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1. 9 26 Restarting daemons Send HUP hangup signal to process kill HUP pid Restart daemon manually etc rc d init d inet restart etc rc d init d network restart Use alias restart inet 9 27 Monitor Kernel Startup Trace with the kernel startup with dmesg This command prints var log dmesg dmesg gt foo 9 28 Strip downloaded text files of DOS linefeeds There are three different systems used for representing the end of the line in text files MS Windows uses ASCII CR LF Macintosh uses CR and Unix uses LF as end of line characters To convert from Windows to Unix use the t r command to strip the file of the excess carriage returns Strip excess carriage returns from Windows file tr d 015 lt fl in gt flout 9 29 Installing Debian 69 To convert from Unix to Windows insert carriage returns in front of line feeds tr 2 lt fl in gt fl out FTP servers attempt to handle these translations automatically when text mode is selected The end of line convention is part of what is Known in Emacs as the encoding Files written with the DOS encoding convention may be reset to the Unix convention within Emacs using C x RET f undecided unix 9 29 Installing Debian Useful mailing list debian user lists debian orghttp www debian org MailingLists A few packages cause many warnings when upgrading Debian These include kbuildsycoca and kio What causes these warnings kio KServicex WARNING The desktop entr
2. CONTENTS 111 9 14 4 13 9 16 9 17 9 18 9 19 9 20 9 21 9 22 223 9 24 9 25 9 26 9 27 9 28 9 29 9 30 9 31 a 9 33 9 34 9 35 9 36 9 37 9 38 9 39 9 40 9 41 9 42 9 43 9 44 9 45 9 46 9 47 9 48 9 49 LUKS cccp aege A EER OER ER SG 41 Install etc initscript to boost stacksizeso CCM can run o 42 Math Libraries lt o eco ea Se ee Oe BE Se Dean 42 Hardware description of Zender group computers 42 SIT A He ah ae GR Ss er ee NF FF 59 Create kr in disk strict re 5 scos Fee Fe a Oe Be Oe RAR RR 59 I wn A 59 NFS mount these disks on local machine oaoa 4545 44 eas 60 still sudo mada RS Oe Oe A e een Haag 62 DIAM IDL md POL to Boe A Rew Flew Geek A Iran 63 SL Pee ed a oe Kee AR ERR ERROR ES 65 PEMLIA rr Sw ER RR Ye Swe Se Ge le Sk ee 2 65 Building new kernel ociosa a Sa a Bu SHEDS 66 LILO configuration lt ses ces ceeace cea Se SOR ESS See Se Rw a 67 Restarting daemons GG REESE a a EH RE Re 68 Monitor Kernel Startup 64 c s2 2 Sa sa RES RRR ae Rw RS 68 Strip downloaded text files of DOS linefeeds 68 Installing Debian a R REED OU NG RG HD GG GU EU RR UA 69 Recreating Server Piles 4 4 2 44 28 4 2 RR RE ROE an an aa ah 74 ORE re Be eR HA NAU NY ANN 76 TNE os ee Oe ewe ee oe ec oe Bee Boe ee ee See 76 A ea ae IR Sk Ba Ba g 76 ok 5 EVEN ee ee t Oe See RO Be NY 77 E IM 71 a a ate Se te Becken NEFYN Be Ar yet 77 BE u bh ek A ne Se
3. sudo chmod arw var cache fonts ls R sudo chmod 666 dev dsp Sound device mode 660 causes permissions errors Make sure cdrom is mount point for dev sg0 in etc fstab Get hardware tools USB mouse reiserfs utilities sudo aptitude install gpm lm sensors smartmontools xfonts artwiz Get narr cd S DATA scp r dust ess uci edu data zender map Allow bds to run Create links to directories in DATA sudo mkdir p fs cgd home0 sudo ln s home zender fs cgd home0 zender sudo mkdir p fs cgd data0 sudo ln s data zender fs cgd data0 zender mkdir p S DATA csm inputdata lnd clm2 S DATA csm input sudo mkdir p fs cgd sudo ln s data zender csm fs cgd csm cd S DATA csm inputdata lnd clm2 scp r dust ess uci edu cd S DATA csm input scp r dust ess uci edu S DATA csm inp sudo mkdir p datashare inputdata csm DATA csm input ut atm dust ess sudo In s S DATA csm inputdata lnd datashare inputdata csm lnd Remove automatic gdm kdm xdm cd etc init d mkdir unused mv gdm unused Install ccache as default compiler sudo cp usr bin ccache usr local bin sudo In s usr local bin ccache usr local bin gcc sudo In s usr local bin ccache usr local bin g sudo In s usr local bin ccache usr local bin icc sudo In s usr local bin ccache usr local bin icpc Commands to set up a basic scientific computing environme
4. JDUnits 103 ID 8 114 nix 68 nmount 23 JP 114 JRL 77 a ESG EE cs E USB 8 USB Flash Drive 8 UTC 40 UUID 94 Virtual Private Network 16 VNC 96 VoIP 104 VPN 16 weet 103 wildcard characters 32 Windows 68 wireless ucar edu 27 wsu edu 27 X 9 12 13 17 39 87 X Window System 10 X org 14 X server 10 18 XDM 18 XFree86 9 14 Xine 77 78 ZIP disk 36 123
5. Nice EGU iwconfig ethl essid EGU2004 1 Nice EGU 192 168 33 181 iwconfig ethl ap 00 02 72 59 D9 0A key s 1122334455 Oslo Carlton Hotel iwconfig ethl essid IUGG R Perugia IAMAS Garden iuggpg4015 X cpra4C iwconfig ethl essid 2WIRE467 Sacramento curtisnet iwconfig ethl essid Free Public WiFi ap 02 18 DE 04 D0 48 San Antonio a iwconfig ethl essid WiFi4public ap 00 90 0E 00 32 C1 San Antonio airport e e iwconfig ethl essid Public Access Wifi ap 00 0D 67 00 5E 6l San Antonio iwconfig ethl essid linksys ap 00 18 39 87 E1 60 San Miguel de Allende cl iwconfig ethl essid default Sutter Creek dadnet 92 9 RSYNC The Intel ipw3945 driver does not automatically associate with the best quality network available e g from multiple UCInet access points You may configure a wireless interface to try access points in a certain order specified in file etc wpa supplicant conf e g o cat etc wpa_supplicant conf ctrl_interface var run wpa_supplicant network ssid name psk pass cat etc network interfaces allow hotplug ethl iface ethl inet dhcp wpa conf etc wpa_supplicant conf 9 44 ARP Address Resolution Protocol The Address Resolution Protocol ARP table maps ethernet addresses to IP addresses Examine the ARP table contents BuH98 p 173 with arp a Sometimes the ARP table contains duplicate or ill defined entries For example pump m
6. encrypt passwords yes in your smb conf file and you must create an appropriate smbpasswd file 9 42 DHCP Dynamic Host Configuration Protocol allows computers to configure as an Internet node with out a static IP address DHCP clients receive their IP address from the DHCP server The net work configuration files must be altered to enable DHCP On Debian systems this is configured in etc network interfaces with a line for the appropriate interface For example to configure et h0 usually the wired ethernet connection for DHCP use iface eth0 inet dhcp The pump command may work when DHCP does not sbin pump i ethO sbin pump i ethl status Inquire settings Note however that pump may corrupt the ARP table Section 9 44 9 43 Wireless 91 9 43 Wireless Wireless is a PITA Logging into wireless access in Starbuck s cafe Barcelona Virga procedure ifdown ethl iwconfig ethl essid UCInet Mobile Access ifup ethl ifdown ethl iwconfig ethl essid mangonet ifup ethl Ashes procedure iwconfig eth2 rate 54M Increase speed on internal broadcom chip iwconfig eth2 rate 5 5M ff Increase speed on internal broadcom chip Alphabetical by city name iwlist ethl scan List available hotspots iwconfig ethl essid any key off Reset wireless interface iwconfig ethl essid 313a2a ap 00 02 2D 31 3A 2A Albuquerque taylornet iwconfig ethl s 13a2a Albuquerque taylornet iwconfig ethl essid sid_ciencieswl
7. 103 113 GDB 103 106 Gettext 103 Ghostscript 103 Ghostview 103 GID 8 114 GLcore 10 globbing 32 glx 10 GMT 40 GNOME 18 GNU 111 GNU Linux 36 Gnuplot 103 Google 10 greenspeedisp net 27 Greenwich mean time 40 GRUB 67 GSL 103 Gzip 103 HDF 103 hibernate 93 high availability storage 24 hostname 40 65 HP printers 95 121 HPCToolkit 14 15 HTTP 96 109 HTTPS 96 HyperWRT 89 IDE 8 23 IDL 18 96 INET 60 initial ram disk 13 Intel 63 Inter Process Communication 98 Internal Server Error 109 IP address 40 87 90 92 112 113 IPC 98 IPCC 97 iPod 8 IPP 96 Java 26 JPEG 18 76 K3b 77 K desktop environment 18 Kai 63 kbuildsycoca 69 KDE 18 77 kernal packages 105 kernel 68 kernel headers 13 kio 69 Kmix 77 Knoppix 23 Lahey 63 109 LCD Projectors 18 Idd 103 LDP 11 LGGE 88 Libtool 103 111 LILO 67 linear 68 Linksys Wireless G router WRT54G 89 Linus Torvalds 114 Linux Documentation Project 11 locate 103 LS120 drive 36 122 LVM 21 M4 103 Mail Transfer Agent 26 Mail Transport Agent 27 Mailman 109 Make 103 malware 113 Matlab 103 Maxtor 19 media resource locators 77 memory leaks 107 Memory Stick 9 37 Mirroring disks 24 Mozilla 27 MPC 98 MPI 98 MPlayer 77 Mplayer 78 MRL 77 MTA 26 27 NACS 16 nameserver 40 NCAR 111 Ncbrowse 103 NCO 26 103 113 Ncview 10
8. cf Exclude backup files from being copied rsync av exclude x home zender cf 38 9 RSYNC There are different types of back ups Often a primary source location contains all impor tant information and is the first repository to remove deprecated files Back ups of this primary repository i e secondary repositories should delete these deprecated files side that rsync av delet xcl rsync av delet xcl rsync av delet xcl Backup to memory sti rsync av delet xcl rsync av delet xcl exclude x exclude x o exclude x so exclude x a exclude x mod exclude a zA Z x home zender media USB20F 9 1 Slink CK Delete files on receiving ded ded ded ded ded are not on sending side data zender snd dust ess uci edu data zender dust ess uci edu data zender snd data zender cvs exclude exclude home zender cf cvs exclude exclude x home zender mems cvs exclude D Backup NCAR CGD uses a tool called slink which makes appear as one whole tree cd data zender gsl 0 7 configure prefix contrib gsl 0 7 make make install cd contrib newgrp contrib co 1 slink conf ci slink conf slink exit 9 2 Documentation numerous separate software installations GNU Linux documentation is a little scattered RedHat and Debian GNU L
9. mailrc file and moreover works with all features of Emacs Remember to change the Emacs SMTP server when roaming setg smtpmail default smtp server smtp uci edu Sometimes it is useful to combine or juggle rmail and Mozilla mail folders cd HOME tar cvzf S DATA tmp mail tar gz mail scp S DATA tmp mail tar gz dust ess uci edu tar xvzf mail tar gz rm HOME mail x 28 5 SOFTWARE Synchronize mail backup repository sand to main repository virga rsync home zender mozilla thunderbird ktwn0dgv default Mail pop uci edu si rsync home zender mozilla thunderbird ktwn0dgv default Mail Local Folder Synchronize current client ashes elnino sand with main repository virg pth_src virga ess uci edu home zender mozilla thunderbird ktwn0dgv defau pth_src sand ess uci edu home zender mozilla thunderbird 1h6xplh6 defaul i pth_ _dst S HOME mozilla thunderbird prznnk5x zender elnino pth_ _dst S HOME mozilla thunderbird lsymr6b9 default ashes pth_ _dst S HOME mozilla thunderbird lh6xplh6 default sand rsync S pth_src Mail pop uci edu pth dst Mail rsync pth_src Mail Local Folders pth_dst Mail My user preferences file prefs js was corrupted on 20060222 Upgrading thunderbird while it is running is usually safe However this major upgrade to version 1 5 appeared to corrupt it See http www mozilla org unix customizing ht
10. smartctl t long dev hda Perform long disk test smartctl l selftest dev hda Check selftest error log The Im sensors package complements the SMART utilities 24 4 DISK MANAGEMENT sudo aptitude install lm sensors Install lm sensors Create devices on the local system cat gt mkdev sh lt lt EOF bin bash number of devices to create max 256 NUMBER 32 Device owner and group OUSER root OGROUP root Set device mod MODE 600 Do not run script if devfs is used if r proc mounts then if grep q dev devfs proc mounts then echo You do not need to run this script as your system uses devfs exit fi fi i 0 while i lt SNUMBER do echo dev i2c i mknod m MODE dev i2c S i c 89 i exit chown SOUSER SOGROUP dev i2c i exit i i 1 done EOF chmod 755 mkdev sh Make mkdev sh executable sudo mkdev sh 4 7 Mirroring Disks Chad Cantwell used hardware RAID 1 to join two Maxtor 150 GB disks on dust as home on dirt ess uci edu Mirroring disks to other disks is a smart strategy for creating high availability storage The RAID status is in proc mdstat mdstat contains a percentage done while setting up and then the final RAID status afterwards This is configured via etc raidtab 4 8 Garbage collection Through time most disks accumulate unwanted files such as core dumps intermediate files and obsolete files U
11. usr sbin exportfs rv By default NFS exports filesystems with a feature called root sguashing enabled With root sguashing enabled processes do not maintain root priveleges when writing to an NFS exported partition on a different machine This is a useful security measure but plays hell with poor man s cron scripts that backup files across machines To override root sguashing use the no_root_squash option in the exports file To export NFS filesystems securely update hosts allow and hosts deny as appropriate In particular hosts allow must allow access to all machines that request INET services from a ma chine with NFS mounted home directories To restrict INET services to specific hosts use e g cat etc hosts allow portmap 128 200 14 25 To allow INET services to all hosts use e g cat etc hosts allow portmap ALL To restrict INET services to all hosts use e g cat etc hosts allow portmap 128 200 14 25 portmap 128 200 14 62 portmap 128 200 14 39 portmap 128 200 86 234 This may prevent errors revealed by gconf sanity check 1 gconf sanity check 1 9 20 NFS mount these disks on local machine Here are the mountpoints to use on lanina when mounting the central fileserver partitions at NCAR sudo mkdir p ncar fs cgd home0 sudo mkdir p ncar fs cgd data0 sudo mkdir p ncar fs cgd csm 9 20 NFS mount these disks on local machine 61 Once these mountpoints exist the mach
12. webalizer 109 xdm 17 18 xf86cfg 9 xhost 17 xine 77 xldb 109 xosview 98 xrestop 9 INDEX xset 12 89 xterm 11 xvidtune 13 Xdefaults 13 bashrc 64 config 67 deb 101 mailrc 27 rhosts 39 shtml 110 ssh 112 boot 14 114 data 21 114 dev modem 38 dev perfctr 15 dev sda1 8 dev ttySO 38 etc X11 default display manager 18 etc X11 gdm gdm conf 17 etc X11 xinit xserverrc 17 etc cups cupsd conf bak 88 etc desktop 18 etc fstab 21 22 61 etc gdm gdm conf 17 etc hosts 40 etc init d nvidia glx 16 ete init d pgi Imgrd 65 etc initramfs tools conf d resume 94 etc inittab 12 18 etc kde Kdm kdmrc 17 etc network interfaces 90 etc pcmcia network opts 65 etc pcmcia network 65 etc pcmcia 65 etc raidtab 24 etc rc firewall 96 etc resolv conf 40 86 etc ssh ssh config 112 etc sysconfig network scripts ifcfg ethO 85 etc sysconfig network 85 etc wpa supplicant conf 92 etc 74 home 22 114 proc mdstat 20 24 proc sys 67 INDEX root 62 sys 9 usr bin perl 103 usr local lib valgrind default supp 108 usr 114 var log XFree86 0 log 14 var log Xorg 0 log 14 var log dmesg 68 var log httpd 109 var spool cron crontabs root 36 var spool cron root 36 var spool cron 36 var spool mqueue client 26 var www html 110 var 114 XF86Config 4 10 14 17 XF86Config 9 10 17 apache2 conf 110 aut
13. Driver synaptics Option SendCoreEvents true Option Device dev psaux Option Protocol auto dev Option HorizScrollDelta 0 Option MinSpeed 0 5 Option MaxSpeed 0 7 Option AccelFactor 0 0350 EndSection Another way to do this is to add Option SHMConfig on and then aptitude install ksynaptics Make sure the 100 dpi fonts are installed or else many xterm and emacs fonts will appear chunky Font management and installation is described by the Linux Documentation Project LDP at http www linuxdoc org HOWTO Font HOWTO html X can be made to use any font desired but the reguired procedures to do so are arcane Here is a skeleton outline ps ax grep xfs Check for running font server xfs xset g Check font path xset fpr unix port_number Add font server xfs port to font path xset fp rehash Rehash font path sudo etc rc d init d xfs restart Restart font server xfs end verbatim None of this should be necessary on a trmidx RedHat GNU Linux machine since RedHat has an automatic way of serving fonts Instead what should be done on all machines is to list in order of preference the valid font directories in the verb Files section of the flidx XF86Config 4 file begin verbatim Section Files 12 3 X AND XFREES6 FontPath usr Xl1R6 lib Xll fonts local FontPath usr Xl1R6 lib Xll fonts misc FontPath usr X11R6 lib X11 fonts 75dpi unsca
14. NTP FAQ is http www eecis udel edu ntp ntpfag NTP a fag htm As of about 1999 few Stratum 1 timeservers will accept synchronization reguests from Stratum 3 machines Stratum 3 machines should synchronize with any publically accessible Stratum 2 server listed for example at http www eecis udel edu mills ntp clock2 htm I chose server 132 239 254 49 ntp ucsd edu Alternatively the ntpdate command works just like rdate and can be used when the NTP daemon itself is unavailable Changing the system timezoneis describedathttp www wikihow com Change the Timezone mv etc localtime etc localtime old Backup old TZ file ln s usr share zoneinfo Europe Amsterdam etc localtime Set new TZ usr bin rdate s time nist gov f Update current system time Set ZONE entry e g America Los_ Angeles in etc sysconfig clock sbin hwclock systohc Set hardware clock 9 13 Perl ln s usr bin perl usr local bin perl 9 14 Links Whenever home is re installed many links must be recreated Links may be listed with ls recursive classify grep Ga For machines at NCAR it is best to store source code in fs cgd home0 zender and create links to HOME so that the larger object files and executables will not consume the expensive space on the central fileserver cd HOME mkdir p lib PVM ARCH 42 9 RSYNC mkdir p obj PVM_ARCH mkdir p bin S PVM_ARCH mkdir include ln s fs cgd home0 zender sh
15. Yes Floating point operations These options are requested as follows hpcrun e PAPI_TOT_CYC 32767 e PAPI_FP_OPS 32767 e PAPI_FP_INS 32767 e PAPI_HW_INT 32767 e PAPI_L2 DCM 32767 lt command_to_profile gt hpcrun profiles everything that results For example command_to_profile is a shell com mand then hpcrun profiles every subcommand in the shell and gives each its own output file in the form of app_name PAPI_TOT_CYC clay ess uci edu 10137 0 Process hpcrun output files into something usable with hpcquick hpcquick is a Perl script that calls some other hpctools to generate the XML database in its own subdirectory that hpcviewer needs src location hpct DB file to process hpcauick I src nco P ncwa PAPI TOT CYC clay ess uci edu 10137 0 View results with Java hpcviewer hpcviewer Open the hpcguick dbxxx hpcguick hpcviewer file To use oprofile on clay reguires a re compiled kernel with the profiling switches enabled Once re compiled the kernel may require a new Nvidia driver This may require un installing and purg ing packages e g aptitude remov purg nvidia glx If the package is not purged then etc init d nvidia glx which runs at each startup may wipe out the TLS links that the new Nvidia driver needs 3 4 Virtual Private Network VPN Use a Virtual Private Network VPN to obtain a UCI net address from an off campus computer sudo etc in
16. a bad block list i e a list of blocks it will not attempt to write to The recommended procedure to create such a list is to first identify the device e g dev hda7 Then logout of any windows accessing that device and unmount it This may be tricky if the partition is used by the umount itself or a dynamic library upon which the executable depends libc for example If this occurs one can presumably boot from a rescue floppy and execute umount from there Then run e2fsck c on the device A highly recommended rescue floppy known as Tom s root boot is available from http www toms net rb home html hjm 1 23 06 updatedb on sand locate is a very useful tool on many ix systems however it can overwhelm you with output especially if it is used on a system that has filesystems and backup directories It is useful to grep the output to for the lead path or remove backup directories from being included in the locate db by entering them in the etc updatedb conf This has been done on sand to avoid cluttering the output with repeated entries from the backup mirrors hjm 5_ Software 5 1 netCDF Browsers There are at last four freely available netCDF file browsers ncview ncBrowse NCVweb and panoply 26 5 SOFTWARE 5 1 1 ncBrowse ncBrowse ncBrowse is a Java application 5 1 2 panoply panoply It functionality is somewhat limited in that logarithmic axes are not allowed 5 1 3 ncview ncview Dave Pierson s exc
17. data lvoll lvcreate lvcreate L 5g dev data Create space for usr local lvcreate L 5g dev data Create space for home lvcreate L 42g dev data Failed due to not enough space lvcreate L 39g dev data Create space for data mkdir mnt home sbin telinit 1 nkdir mnt data 5y nkdir mnt local cd mnt nkreiserfs dev data lvol nkreiserfs dev data lvol2 nkreiserfs dev data lvol3 4 4 4 4 ls usr local mount dev data lvoll mnt home mv home mnt home ls mnt home ls home mount dev data lvol2 mnt local mv usr local mnt local ls mnt local ls usr local umount home local vi etc fstab mkdir data mount data more etc fstab tune2fs j dev hdal Turn ext2 partition into ext3 tune2fs j dev hda6 Turn ext2 partition into ext3 4 6 Knoppix 23 tune2fs j dev hda7 Turn ext2 partition into ext3 more etc fstab tune2fs j dev hda5 Turn ext2 partition into ext3 emacs nw etc fstab Turn home usr local boot data into reiserfs shutdown r now 4 6 Knoppix Knoppix is a Linux distribution useful for previewing hardware and for rescuing downed comput ers Knoppix offers many boot time options Specify these at the boot prompt knoppix lang us Change language from default German to English knoppix 2 Boot to run level 2 knoppix screen 1600x1200 S
18. dmg Mount disk image file cd Volumes OSXvnc 0 6 Look at mounted image cp r OSXvnc app Applications Copy package to software directory cd Volumes OSXvnc 0 6 OSXvnc app Contents MacOS Directory with executal Applications OSXvnc app Contents MacOS OSXvnc amp Run VNC f Window pops up on Macintosh prompts to start VNC server Recommended password is grape hdiutil unmount Volumes OSXvnc 0 6 Unmount disk image file hdiutil unmount dev disk2 Unmount disk image file To view from Linux use vncviewer c 67 169 127 154 client comcast net l IP display Fink URL http fink sf net hdiutil attach Fink 0 6 1 Installer dmg Mount disk image file installer pkginfo pkg Volumes Fink 0 6 1 Installer Fink 0 6 1 A Installer pkg target sw Needs a pkg package Query package info sudo installer pkg Volumes Fink 0 6 1 Installer Fink 0 6 1 Installer pkg target sw Install package requires sudo password hdiutil unmount Volumes Fink 0 6 1 Installer Unmount disk image file hdiutil unmount dev disk3 Unmount disk image file 6 Programming 6 1 Operator precedence The operator precedence of most languages follows that of the C language Table 2 summarizes operator precedence of C Precedence decrease from top to bottom the first line has highest prece dence 6 2 Regular expressions The alphanumeric pa
19. expressions in Emacs is both a pleasure and a problem Some example regular expression search and replaces that work and what they do Replace foo by foo query replace regexp w I MI nil nil nil Replace character foox80 by character 80 foo guery replace regexp character XA V W A 0 9 N character NM2 AI Replace end do I by end do query replace regexp end do lif end 11 nil Replace foo I by foo as long as is not followed by query replace regexp A t n X1 nil Replace floating point number X Y with floating point number X Yf e g query replace regexp 0 9 0 9 L1Dd NMIf nil Replace floating point number X Y with floating point number SX YS e g query replace regexp 0 9 0 9 LlIDd XN SAIS nil Replace command foo bar by command foo ensuremath bar query replace regexp command x command 1 ensuremath 2 One often composes text in an Emacs buffer then copies and pastes that buffer into another program e g a browser or mail program Browser and mail windows often have column width limits imposed so it is helpful to compose with the same column width in Emacs The command to set the maximum buffer width is set fill column The argument to this command is the number of columns Entering the
20. files from one pac dpkg info foo Examine archives dpkg install foo Install package foo Use this not aptitude install dpkg list foox Locate all packages named foo dpkg listfiles foo Which files does installed package foo own dpkg print avail foo Print details about package foo dpkg purge foo Remove package foo deb including configuration files dpkg P foo Remove package foo deb including configuration files dpkg remove foo Remove package foo deb leave configuration files intac 102 9 RSYNC dpkg search foo Which installed package owns file foo dpkg S foox Which installed package owns installed file foo dpkg status foo Print installation status of package foo dpkg vextract foo bar Display filenames contained by package foo in dir dpkg reconfigure foo Re configure installed package foo 9 52 Required software 103 9 52 Required software required software Following is a list of scientific software required for research teaching Most of these packages are installed by default with standard and or power GNU Linux distributions such as Debian and RedHat Since these are free as in no cost software packages it is easiest if they are all installed on all machines i e no differences between servers and clients This Software should be installed in usr local by default This avoids pathname proliferation Packages may be inst
21. gcov sr bin cpp 4 2 usr bin cpp sr bin g 4 2 usr bin g sr bin gcc 4 2 usr bin gcc sr bin gfortran 4 2 usr bin gfortran e MPI MPICH2 distribution recommended MPICH or LAM MPI uci edu data zender tmp mpich2x install S DATA tmp mpich2 doc_1 0 2 3_i386 deb mpich2_1 0 2 lam4c2 lam4 dev lam mpidoc lam runtime install rpm mpich mpich common mpi doc int do yun in stall t in stall au in stall an tomake autoconf bison curl devel tetex fonts tetex dvips texinfo tex flex librx librx devel x r antlr c devel antlr manual do yun do yun n N do yum n N in stall do Packages aptitu scp dust ess uci edu data zender tmp 1f9562 tar gz S DATA tmp Install netcdf by hand sudo aptitu titu de de libdap install gsl gsl devel netcdf nei libnc dap libnc dap devel 0 dev libdap deve bin libgs gs install Install Li uses Fortran90 build finishes C build netcdf perl libxml simple perl Opendap requires de install libcurl3 dev libxml2 dev 12 9 RSYNC Install nr by hand needed by fff Install specfun needed by fff Install udunits needed by NCO cd c make makdep Build makdep only cd nco bld make Build NCO module needed by mie cd nco sre nco_c make f Makefile old i
