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Overview of Computer Facilities and Cluster Configurations in UNIX Environments

This document provides a detailed overview of computer facilities used for scientific computing, focusing on cluster configurations, operating systems, and the software available for various tasks. Key systems include Beowulf clusters and UNIX variants such as AIX and Irix. It covers backup strategies, storage capacities, and network configurations, as well as essential software tools like Amber, NWChem, and various utilities for job management using Portable Batch System (PBS). The information is essential for users engaged in computational chemistry and related disciplines.

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Overview of Computer Facilities and Cluster Configurations in UNIX Environments

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  1. 1) Computerfaciliteiten OAC 2) Beowulf Cluster CCM 3) UNIX 5) ? OAC

  2. OAC(N328) FAR(P275) IBM os: AIX queue: prev. LL server: Iodine network: 144,unsafe backup: none SGI os: irix 6.5 queue: NQE server: (gate-)nonaan network: 148,secure backup: adsm daily inc 30d capacity: 36GB environment: module shell: zsh, csh, ksh g98 (rung98) adf2000 (runadf) amber6 (runsander) XTC os: linux (kernel 2.4) queue: PBS server: xtc0fs network: 144/priv backup: adsm daily inc 30d capacity: 240GB shell: zsh, csh, bash adf2000 nwchem amber6 OAC

  3. NT os: win nt 4 queue: n/a fileserver: cobalt printserver: cobalt network: 144,unsafe backup: occasional Z: //cobalt/home/%username% B: zipdrive Programs *)Office 97 *)Adobe Acrobat reader *)Netscape *)Eudora (depreciated) *)Chemdraw *)Weblabviewer lite *)Platon/Pluton *)SSH/SFTP *)Beilstein (xfire) *)Corel Draw/Photopaint *)Winzip OAC

  4. Firewall type: packet filtering policy: deny all connection- tracking allow: ssh, ftp, chem.vu.nl N 1010 Oct 25 Portmapper portmap-216.169.69.45 N 1011 Oct 25 Portmapper portmap-216.169.69.45 N 1012 Oct 25 Portmapper portmap-web1.gj.net N 1013 Oct 25 Portmapper portmap-web1.gj.net N 1014 Oct 25 Portmapper portmap-202.101.103.111 N 1015 Oct 25 Portmapper portmap-195.68.105.205 N 1016 Oct 25 root*octine sshd-c158-222.cent.net N 1017 Oct 25 root*octine sshd-c158-222.cent.net N 1018 Oct 25 root*far12 sshd-c158-222.cent.net N 1019 Oct 25 root*far12 sshd-c158-222.cent.net N 1020 Oct 26 root*octine pure-ftpd-node08bd.a2000.nl N 1021 Oct 26 Portmapper portmap-64.251.76.91 N 1022 Oct 27 root@propine sshd-194.78.32.252 N 1023 Oct 27 root@propine sshd-194.78.32.252 N 1024 Oct 27 root*octine sshd-194.78.32.252 N 1025 Oct 27 root*octine sshd-194.78.32.252 N 1026 Oct 27 root*far12 sshd-194.78.32.252 N 1027 Oct 27 root*far12 sshd-194.78.32.252 N 1028 Oct 27 root*octine pure-ftpd-d77250.upc-d.chello.nl N 1029 Oct 27 root*octine pure-ftpd-192.117.175.65 N 1030 Oct 27 root*octine pure-ftpd-adsl-62339.turboline.skynet.be N 1031 Oct 27 root*octine pure-ftpd-213.38.171.2 N 1032 Oct 28 root*octine pure-ftpd-.adsl.nerim.net 1033 Oct 28 root*octine pure-ftpd-.abo.wanadoo.fr OAC

  5. SARA TERAS (sgi) os: irix queue: lsf server: teras.sara.nl OAC

  6. SARA SOLO (ibm) os: aix queue: loadleveller server: solo.sp.sara.nl accounts: v61u0012 stol v61u0001 tc v61u0019 vlipzig OAC

  7. Diensten (centrale computerondersteuning) Mail: protocol pop, smtp. server mailhost DNS: 130.37.144.37 ; 130.37.144.39 OAC

  8. OAC

  9. OAC

  10. OAC

  11. OAC

  12. OAC

  13. OAC

  14. OAC

  15. OAC

  16. XTC.CHEM.VU.NL OAC

  17. next generation? OAC

  18. Portable Batch System OAC

  19. #!/bin/sh ### Job name #PBS -N test ### Declare job non-rerunable #PBS -r n ### Output files #PBS -e test.err #PBS -o test.log ### Mail to user #PBS -m ae ### Queue name (small, medium, long, verylong) #PBS -q medium ### Number of nodes #PBS -l nodes=8 # This job's working directory echo Working directory is $PBS_O_WORKDIR cd $PBS_O_WORKDIR echo Running on host `hostname` echo Time is `date` echo Directory is `pwd` echo This jobs runs on the following processors: echo `cat $PBS_NODEFILE` # Define number of processors NPROCS=`wc -l < $PBS_NODEFILE` echo This job has allocated $NPROCS nodes # Run the parallel MPI executable "mpihello" /usr/local/mpich/bin/mpirun -v -nolocal -machinefile $PBS_NODEFILE -np $NPROCS mpihello OAC

  20. Amber 6/sander benchmark for SGI-computers OAC

  21. Stack fault Text- read-only parts of program. Static-preknown memory Arena/Break space-dynamic runtime memory. It consists of heap & unused memory. Stack- whenever a program makes a function call, the current function’s state needs to be saved onto the stack. OAC

  22. OAC

  23. OAC

  24. Why Google? -They're big(ger than Yahoo). -Their search results are relevanced by inbound links. -They run on 10k+ linux boxes. Some RESULTS:: business: 86,900,000 linux: 31,600,000 market: 31,200,000 sex: 28,400,000 god: 24,300,000 microsoft: 20,200,000 ibm: 11,700,000 jesus: 8,800,000 chemistry: 5,210,000 macintosh: 4,860,000 python: 2,080,000 OAC

  25. OAC

  26. OAC

  27. OAC

  28. OAC

  29. OAC

  30. shell wildcards & regular expressions * een willekeurig aantal tekens ? 1 teken [abc] 1 teken uit een lijst [!abc] geen teken uit de lijst $xxx variable xxx $ last line /^The/ start of line /begin/,/end/ statement awk pattern OAC

  31. OAC

  32. FILTERS-1 OAC

  33. FILTERS-2 OAC

  34. FILTERS-3 OAC

  35. Quota’s # repquota -a /dev/dsk/dks2d1s7 (/home): -------------------------- Disk limits File limits User used soft hard timeleft used soft hard timeleft wit -- 145780 0 0 1987 0 0 lette -- 7320 0 0 450 0 0 vernooys -- 531044 0 0 28251 0 0 root -- 370276 0 0 2789 0 0 stol --1650808 0 0 10678 0 0 lammert -- 155180 0 0 4259 0 0 ehlers -- 217076 0 0 3655 0 0 veis -- 12196 0 0 220 0 0 ensing -- 81128 0 0 429 0 0 goumans -- 310612 0 0 4423 0 0 allaart -- 107348 0 0 1107 0 0 berkheij --1387576 0 0 10913 0 0 termaten -- 579912 0 0 6274 0 0 slootweg -- 87924 0 0 670 0 0 borst -- 100084 0 0 1479 0 0 vgisberg -- 12 0 0 4 0 0 vlaar -- 640012 0 0 6382 0 0 bulo --2080136 0 0 12111 0 0 OAC

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