 81.1% usr, 0.4% ker, 0.2% wait, 0.0% xbrk, 0.1% intr Memory: 16G max, 15G avail, 9274M free, 8693M swap, 8687M free swap PID PGRP USERNAME PRI SIZE RES STATE TIME WCPU% CPU% COMMAND 189228 190712 cen 20 1232M 452M run/8 21:20 13.5 99.52 lcdm192 188986 191186 gnedin 20 1491M 1179M run/34 25:28 13.5 99.52 slh 189817 190712 cen 20 1232M 452M run/51 23:54 13.5 99.51 lcdm192 189832 190712 cen 20 1232M 452M run/53 22:56 13.5 99.51 lcdm192 189826 190712 cen 20 1232M 452M run/26 26:09 13.5 99.51 lcdm192 189809 190712 cen 20 1232M 452M run/30 25:12 13.5 99.51 lcdm192 190299 190299 bode 20 92M 69M run/3 93: 48 13.5 99.51 corrv.x 189217 190712 cen 20 1232M 452M run/52 22:24 13.5 99.50 lcdm192 189759 190712 cen 20 1232M 452M run/49 24:18 13.5 99.50 lcdm192 189796 190712 cen 20 1232M 452M run/48 24:39 13.5 99.49 lcdm192 188282 190712 cen 20 1232M 452M run/22 26:41 13.5 99.48 lcdm192 190426 190712 cen 20 1232M 452M run/27 26:14 13.5 99.48 lcdm192 191214 191186 gnedin 20 1491M 1179M run/37 25:32 13.5 99.46 slh 191221 191186 gnedin 20 1491M 1179M run/39 25:32 13.5 99.46 slh 191183 191186 gnedin 20 1491M 1179M run/35 25:32 13.5 99.46 slh

  17. Monitoring tools: osview Osview 2.1 : One Second Average hecate 11:17:12 07/06/99 #1 int=5s Load Average readch 1.2M pgallocs 4.4K 1 Min 52.839 writech 1.1M Scheduler 5 Min 52.900 iget 0 runq 0 15 Min 52.119 System Memory swapq 0 CPU Usage Phys 15.8G switch 2.3K %user 85.71 kernel 535.3M kswitch 2.3K %sys 5.56 heap 292.1M preempt 150 %intr 0.00 mbufs 27.0M Wait Ratio %gfxc 0.00 stream 8.6M %IO 0.0 %gfxf 0.00 ptbl 10.6M %Swap 0.0 %sxbrk 0.00 fs ctl 327.8M %Physio 0.0 %idle 8.73 fs data 3.7G System Activity delwri 46.9M syscall 3.9K free 9.2G read 300 data 2.5G write 300 empty 6.6G fork 0 userdata 2.1G exec 0 reserved 0 1:Sys 2:Cpu 3:Mem 4:Net 5:Other 0:All  Commands!

  18. Monitoring tools: cpu • hecate% cpu --------------------------CPU Usage--------------------------- MODULE n1 n2 n3 n4 1 ( 0- 7) : O H H O F F F F 2 ( 8-15) : O F O F O O O O 3 (32-39) : O O O O O O O O 4 (40-47) : O O O O O O O O 5 (16-23) : F O O O O O O O 6 (24-31) : O O O O O O O O 7 (48-55) : O O O O O O O O 8 (56-63) : O O O O O O O O F: free O: Occupied H: half occupied • (100 - average_idle_time) includes I/O

  19. Monitoring tools: pscpu MODULE 1 MODULE 5 0 - 16 - 1 ssh1 root 17 lcdm192 cen 2 ps ethier 18 lcdm192 cen 3 corrv.x bode 19 lcdm192 cen 4 - 20 lcdm192 cen 5 - 21 lcdm192 cen 6 - 22 lcdm192 cen 7 lcdm192 cen 23 lcdm192 cen MODULE 2 MODULE 6 8 lcdm192 cen 24 lcdm192 cen 9 ssh1 root 25 lcdm192 cen 10 ssh1 root 26 lcdm192 cen 11 - 27 lcdm192 cen 12 mrc jbreslau 28 lcdm192 cen 13 mrc jbreslau 29 lcdm192 cen 14 mrc jbreslau 30 lcdm192 cen 15 mrc jbreslau 31 lcdm192 cen MODULE 3 MODULE 7 32 slh gnedin 48 lcdm192 cen 33 slh gnedin 49 lcdm192 cen 34 slh gnedin 50 lcdm192 cen 35 slh gnedin 51 lcdm192 cen 36 slh gnedin 52 lcdm192 cen 37 slh gnedin 53 lcdm192 cen 38 slh gnedin 54 lcdm192 cen 39 slh gnedin 55 lcdm192 cen MODULE 4 MODULE 8 40 slh gnedin 56 denmax.x bode 41 slh gnedin 57 denmax.x bode 42 slh gnedin 58 denmax.x bode 43 slh gnedin 59 denmax.x bode 44 slh gnedin 60 denmax.x bode 45 slh gnedin 61 denmax.x bode 46 slh gnedin 62 denmax.x bode 47 slh gnedin 63 denmax.x bode

  20. Web pages http://w3.pppl.gov/~xtang/hecate/hecate.html http://astro.princeton.edu/~ognedin/supercomputer/ http://techpubs.sgi.com/

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