22. hda2 101105 30766 65118 33 boot none 1037348 0 1037348 0 dev shm dev hdc2 191440744 73245868 118194876 39 data3 6 7 05 installed Intel icc compiler debugger on soot in opt end soot ess uci subsection SuSE Linux label sxn suse The Zender group server mchidx sand ess uci edu runs trmidx SuSE Linux Professional version 9 0 9 18 Create krein disk structure 59 SuSE offers phone support at 1 510 628 3385 Monday Friday from 9 007AM 3 007PM PST SuSE email support is at url support suse com Our registration logyn is csz and the password is pw _lw Our SuSE software serial number is 48205940904172 Yast Online Update location should be ftp ftp suse com pub suse Configuring printers with SuSE is non trivial but good technical details are given at mchidx portal suse com Search the support database for trmidx CUPS subsection Browsers label sxn moz UCI libraries make many trmidx journal subscriptions available for free on the campus network or from remote locations provided that browser trmidx proxy settings are correctly configured begin verbatim http www lib uci edu services how connect html Describes proxies http www nacs uci edu help proxy UCI proxy instructions Change Preferences gt Advanced gt Proxies gt Automatic proxy configuration to http proxy uci edu proxy_config pac Use for automatic proxy configurati 9 17 1 Firefo
23. http distrowatch com 9 56 2 Upgrading RedHat Linux For network upgrades and installs you must first create a bootnet img floppy to install from and then specify the network address of the RedHat FTP repository dd if bootnet img of dev fd0 bs 1440k ftp ftp uci edu mirrors redhat linux 6 2 i386 RedHat ftp ftp uci edu mirrors redhat linux 6 2 1386 images bootnet img 9 57 Debugging Debugging is an art as much as anything A list of debugging methods sorted by past efficacy is 1 Compile programs on different platforms One compiler may notice errors that another compiler does not report SGI compilers are especially good at finding errors 2 Compile with bounds checking if possible 3 Run with MALLOC_CHECK_ 1 in environment 4 Link to memory debugging libraries like Electric Fence ftp ftp perens com pub ElectricFence or dmalloc http dmalloc com 5 Be sure that the shell has enough resources e g memory to run the program or the crash may be especially mysterious This can involve using the ulimit command e g ulimit s unlimited However this command may require special permissions to execute 6 When all else fails use a symbolic debugger like DDD gdb 89 59 The Electric Fence debugger works very well cith C language programs However Electric Fence may hinder debugging C programs C programs linked to the Electric Fence library libefence a may generate obscure errors within DDD GDB s
24. nc rawdata mksrf_lai nc rawdata mksrf_lanwat nc rawdata mksrf_navyoro_20min nc rawdata mksrf_pft nc rawdata mksrf_soicol_clm2 nc n n n n n rawdata mksrf_soitex 10level nc rawdata mksrf_urban nc rtmdata rdirc 05 srfdata cam clms_64x128_T42_c020514 nc do if f SICSMDATA UCI S f1 then scp babyblue ucar edu CSMDATA NCAR S fl S CSMDATA UCI S fl fi endif done export USER_FC 1f95 cd clm clm sh 4 2 ESS 200B EARTH SYSTEM PHYSICS 2 ESS 200B Earth System Physics Atmospheric Physics and Radiation Course Description Physical processes which mediate the transformation of energy heat and momentum in the Climate system Topics include hydrostatics convection radiative forcing and climate feedbacks Here are topics for the 5 Week ESS Atm Phys Radiation mini course Each bullet is one week and is subdivided into two parts Hydrostatics Thermodynamics Buoyancy Convection Radiance Absorption Flux Emission Scattering Actinic Flux Clouds Direct Effects Aerosols Indirect Effects Earth s Energy Budget T lt gt Climate interactions Oda O DN The text has been chosen to dovetail with other courses Global Physical Climatology by Hartmann Each day s topic Tues Thurs structure comprises the key points enumerated below which are to be illustrated by theoretical and practical examples from the course tex
25. observed spectrum of the clear atmosphere GHGs and the atmospheric window Scattering actinic flux 1 Reflection 2 Direct vs diffuse radiation 3 Particle light interaction 4 Size parameters Mie theory 5 Photochemical radiation 6 PAR NDVI definitions Clouds 1 Formation Lifecycle 2 Cloud climatology cloud classification taught in Hydrology nN 2 ESS 200B EARTH SYSTEM PHYSICS 3 Particle size distributions 4 Radiative properties 5 Liquid ice distinctions 6 Direct radiative forcing LW SW Net Aerosols 1 Formation Lifecycle 2 Global sources 3 Sinks scavenging dry deposition 4 Global distribution amp radiative forcing 7 Vertical flux heating profiles for realistic atmospheres Indirect Effects 1 Daisyworld 2 Indirect forcing via clouds 3 Surface Atmosphere partitioning of absorption 4 Global energy budget including latent sensible heat 2 6 Meridional heat transport atm ocn Nutrient transport T lt gt Climate interactions Physical Climate Change Coupling of troposphere stratosphere change lis 2 Coupling of troposphere land surface change 3 Water vapor feedback 4 Effects of altered lapse rates 5 Thermal expansion of oceans 6 Estimating RF of GHG increases 7 Observed indirect effects Notes on course design Topics which might belong in other courses which assume will b
26. resolv conf should be bearmtn 128 117 24 2 9 38 LGGE The external web homepage at the Laboratoire de Glaciologie G ophysique de l Environnement LGGE in Grenoble France is http www lgge ujf grenoble fr eng LGGE is cordoned off by a firewall The outside facing LGGE SSH server is triolet obs ujf grenoble fr The two step hop to log into ashes from outside the LGGE firewall is ssh triolet obs ujf grenoble fr ssh lgge pcl94 Virga static IP ssh 192 168 102 194 Virga static IP ssh 192 168 102 5 Virga inexplicably drops static and switches to DHCP ftp ftp Triolet is also ftp server login to ftp as zender ftp ftp Triolet is also ftp server login to ftp as anonymous cd pub depot zender ftp ftp pub depot zender The automatic proxy configuration file for accessing the web via a browser inside the firewall is http proxy ujf grenoble fr auto proxy pac The internal LGGE homepage is http www yes you read that correctly The LGGE homepage for Linux is http 1gge pc240 and for printer configuration is http lgge pc240 631 printers My USA UCI printer configuration file is in etc cups cupsd conf bak LGGE supports NFS mounting the Linux partitions on lgge pc240 ls mnt mkdir mnt lgge pc240 mount lgge pc240 usr local mnt lgge pc240 ls 1 mnt lgge pc240 bin ncbo mnt lgge pc240 bin ncbo r Pour imprimer partir du poste linux imprimante Noir et Blanc HP la
27. s extglob 6 3 Bash Use hash to rehash commands in Bash e g hash r This is equivalent to rehash or reset in csh Systemwide defaults are set in etc ssh ssh_config The Bash shell supports a wide variety of built in commands command line editing job con trol and history features 1 s foo bar Repeat previous command substitute bar for foo Il s foo bar Repeat previous command substitute bar for foo foo bar Repeat previous command substitute bar for foo Ifoo s foo bar Substitute bar for foo in most recent command containing 6 4 Internationalization I1 8N 33 6 4 Internationalization I18N Create a local directory structure to hold x mo machine object files created from po portable object by gettext machinery One directory is needed for each language mkdir p HOME share locale es LC_MESSAGES System wide translation database is under usr share locale The installation of gettext is its own documentation Examine usr share gettext intl to see how its done Emacs po mode e1 should be loaded whenever po files are loaded 34 7 FILES 7 Files 7 1 Date conventions This section describes conventions for naming files from geophysical models We adopt the usual convention that DD is a two digit sequence to indicate the day of month DD 01 02 31 MM is a two digit sequence to indicate the month of year MM 01 02 12 and YYYY is the four dig
28. said I m not sure of the total complexity that doing such a thing under SW RAID would have entailed To do this with 2x 4 port controllers would have reguired additional complexity and I m not sure it can be done easily with mdadm And it is possible that I did something wrong in the 3ware rebuild I ll be sending this narrative back to them as well As a postscript to this I should also mention that while most Linux server vendors sell 3ware cards at least one Los Alamos Computers suggests SW raid as being both significantly cheaper and faster They suggest the Promise SATA TX4 for about 70 Newegghasthesupported in kernel SiliconI magechipsettedSyba4portcar df or30 If you remember my previous posts I was surprised to find SW RAID to be a bit 10 20that I probably should have tried the SW RAID on a full 2TB array Well you makes your choices and you takes your chances Currently the 3dm2 SW is running and should be restarted with a reboot commands to re start are in etc init d local Will test to be sure The 3dm2 web interface can be gotten at sand 888 and the password for user read only is Sware The admin password is about a coyote resistant neighbor s cat 6 7 05 noticed that the 3dm2 daemon was reverting to original settings on each reboot It hadn t written a config dir etc 3dm2 3dm2 conf and so was losing the config It also wasn t complaining that it couldn t do it to stdout err to dmesg nor to syslog rsync back
29. set Received at UCI SMU 2007 1221 20071228 Dell Service Tag JB1S8F1 Complete Care until 20111213 Gold support until 20111213 Express Service Code 42026989213 4 year limited warranty plus 4 year NBD on site service and complete care Gold technical support Intel Core2 Extreme CPU X7900 2 8 GHz 800 MHz FSB 17 UltraSharp Wide Screen WUXGA 24x CD RW DVD burner 8x DVD RW DVD ROM Blu Ray Re writable 4 GB RAM NVidia Quadro FX 1600M 512 MB Windows Vista Business Product ID 89576 OEM 7332141 00054 Intel Wireless WiFi 4965AGN Broadcom NetXtreme 57xx Gigabit Con troller MAC address 001C231F2730 wired broadcom MAC address 001DE0289E6D wireless ipw4965AGN Sound controller problems https wiki ubuntu com Gutsy_Intel_HD_Audio_Controller Get video working nvidia glx new UPEK Fingerprint Reader ttp thinkfinger sourceforge net tp packages ubuntu com hardy admin libpam thinkfinger O D Dell site for BIOS updates ttp linux dell com wiki index php Repository firmware udo aptitude install firmware tools firmware addon dell eb http linux dell com repo gutsy dell software ttp direct2dell com one2one archive category 1021 aspx Four steps to firmware updates udo wget g O http linux dell com repo firmware bootstrap cgi bash udo aptitude install firmware addon dell udo aptitude install S bootstrap_ firmware a udo update_firmware Uuuu o Qu D vir
30. the 11 1 o command must be run after installing a kernel and prior to rebooting the machine If it is necessary to rescue a machine that boots with LILO one must construct rather complex 1ilo commands to synchronize the system Find major minor device numbers on other RedHat machine ls 1 dev sdal 1 dev sda3 Create devices with correct numbers mknod dev sdal b 8 1 mknod dev sda3 b 8 3 Create mountpoint directory mkdir mnt root Mount disks with root and kernel images mount dev sda3 mnt root mount dev sdal mnt root boot Change root directory to simplify paths for lilo chroot mnt root Change root from RedHat rescue to disk 68 9 RSYNC chroot mnt sdb3 sh Change root from Knoppix CDROM to disk cd ls Verify we ve changed root sbin lilo Simplest form Unless chroot succeeded lilo may need following arguments b Location of boot device sbin lilo b mnt sdbl C Location of configuration file default etc lilo conf sbin lilo C mnt sdb3 etc lilo conf i Location of bootloader default boot boot b sbin lilo i mnt sdbl boot b When updating the kernel make the old working image available as a backup image boot vmlinuz 2 4 23 label linux image boot vmlinuz 2 2 16 22 label linux 2 2 16 22 lilo conf must specify the linear keyword to boot off a SCSI disk e g dirt ess uci edu
31. usr local bin uci_dcs_lnx_pch pl Replace 7 0 and 1386 with appropriate version and architecture information below then run as root The kernal packages and C library are stored in CPU specific directories for maximum performance Update these directories first e g 1686 instead of i386 Then update the rest of the packages sudo mount ftp uci edu extra ftp mirrors redhat mnt cd mnt linux updates 9 en os i686 CPU specific e g kernel updates rpm Fhv rpm cd mnt linux updates 9 en os i386 rpm Fhv rpm rpm Fhv mnt linux 7 2 en os i386 preview RPMS rpm Fhv mnt linux 7 2 en os powertools i386 RedHat RPMS Remotely update all RedHat RPMs against UCI Redhat Mirror rpm Fhv ftp ftp uci edu mirrors redhat linux updates 7 2 en os i386 w r Remotely update all RedHat RPMs against UCI Redhat Mirror rpm Fhv ftp uci edu mirrors redhat linux updates 7 2 en os i386 rpm When a large number of simultaneous updates are reguired to patch a system the command rpm Fhv rpm may not work In this case break the task down into smaller tasks for rpm e g 106 9 RSYNC for ltrinabcdefghigjkimnopgrstuvwxyZz2ABCD EFGHIJKLMNOPORSTUVWXY Z do rom Fhv 1tr x rpm done Another option is to install the RedHat Rawhide distribution This distribution is available from ftp ftp redhat com pub redhat linux rawhide i386 A useful comprehen sive list of distributions is maintained at
32. 0 UP LOOPBACK RUNNING MTU 3924 Metric 1 RX packets 120 errors 0 dropped 0 overruns 0 frame 0 TX packets 120 errors 0 dropped 0 overruns 0 carrier 0 collisions 0 pppoO Link encap Point to Point Protocol txqueuelen 0 inet addr 128 117 68 69 P t P 128 117 64 227 Mask 255 255 255 2 UP POINTOPOINT RUNNING NOARP MULTICAST MTU 1500 Metric 1 RX packets 621 errors 4 dropped 0 overruns 0 frame 4 TX packets 650 errors 0 dropped 0 overruns 0 carrier 0 collisions 0 zender haze ifconfig a from UCI etho Link encap Ethernet HWaddr 00 10 A4 A0 9D 9D txqueuelen 10 inet addr 128 200 14 62 Bcast 128 200 14 255 Mask 255 255 255 0 UP BROADCAST RX packets 6 TX packets 4 collisions 0 Interrupt 11 RUNNING MULTICAST MTU 1500 Metric 1 18084 errors 0 dropped 0 overruns 0 frame 0 16759 errors 0 dropped 0 overruns 0 carrier 0 txqueuelen 100 Base address 0xe000 lo Link encap Local Loopback inet addr 127 0 0 1 Mask 255 0 0 0 UP LOOPBACK RUNNING MTU 16436 Metric 1 RX packets 28 errors 0 dropped 0 overruns 0 frame 0 TX packets 28 errors 0 dropped 0 overruns 0 carrier 0 collisions 0 9 36 Kernel Modules txqueuelen 0 Modules may be listed with the 1 smod command inserted with insmod probed with modprobe or removed with rmmod lsmod List loaded modules insmod foo Install loadable kernel module modprobe ohcil394 modprobe rawl394 Occas
33. 0 4 DISK MANAGEMENT chunk size 32 device dev hdel raid disk 0 device dev hdgl raid disk d device dev hdil raid disk 2 device dev hdk1 raid disk 3 mkraid dev md0 mke2fs v j b 4096 R stride 8 dev md0 dev md0 raid ext3 defaults 1 2 To check the status of the RAID view proc mdstat o more proc mdstat Personalities linear raid0 raidl raid5 read_ahead 1024 sectors mdQ active raid5 hdel 0 F hdk1 3 hdi1 2 hdgl1 1 480238656 blocks level 5 32k chunk algorithm 2 4 3 _UUU unused devices lt none gt T have had a disk failure a couple of times a RAID failure fixable with raidhotada not an actual problem with the disk Issuing the raidhot add command fixed it first view proc mdstat to see which disk failed raidhotadd dev md0 dev hdel Bootup and shutdown It does not appear that any of the RAID commands raidstart or raidstop appear in any of the startup or shutdown scripts but it all seems to come up and down properly RAID commands raid0run raidhotgenerateerror raidstart raidhotadd raidhotremove raidstop 4 2 Servers Sand Modifications 3 29 05 by hjm 200 gb disk from lanina moved to sand on IDE bus 1 new hoary ubuntu distro loaded on 200gb disk as Filesystem 1K blocks Used Available Use Mounted on dev hdal 10482044 2048572 8433472 20 tmpfs 1786416 0 1786416 0 dev shm dev hda6 105294788 5897208 993975
34. 00 14 62 Dell Inspiron 8000 Dell order 609532437 UCI is Dell customer 6774301 46 9 RSYNC Laptop is UCI PO 0119L03200561 Shipped on 2001 07 31 System Service Tag JGP4R01 Express Service Code 423 685 352 17 Touchpad is PS 2 compatible Two 59 WHR LI ION batteries Pentium III 1 GHz 512 MB SDRAM 48 GB Hard drive Fixed Internal CD RW DVD combination drive 100 MB ZIP drive interchangeable with 3 5 floppy drive 15 UXGA display Video controller NVIDIA GeForce 2 Go Video w 32 MB DDR AGP 4X Grey Microsoft USB mouse with 3 buttons Audio controller ESS Maestro 3 Xircom RealPort 10 100 56K Ethernet Modem Combo PC Card Type 3 PCMCIA tulip_cb driver etc pcmcia config device tulip class network module cb enabler tulip card Xircom RealPort2 10 100 Fast Ethernet version Xircom R2E 100BTX Bought extra battery from http www computergiants com Attached to printer hp5180 zendernet fxm HP Photosmart C5180 All in One Printer Scanner Copier Purchased from Carrefour Echirolles 20070905 Takes 6 pack ink cartridges type part number 363 Hangs off zendernet router MAC address 001a4b954ae8 Serial Number MY6CRO217F04MK Firmware Version R063 1MxNxxN0 Service ID 17249 Problem printing is Network host 192 168 1 2 is busy will retry in 30 seconds Netgear wireless router WGR614v7 Serial 1JS2767T02DC9 MAC address 001B2F5B6BFC Default access http www routerlogin net ESSID zend
35. 03 AC97 modem device forced to iobase_0 0xb400 iobase_1 0xb080 irq 11 http www linuxvoodoo com store index php cPath 45_66 Bought netgear card from Fry s on 20041211 for 45 25 20 NetGear WG511 802 11B G D Link Wireless Cardbus NIC 802 11 g 108Mbps MAC address 00 09 5B E8 C4 El NetGear WG511 802 11B G 20050818 Bad internal disk problem report filed with Dell https wiki ubuntu com HardwareSupportMachinesL suggests pci noacpi acpi noirq biogenic ess uci edu 128 200 14 73 Dell Precision 530 Arrived Jan 10 2002 Serial number HJKZ411 Service Tag HJKZ411 Express Service Code 38189387557 UCI Property 019003703 Intel R Xeon TM CPU 1 50GHz hp5850 ess uci edu 128 200 15 157 44 9 RSYNC Hewlett Packard 5850 Color inkjet printer in Croul 1101 silt ess uci edu 128 200 14 156 clay ess uci edu 128 200 14 158 UCI property number for both as Los Alamos Cluster 059000194 Los Alamos Computers LAC order 014214 Both are dual opterons on a Tyan Tyan S2885ANRF motherboard onboard firewire Dual AMD Opteron 246 2 0 GHz 1M L2 cache 2G PC3200 registered ECC DDR RAM 1 has 2GB of PC2100 one has 4GB of PC3200 nVidia Corpora tion NV34 GeForce FX 5200 128MB RAM w video w DVI 3x 250GB WD SD series SATA disks WDC WD2500SD 01K hdc SONY DVD RW DW D26A ATAPI CD DVD ROM drive 3 5 inch floppy drive Onboard gigabit NIC Multimedia audio controller Advanced Micro De vices AMD AMD 8111 AC97 Audio rev 03 Four port USB 2 0 PC
36. 0312 from CompUSA in Boulder 1100 AMD K6 2 3d Processor at 400 MHz Serial number 1X91CFDH8662 10 GB Hard disk hjm 03 03 05 added 200GB disk added ProMEPIS Debian OS in following partitions hdal 10GB OS hda2 1GB swap hda3 home 78GB hda4 data spare 64 MB RAM hjm 03 03 05 upgraded to 256MB with simms from home 120 MB Super disk aka LS120 mounted as mnt ls120 dev hdd hda WDC AC310000B 9541MB w 512kB Cache CHS 1292 240 63 hda WDC AC310000B ATA DISK drive hdc LTN382 ATAPI CDROM drive hdc ATAPI 40X CD ROM drive 120kB Cache hdd LS 120 COSM 05 UHD Floppy ATAPI FLOPPY drive Floppy drive s fd0 is 1 44M Rockwell HCF 56 kbps DataFax modem on PCI bus COM2 dev ttyS 1 3COM US Robotics 56 kbps winmodem on ISA bus COM 1 dev ttyS0 IRQ4 52 9 RSYNC NIC PCI Fast ethernet DEC 21143 based controller Graphics Rage LT PRO AGP 2X XF86_Mach64 server USB PCI disk controllers Graphics Rage LT PRO AGP 2X 19 Monitor purchased separately 19990901 from CompUSA 350 Horizontal scan frequency 30 95 KHz Vertical scan frequency 47 150 Hz Supports 1024x768 68 6 KHz 85 Hz non interlaced Supports 1280x1024 80 KHz 75 Hz non interlaced Supports 1600x1200 93 7 KHz 75 Hz non interlaced Computed following modeline settings using above info and http www dkfz heidelberg de spec linux modeline V freq 85 00 Hz h freg 68 79 KH
37. 0819 NB Flash differs from Shockwave There is no Linux Shockwave p sudo aptitude install flashplugin nonfree libmad0 totem xine Not available in Ubuntu sudo aptitude install foiltex latex2html tth Install audio player software sudo aptitude install gtkpod xmms Install TightVNC for webcasts sudo aptitude install tightvnc java tightvncserver xtightvncviewer Install acroread not necessarily recommended sudo aptitude install acroread acroread plugins S udo aptitude install xine ui 9 29 Installing Debian xine Watch DVDs Get LaTeX working 73 sudo mv ifdraf sudo mv moviel sudo mv datet sudo mv fmtcoi scp r dust ess uci edu tex cls tex scp r dust ess uci edu usr share texmf tex latex ifdraft scp r dust ess uci edu usr share texmf tex latex moviel5 scp r dust ess uci edu usr share texmf tex latex datetime scp r dust ess uci edu usr share texmf tex latex fmtcount scp r dust ess uci edu usr share texmf tex latex ifsym sudo mv ifsym u scp r dust ess uci edu usr share texmf tex latex revnum sudo mv revnum scp r dust ess uci edu data zender ps erbe_b_s1d012d_8589_0 17 _x_ LS WC scp dust ess uci edu data zender ps uci_fax pdf dust ess uci edu data zen scp r dust ess uci edu tex bst tex cd tex sudo mkdir usr share texmf texlive bibtex bst csz sudo cp bst x
38. 1 Laptop is UCI PO 0120L03002256 Shipped on 2000 01 11 System Service Tag Y20Z8 Express Service Code 572 015 24 Touchpad is PS 2 compatible Pentium mobile III 500 MHz 512 MB 100 MHz RAM 25 GB Hard disk 120 MB Super disk aka LS120 mounted as mnt ls120 dev hdc Display is 15 0 SXGA active matrix color Video controller ATI Mobility P 64 bit AGP 2X w 8 MB RAM ati X org server Controller supports 32 bit color but LCD display limited to 18 bit Infrared IrDA 1 1 port Logitech first mouse 3 button PS 2 compatible Audio controller ESS Technology Maestro 2e Sound Blaster Pro compatible udev DEVPATH bus pci drivers ES 1968 ESS Maestro udev UDEV 1170546089 233339 add module snd_ udev PH YSDEVDRIVER ES 1968 ESS Maestro http occy net taxonomy term 6 from 20 In order to get sound working on my Mom s Dell Inspiron 8200 using Ubuntu Linux I had to do the following edit etc hotplug blacklist add snd intel8x0m edit boot grub menu lst add kopt root dev hdal ro acpi irg isa 7 make SURE you leave in the above run update grub Wireless Lucent technologies Orinoco silver card Orinoco MAC address 00 02 2D 09 82 E2 Xir com 32bit Cardbus Ethernet 10 100 Modem 56 aka CBEM56G 1 03 Xircom MAC address 00 10 A4 08 12 31 PCMCIA tulip_cb driver etc pcmcia config device tulip_ cb class network module cb enabler tulip cb card Xircom CardBus 10 100 Ethernet 56K Modem version Xircom
39. 294788 5897208 99397580 6 dev hda3 73278252 2128912 71149340 3 dev 10482044 2048572 8433472 20none 5120 2836 2284 56 9 17 Hardware description of Zender group computers 53 sand was upgraded to 4GB ram of which 3 5 is available to the system a little mentioned weirdness of Opteron systems is that the 0 5 GB of RAM just below 4 GB disappears into the memory mapping black hole that AMD inherited from INtel After the SW raid experiment sand has 3ware Escalade HW raid card driving eight identical Western Digital 2500jd drives in a RAID 5 config yielding 1 7TB usable It looks to the system like a single SCSI disk 5 13 05 disk failure on sand s RAIDS partition detected on reboot in dmesg not by log or email as expected At this point the data was still intact and SHOULD have been backed up to another system but since it was HW RAID5 AND it was 3ware controller known for reliability HA and robustness HA AND this was acting as the backup for other systems which were still OK AND the data was 200GB at this point I thought it was ok to go ahead MISTAKE First thing was to find the problem of why we hadn t been informed of the failure beforehand The controller a 3ware Escalade 86506 8port driving 8x250GB identical WD disks has like most such cards a BIOS based utility for setting up the RAID which actually worked pretty well except that unlike SW RAID you can t use the raid immediately in degraded mode while it s build
40. 3 NCVweb 26 netCDF 25 26 103 netcdf perl 103 network file system 59 network time protocol 41 NFS daemon 60 NFS lock daemon 60 nfsd 60 NNTP 96 NTP 41 96 nv 93 NVidia 13 93 Nvidia 16 93 nvidia 93 Octave 103 open source 13 OpenGL 10 13 INDEX OpenMP 63 OpenOffice org 95 OpenPGP 99 OpenSSH 112 operator precedence 29 oprofile 16 OS X 28 Panoply 103 PAPI 14 15 PBS 97 98 PCMCIA 8 PDF 37 Perl 16 32 103 PHP 110 Ping 96 poll_idle 15 POP3 96 port 87 96 port 22 92 Postfix 27 PPP ii 38 printing 95 Procfs 67 Promise cards 19 proxy 88 purging 16 Python 26 R 103 RAID 19 RAID 5 19 RAM 114 Rawhide 106 RedHat 17 18 26 36 38 63 65 66 85 95 103 106 regular expression 29 rehash 32 reiserfs 23 relative path 17 required software 103 RHEL 97 rmail 27 Rocks 97 root 60 78 INDEX root user 36 root kits 113 root squashing 60 RPM 97 100 103 RSA 112 RSA1 112 rsync 96 runlevel 12 18 S 103 SCSI 9 23 68 Skype 104 SMART 23 SMP 114 SMTP 26 27 96 SMTP server 27 SourceForge 97 Sourceforge 113 spyware 113 SSH 87 92 96 110 ssh 92 SSI 110 standby 93 suppresions file 108 SuSE 77 suspend 93 suspend to disk 93 suspend to RAM 93 Tar 103 TCP 96 TCP forwarding 17 TEX ETEX 103 tiff 76 TLS 16 27 Tramp 97 Jbuntu 14 26 63 JCAR 111 dev 9
41. 46 PCMCIA Get rid of annoying beep when PCMCIA is inserted Add to etc sysconfig pcmcia CARDMGR_OPTS q kill HUP cardmgr_pid Use cardct1 to notify system of PCMCIA card status changes To suspend eject or resume the card use cardctl suspend Shut down disable power for socket cardctl eject Notify client drivers card will be ejected cut power cardctl resume Restore power to socket re configure for use cardctl reset Send reset signal to socket cardctl status Display current socket status flags cardctl ident Display card identification information cardctl config Display the socket configuration To restart the entire pcmcia subsystem or to remove the eth0 interface use sbin ifconfig eth0 down etc rc d init d pcmcia restart sbin ifconfig eth0 up To trace shell execution use e g sh x etc sysconfig network scripts ifup ifcfg eth0 9 47 core dumps RH6 1 default etc profile uses the ulimit command to limit size of core files with ulimit c 1000000 This causes an error on telnet logins so comment it out 9 48 Printing 95 9 48 Printing RedHat causes spool directories in var spool 1pd to be owned by root with group 1p If this is not the case then printing may fail with permission denied errors comp os linux setup suggested adding to etc conf modules alias parport_lowlevel parport_pc This appears to fix printer gueue permission denied errors on dakine
42. 5s dks9d5s dks9d5s dks9d5s dks9d5s data zender ZENDER dks9d2s dks9d3s dks9d4s dks9d5s dks9d5s dks9d5s dks9d5s dks9d5s dks9d5s dks9d5s 0 B 9 21 Install sudo As root install sudo scp dust scp dust O BIAN match O ZENDER mat O DSS O aca O csm O data 0 dgn O match O tmp IAN match d O ZENDER match O DSS O ZENDER csm d O aca data zen O csm data zen O data data zender data O dgn data zen O match data zender match O tmp data zen data zen O ZENDER csm ch ata zender BIAN match data zender ZENDER match der DSS ata zender ZENDER csm der aca der csm der dgn der tmp ess uci edu etc sudoers etc sudoers ess uci edu usr bin sudo usr bin sudo The sudo command has some subtle problems First sudo does not alter HOME To execute commands with HOME changed to the target user i e root invoke sudo with H root but does not change sudo H foo Change S HOME to root Second sudo carries the user s environment with it Often it is desirable to see a command executed exactly as it would be if it were being execture from a root login shell 9 22 Install IDL and PGI 63 Initialize SHOME SSHELL SUSER SLOGNAME and SPATH Un set all other variables sudo i foo ff Run command as in initial login shell Some GNU Linux distributions such as Ubuntu do not enable the root account by default In ste
43. 80 6 data dev hda3 73278252 2128912 71149340 3 home 4 3 Formatting Disks 21 dev 10482044 2048572 8433472 20 dev none 5120 2836 2284 56 dev hjm 6 7 05 200GB IDE disk moved from lanina failed SMART test replac new spare on same IDE bus Kubuntu ubuntu KDE installed there is currently no floppy on sand dev d0 media floppy0 auto rw user noauto 0 0 4 3 Formatting Disks Ocassionally disks are added or need to be replaced There is a lot one can know about formatting disks Fortunately a few commands suffice for most situations The venerable fdisk family of commands is important The recommended formatting command is cfdisk a curses based disk partition table manipulator The command to build a Linux filesystem is mk fs cfdisk dev hdc Build partition table on dev hdc mkfs t ext3 dev hdcl Build an ext3 filesystem on dev hdc Once the disk is partitioned with cfdisk and formatted with mkfs add an entry to the etc fstab The entry should be for e g dev hdc1 the partition not dev hdc the disk Make sure the mount point exists as a directory e g data before attempting to mount it In May 2007 I formatted a 100 GB replacement disk for elnino as ext 3 using the partition name hdc1 This seemed to work fine for a few reboots until one day in June the hdc1 device could not be found I found the other disk devices were using sda1 style terminology presumabl
44. 9 54 NCO and patches Updating NCO with patches The only difficult thing about patches is remembering the switches used to create and apply them cd nco Create patch relative to top level NCO directory cvs diff c gt feature patch Create patch cd nco Apply patch from top level NCO directory patch p0 lt feature patch p0 Causes patch to use unmodified file names I have simplified remembering the last command by adding 1is patch patch p0 to my bashrc file When patches go wrong they can be unapplied with patch p0 R lt feature patch R Reverse patch patch p0 reverse lt feature patch reverse Reverse patch 9 55 Skype The UCI VoIP FAQ is here Skype is an application which allows free IP based telephony between registered users The skype program package for Debian is at http www skype com download skype linux Once registered simply start sk ype from a console Inspiron 9400 users have found that the audio captured via microphone plugged into the ex ternal jack is almost inaudible on playback One solution is use the command line alsamixer program to set the Capture recording level to 75 75 Apparently the 9400 uses the microphone input for dual purposes and this may eventually be sorted out by software Ekiga is another program that uses VoIP My ekiga address is sip zender ekiga net Ekiga is supposed to work with cameras like my Logitech QuickCam Pro for Notebooks This ca
45. Barcelona UAB ICTA iwconfig eth2 essid IAMAS 2005 Beijing IAMAS iwconfig ethl essid UCAR Boulder NCAR UCAR heartbeat on wireless ucar ed iwconfig ethl essid UCAR ap 00 1B 2A 64 F1 50 Boulder NCAR Director s Con iwconfig ethl essid UCAR ap 00 1B 2A 64 F3 40 Boulder NCAR Chapman Room iwconfig ethl essid UCAR ap 00 1B 2A 64 F3 60 Boulder CMS offices e e iwconfig ethl ap 00 18 F8 FA BD 46 Greenbelt Marriott EOS Aerosol Cloud R e e e Se Sh Sh OSE Se e H iwconfig ethl essid COMINN key s wificomfort38 Grenoble Comfort Inn iwconfig ethl ap 00 0F 24 F1 89 BO Irvine 1103 Croul iwconfig ethl ap 00 0F 24 F1 89 40 Irvine 3101 Croul iwconfig ethl ap 00 0F 24 F1 87 10 Irvine 3228 Croul iwconfig ethl ap 00 0F 24 F1 86 90 Irvine 3103 Croul iwconfig ethl essid UCInet Mobile Access Irvine UCInet access points iwconfig ethl essid panera Irvine Panera iwconfig ethl ap 00 0F 66 8E B6 D3 Irvine mangonet iwconfig ethl essid mangonet ap 00 0F 66 8E B6 D3 Irvine mangonet iwconfig ethl essid Hale_La _Aloa key 6efd8clbee Kona iwconfig ethl essid traveler99 key FEEBED7A49 Lyons cliffnet e e iwconfig ethl essid linksys ap 00 18 39 87 E1 60 Lyons cliffnet iwconfig ethl essid Blue Tile Beach House key s beach Maui iwconfig ethl essid Guest New London iwconfig ethl essid NICEXPO
46. But this is untested on lanina which has given parport errors on bootup in the past If lanina is booted up unconnected to the printer and then the printer is connected later and printing is attempted an error may result such as 2000 12 30 17 13 18 388Get_local_host host When this occurs printing will fail and restarting the print daemon will also fail The solution is simply to rename the machine e g sudo hostname lanina and then restart the printer dae mon and then printing should succeed 9 48 1 CUPS CUPS is the Common Unix Printing System Configure CUPS by pointing a web browser to http localhost 631 The HP4600 network color laser printer is configured to accept IPP as http hp4600 ess uci edu 631 ipp portl The HP4350 network laser printer is configured to accept IPP http 192 168 14 2 631 ipp port1 The Tek850 color printer is tek850 ess uci edu 128 200 24 133 The HP6840 color printer is hp6840 ess uci edu 128 200 24 134 The most informative site for printing on Linux is http www linuxprinting org They sponsor a newsgroup with an email gateway for virtually all types of printer especially HP printers Web Portal to HP printers may be useful aptitude install cupsomatic ppd Install latest CUPS ppd drivers killall HUP cupsd Restart CUPS daemon etc init d cupsys restart Restart CUPS daemon lp plan Print file to default printer lp plan http hp4600 ess uci edu 631 ipp port
47. Huisheng Bian n m p 1 n m p S Schar add n to turn off creation of group name 1 1Scharl i d home kwon g cgdcsm m p SIScharlies d home bian g cgdcsm n N P S1Schar esv c Alf Grini d home alfgr g cgdcsm m p S SlIScharlieSVJFp c Dave Newman d home newman g cgdcsm n c Sarah Bortz d home bortz g cgdcsm m p 1Scharlie VJl c Renato Pajarola c Jorge Talamantes c Dan Stromberg c Francisco Lopez d home lopez g esmfadm c Greg Okin d home okin g cgdcsm m p 1 c Harry Mangalam c Test User d home test g cgdcsm m p 1 c ESMF System Administrator N P d home strombrg g esmfadm S1Schar G users m G users m p Schar esv d home pajarola g cgdcsm m p S 1 cha d home jtalaman g cgdcsm m p S1Sch P ie VJFpv d home hjm g cgdcsm m p S1ScharlieSv c CVS M g cgdcsm u 3562 cvspub c ESS 211 Class Account c Hsun Ying Kao c Gayathri Venkitachalam Schar ieS SVJFpv d home esmfadm g cgdcsm m d home ess211 g cgdcsm m p 1 d home hkao g cgdcsm m p l1 charlies v d home gvenkita g cgdcsm m p c Chao Luo d home chaoluo g cgdcsm m p S1ScharlieSVJF c Oin Han d home qhan g cgdcsm m p S 1ScharlieSVJFpvyB 9 30 Recr
48. I card Logitech Z560 400W speakers 4 satellites sub Chenbro SR10403 enclosure 3 case fans Enermax 460W power supply quiet and dependable disks are mostly in raid5 config Filesystem 1 K blocks Used Avail able Use dev md1 15496084 1864536 12844376 13tmpfs 1028532 0 1028532 O dev mdO 100954 14318 81424 15 dev md2 462259168 34468 438743308 Inone 5120 2708 2412 53where the md devices are setup like this DEVICE partitions ARRAY dev md2 level raid5 num devices 3 UUID b190d39b cad75d67 7abb3ee1 8c71f882 devices dev sda8 dev sdb8 dev sdc8 ARRAY dev md1 level raid5 num devices 3 UUID ba4fb 7ff 85a95d9c 988a6647 1d9d8f8c devices dev sda6 dev sdb ARRAY dev md0 level raid1 num devices 2 UUID c8d86633 d20e14e3 f9025448 de67a792 de vices dev sda5 dev sdb5 Monitors are Viewsonic VP201b 20 LCD Model number VLCDS26064 2W Serial numbers A21050401846 A21050401861 Connections to Cisco 3550 first floor switch are 1 Gb s 1 to jacks 75 sand 48 silt and 56 clay These occupy ports 1 3 of the total 10 jacks In switch closet blue panel goes to station yellow goes to switch dirt ess uci edu 128 200 14 25 Dell Precision 610 Shipped 19990902 from Dell Computer on UCI PO System Service Tag 4R5EJ Express Service Code 7985179 Dual 500 MHz Pentium III Xeon with 512 KB Level 2 cache 1 GB RAM Primary SCSI controller for hard disks Adaptec AIC 7890 Ultra2 Wide LVD controller Adaptec 2940 UW equivalent Two 36 GB SCSI disks QUANTUM Model A
49. IN PGP PUBLIC KEY BLOCK Version GnuPG v1 4 3 GNU Linux mOGiBEVhlbcRBADRCbLu370lsu2cOjckAlAgzvHBjJMYOMtdOjJOe rv9rp6StXyM SNp6GhpwX3b8 amp j6r0NkT6fOgwaUh uvxdTRRlFOJF7tHVAg0n9uYlstKFgROCrcur UP74FgfEvgh5pFL8sI05ay0MO7GZ01h54rO0AO 17TK29ttNDIyg2hpyWwCg7tfm n03gbegdOhC9N1EikO7jCd0EAMg2ceX8ehJv41701dpb4O5zogKYcto7BHULlUPAY v9FYt42MsF1kH6EOXCTrHAA pJ9sfCCrWKZbRtYkZGipJnB8bxl9kxUvlRtPHXSdJ PHyckPOTSeyCAX0 YbyOWMSsZYKMZf2t0VIlEIMLSjTgwpu2OY zSyi0Lx9kr2K8y bUdpBACXoGOSVBZdEX3zZ ck50gan874UbTbOTxB3yw5Ry58CL52eZXaYP0v9pWL9 cCe9hAoVlY2sH5fgZnKwOpT0HeNYcCdcY7wBtVnnW 4bjeljv5MsP2tkgsT2ucYg S4HDpfshfH0OGwpUMHgDgfwXgyO0UG4setLd5jfhct9UVptdZ8tLOfO2hhcmxpZSBa ZW5kZXIgPHplbmRlckBlY2kuZWRlPohgBBMRAgAgBOJFYdW3AhsDBgsJCAcDAgOV AggDBBYCAwECHgECF4AACgkOy5FJrwW9jJXRC60ACgkWtdilBohVmiaxTwGXgstMSF JZUAnApKDwlVOOpTlDUwlCxpCgeAYwRmuOINBEVhlb8OCACyZg28taaSucl0vMSC 7ZB5KOZgrrSDuuEjl9p7Wwu83E6MppsZKOWyhjKJAhmjnAMYAgOexN5xSjgi500Or Df pP rULN4 9Ec 90qu2z B2074NZA3237t 4ATZnMz810saL7R BjtpEK jh43SDOmd 1lD9Da3aNYP04V2tU78F8Iusg3 k66Ppirv9XZrvLsApCgj Bt0PJUbOvznt0cUYBS M4wvUsMzZMB6iffWrCfAo2gaPCsgYEDEvMNlKiM15jOi7wNFCAOtxrs8sWO6LVIH8 VpPaMNCEPIlUrH95FTuPIklnEC2sk8WFzmCNWgRBTP iTeXF5lzvz580OXg7joVoHp oNO0OrAAMGB 9n AOrRMLIv9nSzM R2505VBAiAU vkarllSABpN4H S2F8Br7ehrK OWEo2yuStwcu2Hl F02OwaaNDMZK0sUGMrbgHDGd venbIKu F7mEWfXndP8MbXx eT9tTjD0Oirm42JSTIO7SA6ROg5eX0iPapCGbhrBLemv0OitRl0OE3YBf1t86UELlL6 MzSJUv8xo lodt8FxFvM8nKSEs CAxwYFkAUV 8IrGdmd6ZTgwFcegNSm5Vr811K BBe2xc
50. M which consumes a small amount of power in order to retain its contents so that upon resuming everything is loaded back from the memory and all running applications are restored immediately According to the article the following should be in the device section of xorg conf Option VBERestore true The suspend action may be invoked by e g the suspend sh script in the article The hibernate action saves the state to disk and powers down According to linux com hiber nate is also known as ACPI State S4 or suspend to disk On reboot the kernel senses that a saved state is available and reloads it Experimented with ACPI on Ubuntu 6 06 LTS on 20060604 by connecting the actions to the lid shut button action Results follow Suspend on ashes blanks screen and turns off wireless With nv driver lid up restores without problems except must manually restart wireless interface With nvidia driver lid up get that black melty look and must manually re boot Also both nv and nvidia driver intermittently after a few hours may reboot on ashes This may indicate an xorg conf problem However nv driver seems to have problems with translucency In fact translucency could be a problem with nvidia as well Hibernate on ashes With nv driver saves session to disk and powers down Session restores correctly on re boot except must manually restart wireless interface With Nvidia driver nothing happens no shut down at all Suspend on virga
51. MRLs are similar to URLs with media like protocols Most audio video players do not allow direct control of volume perhaps because the computer speakers are a shared resource Hence it is wise to start the audio controls before the video player Kmix is a fine audio controller to use 9 34 1 MPlayer MPlayer accepts many of the same commands that work with Xine kmix amp Volume control mplayer dvd 1 Quickstart DVD playing mplayer dvd 1 dvdangle 2 Multiangle DVD playing mplayer http mplayer hg example avi Stream from HTTP mplayer rtsp server example com streamName Stream using RTSP mencoder mf jpg mf fps 25 o output avi ovc divx4 Encode all jp mencoder tv driver v4l width 640 height 480 tv o tv avi ovc raw fl Mplayer has difficulty with full screen mode 78 9 RSYNC 9 34 2 dvdrip sudo apt get install lame sudo apt get install dvdrip vcdimager cdrdao subtitleripper sudo apt get install rar unrar sudo ln fs usr bin rar usr bin rar 2 80 rsync data zender snd dust ess uci edu data zender cd data zender rsync dust ess uci edu data zender snd 9 34 3 Xine Xine accepts many of the same commands that work with Mplayer kmix amp Volume control xine dvd 1 Quickstart DVD playing xine dvd 1 dvdangle 2 Multiangle DVD playing xine http mplayer hq example avi Stream from HTTP xine rtsp server example com streamN
52. NkpokPH2Zfam7W7TeoldSvF7RUXGDoEMorkXvuKGkb6rjwv4k j8 krbNu V WGP7GerNFkblJDu3fcC2CFglpvsFfgiEKkEGBECAAkFAkVhlb8CGwwACgkOy5FJ 100 9 RSYNC rW9jJXRAZnwCdHhbbyY0H5bszcM7cj3kXnYoEIPoAn3DXHYEmnSXBZ FJJc0LTG8 WEy6 YKOf END PGP PUBLIC KEY BLOCK 9 51 3 Building RPMs HOWTO build RPMs as a user http myy helia fi karte linux doc rpm build as user html sudo yum y install rpm build etc rpm macros c GPL 2003 Tero Karvinen at sign iki fi o o packager S echo SUSER _topdir echo SHOME rpmbuild _rpmtopdir _topdir name _builddir _rpmtopdir BUILD _rpmdir _rpmtopdir _sourcedir _rpmtopdir _specdir _rpmtopdir _srcrpmdir _rpmtopdir _tmppath _rpmtopdir TMP uildroot _tmppath name root oo AP AP AP AL o9 AL AY AL ol o Build rpms in your home directory without root priviledges Users can copy this file to SHOME rpmmacros to override settings such as packager to Firstname Lastname email Example of typical directory and file hierarchy for rpm building rpmbuild rpmbuild nano replace nano with rpm name rpmbuild nano TMP rpmbuild nano BUILD user must create this dir and files can be extracted from a source rpm with rpm2cpio src rpm cpio dvi rpmb
53. Online http dust ess uci edu doc Updated Linux Cheat Sheet by Charlie Zender University of California at Irvine Department of Earth System Science University of California Irvine CA 92697 3100 Contents Contents List of Tables 1 CCSM Community Climate System Model 1 1 CAM Community Atmosphere Model 1 2 CLM Community Land Model 2 ESS 200B Earth System Physics A 2 Se A 2a CO eke ho eS REE A BR 21 CompactFlash osos HEAR EA 2 2 2 Memory Stick ss ee eee ee hes 3 X and XFree86 3 1 X and XFree86 Configuration 3 2 XFree86 NVidia Graphics drivers 3 3 Performance Profiling e 2 4 ess nen 3 4 Virtual Private Network YPN 2 2 4 244 es 3 3 DE OOO rr a a Raia 3 6 XFree86 Multiple sessions oa x xxx 5 37 LED Protectors 3 2 2er eae heehee EE REE Od 3S II eck ek AAA AAA Gee He Se AIN 4 Disk Management A O ann PEK Does SO Fe HE ak 4 1 1 Hardware 2 200 0 eT ee 4 1 2 Getting Promise cards to work AA nie ee d2 Servers Sad ee Be ae Re a e 4 3 Formatting Disks 2 22 2 2220 2 20 220 2 2824 8 84 Tue 25 Mar 2008 15 36 zender uci edu Voice 949 824 2987 Fax 949 824 3256 ii CONTENTS 44 Creating LVM o co ek ee 254 OER SSS OPA OES SHE OPEL HEELS HX 21 gt LVM GW ashes ooo ot Se a Y A a Sx 22 Ao AIRE TARA 23 4 7 PO BED OE a A ARA RA Boe he Bowe AR RA 24 de TIESTO a pic a ee is EOE Bann 24 49 Diskcorr ption sisas 25 S
54. PPP gateway to UCI Genmask Flags MSS Window 2995729572994 295 UH 2992952992939 UH 299429542950 U 255 0 0 0 U 0 0 0 0 UG oOo OO 0 0 oOo O00 0 with lanina as PPP gateway to UCI Genmask Flags MSS Window 255 255 255 255 UH 209 Zoo 3299 0 U 00 255 0 0 0 U 00 0 0 0 0 UG 00 with lanina as PPP gateway to UCI Genmask Flags MSS Window 295 299 4299200 UH O 0 255299299 30 U O 0 255 0 0 0 U O 0 0 5 0 0 0 UG O 0 from NCAR as dhcp25 cgd ucar edu Genmask Flags MSS Window 295425520 20 U O 0 255 0 0 0 U O 0 0 0 0 0 UG O 0 irtt OO OOO irtt ooo irtt Co CG co irtt 0 0 0 with lanina as PPP gateway to NCAR Genmask Flags MSS Window 259 A PSA LO A UH 0 0 2 99 0 0 0 U O 0 0 0 0 0 UG O 0 irtt 0 0 0 If et et If et PP et PP If pp et PP If et et et If PP PP 9 35 Network ifconfig a zender ashes ifconfig a dummy 0 etho ethl lo Link encap Ethernet BROADCAST NOARP RX packets TX packets collisions RX bytes 0 Link encap inet addr 128 200 14 90 at UCI MTU 1500 HWaddr 00 81 wired working wireless not quite 00 00 00 00 00 Metric 1 0 errors 0 dropped 0 overruns 0 frame 0 0 errors 0 dropped 0 overruns 0 carrier 0 0 0 0 b Ethernet UP BROADCAST RUNNI TX bytes 0 HWaddr 00 Beast NG MULTICA
55. ST 0 0 b 0B DB 17 83 0D 128 200 14 255 Mask 255 255 255 0 MTU 1500 Metric 1 RX packets 9379086 errors 0 dropped 0 overruns 0 frame 0 TX packets 1543592 errors 0 dropped 0 overruns 0 carrier 0 collisions RX bytes 1840313132 Link encap 20 1 7 GiB Ethernet HWaddr 00 MTU 1500 BROADCAST MULTICAST RX packets TX packets collisions RX bytes 0 Link encap inet addr 127 0 0 1 0 errors 0 errors 0 0 0 b TX bytes 1113652359 1 0 GiB 90 4B B2 09 86 Metric 1 0 dropped 0 overruns 0 frame 0 0 dropped 0 overruns 0 carrier 0 TX bytes 0 Local Loopback Mask 255 0 0 0 UP LOOPBACK RUNNJ RX packets TX packets collisions RX bytes 1488519751 ING MTU 16436 0 0 b Metric 1 errors 0 dropped 0 overruns 0 frame 0 errors 0 dropped 0 overruns 0 carrier 0 zender dust dotS ifconfig a etho lo Link encap inet addr 128 200 14 25 UP BROADCAST RUNN I 13954461 13954461 0 1 3 GiB Ethernet HWaddr 00 Bcast NG MULTICAST RX packets 5406688 errors 2103 TX packets 1398865 errors 0 dropped 0 overruns 0 carrier 24 collisions 62451 txqueuelen 100 Link encap Local Loopback inet addr 127 0 0 1 UP LOOPBACK RUNNI TX bytes 1488519751 1 3 GiB C0 4F 60 73 8D 128 200 14 255 Mask 255 255 255 0 MTU 1500 Metric 1 dropped 0 overruns 0 frame 3179 Interrupt 17 Base address 0xdc00 Mas
56. TLAS 10K 36WLS Secondary SCSI controller for CDROM Adaptec AIC 7880 internal Ultra Narrow and external Ultra Wide Adaptec 2940 UW equivalent SCSI CDROM NEC Model CD ROM DRIVE 466 Audio System board integrated 16 bit Crystal CS4237B audio controller chip which emulates Sound Blaster Pro card from Creative Laboratories Inc NIC 3Com 3C905b TX Wakeup On LAN capable uses a 3Com 3C918v2 ASIC 24 Dell UltraScan P1690 1920x1200 60 Hz 75 0 kHz hsync See http support dell com oti monitors P 1690 En specs htm Dell warranties monitor syncs at 1920x1200 resolution with hsync 95 kHz vsync 76 Hz dot 9 17 Hardware description of Zender group computers 45 clock 245 5 MHz horizontal vertical sync polarity Video controller Diamond Viper 770D AGP PCI video adapter with 16Mb of SGRAM This controller is based on the NVidia RIVA TNT2 chipset and uses the XF 8 6_ SVGA driver IOmega 250 MB ZIP drive elnino ess uci edu 128 200 14 97 Dell Precision Mobile Workstation M50 4400 Arrived 20030129 Service Tag 4RPK921 Express Service Code 103 826 513 53 UCI Property 039003413 1 GB RAM 15 UXGA IEEE 1394 elnino inherited haze s second battery which is a 66 Whr JP 04M778 42016 2CR 1656 24x CD R W 8x DVD ROM nVidia Quadro 4 500 GoGL 64MB VGA Intel Mobile Intel R Pentium R 4 M CPU 2 20GHz stepping 07 512B L2 Cache hda IC25T060ATCS05 0 ATA DISK drive hdb Samsung CD RW DVD ROM SN 324B ATAPI CD DVD ROM drive NB hdb requi
57. TOPOINT RUNNING NOARP MULTICAST RX packets TX packets collisions MTU 1500 Metric 1 216 errors 1 dropped 0 overruns 0 frame 1 221 errors 0 dropped 0 overruns 0 carrier 0 0 txqueuelen 10 zender lanina ifconfig a from NCAR as dhcp25 cgd ucar edu etho lo Link encap inet addr 128 117 22 248 UP BROADCAST RUNNING MULTICAST RX packets TX packets collisions HWaddr 00 10 A4 08 12 31 Bcast 128 117 255 255 Mask 255 255 0 0 Ethernet MTU 1500 Metric 1 9198 errors 0 dropped 0 overruns 0 frame 0 529 errors 0 dropped 0 overruns 0 carrier 0 28 txqueuelen 100 Interrupt 11 Base address 0x200 Link encap inet addr 127 0 0 1 Local Loopback Mask 255 0 0 0 UP LOOPBACK RUNNING MTU 3924 RX packets TX packets collisions zender lanina dots etho Link encap inet addr 192 168 1 2 Metric 1 468 errors 0 dropped 0 overruns 0 frame 0 468 errors 0 dropped 0 overruns 0 carrier 0 0 txqueuelen 0 ifconfig a with lanina as PPP gateway to NCAR Ethernet HWaddr 00 10 A4 08 12 31 Bcast 192 168 1 255 Mask 255 255 255 0 BROADCAST MULTICAST RX packets TX packets collisions MTU 1500 Metric 1 0 errors 0 dropped 0 overruns 0 frame 0 0 errors 12 dropped 0 overruns 0 carrier 12 0 txqueuelen 100 84 Interrupt 11 9 RSYNC Base address 0x200 lo Link encap Local Loopback inet addr 127 0 0 1 Mask 255 0 0
58. The web interface software however while it started up and presented an optimistic login screen gave no indication of what the passwords should be or where to go to set them After looking in the config file etc 3dm2 3dm2 conf only to find encrypted passwords I then wandered around the 3ware web site trying to find documentation about how to set or even find out what the initial passwords were There were no docs or help files or README s with teh software it s 3ware for those of you going thru the same hell you can change them via the web interface when you finally get in Re the passwords nothing or at least nothing I could find in about an hour s searching I finally decided to look in the installation script bingo The passwords are set and encrypted into the config file from there SO after setting them to what I wanted FINALLY I was able to log into the web interface and talk to the controller And in fact after being able to log in the help file DOES tell you what what the password is and how to change it Actually the tw_cli app also works but it s pretty ugly altho give them credit they DID make 2 linux specific clients The one that I needed was the 3ware 9000 series 3DM2 Linux64 bit one helpfully on the web page I eventually found http 3ware com support downloadpageeng asp SNO 4 both the 32 bit and 64 bit one are named the SAME THING So here I am talking to the 3ware controller via the web interface
59. ZZZ_MM Ensemble mean of month MM from years YYYY through ZZZZ one record 10 caseid _YYYYZZZZ_0112 Ensemble mean of seasonal cycle sampled from years YYYY through ZZZZ twelve records 11 S caseid _YYYY_ZZZZ_MM Timeseries of month MM from years YYYY through ZZZZ ZZZZ YYYY 1 records 12 S caseid _YYYY_ZZZZ_ MMNN Timeseries of month MM through month NN means from years YYYY through ZZZZ ZZZZ YYYY 1 records 7 1 13 14 15 16 17 18 19 20 21 22 23 Date conventions 35 caseid _YYYY_ZZZZ_0305 Timeseries of Springtime means from years YYYY through ZZZZ ZZZZ YYYY 1 records caseid _clm_0112 Twelve month seasonal cycle caseid _YYYY_0112 Annual mean seasonal cycle 12 records Note this is an ex ception to the general rule It is unambiguous however because the mean of all twelve months is simple representable by the caseid _YYYY convention caseid _YYYY_MMNN Mean of months MM through NN 1 record caseid _YYYY_0305 Springtime mean 1 record caseid _YYYY_ZZzZZ Annual mean timeseries multiple records Stcaseid _YYYYMM ZZZZNN Monthly mean timeseries from YYYYMM to ZZZZNN inclusive multiple records caseid _ YYYYMMDD_ ZZ ZZNNEE Daily mean timeseries from YYYYMMDD to ZZZZNNEE inclusive multiple records S caseid _YYYY_ZZZZ_t Mean of annual mean timeseries from YYYY to ZZZZ inclu sive single record Stcaseid _YYYYMM ZZZZNN_t Mea
60. a is fixed IP lanina ess uci edu running Linux Execute following commands on lanina This topology setup works but lanina does not resolve names on local ssh dust ess uci edu works but ssh dust does not hostname lanina ess uci edu hostname i v sbin ifconfig eth0 down sbin ifconfig eth0 1 down sbin ifconfig eth0 lanina zender org Connect IP address with Ethern sbin ifconfig ethO inet 128 200 14 80 Connect IP address with Ethern sbin ifconfig eth0 netmask 255 255 0 0 broadcast 128 200 14 255 Creating eth0 1 puts potentially troublesom ntries in route table These entries may cause problems when machine is again connected to h sbin ifconfig eth0 1 lanina ess uci edu Connect IP address with Eth Route to gateway host all datagrams bound for hosts outside intranet fxm metric 1 argument appears necessary sbin route add default gw 128 200 14 1 metric 1 elnino is wireless on Harry s Earthlink net DSL network elnino uses ethO for wired con nection and eth1 for wireless lanina is wireless on Harry s Cox DSL network Make sure etc resolv conf contains the cox net nameserver nameserver 68 4 16 25 nameserver 68 2 16 30 nameserver 68 5 16 30 lanina is 192 168 1 73 on Harry s network elnino is 192 168 1 74 on Harry s network ashes is 192 168 1 75 on Harry s network Harry s router is 192 168 1 1 Following lines switch lanina to work on wirele
61. accept license action fillOut amp file id 7 Use CVS to check out model if you have an NCAR login cvs d ext zender goldhill cgd ucar edu fs cgd csm models CVS REPOS co r clm2_deva_52 d clm2_deva_52 clm2 Create model run space sudo mkdir ptmp sudo chmod 777 ptmp if n S LOGNAME then export LOGNAME S USER fi mkdir ptmp LOGNAME Create and populate boundary condition directories export CSMDATA NCAR fs cgd csm inputdata lnd clm2 export CSMDATA UCI datashare csm inputdata lnd clm2 export CSMDATA UCI ptmp S USER inputdata lnd clm2 export CSMDATA UCI S HOME tmp inputdata lnd clm2 if d S CSMDATA UCI then sudo mkdir p S CSMDATA UCI fi data drc fll lst NCEPDATA Directories to be copied in full Directories to selectively copy data_drc_prt_lst inidata_2 1 cam srfdata cam pftdata rawdata rtmdata Create all boundary condition directories for dre in S data drc fll lst S data_drc_prt_lst do mkdir p S CSMDATA UCI S drc done Populat ntire directories for dre in S data drc fll lst do scp r babyblue ucar edu CSMDATA_NCAR S drc x S CSMDATA UCI S drc done done populating directories Populate selected directories with selected files for fl in inidata_2 1 cam clmi_0000 09 01_64x128_T42_c021125 nc A 1 2 CLM Community Land Model 3 pftdata pft physiology rawdata mksrf_glacier
62. ache 4 GB USB 2 0 Flash drive on 20060729 I bought a second PNY Technologies Attache 4 GB USB 2 0 Flash drive on 20071006 3 X and XFree86 X tends to have large memory leaks Sometimes the problems are due to the X server and some times the problems are due to programs which never free graphics space reguested by the X server The xrestop monitors resources consumed by the X server 3 1 X and XFree86 Configuration A configuration tool has been built directly into the XFree86 server accessible with XFree86 configure XFree86 configure generated a perfectly working XF86Config file for lanina and is the method I now recommend XFree86 4 0 1 also has a different and new configu ration tool x 86cfg xf 86cfg9 did not generate a working optimal configuration file for lanina 10 3 X AND XFREES6 so I do not recommend this method Both these methods should generate fairly good configuration files which must be stored as XF86Config 4 e g etc X11 XF86Config 4 Note the extra 4 which indicates suitability for XFree86 4 x Version 4 uses dynamically loaded modules for each particular chipset so there is no need to symbolically link the X Window System server e g etc X11 X to anything XFree86 version 3 3 x uses the file etc X11 XF86Config which may be generated by Xconfigurator Xconfigurator cp etc X11 XF86Config HOME linux cp S HOME linux XF86Config etc X11 In XFree86 version 3 the correct X server should
63. ackages so called deb s dot debs are manipulated with the apt command apt cache search foo Which packages relate to subject foo apt cache search XML Simple Which package contains XML Simple apt file update Refresh apt file database apt file search foo Which non installed package installs provides file aptitude help aptitude t unstable install foo ff Install package foo from unstable aptitude autoclean Remove only package files that can no longer be downlo aptitude clean Remove everything except lock files from var cache apt aptitude dist upgrade Smarter version of upgrade aptitude install apt show versions u b grep unstable Upgrade unstab aptitude install foo Locate download and install package foo aptitude install foo http marillat free fr Locate download and insta aptitude install foo x y Locate download and install package foo versio aptitude remove foo Uninstall foo x y deb aptitude update Resynchronize package index files from sources aptitude upgrade Install newest versions of all packages currently instal aptitude upgrade foo Install newest version of package foo dpkg configure foo Configure unpacked package foo dpkg contents foo Examine contents of archive dpkg force help Help on force actions dpkg install force overwrite Install and overwrite
64. ad Ubuntu expects the first user created to use sudo to perform administrative tasks In such situations it may be useful to create a shell with root privileges sudo s Create shell with root priveleges Another option is to enable the root accounta sudo passwd root Enable root account sudo passwd l root Lock root account after enabling it hjm 08 18 05 I ve had a continuing problem with sand periodically complaining about my ICEauthority and Xauthority files being screwed up and then refusing to let me log in on the console This may not affect you two too much as you probably never use GUI tools to admin the system but I do and this is the reason Since sand has no root user it manipulates the user s Xauthority to enable X to open displays That changes the permission of the file and thus prohibits a console login because xdm needs to write to that file So if you use an X app as root you will need to explicitly change the permissions on these files before you will be able to log in I ve added the following into my alias file which fixes but does not solve the problem alias chice sudo chown hjm cgdcsm home hjm ICEauthority home hjm Xauthority 9 22 Install IDL and PGI Intel recently purchased Kai software and is now distributing their compilers for Linux http www intel com software products compilers flin noncom htm http www coyotegulch com hpc intel_ lst_look html Select the non commercial uns
65. ager Convenient GUI for WiF configuration moon is visible to the internet but mine is not since all IP packets are masguerading as Harry s machine Hence two consecutive SSH s are reguired unless moon is contacted on port 261 This port forwards SSH reguests directly to elnino s DHCP address of 192 168 1 226 ssh p 262 68 109 196 84 ssh p 263 68 109 196 84 Forward to ssh p 264 68 109 196 84 Forward to ssh p 265 68 109 196 84 Forward to Forward to se HE 192 168 1 73 to haze from outside 192 168 1 74 to elnino from outside 192 168 1 75 to ashes from outside 192 168 1 76 to virga from outside ssh p 262 192 168 1 1 Forward to 192 168 1 73 to haze from inside ssh p 263 192 168 1 1 Forward to 192 168 1 74 to elnino from inside ssh p 264 192 168 1 1 Forward to 192 168 1 75 to ashes from inside ssh p 265 192 168 1 1 Forward to 192 168 1 76 to virga from inside bonk s network sometimes gets into strange states which dramatically reduce network speed If you suspect this might be the case log into bonk and do a 88 9 RSYNC sbin ifconfig ethl If it shows errors alert Harry The fix is often simply a quick ifdown ifup cycle NCAR standard for routers on each subnet is 128 117 xxx 251 CGD router is 128 117 22 251 or 128 117 24 251 The default gateway should be the router The default nameserver in
66. alled in usr when installation is automated so that the package becomes indistinct from one supplied with the base operating system This is true of most debs and RPMs for example When any administrative intervention is required the package is best installed in usr local For this reason it is wise to back up usr local and unnecessary to back up usr Packages which have up to date pre compiled binaries for most Linux distributions 1 TEX ETEX Autoconf Autoheader Automake Bash Bison CVS DDD Emacs Flex GCC GDB GSL Gettext Ghostscript Ghostview Gnuplot Gzip Libtool M4 Make Octave Matlab clone Perl must be executable as usr bin perl R S clone Tar wget Idd locate Packages which may not have up to date pre compiled binaries for most Linux distributions Adobe Acroread Intel Fortran 95 and C compilers Java runtime environment 1 4 NASA Panoply NCSA HDF NOAA Ncbrowse Sourceforge NCO UCSD Neview Unidata netCDF must be compiled with gcc g netcdf perl UDUnits DODS vosnsaurwuvn 104 9 RSYNC 9 53 Packages installed in usr local some RPM some tgz some propri etary DODS Distributed Oceanographic Data System dx IBM Data explorer hdf Hierarchical Data For mat gnuplot Gnuplot for DDD java Java ncBrowse ncBrowse 1 2 1 ncarg NCAR graphics pgi PGI Fortran rsi Research Systems International Interactive Data Language IDL udunits Unidata units conversion package
67. am one must open the Execution View window Also in the Views menu is the Variable Browser which does what it says Click ing on the variable names in the Variable Browswer will bring up a nice Array Browser for arrays Breakpoints are set in the Traps menu in cvd On AIX use the x1db debugger Invoke with export DISPLAY ashes ess uci edu 0 0 xldb which swnb2 drc_in S DATA aca D 1 E e 1603 d foo nc dbx d 100 which mie The Lahey 1 95 compiler comes with the db debugger Invoke with fdb which fff amp 9 60 Mailman Mailman is used to create and manage mailing lists First run mailman to create the site list newlist mailman 9 61 Web Servers The DEAD box model is interactively served on the web Doing so requires coordination between model scripts the HTTP server Apache and system permissions The Apache server keeps its transaction logs in var log httpd Users will get an Internal Server Error if the CGI script fails tail var log httpd access_log RedHat tail var log httpd error_log RedHat tail var log apache2 access log Debian tail var log apache2 error log Debian Track web server usage using webalizer scp linux etc webalizer conf etc mkdir p var www html usage chmod R 755 var www html usage webalizer 110 9 RSYNC 9 61 1 Group Web Server The group relies on a number of non default webserver features M
68. ame Stream using RTSP Xine provides trouble free operation in full screen mode usr share doc libdvdread2 examples install css sh aptitude install xine ui Make sure the DVD is in the drive an mounted udo ln s f dev sr0 dev cdrom ashes udo ln s f dev sr0 dev dvd ashes udo mount t iso9660 o ro user noauto unhide dev cdrom cdrom do mount t udf o ro user noauto unhide dev dvd dvd udo mount t udf o ro user noauto unhide dev dvd dvd Xine mounts DVDs like this on elnino udo mount t udf o ro noexec nosuid nodev dev scd0 cdrom vn Fu nm un nm O xine generates lots of warning messages Run xine as root until permissions are straightened out libdvdcss error failed opening raw device continuing main probing lt aadxr3 gt video output plugin load_plugins failed to load video output plugin lt aadxr3 gt main probing lt dxr3 gt video output plugin load_plugins failed to load video output plugin lt dxr3 gt main probing lt xv gt video output plugin main probing lt alsa gt audio output plugin load_plugins failed to load audio output plugin lt alsa gt main probing lt oss gt audio output plugin xine_interface unknown param 10 xine_interface unknown param 10 9 35 Network 79 xine_interface unknown param 10 xine_interface unknown param 10 vo_scale invalid ratio using 4 3 vo_scale unknow
69. and while it s not fantastic it s really not bad And one disk has been marked bad So now I have to replace the bad disk I m just about to bring the system down to do this when I realize the disks are sitting in the expensive hotswap cages we bought for this specific purpose so after unmounting the filesystem I take a deep breath and pop the offending disk nothing happens the system doesn t freeze or explode or anything it looks like it has actually worked and the 3dm2 interface shows that the bad disk is now gone GREAT I guickly replace the disk with a spare and slam it back in again and there it is on the web interface Now isolated all by itself Now how to go about adding it back to the RAID The Web interface is a bit dodgy on how to go about adding this disk back into the array And the help pages are not particularly helpful the Maintenance help page sort of obliguely refers to this scenario but certainly doesn t give any specific step by step instructions You d have thought that since one of the primary reasons for buying such an expensive controller is to be able to replace a RAIDS disk on the fly they might have a specific mention of such an eventuality The way I did it is to add the disk to a new UNTT and then add that UNIT to the previously defined RAID5 UNIT and reguest that the new combined unit be rebuilt That seemed to work and the controller went about integrating the new disk into the raid 5 array Agai
70. argument to Emacs commands is non trivial The example of setting the number of columns to 80 show this ESC 80 ESC x set fill column RET This command might be written in Emacs short hand as 32 6 PROGRAMMING M x set fill column Bash supports a wide variety of pattern operators for shell filename expansion aka globbing These globbing operations filter all files and directories present through a filter including one or more wildcard characters for El Hin Ths Gst25 858 9 27 ne do mv fl S fl 8589_ _ clm Change 8589_ to clm in filenames done for fl in ls khus jpg do mv f1 S fl khus kuhs Change khus to kuhs in filenames done for fl in ls Johnson Jack do mv fl S fl Johnson _ Jack Jack_ Johnson done On machine with temporary mail e g ashes cd mail for fl in bin ls do mv S fl S fl foo done On machine with archived mail e g elnino cd mail scp ashes ess uci edu mail foo mail for fl in bin ls foo do cat S fl foo S fl gt S fl foo new mv f S fl foo new S f1 done I also have a custom Perl script fl rnm pl for renaming files The most common shell pattern matching operators such as and have minimal function ality as regular expressions The Bash shell supports extended regular expressions in filename globbing via the shell option ext glob Activate this functionality using the shopt command shopt
71. ay corrupt the ARP table One symptom of this is when ssh to a working host fails with e g ssh connect to host ashes ess uci edu port 22 No route to host When this occurs the first thing to check is that the sshd daemon is installed and running Many security conscious operating systems ship by default with very few services running Another cause of this message is incorrect network configuration The suspect device is ethO or eth1 Ensure that only one Ethernet device is configured The best solution is to remove the offending entry sudo arp delete ashes ess uci edu A simple but dangerous fix is to bring down and then up the offending device This does not work remotely since the machine will be off the network ssh and scp will also fail with the error ssh connect to host ashes ess uci edu port 22 No route to host when the sshd server is not running To check whether sshd is running use ps To check wheter port 22 is open for SSH connections use the nmap command ps ef grep sshd sudo nmap sS F localhost 9 45 Hibernate 93 9 45 Hibernate Laptops these days have various power consumption options controlled by the Linux Advanced Configuration and Power Interface ACPI The states are standby suspend and hibernate The standby action causes the screen to go blank The suspend action invokes ACPI state S3 aka suspend to RAM According to linux com everything in the system enters a low power state except for RA
72. be dynamically linked to the generic server file e g ln sf usr X11R6 bin XF86_I128 etc X11 X The Google googleearth application requires correctly functioning OpenGL drivers The xorg conf file instructs X to load these drivers with Section Module Load glx Load GLcore EndSection It is important that glx precede GLcore The glxinfo command reports the OpenGL driver status Use import to save an X window to an image format import import san_antonio gif guality 100 san_antonio png Tweaking the default XF86Config file is often necessary for special performance The follow ing tweaks to swcursor and XkbOptions are useful 1 Software cursor to allow large cursors In Section Device add csz 19991005 swcursor required for 96 x 94 pixel lightning cursor Option swcursor csz 2 Swap positions of capslock and control keys Inthe InputDevice section for the keyboard add csz Swap positions of capslock and control keys XkbOptions ctrl swapcaps csz In the InputDevice section for the keyboard add 3 1 X and XFree86 Configuration 11 csz Make pressing both touchpad buttons at same time emulate middle button on 3 button mice Option Emulate3Buttons on csz Adjust the speed of the t ouchpad mouse using the MinSpeed MaxSpeed andAccelFactor options in the Touchpad section Section InputDevice Identifier Synaptics Touchpad
73. bin sh s fs cgd data0 zender match match s fs cgd data0 zender match dst dst aer s fs cgd home0 zender aca aca s fs cgd home0 zender c c s fs cgd home0 zender c c s fs cgd home0 zender ck ck fs cgd home0 zender dot dot s fs cgd home0 zender f f s fs cgd home0 zender fsf fsf s fs cgd home0 zender idx_rfr idx rfr s fs cgd home0 zender mk mk s fs cgd home0 zender nco nco s fs cgd home0 zender perl perl ba ll Ka GG Ka Ks Ka pa ps ps ps H H H H H H H H H H H H H a A pe gt De ao ie es o ae 4 u 9 15 Install etc initscript to boost stacksize so CCM can run 9 16 Math Libraries Compile libspecfun a Normally the double precision version of libspecfun a located in src dp should be built and used However on Alpha chips using f90 this results in gamma_ being un defined In this case build the single precision source and hence function names using double precision flags cd specfun src sp setenv FFLAGS r8 i4 make e f Makefile unix cp libspecfun a SMY_LIB DIR 9 17 Hardware description of Zender group computers Dell Support 1 800 624 9896 general 1 800 234 1490 x69080 general http premiersupport dell com For all machines Netmask 255 255 255 0 Default gateway subnet 14 128 200 14 1 Default gateway subnet 24 128 200 24 1 Broadcast subnet 14 128 200 14 255 Primary nameserver UCI 128 200 1 201 Seco
74. c fstab krein krein krein krein math math math math uci uci uci uci edu dks9d2s0 edu dks9d3s0 edu dks9d4s0 edu dks9d5s0 Mount these partitions interactively the first time mount mount mount mount krein krein krein krein math uci math uci math uci math uci edu dks9d2s0 edu dks9d3s0 edu dks9d4s0 edu dks9d5s0 s cgd home0 s cgd data0 s cgd csm mountpoint mountpoint ct ct ct mountpoint o o o o t mountpoint edu dks9d2s0 dks9d3s0 dks9d4s0 dks9d5s0 dks9d2s0 dks9d3s0 dks9d4s0 dks9d5s0 dks9d2s0 dks9d3s0 dks9d4s0 dks9d5s0 nfs nfs nfs nfs exec dev suid rw exec dev suid rw exec dev suid rw exec dev suid rw 62 9 RSYNC Create softlinks on local machine e g dust ess uci edu so these directories may be ac cessed identically on krein and on local machine BRWN Disk dks9d2s0 is for match runs BIAN match Disk dks 9d3s0 is for match runs ZENDER match Disk dks9d4s0 is for NCEP data DSS Disk dks9d5s0 is for boundary data DATA data diagnostics DATA dgn DATA aca DATA map and csm runs ZENDER csm and all run directories data zender match data zender csm 4 j EG ge bw De EU BA DDA EU e TP y rj ry FA bo ba ba bb Eo pb ol F F F F F F F F F F 5 5 5 5 5 5 5 5 5 Dd dks9d2s dks9d3s dks9d4s dks9d5s dks9d5s dks9d
75. ce ftp in nearly every situation bin rm r data zender tmp rpm mkdir data zender tmp rpm cd data zender tmp rpm ncftp ftp uci edu This will circumvent NCAR s firewall cd mirrors redhat updates 8 0 en os i386 get rpm set passive yes ff Other firewalls may reguire this command bye sudo usr local bin uci_dcs_lnx_pch pl data zender tmp rpm 9 63 Accounts 111 9 63 Accounts When GUIs go bad accounts need to be added by hand The following commands work to add accounts and appropriately cross mounted home directories to the cluster udo groupmod g 2400 cgdcsm udo useradd D g cgdcsm udo useradd d dhome mflanner g cgdcsm n u 3563 mflanner udo usermod p S 1ScharlieSVJFpvyBLLZzEvLkainaFW chaoluo udo usermod L daniellj Lock user pasSsword udo usermod a G adm admin audio cdrom cgdcsm dialout dip floppy lpadmin j un oo oo ao When adding an account to the home directory server itself dust ess uci edu the default home directory should be home 4USER rather than dhome USER The userdel command is for deleting user accounts userdel foobar ff Delete account userdel r foobar Same and remove all files in S HOME and mail spool 9 64 NCAR Over the years NCAR has developed a number of idiosyncratic procedures for managing user accounts One way to gain access to any NCAR machine is to connect through the gatekeeper machine gate ucar edu ssh gate uca
76. ces in sources list 70 9 RSYNC sudo aptitude install auctex metamail preview latex tramp Install Emacs a sudo ln s usr bin mimencode usr local bin mmencode Rmail uses mmencod emacs amp Edit dot files to contain new system name cd dot make dot bashrc cd Install dot files load custom bash settings ssh keygen t rsal Generate RSAl key ssh keygen t rsa ff Generate RSA key ssh keygen t dsa ff Generate DSA key cd dot cp authorized keys authorized keys2 known_hosts known _hosts2 ss Edit known_hosts and authorized keys Insert ssh id_dsa pub ssh id_rsa pub into authorized keys2 SSH to remote machine copy value from ssh known_hosts on remote machine into known_hostsx Or take values directly from etc ssh ssh_host cd dot make ssh cd Directories for personal machines cvs d ext zender esmf ess uci edu u zender cvs co kk aca aeroce aeronet afgl anl anv arese avhrr bxm c c cld clm crr dmr dst esmf ess ess_acc ess_atm ess_bnd ess_ccc ess_ccp ess_lsp ess_phz ess_prc ess_rdn f fsf grd hdf hire idea idl idx rfr igbp igpp improve job jrn lsm ltr YA map match matlab mie mk mny ncep ncl perl phd poetry pr prp rvw sdn slr_spc tex time toms uci www Directories for computational machines cvs d ext zender esmf ess uci edu u zender cvs co kk aca acia afgl anl c c cld clm crr dst f fsf icr idx_rfr map mie mk mtrdst ncl perl slr_spc time Papers cvs d ext zender es
77. command serves this purpose Shut down all X processes with telinit 3 Restart all X processes with telinit 5 Set the default system runlevel in etc inittab This is what determines whether X automatically starts on reboots Some computers have terrible default X settings which may be corrected by use of xset usually done in 7 xinitrc For example lanina has DPMS turned off by default and very slow key repeat settings so its xinitrc contains xset q Show current settings xset dpms Enable DPMS xset dpms 300 600 1200 Seconds until Standby Suspend Off xset mouse 4 4 Mouse acceleration and threshold 3 2 XFree86 NVidia Graphics drivers 13 The keyboard repeat rate may be changed with the kbdrate command The r options sets the repeat rate in characters per second The maximum allowed rate 30 cps gives a nice response kbdrate r 30 Set keyboard repeat rate to 30 cps The default mouse movement rate is also susceptible to fubaration xvidtune generates modelines which center the picture on the monitor The XAPPLRESDIR contains X defaults for various programs mkdir S DATA app defaults export XAPPLRESDIR X11 lib X11 app defaults DATA app defaults These defaults may be over ridden on a per user basis by implementing X resources in the Xde faults file 3 2 XFree86 NVidia Graphics drivers Source code drivers that support all of the advanced features of theubiquitous NVidia graph
78. dia USB20FD S HOME media USB20FD S DATA sudo chmod 755 media USB20FD S HOME media USB20FD DATA sudo chown zender media USB20FD S HOME media USB20FD DATA sudo chgrp cgdcsm media USB20FD S HOME media USB20FD DATA To quickly backup and copy material from virga to my grey Attache memory stick use sudo mkdir p media disk S HOME media disk DATA sudo chmod 755 media disk S HOME media disk DATA sudo chown zender media disk S HOME media disk S DATA sudo chgrp cgdcsm media disk S HOME media disk S DATA In the old days to mount a Memory Stick one did this Install necessary sysfs utilities aptitude install hotplug sysfsutils udev Create a mountpoint for sysfs cd mkdir sys mount t sysfs none sys Mount USB Memory Stick sudo mkdir m 777 memstick sudo mount t vfat o umask 022 uid 3555 gid 2400 dev sdal memstick Ash sudo mount t vfat o umask 022 uid 3555 gid 2400 dev sdbl memstick Vir For Linux 2 6 kernels make sure to install udev The Memory stick with a USB adaptor appears automatically in the sys filesystem as a SCSI drive zender elnino more sys block sda device model IntelligentStick zender elnino more sys block sda device vendor I Stick2 It must still be mounted See the rsync description in Section 9 for examples of how to back up to CompactFlash and Memory Stick media I bought a PNY Technologies Att
79. dust ess uci edu var www sudo scp linux etc apache httpd conf dust ess uci edu etc httpd conf htt sudo chown R zender x sudo chgrp R cgdcsm sudo etc init d httpd restart Rebuild contents doc ppr facts bxm nco Restore BXM cd bxm sudo make bxm cd cd bxm sudo make bxm_aerjcd sudo mkdir p var ftp dead sudo chown apache var ftp dead sudo chgrp apache var ftp dead 76 9 RSYNC Restore NFS Crossmounts sudo etc init d nfs restart sudo usr sbin exportfs rv sudo mount a Restore Scientific computing sudo rpm i gsl 1 4 5mdk src rpm netCDF Restore FTP cd var ftp pub sudo mkdir zender sudo chown zender zender sudo chgrp cgdcsm zender 9 31 iS500s Inspiron 8500 Use the xev program to find the keycodes for the volume keys In my case they turned out to be 174 lower and 176 raise Ran the commands xmodmap keycode 174 XF86AudioLowerVolume and xmodmap keycode 176 XF86AudioRaiseVolume to map the buttons to the right key symbols Configured the Sawfish window manager to run the command aumix c 5 on lower and aumix c 5 on raise Tried it and it worked Put the commands into xsession to make this permanent 9 32 Images Images refers to all still images including JPEG tiff etc The best program to use for viewing images depends on your intent For image processing use gimp For slideshows of raster images use gimp 9321 Gimp The gimp
80. e startx depth 24 1 To create a second display using a test XF86Config file use startx xf86config linux etc X11 XF86Config 4 elnino 1 For secutrity reasons the path to the XF86Config file must be a relative path not an absolute path Table I summarizes the keystroke commands related to X Windows Accessing virtual consoles and starting multiple sessions is the same in XFree86 4 x as XFree86 3 x However the specification of the color depth has changed from bpp to depth To start X with 24 bit color the command is startx depth 24 Display managers such as xdm kdm and gdm start X themselves and require that non default options be passed directly to the X server in the configuration file e g etc X11 gdm gdm conf or etc Kde kdm kdmrc Before configuring display managers individually however it is wise to consider setting many parameters in the system wide X configuration file XF86Config 4 For ex ample adding DefaultColorDepth 24 toSection Screen should cause the X server to always run with 24 bit planes 18 3 X AND XFREES6 Table 1 Funky Keystrokes Key Description Ctl Alt F1 F5 Virtual consoles Ctl Altar X display 0 0 Ctl Alt F8 X display 0 1 Ct1l Alt Change X Resolution Ctl Alt Change X Resolution Use em or lose em gt This must be the plus key on the numeric keypad On most laptops this requires a four key combination since the numeric key
81. e argument is an integer This may only be neccessary when argument is type long To display this array in the display window highlight grd 0 grd_nbr 0 so that it appears in the argument line at the top next to Then click the display button The required specification can be tedious especially when indirection and class structures are involved e g tst_obj gt flx_slr_frc_in 0 tst_obj gt wvl_nbr_in or for say N 3 elements the even more complex t st_obj gt flx_slr_frc_in 0 tst_obj gt w Setting conditional breakpoints can be done with the wat ch function For example consider the problem of breaking inside of a loop once the value of the counter idx is 37 The GDB command is watch idx which sets a watchpoint on idx A watchpoint is a breakpoint that is called whenever the expression changes value 9 60 Mailman 109 Stepping through C code is tedious because GDB takes the long route through all the inter face files Instead set breakpoints at the start of the desired function with e g break rt_cls var_put Using gdb on G95 code is possible but not pretty Symbols are case sensitive use lower case Dummy arguments are actually pointers Module variables have a modulename_MP_ prefix Module procedures have the same plus an underscore _ suffix On SGI 64 bit machines dbx and gdb do not work and one must use the cvd debugger This debugger is powerful but non intuitive To view the stdout stre
82. e covered here and thus might be duplicated Buoyancy convection maybe in Boundary layer Topics which might belong here but which I assume will be covered in other courses and thus might fall through the cracks Ice albedo feedback Hydrology cryosphere Mass continuity equation Dynamics Advection Dynamics or Geosci Model Diffusion Dynamics or Geosci Model Box models feedbacks residence times Hydrology Aerosol composition nutrients pH Chemistry Gibbs Helmholtz energy Terr BGC lt NYO OB WN FP Topics which might belong here but which I assume will not be covered in any first year unit due to time contraints These topics should be available in an advanced graduate course di 2 3 4 Formulation of RT Eguation Solution for pure absorbing atmosphere with reflecting lower boundary Definition of single scattering asymmetry Radiative convectiv guilibrium 8 2 ESS 200B EARTH SYSTEM PHYSICS 2 1 iPod The primary reference for using the Apple iPod with Linux is http www cavecanen org linux ipod Two Linux applications for managing iPod music are GNUpod and gtkpod 2 2 Cameras If your Linux uses modules load the following modules Support for USB Also select either UHCI Intel PHX4 VIA support UHCI Alternate Driver JE support or OHCI HCD Compaq iMacs OPTI SiS ALi support usbcore o usb uhci o uhci o or usb ohci o In
83. eating Server Files 75 udo useradd c Scott Capps d home scapps g cgdcsm m p SIScharlie V Oops got to change Robynn s UID udo useradd c Robynn Zender d home robynn g cgdcsm m p 1 charlie udo useradd c Mike Brown d home brownmc g cgdcsm m p SIScharlie V udo useradd c Danielle Johnson d home daniellj g cgdcsm m p 1 ch udo useradd c Mike Tosca d home mtosca g cgdcsm m p SIScharlie VdJ udo useradd c Henry Butowsky d home hbutowsk g cgdcsm m p l char udo useradd c Olivia Zender d home olivia g cgdcsm m p S 1Scharlie udo useradd c Daniel Wang d home wangd g cgdcsm m p SIScharlie VdJ An HA HAHN WH Oo Create work directories and change permissions for usr in mtosca do sudo chmod 755 home S usr sudo mkdir data S usr cd data sudo chown usr Sf usr sudo chgrp cgdc sudo mkdir var www html S usr cd var www html sudo chown S usr S usr done Patch RPMs Restore usr local includes NCAR graphics Lahey fortran PGI RST cd usr tar cvzf local tar gz local sudo scp local tar gz dust ess uci edu usr cd usr tar xvzf local tar gz Restore CVS sudo mkdir var lock cvs sudo chmod 777 var lock cvs sudo scp linux etc xinetd d cvspserver etc xinetd d sudo etc rc d init d xinetd restart Restore WWW sudo bin rm r var www html fsudo scp r var www html
84. ecurity do aptitude do chkrootkit do rkhunter c Packages for building NCO debs do aptitude install install xosview hddtemp gkrellm chkrootkit clamav rkhunter install antlr autoconf autoconf doc automakel 9 ccache debhelper debootstrap devscripts dput debian policy dupload figlet fakeroot flex gnu pbuilder FU O ao a ao O num u nn un a scp cd An HAHAH run o sudo api do aptit do aptit do aptit do aptit do aptit do aptit do aptit do aptit do do do do do MPI au Jas ar kur er F F F F F 5S 5H 5 5 5 do aptitu do aptitu Install reportbug wdiff de install man plot libantlr dev libtool linda lintian pages dev glibc doc d d remov qecc 3 030g 3 3 libstdc 3 3 dev 5 6 de de de de de If necessary gt D f gt E Choose st ess DATA tmp sudo dpkg install de de GSL do yun in stall remov install install install gcc 4 0 g 4 0 libstdc 4 0 dev gfortran 4 0 libstd gcc gcc 4 2 gcc doc gcc 4 2 locales g g 4 2 libstdc 6 4 2 doc gfortran 4 1 Needed for NCL NCAR Graphics in stall install gfortran gfortran 4 2 gfortran doc gij gcj link u u u u u on default executables to appropriate Ubuntu binaries sr bin gcov 4 2 usr bin
85. eenmtn e0 nameserver 128 117 64 22 NCAR PPP router nameserver 128 200 1 201 csi ns nts uci edu nameserver 128 200 192 202 cpl2 ns nts uci edu 911 C development kernel headers and glibc devel are required to develop C language programs but not installed by default rpm ivh mnt cdrom RedHat RPMS glibc devel 2 0 5c 10 i386 rpm rpm ivh mnt cdrom RedHat RPMS kernel headers 2 0 32 2 i386 rpm 9 12 Time and TimeZone Use utc option to indicate that HW clock is kept in coordinated universal time or UTC which is virtually identical to Greenwich mean time or GMT This option is set during the installation of GNU Linux 9 13 Perl 41 sbin hwclock debug sbin hwclock test set date 08 13 98 04 38 00 Tests the command sbin hwclock set date 04 09 00 15 41 00 A better option seems to be using rdate to set the system clock and then hwclock to set the hardware clock to the system clock sudo usr sbin rdate s time nist gov sudo usr sbin rdate s ntp ucsd edu sudo sbin hwclock systohc Note that time nist gov may refuse connections so consider alternatives like ntp ucsd edu In serting this command in etc rc d rc local ensures time is set correctly on each reboot assuming machine is on network at boot time I think this resets the hardware clock and not just the system time The preferred solution is to use NTP the network time protocol The NTP homepage is http www eecis udel edu ntp andthe
86. ellent ncview software must be installed by hand Since it relies on UDUNITS it is important to build that as well sudo scp usr local bin ncview dust ess uci edu usr local bin sudo scp r usr local lib ncview dust ess uci edu usr local lib ncview allows logarithmic transformation of coordinates 5 1 4 NCVweb The NCVweb package is designed specifially for viewing netCDF files produced by the Atmo spheric Radiation Measurement ARM Program NCVweb is for web based visualization It uses NCO for aggregating data fxm 5 2 Python The netCDF interface to Python is Python has at least 2 actively maintained netCDF interfaces http met www cit cornell edu noon ncmodule html by Bill Noon and http starship python net crew hinsen netcdf html by Konrad Hinsen 5 3 Mail My Linux servers run sendmail or the post fix interface to sendmail This program like other daemons can be restarted using killall HUP sendmail To start the program use the RedHat control panel The outgoing SMTP server is set in the file etc sendmail cf or etc mail sendmail cf in the line beginning with DS Mail that has not yet been delivered is stored in the var spool mqueue directory Incoming mailbox e g var spool mail zender must be known to Emacs There is a good example of how to set up post fix for Ubuntu machines at http www ubuntulinux org wiki DialupEmailHowto This example works for ashes ess uci edu All too often mail does not ge
87. ernel headers 40 kgcc 66 kpdf 90 krein 62 ldd 28 1 95 109 lilo 67 llcancel 39 lg 39 lsubmit 39 lm sensors 23 lmremove 65 lmstat a 65 lmutil 65 lp 95 ls la dev disk by uuid 94 lsmod 84 mailman 109 malloc 107 man 107 mkfs 21 117 mk swap 94 modprobe 15 84 mount 23 61 mozilla thunderbird profilemanager 28 mplayer 77 cBrowse 25 cap 31 cbo 15 cftp 110 cgen 31 cview 25 etscape 36 fslock 60 map 92 m 40 o_root_squash 60 oauto 61 slookup 40 tpdate 41 vidia 13 v 13 oprofiled 14 3 9 9 BS SS 9 9 99 eS BB SS oprofile 14 otool 28 panoply 25 pbsnodes 98 perfetr 13 postfix 26 pppd 39 ps 92 pump 90 92 qdel k 39 qstat 39 qsub 39 raid0run 20 raidhotadd 20 raidhotgenerateerror 20 raidhotremove 20 raidstart 20 raidstop 20 rep 97 rdate 41 rehash 32 reset 32 118 rkhunter 113 rmmod 84 root 23 rpm 100 105 rsync 9 37 scp 92 113 sendmail 26 set fill column 3l shopt 32 skype 104 smartctl 23 smartmontools 23 ssh copy id 112 sshd 39 92 ssh 92 97 98 112 startx 17 sudo 1s 15 sudo 62 suspend sh 93 swapon s 94 swcursor 10 sysctl 67 telinit 12 telnetd 39 thunderbird 27 28 top 98 touchpad ll tramp 97 tr 68 ulimit 94 96 106 umount 22 25 61 update initramfs u 94 userdel 111 usermod 113 v412 104 valgrind 107 vfat 8
88. ernet Router settings date stamped and saved to virga S DATA tmp netgear_wgr614v7_20070916 cfg S DATA tmp netgear_wgr614v7_20070923 cfg cp home zender Desktop netgear cfg S DATA tmp netgear_wgr614v7_20070923 c Came with WG111v2 USB 802 11g card MAC address 00184DFF1D2C S N 1AC174BP09583 9 17 Hardware description of Zender group computers 47 Comprehensive Wireless MAC list for zendernet router airlink_ awlc3026_pcmcia 00032F36D551 ashes_trumobilel400 00904BB20986 elnino 00022D855C3E linksys_dlink pcmcia fxm netgear_wglllv2_usb 00184DFF1D2C netgear_wg5ll_pcmcia 00095BE8C4E1 orinoco_silver_ pcmcia 00022D0982E2 virga_ipw3945 0013020A7CE5 zyxel_a200_pcmcia 00A0C5B810C7 neige_ipw4965 001DE0289E6D hp5180_printer 001a4b954ae8 wired zendernet router reserved IPs 192 168 1 2 hp5180 192 168 1 3 virga 192 168 1 4 elnino 192 168 1 5 neige 192 168 1 6 ashes 192 168 1 7 ashes 192 168 1 8 neige ipw4965 trumobile1400 broadcom netgear wg511_pcmcia broadcom netXtreme 57xx Gigabit Controller hp4600 ess uci edu 128 200 14 123 COLOR LASERJET 4600DN 17PPM 96MB PAR ENET 2 EIO PS3 PCL6 5C Purchased from GST Inc 17707 Valley View Ave Cerritos CA 90703 7004 Arrived Jan 23 2003 Serial number JPBKB18664 UCI Property 039003414 17 ppm clr 600x600 DPI 96 MB RAM 10 GB disk 81 0180 EIO 1 ERROR messages If yo
89. ery desirable to turn off not just the sound server but all audio beeps For this purpose the xset command does very nicely xset b 0 Turn off sound xset b off Turn off sound Set beep parameters maximum volume pitch Hz duration ms xset b 20 440 50 90 9 RSYNC http ariesl7 uwaterloo ca dmg brick suggests adding alias sound maestro options sb io 0x220 irg 5 dmg 1 to etc conf modules for Dell Inspiron 7500 Sometimes the sound device gets controlled by processes that do not play well with others One symptom of this is when amarok complains that the sound device is unavailable When this occurs try to kill the errant processes revealed to be controlling the sound device To find those processes follow these steps 1 Open the system monitor System Administration System Monitor 2 Open in the menu Monitor Search for open files 3 In the text box enter dev snd then click on Find On 20080325 kpdf of all things was responsible for stealing the sound outputs 9 41 dakine msw lanina linux List dakine msw shares accessible via Samba on lanina lanina smbclient L dakine Work interac tively in FTP like environment with msw shares lanina smbclient dakine home Ability to browse Linux from Windows is determined by etc smb conf hosts allow 192 168 1 128 200 14 127 128 117 24 printers browseable yes Specifically you must set up encrypted passwords by using the line
90. esses owned on each ESMF node Running and killing MPI jobs can leave clusters with un released resources such as shared memory allocations and shared semaphores This unclean state may block further MPI execution To clean up the leftover state use Inter Process Communication IPC management commands such as ipcs On interactive node ipcs m awk 0x print 2 xargs n 50 ipcrm shm ipcs s awk 0x print 2 xargs n 50 ipcrm sem 9 51 RPM packages in usr that were installed and may need to be uninstalled or reinstalled by hand 99 To compute nodes cluster fork ipcs m awk 0x7 print s2 4 xargs n 50 ipcrm shi cluster fork ipcs s awk 7 x0x print s2 I xargs n 50 ipcrm set As its name implies cLuster fork issues its argument as a command to all cluster nodes 9 51 2 GPG GNU Privacy Guard The OpenPGP standard defines the cryptographic authentication protocol that gpg implements gpg export a Charlie Zender a Add ASC armor gpg keyserver pgp mit edu send keys 6F635D10 gpg keyserver pgp mit edu search keys Charlie Zender gpg list public keys Type Bits KeyID Date User ID pub 1024D 6F635D10 2006 11 20 Charlie Zender lt zender uci edu gt sub 20489 9148C6AF 2006 11 20 Key fingerprint DBDO E788 E13C 56A2 6C5D 2C62 CB91 49AD 6F63 5D10 s BEG
91. estern Scientific installation usr local src Source tarball etc init d pgi lmgrd daemon to start FlexLM usr local pgi 5 1 3 license dat License var tmp flexlm log License daemon error messages The server s hostname configuration is very important When the hostname changes then update the license file accordingly 923 PCMCIA cd usr src tar xvzf pcmcia cs 3_x_x tar gz cd usr src linux pcmcia cs 3 x x make config make all make install Customize in etc pcmcia if neccessary For RedHat systems read Section 2 5 2 p 12 of PCM CIA HOWTO As recommended delete or comment out contents of default etc pcmcia network opts and replace with script given in HOWTO This fix enables ethernet connections on power up Alternatively I modified etc pcmcia network with two suggestions from PCMCIA Xircom Hy permail list but as stated in the HOWTO RedHat may not actually run this script JWZ has similiar card and uses three commands 66 9 RSYNC usernetctl eth0 down etc rc d init d pcmcia restart usernetctl eth0 up 9 24 Building new kernel Before building kernel make sure default compiler is known to build stable kernels For RedHat 7 0 systems use kgcc not gcc New kernel 2 2 18 Makefiles do this automatically but just in case do this as root export CC usr bin kgcc For guaranteed kernel stability GCC version 2 95 is recommended export CC usr bin gcc 2 95 Final
92. for passwords For ncbo assuming ncbo has been com piled with the g option sudo opcontrol reset Reset counters ncbo 0 op_typ r p S DATA nco_bm A gcm_T85 nc gcm_T85_00 nc DATA nco_bm ipcc diff nc opreport exclude dependent demangle smart symbols gt oprofile report full ncbo The output is a text file that gives the time spent in each function The poll idle time is that time which the CPU s has spent doing nothing i e idling For a lightly loaded dual CPU machine you would expect to obtain about 5090 in poll idle running a single serial job To use HPCToolkit make sure that oprofile is not loaded and load the perfctr module lsmod grep oprofile sudo opcontrol deinit Unload oprofile if loaded modprobe perfctr Load perfctr module The PAPI API has access to necessary hardware counters once the perfctr has been loaded After this profiling is relatively straightforward To profile a command prefix it with hpcrun e g hpcrun options ncbo 0 op_typ p S DATA nco_bm gcm_T85 nc gcm T85_00 nc DATA nco_bm ipcc diff nc The hpcrun options are typically a set of hardware counters you want to access during the run hpcrun L grep Yes List available hpcrun options PAPI_L2 DCM Ye
93. ga ess uci edu 128 200 14 189 Dell Inspiron 9400 Received at UCI 20060221 Dell Service Tag F1NOJ91 9 17 Hardware description of Zender group computers 49 Express Service Code 327 508 573 33 4 year limited warranty plus 4 year NBD on site service and complete care Gold technical support Intel Core Duo Processor 2 GHz 667 MHz FSB 17 UltraSharp Wide Screen UXGA WUXGA 8x CD DVD burner DVD RW with double layer DVD R write capability 2 GB RAM Logitech MX1000 Laser Cordless mouse 29 1 ROM GP Logitech Resolution 800 DPI 5 8 MP s 1 Logitech S N LZB533350679 MAC address 00 14 22 EF 61 8E wired MAC address 00 13 02 0A 7C E5 wireless ipw3945 Bluetooth Dell Wireless 350 Bluetooth Internal 2 0 enhanced data rate Bluespoon AX2 Logitech QuickCam Pro for notebooks IEEE 1394 scsi0 ata piix Vendor ATA Model Hitachi HTS72101 Rev MCZO scsil ata_piix Vendor NEC Model DVD RW ND 6650A Rev 102C SCSI device sda 192426570 512 byte hdwr sectors 98522 MB 1 PCI Express card slot Zero pcmcia slots Video 256 MB Nvidia GeForce Go 7800 eth0 Broadcom 4400 10 100BaseT Ethernet 00 14 22 ef 61 8e Intel PRO Wireless 3945 80211a g minicard Sound http wiki ubuntu com DebuggingSoundProblems Turn off internal speakers when headphones plugged in echo options snd hda intel model ref sudo tee a etc modprobe d alsa base Ubuntu wireless cards https wiki ubuntu com HardwareSupportComponentsWirelessNetworkCards This he
94. h The top command shows the load on all processors in the line labeled Cpu s near line 3 This mode presents statistics as a fraction of total avail able resources for all CPUs so that full usage of 1 CPU on a dual CPU system shows up as 50 user usage and 50 idle The load average uppermost line on the otherhand is shown as a fraction of maximum load for one CPU Pressing 1 while t op is running toggles the presentation mode between a single line Cpu s summary and multiple lines of per CPU summaries The load average in the top most line ap proaches N when an N processor node is fully utilized e g about 4 0 for a guad CPU system The free and xosview commands are also useful at monitoring system usage The PBS batch queuing system may be interrogated with a number of commands such as pbsnodes cluster ps Connects to all computes nodes and does ps free nodes Display all free compute nodes MPC job uptime Show load averages for all user running jobs on Torque pbsnodes a Display all compute nodes and jobs assigned to them gadel 161608 Cancel job number 161608 in queue gmon amp GUI for gstat functionality for SGE gstat a Display all jobs running queued gstat r Display all running jobs gstat r grep ipcc Display all running jobs asub I q opteron Request interactive node from Opteron pool esmfusers display proc
95. hift Left to right gt gt Right shift Left to right lt Less than Left to right lt Less than or equal to Left to right gt Greater than Left to right gt Greater than or equal to Left to right Equal to Left to right Not equal to Left to right amp Bitwise AND Left to right Bitwise XOR Left to right Bitwise OR Left to right amp amp Logical AND Left to right Logical OR Left to right 2 Conditional Right to left Assignment Right to left x amp lt lt gt gt Compound assignment Right to left r Comma Left to right 6 2 Regular expressions 31 e Complemented character set e Match beginning of line e Match end of line e Quote special characters e w Matches any word constituent character e w Matches any non word constituent character In the replace expression amp stands for the match found for the whole regular expression and AN stands for the match to the Nth occurence of the XA pair A floating point number match is Friedl 1997 p 128 0 9 0 9 0 9 The makes the negative sign optional The regular expressions used for lexically recognizing doubles in ncap and in ncgen respectively are 0 9 0 9 eE 0 9 L1Dd 0 9 eE 0 9 L1Dd 0 9 0 9 exp L1Dd 0 9 exp L1Dd Using regular
96. horized keys2 112 authorized keys 112 113 bck pl 36 cgi bin 110 core 24 crontab 36 eth0 1 85 ethO 86 92 eth1 86 92 exports 59 60 fl rnm pl 32 fstab 61 94 gdm conf 17 hdc1 21 hosts allow 60 hosts deny 60 httpd conf 110 id dr sa pub 112 identity pub 112 index html 110 index shtml 110 initrd 13 interfaces 96 known hosts 112 lanina 9 libefence a 106 libspecfun a 42 119 lilo conf 68 Itx ps 39 ltx tex 39 mail greenspeedisp net 27 mail wsu edu 27 mailhub cgd ucar edu 27 mdstat 24 menu lst 13 ncview 26 nvidia 14 nv 14 oprofile 14 perfctr 14 pop uci edu 27 prefs js 28 59 raidtab 19 resolv conf 88 sda1 21 sdb1 21 sk98lin 52 smtp uci edu 27 smtp west cox net 27 suspend sh 93 user js 59 valgrind txt 108 vmlinuz 14 xorg conf 10 93 xserverrc 17 xinitre 12 Ky he 18 g La 18 1 98 80 31 2 32 DD 34 ESC 31 MM 34 Pg Dn 77 RET 31 YYYY 34 set fill column 31 x 31 128 117 22 251 88 120 128 117 24 251 88 128 117 24 2 88 128 117 xxx 251 88 ashes ess uci edu 22 ashes 23 86 88 93 bearmtn 88 biogenic 19 clay 14 dirt ess uci edu 24 68 elnino ess uci edu 77 elnino 86 ess1 ess uci edu 110 gate ucar edu 111 hp6840 ess uci edu 95 https vpn nacs uci edu 16 ipcc ess uci edu 97 lanina 86 Igge pc240 88 localhost localdomain 27 localhost 27 lunada ps
97. ics cards are unavilable Two type of drivers are available First the XFree86 project nv driver is open source and works well with all 2D drawing commands Second NVidia supplies binary only nvidia drivers which support full 3D acceleration and OpenGL graphics The nvidia kernel modules are closed source prone to errors and must be re installed after the kernel is recompiled Since there is no easy mechanism to retain multiple nvidia modules for multiple kernels on one machine e g for testing the constraints of the closed source modules are bothersome Since these drivers are modules installing them requires kernel recompilation which in turn requires kernel headers dpkg list x686x apt cache search kernel grep 2 6 15 grep 686 Ubuntu Breezy Badger uname_r uname r aptitude install linux image uname_r linux restricted modules uname_r aptitude remove linux image S uname_r linux kernel headers S uname_r linu Note that recent Debian kernel packages require the initial ram disk initrd to be specified in the GRUB menu lst aptitude install libncurses5 dev cd S DATA zender tmp svn checkout http powertop googlecode com svn trunk powertop cd DATA tmp powertop make sudo make install Linux experts re compile their own kernals frequently GNU Linux will not boot into X until the correct X server module is available for the current kernel Download NVidia drivers from http www n
98. ine is on the NCAR network and the mount options are listed in the etc fstab file the partitions may be mounted with the following commands sudo mount fil sudo mount fil sudo mount fil leserver n8 ucar edu fs cgd home0 leserver n8 ucar edu fs cgd data0 leserver n8 ucar edu fs cgd csm Note that the partitions should not be automatically mounted at boot time since usually the laptop is not directly on the NCAR network The noauto option to mount accomplishes this Thus the appropriate fstab entries are ileserver n8 ucar edu fs cgd home0 ileserver n8 ucar edu fs cgd data0 ileserver n8 ucar edu fs cgd csm ncar fs cgd homeO0 nfs exec di ncar fs cgd dataU nfs exec di ncar fs cgd csm nfs exec di When disconnecting the laptop from the network it is best to umount these partitions so that the NFS related daemons do not waste time looking for them when the laptop is turned on again somewhere off the network sudo umount fil sudo umount fil sudo umount fil leserver n8 ucar edu leserver n8 ucar edu leserver n8 ucar edu Here are the mountpoints on krein mount mount mount Ch CE ct mount Create mountpoints on local machine e g dust ess uci mkdir mkdir mkdir mkdir krein krein krein krein ma ma ma th uci ERSUCT th uci math uci dks9d2s0 dks9d3s0 dks9d4s0 dks9d5s0 edu dks9d2s0 edu dks9d3s0 edu dks9d4s0 edu dks9d5s0 Add mount commands to et
99. ing the checksum info across the raid you have to let it sit there for hours it s a 1 6 TB array while it checksums the entire array even tho there s nothing on it to begin with That done it looks like a giant scsi disk to the OS so far so great 3ware also comes with a web frontend utility called 3dm and a commandline utility called tw_cli When I had installed the 3dm I had gone thru the installation script checked that there were no error messages checked that I got an email verification and then forgot about it altho thinking about it I must have gotten the email from the script not the app I did not check that the web server interface was working as I didn t think I d ever use it MISTAKE Now I DID need to talk to the controller and the 3dm tw_cli were the only things that could while the OS was running THIS is one of the downsides of a hardware RAID you re stuck with the tools that the vendor gives you Since I was running on a 64 bit SMP Linux Ubuntu dual opteron the installation bash script ran fine but the monitoring daemon silently failed 32 bit code and I was running a 64 bit only OS So nothing was hearing the controller screaming that a disk had died and the RAID was now running in degraded mode as noted above the only thing that let us know this was an entry in dmesg on a reboot After verifying that this software was in fact incompatible with the OS I tried to find an up grade that WOULD let me talk
100. inux install program specific documentation in usr share doc 9 3 PPP Modem is dev ttyS0 which should be linked to dev modem dev modem must be usable by all This should be set with control panel Must get correct permissions and ownerships on various files and directories Line speeds etc have not changed from RH5 defaults Permissions are a major security issue 9 4 Batch Queues 39 cd S HOME linux usr local bin sudo cp ppp go ppp off ppp on dialer usr local bin Or usr local sbin cd HOME linux etc ppp sudo cp options chat secrets etc ppp Some security configurations may require that pppd be run with the setuid root bit set and some distributions ship pppd with mode 6 44 In this case use e g chmod s usr sbin pppd 9 4 Batch Queues Two batch queue handlers are in use at NCAR and UCI the NOS Network Queueing System and the AIX LoadLeveler system LoadLeveler is described at http www scd ucar edu docs blackforest batch html The commands to submit jobs in these systems are qsub and 11submit respectively The commands to query jobs in these systems are qst at and 11a respectively The commands to cancel jobs in these systems are qdel k and llcancel respectively astat a h ute Check batch queues on ute from utefe gadel h ute 12978 ute Delete jobs on ute from utefe 9 5 Remote shell service rcp rsh ssh telnet Make sure rhosts is installed and NOT group other writable Turn o
101. ionally it is necessary to ins ert standalone kernel modules First bring down interface to avoid interface busy errors ifconfig eth0 down 9 37 Change network topology 85 Remove current module from kernel rmmod tulip Insert new module into kernel insmod home zender tulip o Examine messages tail 10 var log messages 9 37 Change network topology Linux Network BuH98 p 138 Linux Bible p 374 Following scenarios include possibly super fluous commands to shut down eth0 1 If ethO 1 is not shutdown and is running route table may be bad Machine which runs PPP calls ISP tries to set default route to ppp0 interface If default route 0 0 0 0 on PPP host is preset to ethO PPP fails doing this Hence unset and preset eth0O default route on PPP host before ydialing On RedHat systems the key networking information is kept in etc sysconfig network and in etc sysconfig network scripts ifcfg ethO Things such as GATEWAY NETMASK must be set correctly in these files These files are easiest to change by hand 1 dakine is PPP dialin host and gateway for home LAN Execute following commands on lanina Delete existing Ethernet interface s if any sbin ifconfig eth0 down sbin ifconfig eth0 1 down sbin ifconfig eth0 lanina zender org Connect IP address with Etherne Add entry to kernel routing table which directs all datagrams to any sbin route add net 192 168 1 0 Route to gateway host all datag
102. isk Management 4 1 RAID RAID is Redundant Array of Independent Disks Reference http en tldp org HOWTO Software RAID HOWTO html 4 111 Hardware Will Kitto helped with this setup The RAID on biogenic consists of 4 x 150 GB Maxtor disks There are two Promise disk controller cards installed in biogenic with two disks connected to each card The jumpers on each disk were set appropriately All disks are master not slave so the disks have the following IDs Card which drive 1 ml hde sl hdf does not exist m2 hdg s2 hdh does not exist 2 ml hdi sl hdj does not exist m2 hdk s2 hdl does not exist 4 12 Getting Promise cards to work The Promise cards were not supported by the kernel that comes with RH7 2 A patch was found to support the Promise chipset and a new kernel was made with all the RAID modules included I do not know if RH8 0 has support for the Promise cards but I would guess yes 4 1 3 Software The devices were setup to run software RAID 5 i e not RAID done in hardware This means that of the 4 disks only the capacity of 3 i e 450 GB is available for users the other 150 GB are for redundancy I followed the instructions that you d see in any typical RAID howto e g as per the reference The raidtab was setup o more etc raidtab raiddev dev md0 raid level nr raid disks nr spare disks persistent superblock RO 0 parity algorithm left symmetric 2
103. it Common Era year It is often useful to select files based on their date convention In such cases it is useful to have regular expressions cf 6 2 for each date convention Date components like MM and YYYY are not just keyboard inputs they are also variables since useful information may be derived from them For example the number of years N in a file containing data from years YYYY and ZZZZ is N ZZZZ YYYY 1 Valid replacements for DD are 0123 0 9 Valid replacements for MM are 01 0 9 Valid replacements for YYYY are 0 9 0 9 0 9 0 9 Climatological values are abrreviated clm which is best interpreted as all of the available data present when the command was run Syntactically c1m works equivalently to YYYY However cIm is only three characters while YYYY is four characters This distinction helps reduce errors when commands use globbing to do the right thing e g ncra caseid 01 nc caseid clm0l nc OK globbing ncra caseid_ 0 9 0 9 0 9 0 9 01 nc caseid clm0Ol nc Better ncra caseid 0 9 4 01 nc caseid clm0l nc Preferred 1 S caseid _YYYY Annual mean S caseid _YYYYMM Monthly mean S caseid _YYYYMMDD Daily mean S caseid _YYYYMMDDHH Hourly mean caseid _YYYYMMDDHHMM Minute mean S caseid _YYYYMMDDHHMMSS Second mean Al Dn O A Q N S caseid _clm Climatological mean 8 caseid _clmMM Climatological monthly mean 9 S caseid _YYYYZ
104. it appears to be running more stably printing hint for remote use kcmshell printmgr will bring up the KDE print manager in full DODS server on sand The DODS server on sand is not a server at all but just a series of cgi scripts that are active as soon as the apache server comes up DODS urls are constructed as http sand ess uci edu cgi bin dods nph dods dodsdata in nc dds server name Be AIT gy eA O YAR DODS er where the DODS cgi are kept If the license manager screws up infreguent but not unknown file name ext name of the subdir in the cgi to define acti data file name you can t just kill the flexlm daemon and restart it as it sets up l 9 17 Hardware description of Zender group computers 57 subdir rooted from htmlroot actual files live name of the cgi script that is called this is the same across zender DODS servers seasalt ess uci edu 128 200 14 39 Dell Dimension T Minitower 800 MHz PIII Arrived 20000615 System Service Tag DS8J10B Express Service Code 300 055 479 95 Intel Pentium III Coppermine 800 MHz 256 MB RAM 40 GB Ultra ATA 7200 RPM with ATA 66 controller NIC 3Com EtherLink 10 100 PCI PCI For Complete PC Management 3c905c TX Microsoft PS 2 Mouse Intellipoint Promise Technology Inc Ultra66 IDE Controller Intel 82371 AB EB PCI Bus Master IDE Controller 120 MB Super disk aka LS120 Sony 8X 4X 32X CD RW drive G
105. it d vpnclient_init start Load kernel module sudo vpnclient connect UCI Start VPN connection sudo vpnclient connect UCIFull Start VPN connection full mode NACS uses allows browsers to request a VPN by logging into the UCI VPN Proxy at https vpn nacs uci edu 3 5 XFree86 Security 17 3 5 XFree86 Security X supports a number of security measures not all of them helpful By default the Debian distri bution prohibits X connections connections from any processes not started by the current desktop owner Apparently this is enforced through so called TCP forwarding TCP forwarding may be prohibited with the nolisten tcp argument to the X server To permit other users access to your desktop display remove this argument from appropriate file s Debian starts the X server from xserverrc etc X11 xinit xserverrc The gdm conf file etc gdm gdm conf may also need to be modified usr bin Xl1 X dpi 100 nolisten tcp Another way of allowing access to your X desktop is to authorize access from all clients using the xhost command xhost Allow connections from any server This may be risky unless the desktop sits behind a firewall or is offline 3 6 XFreeS6 Multiple sessions Default X display is accessible as Ctl Alt F7 on RedHat Linux For a different number of bitplanes on default display use e g startx startx depth 24 To create a second display at say 24 bits per pixel accessible as Ctl Alt F8 us
106. k 255 0 0 0 ING MTU 3924 Metric 1 RX packets 59429 errors 0 dropped 0 overruns 0 frame 0 82 9 RSYNC TX packets 59429 errors 0 dropped 0 overruns 0 carrier 0 collisions 0 txqueuelen 0 zender lanina ifconfig a Link encap Ethernet inet addr 192 168 1 2 UP BROADCAST RUNN etho from UCI HWaddr 00 10 A4 08 12 Bcast 192 168 1 255 NG MULTICAST MTU 1500 3 Mask 255 255 255 0 Metric 1 RX packets 674 errors 0 dropped 0 overruns 0 frame 0 TX packets 541 collisions 73 txqueuelen 100 Interrupt 11 Base eth0 1 inet addr UP BROADCAST RUNN I Interrupt 11 Link encap Ethernet 128 200 14 80 NG MULTICAST Base lo ING MTU 3924 address 0x200 HWaddr 00 10 A4 08 12 Beast 128 200 255 errors 2 dropped 0 overruns 0 carrier 2 MTU 1500 address 0x200 Link encap Local Loopback inet addr 127 0 0 1 UP LOOPBACK RUNN Mask 255 0 0 0 Metric 1 31 255 Mask 255 255 0 0 Metric 1 RX packets 45 errors 0 dropped 0 overruns 0 frame 0 TX packets 45 errors 0 dropped 0 overruns 0 carrier 0 collisions 0 txqueuelen 0 zender lanina dots etho eth0 1 lo Link encap Ethernet inet addr 1 ifconfig a 92 168 1 2 UP BROADCAST RUNNI NG MULTICAST MTU 1500 HWaddr 00 10 A4 08 12 31 Bcast 192 168 1 255 Mask 255 255 255 0 Metric 1 RX packets 897 errors 0 dropped 0 overruns 0 frame 0 TX packe
107. l Specify printer lp plan http xerox ess uci edu 631 ipp portl Specify printer lp plan http tek850 ess uci edu 631 ipp portl Specify printer lp plan http hp6840 ess uci edu 631 ipp portl Specify printer Xerox drivers http www office xerox com perl bin opb_ drivers pl lp plan http xerox ess uci edu Xerox Phaser 4500 is 128 200 24 127 lp o docs plan Print printer options to printer lp dhp4600 hp4600t oraw GIMP2 uses this by default lpr z InputSlot Trayl CUPS command line option to send to Tray 1 lpr P XeroxPhaser4500 plan Xerox Phaser 4500 is xerox ess uci edu 1 lpr P hp4600 plan HP4600 is hp4600 ess uci edu Enabling extra printers in OpenOffice org sudo ln s usr lib openoffice program spadmin usr local bin spadmin 96 9 RSYNC PATH S PATH N usr lib openoffice program usr lib openoffice program spadmin Set printer to standard input kprinter stdin The Xerox Phaser 4500 printer is set up as Xerox Docuprint 4508 lpd xerox ess uci edu 515 Add port 515 LPD port to etc rc firewall the same way 631 is added Add port 9100 JetDirect port to etc rc firewall the same way 631 is adde On 20061108 ESS installed a new printer for faculty on a private network This reguires modifying the interfaces file to start a new interface solely for this printer HP4350 DTN printer in ESS mail room IP 192 168 14 2 iface eth2 inet
108. led FontPath usr X11R6 lib X11 fonts 100dpi unscaled FontPath usr X11R6 1ib X11 fonts Typel FontPath usr X11R6 lib X11 fonts CID FontPath usr X11R6 lib X11 fonts Speedo FontPath usr X11R6 1ib X11 fonts 75dpi FontPath usr X11R6 lib X11 fonts 100dpi FontPath usr share AbiSuite fonts FontPath wnd windows fonts EndSection Also make sure the X server loads the modules to handle freetype and Type 1 Adobe fonts This is accomplished by having Section Module Load freetype Load typel EndSection Notice that the font server can use the MS Windows fonts directly from the Windows fonts direc tory wnd windows fonts However the fonts in this directory first must be prepared for use by running a few commands in that directory cd wnd windows fonts ttmkfdir o fonts scale mkfontdir Also make sure all the fonts are world readable When fooling with X configurations it is convenient to have a clean way to shut down and restart all X processes This can be done by initializing the system to a new runlevel Most Unices start multi user mode and all network applications except the X server in runlevel 3 Runlevel 5 starts the same processes as runlevel 3 and starts the X server as well Thus initializing a system to a different runlevel usually 3 or 5 is a clean way of starting an stopping X processes The telinit
109. ll SG 22a we RG SER SEAS EHS 9 56 1 Updating RedHat Linux with latest patches 9 50 2 Upgrading RedHat LIE os cw ede ehren Debugging es ere Pe he ee WR SRK Ve We Soe Gols Soe AN AO OO YO O U d NM III EE i hh Re Ree i OE ee ER ER YU Y YG EYN YUA Mailmaat oo Hb eR an CEES EEE CAREER OR EES Web LVRS oe ae ah Y 9 RAC HOR EER AE WERE WiC aR KA 9 61 1 Group Web Servet 646 4654 DRE RR be REE EG Lee eS SSL2 ESS Web Server lt lt arar nenn a FTP and firewalls y eoc e O O re a Nom este Bae Wr She p Sii PRO She oS SAS GS AeA eS be Oe YE I AEN Y NU us NCAR so ec ee me eth oe ee ee ee be eo ke O n o oa ee er Gh ddd O y n he ydy de do n di Bade GOES du A Soe ee Bee Swe Bee Grek ips Gace oe Ble ee I LE A pr dr rs Ba na E YR Bey Be A PT Bi E Bibliography Index List of Tables BRWN re F nky Keystrokes 6 oo se ek OR OP EE ORE OHS AAA FO Commalids 2 22424 624244654 62 du 245 oe Fem e aes GDB Commands gt e nic a She a a N RE eee in PICOS o ma ooh ee a eS Oe eee ESS ROBES SS 2 1 CCSM COMMUNITY CLIMATE SYSTEM MODEL 1 CCSM Community Climate System Model Preliminary system modification sudo In s usr bin make usr bin gmake aptitude install netcdf mpich mpi doc Debian GNU Linux 1 1 CAM Community Atmosphere Model 1 2 CLM Community Land Model Make Linux workstation capable of running CLM offline ca Download and unpack CLM 2 1 source code into your home directory http www cgd ucar edu 8080
110. lpful site http www thinkwiki org wiki Intel_ PRO Wireless_3945ABG Mini PCI_ Express_ A mentions that the correct driver is available from sourceforge at http ipw3945 sourceforge net The upshot is that the ipw3945 driver is expected to be available Ol 2006 When complete Intel Linux wireless drivers are available at http support intel com support notebook sb CS 006408 htm Thinkwiki used to 20060215 recommend using the ipw2200 driver Here s what happens when you try that http www thinkwiki org wiki Ipw2200 Installation_on_Debian aptitude remove linux headers 2 6 15 18 686 linux headers 2 6 15 18 aptitude install linux headers 2 6 15 20 686 sudo aptitude install ieee80211 source sudo module assistant t build ieee80211 source sudo aptitude install ipw2200 source sudo module assistant t build ipw2200 source Install firmware cd DATA tmp sudo tar xzvf ipw3945 linux 1 0 0 tgz cd DATA tmp intel ipw3945 1 0 0 C lib hotplug firmware modprobe ipw2200 iwconfig 50 9 RSYNC lsmod grep ipw Module loads but ethl does not show up in ifconfig flyash ess uci edu originally named lanina usually dhcp 14116 ess uci edu dhcp 14118 ess uci edu wired or dhcp 086159 mobile uci edu dhcp 086183 mobile uci edu wireless Dell Inspiron 7500R Dell order 320036478 UCI is Dell customer 677430
111. ly the System map file must be copied along with the kernel cd usr src linux f Choose _one_ of the following cp cnf fl usr src linux config Use archived config file nake clean remove old object files nake oldconfig Use config file or nake config Create modify config file text or nake menuconfig Create modify config file curses or nake xconfig Create modify config file Xwindows nake mrproper Remove config CAREFUL clean up disk Enable APM ACPI ISA LVM UDF USB DHCP requires CONFIG_PACKET and CONFIG_FILTER USB requires fxm DVD and CD ROM requires UDF filesystem Following steps are mandatory make dep Dependency check make Create bzImage NB bzImage not zImage make modules make modules_install make install Copy bzImage to boot Rename it intelligently This automagically does the following three steps cp usr src kernel source 2 4 23 arch i386 boot bzImage boot vmlinuz 2 4 2 cp usr src linux arch i386 boot bzImage boot vmlinuz 2 4 23 cp usr src linux System map boot System map 2 4 23 make clean remove old object files rm boot vmlinuz rm boot System map ln s boot vmlinuz 2 4 23 boot vmlinuz ln s boot System map 2 4 23 boot System map sbin lilo shutdown r now F Exit X the rebuild NVidia driver cd usr src sh NVIDIA Linux x86 1 0 4496 pkg2 run Get 2 6 kernel patches f
112. mbly language file sx 114 9 RSYNC Table 4 Partition sizes used on various computers Computer wnd usr usr local home tmp swap data var boot GB GB GB GB GB GB GB GB GB GB seasalt 5 0 5 2 2 2 0 5 0 5 27 dust 10 20 2 33 lanina 5 0 1 2 2 3 0 2 0 4 11 5 dakine ashes biogenic elnino haze soot 9 69 Groups Make default group cgdcsm with GID 2400 It is also helpful to have a consistent user ID or UID across all systems My CGD UID is the same as my NCAR scientist number 3555 as can be seen on Solaris with the ypcat passwd grep zender 9 70 WINE cd wnd Program Files Microsoft Office Office win xcel exe 9 71 Partitioning Linus Torvalds recommends setting swap partition size equal to twice the amount of RAM Table 4 shows the partitioning schemes used on various computers 1 usr 4 GB may not be enough on Debian 10 GB would be better 2 boot 100 MB is insufficient as having up to five kernels is reasonable i e UP and SMP versions of old and new kernels plus one extra for testing 3 var 1 GB is too small Web server may grow to 5 GB soon Use aptitude clean to free space used by Debian package installation 4 data All remaining space 5 home 10 GB seems adequate BIBLIOGRAPHY 115 Bibliography Friedl J E F Mastering Regular Expressions O Reilly Sebastopol CA 1997 6 2 Index deb 103 bpp 17 depth 17 nolisten tcp 17 dmg 28 etc init d sma
113. mera works with Ubuntu out of the box if one selects the v412 driver Otherwise compile and install the driver yourself with sudo apt get install linux headers uname r linux restricted modules unal cd DATA tmp svn checkout http svn berlios de svnroot repos linux uvc cd linux uvc linux uvc trunk make sudo make install Start ekiga with debugging option 9 56 Installing RedHat Linux 105 ekiga d 1 amp Plug in camera look at dmesg for the device listing e g dev videol f Point your application at that device and see if it works If the video device does not work try restarting the module sudo rmmod uvcvideo sudo modprobe uvcvideo trace 15 dmesg grep uvc New method vncviewer via tephra ess uci edu shared localhost 15 f Enter password when asked f Old method ssh L5915 localhost 5915 zender tephra ess uci edu Start tunnel to on te vncviewer 15 Open VNC window on local machine 9 56 Installing RedHat Linux Get following non default packages Disk 1 openssh server ElectricFence X100dpifonts DisXk 2 sudo xsanegimp Powertools ddd openmotif openmotif devel acroread dxpc octave blas la pack Other gsl RealPlayer abisuite HDF Do not install netcdf RPM as it is built with double underscore versions of all Fortran functions 9 56 1 Updating RedHat Linux with latest patches Read UCI instructions at http www dcslib uci edu linux index html Script is installed as
114. mf ess uci edu u zender cvs co kk ppr_BiZ03 ppr_BiZ04 ppr_GrZ04 ppr_ZeK05 ppr_ZeM07 ppr_Zen08 ppr_ZMT04 ppr_ZeT06b ppr_ZeT06 sltsbl cvs d ext charlesz hox uio no mn hox dl alfgr CVS co kk ppr_GMZ05 Mark s papers cvs d ext biogenic ess uci edu home mflanner cvs co kk ppr_F1Z06 cd tex scp biogenic ess uci edu home mflanner tex mflanner bib cd ppr FlZ05 scp biogenic ess uci edu home mflanner ppr FlZ05 fgr eps cvs d esmf ess uci edu u zender cvs co kk r prp itr d prp itr prp arl cvs d esmf ess uci edu u zender cvs co kk prp_ans prp ids Other Proposals cvs d ext visa eng uci edu home cvs user co kk d prp_JZK05 SE 05 cvs z3 d ext zender nco cvs sourceforge net cvsroot nco co kk nco svn checkout https swamp googlecode com svn trunk swamp username charl cvs d ext zender goldhill cgd ucar edu fs cgd csm models CVS REPOS co r ccm_brnch_dst kk ccm_dst cvs d ext zender esmf ess uci edu u zender cvs co kk r match_brnch_dst cd crm cvs d ext zender goldhill cgd ucar edu fs cgd csm models CVS REPO co r ccm brnch_crm kk crm 9 29 Installing Debian 71 sudo mkdir data cd data sudo mkdir zender sudo chown zender zender sudo cl cd data zender mkdir p mie ps tmp Create data directories which may be Hardware monitoring S vn U 20 ao binutils multiarch bison do aptitude S
115. ml prefs Create anew profile with mozilla thunderbird profilemanager To see all your firefox settings view the URL about config ina Firefox browser act_src prznnk5x zender elnino act_dst ktwn0dgv default virga pth_src HOME mozilla thunderbird act_src pth_dst HOME mozilla thunderbird act_dst bin cp p f S pth_src mab pth dst bin cp p f S pth_src cert8 db pth_dst bin cp p f pth_src key3 db pth dst bin cp p f S pth_src 63760765 s pth dst bin cp p f pth_src mimeTypes rdf pth dst bin cp p f S pth src training dat pth_dst bin cp p f pth_src virtualFolders dat pth dst bin cp p f S pth src Mail pop uci edu S pth_dst Mail pop uci edu bin cp p f S pth_src Mail Local Folders S pth_dst Mail Local Folde 5 4 Macintosh OS X OS X is based on FreeBSD The OS X equivalent to 1dd is otool otool L which ncks 5 4 1 Fink Fink is a Debian based system for installing packages on OS X Fink comes as a disk image file with a dmg suffix Clicking with the pointer on a disk image file causes a sequence of actions to occur the file is mounted the contents appear as icons etc The same effect may be achieved from the command line with the hdiutil and installer commands 29 man hdiutil man installer OS X VNC URL http netmath math uiuc edu VNC osx htm http www realvn hdiutil attach OSXvnc 0 6
116. n it was not possible to mount the array and use it while it was being integrated like you can do with SW RAID under linux This took several hours and in the end it FAILED That was the just about the last straw After spending and time on this escapade that s what the Escalade series SHOULD be named the thing fails to rebuild the array But at least it now reports via email that it has failed So now what The filesystem was a reiserfs to begin with As a last resort I try to rescue the thing with a fsck reiserfs After reading the dire warning about this being the last thing you should try I give it the rebuild tree option and go home This being 2TB of disk it takes a while Later that night I see it s completed and try to mount it To my astonishment it mounts I do a df hmm that s not good only 3started the raid had only been running a short while I m not at all happy to see that it the only directory on the partition is lost found This dir contains the rubble of what used to be about 200GB of expensive and carefully groomed earth sensing and atmospheric data 9 17 Hardware description of Zender group computers 55 So go ahead ask me Am I happy that I spent the extra tobuyahardwareraidcardratherthantwo30 4port sata controllers and using SW RAID I probably couldn t have done all this disk hot swapping with a non HW RAID card but the cost of a reboot for most of us is not that big a deal That
117. n Gateway Genmask Flags MSS Window irtt 128 200 14 0 0 0 0 0 2552259 25 9 0 U 192 168 82 0 0 0 00 299295729970 U O 0 0 12707050 0 0 0 0 255 0 0 0 U O 0 0 OO O 128 200 14 1 0 0 0 0 UG O 0 0 zender lanina dot netstat rn with dakine as PPP gateway to UCI DEFOD OH todd If et vm et 80 Kernel IP routing table Destination Gateway 192 168 1 0 0 0 0 0 127 0 0 0 0 0 0 0 0 07 00 1 92 168 L 1 zender dakine dot netstat rn Kernel IP routing table Destination Gateway 192 168 1 1 0 0 0 0 128 195 187 2 0 0 0 0 192 168 1 0 0 0 0 0 127 0 0 0 0 0 0 0 0 0 0 0 128195 187 2 zender8lanina dotS netstat rn Kernel IP routing table Destination Gateway 128 195 186 2 0 0 0 0 192 168 1 0 0 0 0 0 1 20 0 0 0 0 0 0 0 0 0 128 195 186 2 zender dakine dot netstat rn Kernel IP routing table Destination Gateway 192 168 1 1 0 0 0 0 192 168 1 0 00 00 T270 00 0 0 0 0 0 0 0 0 192 168 1 2 zender lanina netstat rn Kernel IP routing table Destination Gateway 128 117 0 0 0 0 0 0 1270 4 OO 0 0 0 0 0 0 0 0 Leu MTI zender lanina dotS netstat rn Kernel IP routing table Destination Gateway 128 117 64 227 0 0 0 0 127 0 0 0 0 0 0 0 0 0 0 0 128 117 64 227 9 RSYNC Genmask Flags MSS Window 2252592950 U O 0 255 0 0 0 U O 0 0 0 0 0 UG O 0 with dakine as
118. n aspect ratio 0 in stream gt using 4 3 load_plugins plugin dxr3 spudec failed to instantiate itself libspudec init_plugin called liba52 No accelerated IMDCT transform found 9 35 Network Linksys Etherfast 10 100 hub netstat rn BuH98 p 177 Destination 0 0 0 0 is default destination of all datagrams not explicitly routed elsewhere Flags U Route is Up or Usable G Route uses a gateway H Route targets a host Sometimes connectivity to a host or a subnet can be lost when a static route gets stuck in the routing table This has happened twice in the past when system administrators log into lanina and manipulate the routing table In such cases the static route must be manually removed from the routing table as follows Assuming 128 200 14 0 is unreachable zender lanina S S sbin route n Kernel IP routing table Destination Gateway Genmask Flags Metric Ref Use Ifa 128 200 14 0 0 0 0 0 255 25b5 255 O U 0 0 0 eth zender lanina S sudo route del net 128 200 14 0 netmask 255 255 255 0 eth zender dust dotS netstat rn Kernel IP routing table Destination Gateway Genmask Flags MSS Window irtt 128 200 14 25 0 0 0 0 255 255 25 225 UH O 0 128 200 14 0 0 0 0 0 2592209 LOTO U O 0 0 LL20 050 0 0 0 0 255 0 0 0 U 0 0 0 0000 128 200 14 1 0 0 0 0 UG O 0 0 zender lanina netstat rn lanina at UCI Kernel IP routing table Destinatio
119. n of monthly mean timeseries from YYYYMM to ZZZZNN inclusive single record caseid _ YYYYMMDD_ ZZ ZZNNEE_t Mean of daily mean timeseries from YYYYMMDD to ZZZZNNEE inclusive single record 36 8 SYSTEM ADMINISTRATION 8 System Administration 8 1 Backups Simple but effective system backups are made each night The Cron system performs specified actions at regular intervals The cron program checks for actions to perform once per minute Currently all backups are handled by the crontab file of the root user Use the crontab program to alter any user s crontab crontab e sudo crontab u root e The crontab program stores each user s crontab in var spool cron For the root user this is var spool cron root and var spool cron crontabs root for RedHat and Debian GNU Linux respectively Currently this system backup crontab file is 15 2 x x x usr local bin bck_home sh zender 45 2 x x x usr local bin bck_home sh bian 15 3 x x x usr local bin bck_home sh alfgr 45 3 x x x usr local bin bck_home sh mflanner 15 4xx x usr local bin bck_home sh kwon 45 4 xxx usr local bin bck_home sh strombrg 15 5x x xk usr local bin bck_home sh lopez 45 5x x x usr local bin bck_home sh jtalaman 15 6x x x usr local bin bck_home sh okin 45 6x x usr local bin bck_home sh pajarola 30 5x x x usr local bin bck_data sh 35 5x x x usr local bin bck_etc sh 40 5x
120. n sshd telnetd httpd in at least run levels 3 5 Turn on services in runlevel 2 if they should be running even when the X server is not 9 6 Root Change shell to tcsh using control panel chsh s bin tcsh root Install abbreviations to root s cshrc file e g lias m less lias h history lias csrc source tcshrc lias cd cd x set prompt S cwd ROOT lias dir ls lga setenv PATH usr sbin sbin bin usr bin usr local bin SPATH 9 oo o o 9 7 BIFX All ETEX notes are contained in Itx tex and Itx ps 40 9 RSYNC 9 8 Library Often unresolved external links are reported by a loader and the required library must be located A useful procedure to follow is to change to the library directory and use the nm command to search for the missing subroutine sbr foo cd usr lib for lib in libx a do printf Searching lib for sbr n nm lib grep sbr done end loop over lib 9 9 Info After installing packages in usr local which install info in usr local info you need to update usr local info dir 9 10 Networking nslookup returns information about the machine on the Internet with a given name or IP address Use control panel to set network parameters such as hostname in etc hosts e g 128 117 91 216 lanina ppp ucar edu lanina and the nameserver in etc resolv conf nameserver 128 117 24 2 bearmtn e0 nameserver 128 117 24 3 gr
121. nc cd Build libnco_c need cd ctt make Build c module including getopt_bsd cd c make Build c module cd mie make Build mie module cd f make Build f module cd dead make Build dead module Copy important data directories wholesale for drc in aca arese avhrr cccac data dst fgr hitran lsmdata map mny no2 pp rsync av dust ess uci edu data zender drc DATA printf Copied dust ess uci edu data zender idrcjin done Mount dev sg0 as cdrom to enable CD burning done in fstab Install packages not on default Debian unstable install Printing web A V related sudo aptitude install cupsys cupsys client cupsys driver gimpprint gimp foomatic filters ppds foomatic filters imagemagick kaffe pump sane traceroute vncserver xvncviewer xrestop xsane Debugging sudo aptitude install ddd ddd doc gdb graphviz valgrind valgrind callgrind graphviz kcachegrind kcachegrind converters TeX document related sudo aptitude install bibtool bibtex2html cmatrix xfont dvipng emacs intl f Video sound related te sudo aptitude install ubuntu restricted extras includes flashplugin nonfr sudo aptitude install regionset kubuntu restricted extras sudo aptitude install libdvdcss2 this comes from medibuntu sudo usr share doc libdvdread3 install css sh redundant with libdvdcss 2007
122. ndary nameserver UCI 128 200 192 202 UCI News server news service uci edu 9 17 Hardware description of Zender group computers 43 UCI POP server newer should work pop uci edu UCI IMAP server imap uci edu UCI SMTP server smtp uci edu ashes ess uci edu 128 200 14 90 Dell Inspiron 8500 Arrived 20030408 Service Tag C2PNM21 Express Service Code 26285412457 UCI Property 039003448 Pentium IV 2 4 GHz 512 KB L2 Cache Wireless card is TrueMobile1400 MAC address 00 90 4B B2 09 86 wireless internal chip TrueMobile1400 MAC address 00 0b db 17 83 0d wired aptitude install bemwl5driverloader Broadcom wireless card http www linuxant com drivers_bcemwl bemw15 downloads license php Installed driver Broadcom 01 09 2003 3 10 39 0 ndiswrapper driver for Broadcom wireless chip installed 20061216 as aper http ubuntuforums org showthread ph cdrom Setup I 500 bcmwl5 inf cdrom Setup bcmwl5 sys License Key 87 A7 39 A4 18 C0 email address zender uci edu Registered as ethl hda FUJITSU MHS2060AT ATA DISK drive 60 GB hdc HL DT STCD RW DVD ROM GCC 4240N ATAPI CD DVD ROM drive hdc ATAPI 24X DVD ROM CD R RW drive 2048kB Cache UDMA 33 Intel 810 AC97 Au dio version 0 24 04 35 38 May 6 2003 Broadcom 4401 Ethernet Driver bcm4400 ver 2 0 0 03 25 03 eth0 Broadcom BCM4401 100Base T found at mem faffe000 IRO 11 node addr 000bdb17830d O nvidia loading NVIDIA Linux x86 nvidia o Kernel Module 1 0 4349 Thu Mar 27 19 00 02 PST 20
123. ne This section falls out of date quickly Tramp filename conventions have changed at least three times in three years 9 51 RPM packages in usr that were installed and may need to be unin stalled or reinstalled by hand opendx 4 1 0 1 i386 rpm opendx docs 4 0 10 1 i386 rpm sgi opengl 1 2 1 1 i386 rpm ImageMagick 5 1 1 1 i386 rpm ghostscript 6 01 1 i386 rpm ghostscript fonts 6 0 2 noarch rpm 9 51 1 IPCC and PBS configuration The IPCC and PBS clusters ipcc ess uci edu and pbs ess uci edu run Rocks Rocks based clusters use the Community Enterprise Operating System CentOS a re packaged version version of RHEL CentOS is an RPM based system Copies of CentOS are kept on the system so that new RPMs may be easily installed 98 9 RSYNC Get CentOS bison locally or from the net data centos 4 3 os x86_64 CentOS RPMS bison 1 875c 2 x86_64 rpm cd DATA tmp wget ftp ftp nluug nl pub os Linux distr CentOS 4 3 os x86_64 CentOS RPMS sudo rpm ivh bison 1 875c 2 x86_64 rpm Rocks names compute nodes in a 1 based enumerated format so a 26 compute node cluster has nodes compute 0 1 compute 0 2 compute 0 3 compute 0 26 Some IPCC compute nodes are loaded by the Medium Performance Cluster MPC MPC names compute nodes in a 1 based enumerated format so a 26 compute node cluster has nodes ipce nl ipce n2 ipcc n3 e 1pec n26 Each node is by default accessible via ss
124. nless care is taken a substantial portion of free disk space may be used by un wanted files The following short script uses find to locate and sort in order of descending size the largest 100 files within the drc hierarchy 4 9 Disk corruption 25 drc DATA drc S HOME find drc type f xec ls 1 Xy sort r n k 5 head 100 gt tmp bgf_foo txt The results are stored in tmp bgf_foo txt Find files that contain foo in their names find name html tmp bgf_foo txt 4 9 Disk corruption Disks die occasionally and it is prudent to gain familiarity with disk recovery strategies although these are no substitute for making regular off site backups Disk blocks that are unwritable are known as bad blocks When disks develop bad blocks they may still function for guite a while but restarting the system may become tedious as manual fsck s become mandatory Specific disk repair commands are filesystem dependent The default Linux filesystem is ext2 which is supported by a package of utilities known as e2fsprogs The dumpe2fs command displays useful information about a device such as the block size chunk size etc The e2 sck command is used to monitor and repair ext2 filesystems dumpe2fs b dev hda7 Print bad block list umount dev hda7 e2fsck c dev hda7 Write bad blocks to list e2fsck p dev hda7 Automatically preen filesystem without prompting Ext2 filesystems support the notion of
125. nt mkdir p bin bin cp r zender sh export PVM_ARCH sh pvmgetarch mkdir p bin PVM_ARCH include lib PVM_ARCH obj cp zender bin PVM_ARCH makdep bin PVM_ARCH cp zender sh pvmgetarch sh S PVM_ARCH 74 mv cp bashre zender bashrc 7 bashrc old 9 30 Recreating Server Files 9 RSYNC Server port to leave open when registering over UCInet 29659 NCO 1700 PGI DL license servers 7143 PathScale licence server on IPCC When the system goes down and takes the etc partition with it the system services must be re installed from scratch sudo mv home backup etc passwd etc passwd ls home backup Reset SSH keys to ease work on remote machine Reinstall sudo permissions sudo scp biogenic ess uci edu etc sudoers dust ess uci edu etc sudoers it S S S S S S S S S S su S S S S S S S S S S S S Restore accounts do do do do do do do do do do do do do do do do do do do do do do do RedHat Linux groupadd g 2400 cgdcsm Create group cgdcsm groupadd g 1965 esmfadm Create group esmfadm seradd seradd seradd seradd seradd seradd seradd seradd seradd seradd seradd seradd seradd seradd seradd seradd seradd seradd seradd seradd seradd c Charlie Zender d home zender g cgdcsn c Mark Flanner d home mflanner g cgdcsn c Eun Young Kwon c
126. oftware 25 o 1 nEICDF Browsers eu ch ee a aan nen ae nen BA A WLR Wn 8 25 odl dCBrowmb serra ee te e e o Be es Bete Boe Be ade 8 26 as 2 3 ea NE e FAR 26 AMS CYIG caos eed wg wee rg ee Ee GN Sy tea Ryd 26 Sed NOW WE Se rea diaa e aa e e a ee ee Oe Y PE 8 26 52 FO kn Be PRS SSS Se ChE Se OSE SESS ESSE EE He HSS 26 Ia Mal 4 oy oh ee Oe ek i dio me es Ge ae A 26 a4 Macintosh OS 2 2 2 ves eed wea e Oe Ree hee Bee bu Gu a 28 SAN a eC re ra ar a Ba NN 28 Programming 29 BL Deal Dre ee rn an a aa Ew OO nd 29 6 2 Regular expressi ns aaa aaa RWE RHS AAA 29 ue IE see ee a Ge he ae we Gok de ROE e Gok ar ae Goa arena la ee are 32 6 4 JntemationalizatonIl8N nn 33 Files 34 Ll Die cusco re en ee ee oe eee eas 34 System Administration 36 RH EF ee ee Ge Sto Dek Bite Diente EYN A nd Soe er 36 Ce WN oa oo ee RAR EAR AAA AEREA RA 37 rsync 37 IE SE er O a A RR RAF A re re 38 92 Documentation s m a u we ann en en NF SO A 38 VE ee ee ee ee he DR cay das He GYN Ee tap tbs He O DD Go Gl ag de dug 38 OA Batch Queues cc a ew 39 9 5 Remote shell service rcp rsh ssh telnet o oe be REE REO REE OES 39 Oe Wie ee whee Poe be he bee a ee Oe 39 A ee Hs we FWG Bh oe dU GE DDI BO FO UU RR o FD CRE Feb E 39 F5 LDF lt lt ek eS en ee ra AA AE d 40 e Y A A AR 40 A o o a Y CE CR od RE a RIN ER ee 4 40 9 11 C development occ Er RR REE AA 40 9 12 Time and TimeZone 2 0a ee ee EG 40 ALS POL cosa bw tole bs eee bs CAM EERE SMe R 41
127. oprofile module available but we are not aware of any with the more exciting perfctr patch applied and the perfctr module available The Oprofile homepage is http oprofile sourceforge net docs Oprofile first requires sudo modprobe oprofile Second initialize the oprofiled daemon and start it collecting info This command depends on your exact hardware software configuration opcontrol vmlinux path to vmlinux Normal generic opcontrol no vmlinux No vmlinux exists The path must lead to the uncompressed linux ELF executable not to typical vmlinuz compressed boot sector that is installed in the boot directory For clay ess uci edu sudo opcontrol vmlinux usr src linux 2 6 ll vmlinux Explicitly say one CPU sudo opcontrol separate none vmlinux usr src linux 2 6 ll vmlinux separate cpu reports counts on both CPUs sudo opcontrol separate cpu vmlinux usr src linux 2 6 ll vmlinux Once separated must explicitly shut off for succeeding runs sudo opcontrol start Next line kills daemon removes small amount of overhead sudo opcontrol shutdown Remove profile module needed for hpcrun opcontrol deinit 3 3 Performance Profiling 15 In order for hpcrun to work per ct r module must be modprobe loaded and dev perfctr must be mode 644 When ready to collect info do a sudo 1s to initialize the timeout on the sudo command so later commands do not ask
128. or NVidia drivers 9 25 LILO configuration 67 http www minion de files I like the make xconfig method It is very clean and allows storing and retrieving configuration files By default the configuration file is saved as config in the top level make directory Save a visible version of the configuration file as e g home zender linux usr src linux config lani or config lanina 2 4 23 20010322 andthencp usr src linux config lanina 2 4 23 Specific configuration options which are not the default must be set 1 Block Devices CONF IG_BLK_DEV_IDEFLOPPY for LS 120 Iomega Zip support 2 Sound CONFIG _SOUND_MAESTRO for Lanina soundcard 3 Networking Options for IEEE 1394 Firewire 4 IrDA infrared support CONFIG_IRDA 5 USB support Various Important for futurre goodies like mouse joystick 6 Character devices CONFIG PRINTER 7 Filesystems CONFIG_FAT_FS CONFIG_VFAT_FS for MS Windows filesystem support The sysct1 command allows one to print and set kernel parameters at runtime The Procfs file system which displays Droc sys is required for sysct1 to work sysctl a Print all kernel configuration values in proc sys 9 25 LILO configuration The LILO linux loader system is a venerable method of loading Linux which has lately been superceded by GRUB One problem with the LILO method is that
129. or malloc for more information MALLOC_CHECK_ 0 ccc tst mmr Heap corruption silently ignored MALLOC_CHECK_ 1 ccc tst mmr Heap corruption prints diagnostics to stder MALLOC_CHECK_ 2 ccc tst mmr Heap corruption causes immediate abort Many commercial tools are available to find memory leaks ccmalloc is a free tool Simply link with ccmalloc g and then run with MALLOC_CHECK_ 1 to produce a report ccmalloc g o ccc ccc o gcc o ncks ncks o usr local lib ccmalloc gcc o L usr local lib lccmallo g o ccc ccc o usr local lib ccmalloc g o L usr local lib lccmalloc MALLOC_CHECK_ 1 ccc ccmalloc generates a report and the number of memory leaks in the program is shown in the garbage column http ieee uow edu au mjp16 prog memleak html describes the procedure 9 58 Valgrind The most useful memory debugging tool since about 2002 has been valgrind Simply precede the program invocation with valgrind options valgrind ccc gt foo 2 gt amp l valgrind leak check yes ccc gt foo 2 gt amp 1 Print location of likely leaks valgrind toolzmemcheck ccc gt foo 2 gt amp 1 2The term is from Norse mythology and is pronounced val grinned 108 9 RSYNC Table 3 GDB Commands Command Result start Break at beginning of program all languages break rt_cls var_put Break at start of function rt_cls var_put break nco_var_fll Break at start of functionnco_var_fll break s
130. ost of these requirements can be met by small modifications of the apache2 conf or httpd conf files 1 DirectoryIndex should include index html and index shtml 2 PHP should be enabled although not currently used 3 Processing of server side includes SSI should be enabled This handles processing of shtml files The apache2 conf handles this hjm to include handling for server parsed files shtml lt IfModule mod_mime c gt AddType text html shtml AddHandler server parsed shtml lt IfModule gt 4 DocumentRoot top directory of webpage hierarchy should be var www html 5 DODS OPeNDAP access must work This may require enabling web server usage of CGI scripts in the cgi bin directory 6 Webserver must re start automatically on reboots 9 61 2 ESS Web Server The ESS webserver is www ess uci edu It does not support remote SSH access The ESS server ess1 ess uci edu allows remote SSH access Both the webserver and the department server are virtual hosts which appear to be hosted by the same physical hosts The physical hosts which support SSH access include swamis ps uci edu and lunada ps uci edu Physical hosts which firewall SSH include mavericks ps uci edu 9 62 FTP and firewalls On Linux the ncftp client may be used to circumvent firewalls ncftp supports most of the commands as the standard ftp client but many more intuitive commands as well Experience shows that ncftp should repla
131. pad requires a key to activate This must be the minus key on the numeric keypad 3 7 LCD Projectors LCD Projectors interact with X in strange ways The ESS Department projector works best at resolution fxm The IGPP projector works best at resolution fxm 3 8 Desktop The X server automatically starts at the specified system runlevel The default runlevel is specified in etc inittab and is OS dependent In a given runlevel RedHat uses runlevel 5 for this De bian uses runlevel 2 X automatically starts the display manager specified in etc desktop The most common choices are GNOME KDE and XDM These choices invoke the display managers gdm kdm and xdm respectively These display managers are capable of starting any desktop on the system as determined in their configuration settings Naturally they default to their appro priate desktops e g kdm starts the K desktop environment This default may be over ridden by etc X1 1 default display manager cat etc X11 default display manager usr bin kdm 3 9 JPEG Processing JPEG files produced by IDL for fl_stb in ls jpg perl p e s x x1 3pg 1 g do echo Converting f1_stb Jpg to fl_stb pnm jpegtopnm S fl_stb jpg gt S fl_stb pnm echo Converting f1_stb pnm to f1_stb png pnmtopng f1_stb pnm gt S fl_stb png echo Converting f1_stb pnm to f1_stb png pnmtoppm S fl_stb pnm gt S fl_stb ppm done 19 4 D
132. particular CompactFlash relies on the USB driver 2 2 1 CompactFlash To transfer files from your Camera s CompactFlash to disk first mount the CompactFlash card as avfat file system mount t vfat dev hdel cf CompactFlash root only This CompactFlash is enumerated as an IDE drive here because it is inserted into the system on the PCMCIA bus in a PCMCIA adaptor CompactFlash to USB adaptors are at least as common The USB sub system uses SCSI drivers so CompactFlash drives will be enumerated as SCSI drives e g dev sda1 when mounted through a USB port By default CompactFlash devices require root priveleges they are not user writable unless opened with the appropriate mask mount t vfat o umask 022 dev hdel cf CompactFlash users R W In this mode users may read and write files but can not actually own files or directories The vfat filesystem does not support multiple user identities and priveleges However the device may be mounted with a particular UID and GID which will allow full user read write access sudo mount t vfat o umask 022 uid 3555 gid 2400 dev hdel cf CompactFl This is the recommended way to mount CompactFlash used for backup and file transfer purposes 2 22 Memory Stick A Memory Stick aka a USB Flash Drive is very similar to CompactFlash device As always the Flash Memory HOWTO is very useful To guickly backup and copy material to my black attache memory stick use sudo mkdir p me
133. pc_slr cc spc_slr_cls spc_slr_cls Break at start of function spc_slr_cls of class print grd 0 grd_nbr 0O Print first grd_nbr items of array grd print varprc idx gt val fp 0 Print first item of array var _prc idx gt val watch idx Set watchpoint on idx break dstmbl MP dst_mbl_ Set breakpoint on G95 compiled module procedur print dstctl MP nstep Print G95 compiled Module Procedure MP varia Since there are many errors in the default GNU compilers and libraries these errors may be sup pressed using the To make it easier to write suppressions tell valgrind to print the suppression command for each error it encounters valgrind guiet gen suppressions yes ccc ff Generate suppression messages In this mode val grind queries whether to print suppression text for each The default suppressed warnings are contained in usr local lib valgrind default supp and Store additional suppressions you wish to ignore in a suppresions file e g valgrind txt Multiple suppressions files may be used by specifying them with the suppressions flag valgrind v suppressions S HOME c t valgrind txt ccc gt foo 2 gt amp 1 9 59 DDD DDD has many obscure capabilities especially when running in GDB mode Table 3 summarizes frequently used GDB commands GDB does not know the size of dynamically allocated arrays To print the first grd _nbr items of array grd use print grd 0 grd_nbr 0O The 0 is necessary to get DDD to recognize that th
134. pecify screen resolution Knoppix is very useful for restoring corrupted systems Typically this requires mounting the disks on the filesystem Knoppix does this automatically by double clicking on the disk icon alterna tively on may use the mount command Then the disk must be set to enable writing Knoppix makes this available through the mouse menu Finally it is usually necessary to change from user knoppix to user root before doing any serious repairs The command sequence to fix a bad sector on a reiserfs partition on ashes was su root reiserfsck dev hdal Assuming corruption is found and the disk may want to unmount the disk and attempt to rebuild the filesystem tree umount dev hdal reiserfsck rebuild tree dev hdal Many ATA 3 and later ATA IDE and SCSI 3 hard drives include Self Monitoring Analysis and Reporting Technology SMART utilities The smartmontools package uses these capabilities to monitor and tests for disk problems The command line program is smart ct 1 and the daemon is etc init d smartmontools which uses the configuration in etc init d smartmontools start usr sbin smartctl all dev hdal smartctl i dev hda Print disk information smartctl H dev hda Print health status smartctl l error dev hda Print error log from test smartctl t offline dev hda Perform offline test then check error log smartctl t short dev hda Perform short disk test
135. program is excellent for viewing and editing images However it has now slideshow capabilities 933 CDs 77 9 32 2 KView 9 32 3 Kuickshow Kuickshow is a very fine tool with excellent preview and slieshow modes In preview mode just click on a filename and keep hitting Pg Dn to see new pictures The slideshow mode has an appropriate delay betweeen slides Remember to de activate power saving and screen blanking before expecting the slideshow to continue unattended 9 33 CDs Compact Disks CDs store up to 700 MB Formatting and writing data to the CD known as burning is not always straightforward with Linux The program cdbakeoven has an intu itive interface It provides continuous real time status reports during burning and sometimes works when K3b fails On sand ess uci edu K3b tends to fail yet cdbakeoven works On elnino ess uci edu K3b tends to work and cdbakeoven fails The KDE CD DVD burning utility is called K3b It automatically loads when it detects a blank CD in a writable drive However K3b does not have a completion meter and just hangs when it fails to burn CDs at least under SuSE This is annoying because one does not know whether the program is working and how long until completion 9 34 DVDs I use xine and mplayer to play DVDs Due to legal concerns few Linux distributions automat ically install DeCSS the pre requisite library for decrypting DVDs Multimedia software works with media resource locators MRLs
136. protocol version 1 2 authorized keys2 contains RSA and DSA public keys of authorized users gathered from the id_dsa pub files on remote machines These keys employ SSH protocol version 2 3 known_hosts contains RSA1 public keys of authorized machines gathered from the etc ssh ssh_host key files on remote machines These keys employ SSH protocol version 1 4 known_hosts2 contains DSA public keys of authorized machines gathered from the etc ssh ssh_host_dsa and etc ssh ssh_host_rsa_key pub files on remote machines These keys employ SSH pro tocol version 2 5 Note that the system wide configuration files e g etc ssh ssh_config may disallow rec ognizing user specific known hosts Execute ssh keygen t rsal to generate identity and identity pub files Execute ssh keygen t rsa to generate id_rsa and id_rsa pub files Execute ssh keygen t dsa to generate id_dsa and id_dsa pub files When upgrading or renaming a server one may need to re generate the server s keys cd etc ssh ssh keygen t rsal f etc ssh ssh_host_key ssh keygen t rsa f etc ssh ssh_host_rsa_key ssh keygen t dsa f etc ssh ssh_host_dsa_key To exercise all the various keys force ssh to use the different algorithms ssh 1 Use SSH version 1 protocol only ssh 2 Use SSH version 2 protocol only Recently OpenSSH added some useful commands The command ssh copy id automates the process of installing the identity pub and id_ d
137. r edu This machine will open a proxy to any other machine at UCAR 9 65 Autotools The GNU Autotools refers to an integrated set of software development and portatibility tools including Libtool cd DATA cvs z3 d pserver anoncvs subversions gnu org cvsroot libtool login cvs z3 d pserver anoncvs subversions gnu org cvsroot libtool co r bran cd DATA libtool bootstrap configure prefix usr local make sudo make install hash r cvs z3 d pserver anoncvs subversions gnu org cvsroot autoconf login cvs z3 d pserver anoncvs subversions gnu org cvsroot autoconf co r AUT cvs z3 d pserver anoncvs subversions gnu org cvsroot m4 login cvs z3 d pserver anoncvs subversions gnu org cvsroot m4 co r m4 1_40 m 112 9 RSYNC 9 66 SSH Most Unices use OpenSSH from the FreeBSD folks Systemwide defaults are set in etc ssh ssh_config The directory ssh contains authorization files which make passwordless access possible An authorized_keys file if present on machine A contains public keys of users generated on ma chines B Z These users will be allowed to log in to machine A without entering any password A known hosts file if present contains public host keys of known remote machines These keys were generated on remote machines 1 authorized_keys contains RSA1 public keys of authorized users gathered from the iden tity pub files on remote machines These keys employ SSH
138. r local ess uci edu data zender tmp rsi tar gz usr local pgi tar gz rsi tar gz rsi idl_5 6 rsi idl IDL and PGI are handled by FlexLM ted in etc rc d rc local Running lmgrd as root is not recommended but is expedient IDL lmgrd starts vendor specific license daemons for both IDL and PGI This is because contents of PGI license file are in IDL license file CENSE_FILE environment variable point to both license S PGI li ess uci edu ess uci edu LE is undefined with unset LM_L CENSE_F CENSE_F CENSE_FILE appear to override searching for 9 23 PCMCIA 65 PGI style node locked licenses first Since LM_LICENSE_FILE must be defined to allow net work access to the IDL software this means it will be difficult if not impossible to get PGI and IDL both working on lanina at the same time To remove a checked out license use the Imremove option to the lmut il command lmutil lmremove c license file list feature user user_host display lmutil lmremove idl zender lanina ess uci edu dev pts 0 The argument to Imremove were obtained from the Imstat a command which is now obso lete Instead give sub commands arguments directly to lmut il e g lmutil lmstat 9 22 1 PGI on sand So that any system user may run the software we create a FlexLM license daemon etc init d pgi Imgrd A corresponding user f 1ex1m runs this daemon usr local pgi 5 1 3 W
139. r sa pub files in a remote machine s autho rized keys and authorized keys2 files ssh copy id i identity_file user machine Some machines have multiple IP addresses blackforest ucar edu has four IP ad dresses The entries in the known_hosts files might conflict with one another and lead to warnings like POSSIBLE DNS SPOOFING DETECTED or REMOTE HOST IDENTIFICATION HAS CHANGED Machines with mulitple IP addresses and multiple host keys should be entered in the known_hosts files in one of two ways First one may omit the optional FODN from the entry and specify only the IP address es associated with the host When SSH looks at IP addresses only 9 67 Security 113 it cannot get confused Second one may enter the optional FQDN with the IP address but in this case one must make sure that entries for each possible IP address are present Otherwise the above warnings will result if one tries to use one of the missing addresses Misconfiguration of the login shell e g causing bashrc to print will cause scp to fail with alost connection error The NCO project uses the Sourceforge shell and CVS servers nco sf net and nco cvs sf net respectively Set SSH keys for these machines by uploading keys to the Sourceforge web interface athttps sourceforge net account Uploading keys directly e g with scp to the shell server is allowed but discouraged Uploading keys directly to the Sourceforge CVS server is not allo
140. rams bound for hosts outside intranet fxm metric 1 argument appears necessary sbin route add default gw 192 168 1 1 metric 1 Execute following commands on dakine sbin ifconfig eth0 down sbin ifconfig eth0 1 down sbin ifconfig eth0 dakine zender org Connect IP address with Etherne Ensure default route interface is not preset to eth0 before dialing sbin route del default gw 192 168 1 1 metric 1 PPP JO etc ppp chain start Turn on IP masquerading 2 lanina is PPP dialin host and gateway for home LAN Execute following commands on lanina Delete existing Ethernet interface s if any hostname lanina zender org hostname i v sbin ifconfig eth0 down 86 9 RSYNC sbin ifconfig eth0 1 down Ensure default route interface is not preset to eth0 before dialing sbin route del default gw 192 168 1 1 metric 1 PPP JO sbin ifconfig ethO lanina zender org Connect IP address with Etherne etc ppp chain start Turn on IP masquerading Execute following commands on dakine Point dakine to lanina gateway sbin ifconfig eth0 down sbin ifconfig eth0 dakine zender org Route to gateway host all datagrams bound for hosts outside intranet fxm metric 1 argument appears necessary sbin route add default gw 192 168 1 2 metric 1 These commands plus some other goodies clock synchronization are executed by the lanina sh script lanin
141. raphics NVIDIA TNT2 M64 4xAGP with 32MB RAM 07 12 05 hjm modified the xorg conf to read Section Device Identifier NVIDIA Corporation NV5M64 RIVA TNT2 Model 64 Mode Driver nvidia BusID POL LeO 20 Option BackingStore True lt allows covered windows to refresh Option SaveUnders True lt ditto Option RenderAccel true lt allows better HW acceleration EndSection 19 Dell M990 purchased with computer See http support dell com docs monitors m990 En Index htm Video controller NVIDIA TNT2 M64 4xAGP with 32MB RAM Uses XF86_SVGA driver Horizontal scan frequency 30 96 kHz automatic Vertical scan frequency 50 160 Hz automatic Optimal preset resolution 1024x768 at 75 Hz or 85 Hz Highest preset resolution 1600x1200 at 75 Hz Highest addressable resolution 1600x1200 at 75 Hz Preset modes Supports 1024x768 68 7 kHz 85 Hz Supports 1280x1024 80 0 kHz 75 Hz Supports 1280x1024 91 1 kHz 85 Hz Se ose od de de de de de de Se de Se e 58 9 RSYNC Supports 1600x1200 93 7 kHz 75 Hz Computed following modeline settings using above info and http www dkfz heidelberg de spec linux modeline V freq 85 00 Hz h freg 68 79 KHz Modeline 1024x768 97 40 1024 1072 1192 1416 168 768 771 809 HSync V f
142. re locked to the username that installed the compilers and to the hardware configuration in ex istence when the compilers were installed The PGI style hostid can be found by running the command S PGI linux86 bin pghostid unset LM_L CENSE_F LE The host ID must match that in the license file To copy files from dust to other machines e g lanina udo scp dust udo scp dust d usr local udo udo udo In s tar xvzf tar xvzf un 0 0000 tar cvzf data zender tmp pgi tar gz tar cvzf data zender tmp rsi tar gz pgi Est bin rm rsi idl_linux tar gz Add the following to bashrc Se E de OSE Se HR Licenses for FlexLM is start Users must have LM_L case S HOST in dustx export LM OL CENSE_F LE S IDL DIR license licens o vy dakinex Randerson s server endif using licenses directly on license server Zender s server lanina seasaltx dhcp ras cgd85 export LM_LICENSE_FILE S PGI license dat 1700ftessl CENSE_FILE S PGI license dat 1700 dust export LM_L ee vy esac endcase S HOST PGI Fortran may not run on lanina unless LM_L This is because any licenses specified in LM_L endif using network licenses dat ess uci edu data zender tmp pgi tar gz us
143. req 80 00 Hz h freg 86 05 KHz Modeline 1280x1024 167 97 1280 1368 1576 1952 1024 1024 1027 1075 Hsyn V freq 85 00 Hz h freg 91 72 KHz Modeline 1280x1024 185 64 1280 1376 1600 2024 1024 1024 1028 1079 HSyn V freq 75 00 Hz h freg 94 24 KHz Modeline 1600x1200 242 01 1600 1728 2024 2568 1200 1200 1204 1256 HSyn Linux 2 2 x kernels do not recognize the ATA66 controller but patches and workarounds are avail able HHPT366 HOWTO at http www csie ntu edu tw 7Eb6506063 hpt366 UDMA Mini HOWTO http www linuxdoc org My solution was to plug the hard drive directly into the IDE controller on the motherboard and then install linux i e I bypassed the ATA66 controller soot ess uci edu 128 200 14 98 Dell Precision Workstation 650n Minitower Arrived Jan 23 2003 Service Tag GC9L921 Express Service Code 35570219545 UCI Property 039003412 Dual Xeon 2 8GHz 2 GB RAM hjm 4 11 05 added etc init d httpd restart to etc rc local to restart web server on reboot hjm new 200 GB disk added 4 14 05 on same IDE bus as 1st suboptimal but physically tricky to take over other IDE bus If very slow will try to move it 6 1 05 moved 2nd disk to other controller channel much faster 1024 df Filesystem 1K blocks Used Available Use Mounted on dev mapper VolGroup00 LogVol00 113177264 94615204 12812916 89 dev
144. res ide scsi driver hdb mounts as sr0 hdc HITACHI_DK23EB 40 ATA DISK drive hde SanDisk SDCFB 1024 CFA DISK drive Floppy drive s fd0 is 1 44M Attached scsi CD ROM sr0 at scsi0 channel O id O lun O sr0 scsi3 mmc drive 0x 24x writer cd rw xa form2 cdda tray agpgart Detected Intel i845 chipset Intel 810 AC97 Audio version 0 21 09 15 48 Aug 14 2002 eth0 3c59x eth1 Looks like a Lucent Agere firmware version 8 10 Uses hermes orinoco and orinoco_cs modules MAC address 00 08 74 E4 EC 3F wired MAC address 00 02 2D 85 5C 3E wireless Firewire IEEE 1394 uses ohci1394 Linksys Wireless G Broadband Router S N CDF80E406886 MAC 0013107D321C Ownership ID 4HFFS4BW Device ID 5ZRJG2FV ZyXel AG200 Wireless 802 11a b g USB adaptor Based on Atheros chipset S N S510500149 MAC 00A0C5B810C7 http www zyxel com product Cleaned fans 20070917 using on line ser vice manual Found with search for Dell Precision M50 Service Manual http support dell com support edocs sy elnino s internal 60 GB disk drive died 20080120 This was an IBM travelstar Model IC25TO60ATCSOS 0 5400 RPM Received replacement 80 GB disk drive died in 20080205 This was an Samsung esmf ess uci edu 128 200 197 165 Sony DSCF828 Digital Camera SanDisk ImageMate USB 2 0 Reader Writer for CompactFlash Type I amp II Model SDDR 91 Part Number 20 90 00091 1 year warranty SanDisk CompactFlash 1 0 GB www sandisk com reg 5 year warranty Sony Camera Case LCS VA3 haze ess uci edu 128 2
145. rtmontools 23 AccelFactor 11 Bash 32 CR LF 68 CR 68 DefaultColorDepth 24 17 DirectorylIndex 110 DocumentRoot 110 Emacs 26 31 69 GATEWAY 85 GNUpod 8 HOME 62 InputDevice 10 LF 68 LoadLeveler 39 MALLOC_CHECK_ 107 Macintosh 68 MaxSpeed 11 MinSpeed ll NCVweb 25 NETMASK 85 NOS 39 PPP 85 Tau 14 XAPPLRESDIR 13 XFree86 4 x 10 X server 12 Xconfigurator 10 XkbOptions 10 alsamixer 104 amarok 90 aptitude clean 114 apt 101 blackforest ucar edu 112 cardctl 94 cat 27 ccmalloc g 107 ccmalloc 107 cdbakeoven 77 cfdisk 21 cgdcsm 114 chkrootkit 113 cluster fork 99 control panel 26 crontab 36 cron 36 60 csh 32 cvd 109 ddd 36 dmalloc 106 dmesg 68 dumpe2fs 25 e2fsck 25 e2fsprogs 25 ekiga 104 emacs 11 97 eth0 90 exportfs 60 extglob 32 fdb 109 fdisk 1 93 fdisk 21 find 24 firefox 28 flexlm 65 free 98 fsck 25 ftp 11 g 96 gcc 66 gconf sanity check 1 60 gdm 17 18 gimp 76 gkrellm 93 glibc devel 40 glxinfo 10 googleearth 10 gpg 99 gtkpod 8 guarddog 96 harry sh 87 116 INDEX hash 32 hdiutil 28 hpcquick 16 hpcrun 14 15 hpcviewer 16 httpd 39 hwclock 41 i8kbuttons 93 i8kctl 93 i8kmon 93 i8kutils 93 i8k 93 icc 63 ifc 63 ifdown 88 ifup 88 import 10 insmod 84 installer 28 ipcs 98 iptables 96 ipw3945 92 kbdrate 13 kdm 17 18 k
146. s Level 2 data cache misses PAPI_L2 ICM Yes Level 2 instruction cache misses PAPI_FPU_IDL Yes Cycles floating point units are idle PAPI_TLB_DM Yes Data translation lookaside buffer misses PAPI TLB IM Yes Instruction translation lookaside buffer misses PAPI_L1_LDM Yes Level 1 load misses PAPI_L1 STM Yes Level 1 store misses PAPI_L2_LDM Yes Level 2 load misses PAPI_L2 STM Yes Level 2 store misses PAPI_STL_ICY Yes Cycles with no instruction issue PAPI_HW_INT Yes Hardware interrupts PAPI_BR_TKN Yes Conditional branch instructions taken PAPI_BR_MSP Yes Conditional branch instructions mispredicted PAPI_TOT_INS Yes Instructions completed PAPI_FP_INS Yes Floating point instructions PAPI_BR_INS Yes Branch instructions PAPI_VEC_INS Yes Vector SIMD instructions 16 3 X AND XFREES6 PAPT_RES_STL Yes Cycles stalled on any resource PAPI_TOT_CYC Yes Total cycles PAPI_L2_DCH Yes Level 2 data cache hits PAPI_L1 DCA Yes Level 1 data cache accesses PAPI_L2 DCR Yes Level 2 data cache reads PAPI_L2 DCW Yes Level 2 data cache writes PAPI_L2 ICH Yes Level 2 instruction cache hits PAPI Ll1 ICA Yes Level 1 instruction cache accesses PAPI Ll1 ICR Yes Level 1 instruction cache reads PAPI_ FML INS Yes Floating point multiply instructions PAPI_FAD_ INS Yes Floating point add instructions PAPI_FP_OPS
147. serjet 4250 au ler tage couloir format papier A4 recto verso duplex 192 168 101 39 Photocopieuse Canon 3570 deux ieme tage salle reprographie format A4 et A3 recto verso duplex 192 168 101 36 Imprimante couleur Dell 3110CN deuxieme tage salle reprographie format A4 recto verso duplex 192 168 101 42 9 39 Router 89 9 39 Router Whistlernet routers Linksys Wireless G router WRT54G Install HyperWRT Linux router distri bution from http www hyperwrt org 1 Connect ethernet of laptop to router Log into router Login password when shipped is admin admin Destination is http 192 168 1 1 BR o N Router Name is zender WRT54G 5 Local Address is 192 168 1 5 6 Internet Address is 192 168 1 6 7 Subnet Mask is 255 255 255 0 8 Enable DHCP server 9 Starting IP address 192 168 1 160 10 Ending IP address 192 168 1 179 11 Static DNS 128 200 1 201 64 4 16 25 12 Router password dakinenet 13 Wireless Network Name SSID zendernet 14 Setup to use MAC based filtering 15 Startup script for each router to bond to eachother usr sbin wl lazywds 0 Give Mangonet MAC to zendernet usr sbin wl ws 00 0F 66 8E B6 D2 9 40 Sound Audio can be one of the most pleasant features of a computer or its most annoying Usually Linux does recognize the special keys many keyboard manufacturers have added to automatically control audio features In public places such as planes meetings and libraries it is often v
148. sing guarddog with the Logging panel surprising 56 9 RSYNC That stops 99 of the lines hjm flexlm license manager running on sand test the status usr local rsi idl bin lmstat if it needs to be restarted bring it down smoothly with usr local rsi idl bin lmdown q oo se He files all over the place After it comes down restart it via su c usr local rsi idl bin lmgd hjm or su c usr local rsi idl bin 1mgd cluo the manager has to run as a regular user not as root installed gnome as well for Dan Just as well kde has some issues with the kernel 2 6 11 1 SMP installed extras include libxml2 dev libxml2 doc libxml2 utils bonnie xosview tkdiff Kompare kdesdk doc html ssh apcupsd guarddog vncserver synaptic ddd ddd doc pydb glibc doc gnuplot libgt3 dev tree nedit joe gnome sand is now sitting behiind a pretty restrictive firewall so if things don t work that may be the reason In fact it was preventing the nco bm server from getting data on udp port 29659 until guarddog was changed to address that issue also running ubuntu kernel 2 6 11 1 smp sort of successfully but it kills the usb connectivity so apcupsd doesn t see teh ups And then it did ANd then it didn t Then it did Then it didn t Still to be resolved 07 13 05 hjm Now runnning 2 6 10 5 smp k8 more or less successfully een with the USB also upgraded all the KDE stuff so now
149. ss network 9 37 Change network topology sbin ifconfig eth0 down sleep 1 sbin ifconfig eth0 add address 87 192 168 1 73 add netmask 255 255 255 0 Goel sbin route add default gw 192 1 These commands plus some other goodies clock synchronization are executed by the harry sh script Harry s DSL server moon is assigned a permanent IP address by cox net Since I masquer ade as moon it may be useful to try to display X programs from other machines on my laptop As of 20050504 Hiperstore 128 195 169 30 export DISPLAY ip68 109 196 84 oc oc cox net Cliff s house in Lyons as of 20041221 65 112 206 3 Harry s Cox DSL ssh ip68 109 196 84 oc oc cox net to moon from outside LGGE Static DHCP ssh lgge pcl94 lgge obs ujf grenoble fr 192 168 102 194 to virga static ssh lgge pcl94 obs ujf grenoble fr 192 168 102 194 to virga static IP fr ssh lgge asa50 obs ujf grenoble fr SMU ADSL ssh 62 147 226 50 neige appears as ssh p 265 62 147 226 50 Forward to virga appears as this from outside this from outside 192 168 1 4 to neige from outside ssh 62 147 226 50 Forward to 192 168 1 4 to neige from outside UCI wireless for ashes as of 2005041 sbin route del default gw 192 168 33 1 Delete gateway sbin route add default gw 192 168 0 1 Add gateway kwifiman
150. static address 192 168 14 2 broadcast 192 168 14 255 netmask 255 255 255 0 Printing protocols may be enabled and disabled by firewall controls on particular ports On Debian compatible GNU Linux systems with 2 6 Kernels the firewall is built with iptables The iptables rules are set in etc rc firewall iptables L Print IP tables configuration iptables F Flush IP tables iptables X Delete extra chains iptables P OUTPUT ACCEPT iptables P INPUT ACCEPT iptables P FORWARD ACCEPT ip route flush cache Flush existing routes ip route show cache Show existing routes Under Debian use the guarddog program to configure firewalls At a minimum allow these protocols DNS FTP HTTPS HTTP IPP NNTP NTP POP3 Ping rsync SMTP SSH VNC Systems without these protocols set will not behave well License daemons on other monstrosities will usually need to be configured by hand For instance the IDL license daemon wants to send and receive TCP packets on port 1700 This must be defined as a new User Defined protocol under Advanced Settings and then manually enabled in all intervening network zones 9 49 Virtual Memory When compiling large programs like mie cc g may fail with an error like virtual memory exhausted This may be due to having to small a swap partition To see system parameters use ulimit e g ulimit a According to Linus the size of the swap par
151. t forwarding is to redirect traffic on the local port to the hostport on the remote host This forwarding is done via encrypted tunnel so the remote_client must have trusted access to the remote server This command forwards 2025 traffic on localhost to port 25 on the SMTP server The tunneling is done on a trusted remoted client ssh L localport remote_server server_port remote_client ssh L 2025 smtp uci edu 25 sand ess uci edu Access PBS cluster firewalled httpd First ssh to pbs then open local browswer to http localhost 2026 ssh L 2026 pbs ess uci edu 80 pbs ess uci edu The tunnel must remain open for this port forwarding to work do not close the window The second option is to login to an authorized SMTP server All non UCI SMTP servers must use port 587 Clients directly connected to wsu edu should use mail wsu edu WSU blocks mail routed through localhost localdomain SMTP servers Clients directly connected to Cox net should use smtp west cox net Clients directly connected to cgd ucar edu or to wireless ucar edu should use mailhub cgd ucar edu Clients directly connected to greenspeedisp net should use mail greenspeedisp net Setting the SMTP server in Mozilla is non intuitive Select the Outgoing Server SMTP setting at the bottom of the accounts menu presented by Edit Mail and Newsgroups Account Settings Emacs rmail mode provides an excellent environment for editing and sending mail rmail understands your
152. t and from current research Hydrostatics 1 Mass density pressure 2 Ideal gas law 3 Hydrostatic equilibrium 4 5 Dry lapse rate Realistic T profiles Thermodynamics 1 Work Expansion compression 2 Heat heat capacity 3 Adiabatic vs Diabatic 4 Saturation 5 Condensation Evaporation 6 Latent heat 7 Moist lapse rate Earth s Energy Budget 1 Planetary Radiative Equilibrium 2 Energy Transformations 3 Dry Moist Static Energy 4 Gravitational Potential Energy 5 6 Available Energy Global Mean Energy Storage Climate Models NTO OF O N FP Planetary Radiative Equilibrium Boltzmann s Law Effective Temperature Solar and Infrared Radiative Budgets Greenhouse Effect Forcing Response Sensitivity 0 D 1 D Climate models Multiple Climate Equilibria Buoyancy Convection Tg Os O N Dry Moist static energy Stability Instability Convectively Available Potential Energy Simple convection Adiabatic adjustment Convective redistribution of heat vapor tracers Flux Emission O FWN Solid angles Radiance Isotropy Blackbody radiation Radiance Flux relationships Boltzmann s law Radiative eguilibrium T structure of grey atmosphere Absorption Extinction Molecular cross sections spectra NOR WN FP Absorption Vibration rotation bands Extinction Beer s law Explaining the
153. t delivered Thus it is very important to keep a file copy of all messages before entrusting them to the Mail Transfer Agent MTA At the very least CC yourself on all mail you send If it does not reach you it did not reach its intended recipient Undelivered mail is stored in var spool mqueue client Undelivered messages have non zero sizes 5 3 Mail 27 Occasionally it is necessary to move mail between machines Mail folders which are in stan dard format can be simply joined together using the cat command As of September 2002 the correct UCI POP server to use for incoming mail is pop uci edu The SMTP server to use for outgoing mail depends on the Internet address of the client In general setting SMTP server to localhost localdomain works fine This requires correctly configuring a Mail Transport Agent MTA such as Postfix first When configuring the SMTP client e g thunderbird delivery protocol a good option to select is TLS in particular the TLS if available option Clients directly connected to UCI may use smtp uci edu See http www nacs uci edu computing e4e html for additional UCI details Clients at remote locations have two basic options for for sending mail from the remote location port forwarding or changing mail servers Port forwarding works from any remote location Being portable it is recommended for all short term trips where there is no advantage to being on a local mail server The goal of por
154. ta 9 rsync rsync is fhe program to synchronize non archived files among remote machines Files and di rectories which are not controlled by a source code control system are notoriously hard to keep synchronized Examples are my directory of PDF journal papers BIEX class files and web direc tories The general syntax of rsync is rsync src dst A common mistake is to use the same path depth in src and dst arguments when normally the src path should be one level deeper than the dst path rsync source drcl drc2 drc3 destination drel dre2 rsync source drcl drc2 drc3 destination drel dre2 dre3 The previous two commands are equivalent and the first form is preferred Specifying av is usually recommended for recursive synchronization without modifying file attributes Hence the typical commands to keep machines in sync are Rsync synchronization methods a equivalent to rlptgoD Copy recursively preserve file modes amp time v Verbose rsync av data zender cccac dust ess uci edu data zender rsync av data zender ppr dust ess uci edu data zender Often backups are made to CompactFlash or Memory Stick devices described in Sections 2 2 1 and 2 2 2 Backup home directory to compact flash bin cp r home zender cf Backup for dummies Rsync backup methods a equivalent to rlptgoD Copy recursively preserve file modes amp time v Verbose rsync av home zender
155. tition should be twice the amount of RAM see 89 71 Here is an untested way to use a swapfile instead of repartitioning 9 50 tramp el 97 Make a swap file large enough to work around virtual memory exhausted e SSIZE is number of kilobytes SSWAP is name of swapfile S dd if dev zero of SSWAP bs 1024 count SIZE amp amp chmod 0600 SSWAP amp amp sync 9 50 tramp el Tramp stands for Transparent Remote file Access Multiple Protocol Ita most excellent Emacs extension which facilitates editing files on remote machines in a local emacs session using ssh rcp or any number of other protocols to transfer edits to the remote machine Checkout t ramp from the SourceForge archive cd DATA cvs d pserver anonymous cvs sourceforge net cvsroot tramp login cvs d pserver anonymous cvs sourceforge net cvsroot tramp co kk tramp Here are Tramp formats that appear to work dust ess uci edu plan esmf ess uci edu plan nco sf net home groups n nc nco nco doc nco texi scp zender krein math uci edu home ess zender zender plan scp krein math uci edu home ess zender zender plan zender krein math uci edu home ess zender zender plan krein math uci edu home ess zender zender plan multi ssh zender dust ess uci edu ssh zender krein math uci edu plan multi ssh zender dust ess uci edu ssh zender krein math uci edu plan Yes Tramp does expand correctly i e on the remote machi
156. to the controller I figured that 3ware being a vendor of high end hardware my kind of machine would be among their main targets And I was right BUT Trying to find the software that was compatible with my system was an exercise in frustration 3ware s web site is walled off from google s bots like almost all corporate sites and since 3ware is relatively high end hardware there are not a lot of messages on the linux BBSs about such failures and how to deal with them So after a couple hours of browsing I had to go back to the 3ware site and deal with their oh so cool web design that doesn t show URLs in any way different than regular text The text only shows up as a hyperlink if you mouse over it I noticed this and then had to mouse over entire pages of text line by line to search for likely hyperlinks The one that finally took me to the page I needed was buried in a paragraph that I almost overlooked Turns out the SW does exist but is NOT specified for the controller I have 8506 8 but the 9000 series controller which is noted in the fine print as being backwards compatible with the 8000 series ALso it s not released SW it s being In Engineering Phase To make a long story shorter I ended up downloading and trying several versions of software until I finally stumbled 54 9 RSYNC over the right software the 64bit versions of the 3dm2 and cli for the 9000 series controllers This installed OK and apparently ran
157. ts 1029 errors 0 dropped 0 overruns 0 carrier 0 collisions 0 txqueuelen 100 Link encap Ethernet 128 200 14 80 NG MULTICAST 1 Base address 0x200 inet addr UP BROADCAST RUNNI Interrupt 1 Interrupt 11 Link encap Local Loopback inet addr 127 0 0 1 UP LOOPBACK RUNNJ Base address 0x200 HWaddr 00 10 A4 08 12 31 Beast 128 200 255 255 Mask 255 255 0 0 MTU 1500 Mask 255 0 0 0 ING MTU 3924 Metric 1 Metric 1 RX packets 2982 errors 0 dropped 0 overruns 0 frame 0 TX packets 2982 errors 0 dropped 0 overruns 0 carrier 0 collisions 0 txqueuelen 0 zender dakine ifconfig a 9 35 Network etho lo ppp0 Link encap inet addr 192 168 1 1 83 HWaddr 00 40 D0 0B E9 E4 Beast 192 168 1 255 Mask 255 255 255 0 Ethernet UP BROADCAST RUNNING MULTICAST MTU 1500 RX packets TX packets collisions Metric 1 2290 errors 0 dropped 0 overruns 0 frame 0 1273 errors 0 dropped 0 overruns 0 carrier 0 0 txqueuelen 100 Link encap inet addr 127 0 0 1 Interrupt 10 Base address 0x2000 Local Loopback Mask 255 0 0 0 UP LOOPBACK RUNNING MTU 3924 RX packets TX packets collisions Link encap inet addr 128 195 187 37 Metric l 222 errors 0 dropped 0 overruns 0 frame 222 errors 0 dropped 0 overruns 0 carrier 0 0 txqueuelen 0 Point to Point Protocol P t P 128 195 187 2 Mask 255 255 255 2 UP POIN
158. ttern specifying a group of strings is called a regular expression Special characters are x and e Matches any character except newline e x Match smallest possible preceding regular expression as many times as possible e Match preceding regular expression at least once e gt Match preceding regular expression once or not at all e Character set 30 6 PROGRAMMING Table 2 C C Operator Precedence Operator Description Associativity cia Unary scope resolution Left to right atb Binary scope resolution Left to right arr Post increment Left to right a Post decrement Left to right a Function call Left to right a b Array element Left to right a gt b Pointer to structure member Left to right Structure or Union member Left to right a Pre increment Right to left Pre decrement Right to left la Logical NOT Right to left a Bitwise NOT Right to left a Unary minus Right to left a Unary plus Right to left amp a Address Right to left xa Indirection Right to left sizeof a Size in bytes Right to left new Allocate memory Left to right delete De allocate memory Left to right type Typecast amp all C cast operators Left to right ae Pointer to member objects Left to right gt x Pointer to member pointers Left to right Multiply Left to right Divide Left to right Remainder Left to right Add Left to right Add Left to right lt lt Left s
159. u ea ee en eS 71 SAL MPT ner Ra Be Re Re Sr Ra Sera 11 Va ee ae ERS ERR ara 78 ee es ck PRR Ou eR RR Ye Gow ee De ee 78 DONDE via EERE NE change 79 Kernel Modules c ss r eK EKER EEK ARA RR AR a 84 Change network topology 25 a aan 85 E be ia e NR 88 Router oa ee a ee OOS Oe OS OG a a a As ose a 89 BOW oe ee ed ee a Re AAA ER h 89 dakine msw lanina linux 42 area ana aan 90 DEC o og koe ee re OS ee Bee AA A AA 90 We Sn Wie ae O Y EC Be eee Cee ee we ee 91 ARP Address Resolution Protocol FD 92 tu AA 93 PEONICIA a os ee Be ae YOU BEU BO e BLU eB RD DU A RS OO A 94 a a eS See Be he Be Ge Be a Gee GG eh Yh 94 Hn EII 95 sr CUPS ask en Ge Da BH Re Ra RES eA Ble ES eh CW Se 95 Virmal Memory e oo oe teeta ea ee a FF 96 9 50 9 31 9 52 9 53 9 54 9 55 9 56 9 57 9 58 9 59 9 60 9 61 9 62 9 63 9 64 9 65 9 66 9 67 9 68 9 69 9 70 9 71 Ee A E EERE ER SHE Se REED EE RPM packages in usr that were installed and may need to be uninstalled or rein o o e sog oeei e a ere BER Oe es 9 51 1 IPCC and PBS configuration na ana RAOR FE RR UR a 9 51 2 GPO GNU Privacy Guard arena ei BR BO EUR 8 9 51 3 PO RPMS 0 c e r cce HHO a ace a oos dooa Goa o3 9514 RPM commands lt c saoe a GR YN ES RA Be A R ZILS APT CN AAA A Reguired MWS o o n e a ke REAR nen E e FEN Packages installed in usr local some RPM some tgz some proprietary N Gand MA A a a o A ah ly ny a en ea Installing RedHat Linux
160. u have a 615N J6057A card and you get EIO errors open a ticket for your free replacement You have a bad card 1 800 HPINVENT https forumsl itrc hp com service forums guestionanswer do threadId 71839 My card is an HP615N J6057A card S N SG2B303C8E Case 1 3213917944 Case 2 3213977696 CSO 2689174068000 Called second time on 20060223 switched from port 2 to port 3 Green Laser Pointer Originally with three Vinnic L1154 batteries http www batterymart com battery mv p B LR44 has a picture of these batteries and gives their technical specifications as Volts 1 5 mAh 120 Chemistry Alkaline Dimensions 11 6 X 5 4 Dia x Ht MM The bumpy negative side 48 9 RSYNC faces into the pointer against the spring The flat positive side faces out of the pointer toward the chain I believe the pointer came with three L1154 batteries The pointer does not work with three Rayovac 303 357 batteries The pointer does work with four Rayovac 303 357 batteries but the lid will not shut Hence the problem seems to be that the aggregate power is not enough The Rayovac is a Silver Oxide chemistry like the Vinnic 1154 but not the L1154 ipcc ess uci edu ipcc calit2 uci edu 128 195 185 75 pbs ess uci edu pbs calit2 uci edu 128 195 185 76 The Wiki for PBS is at http tephra ess uci edu PBS Wiki tephra ess uci edu 128 200 14 171 neige ess uci edu 128 200 14 fxm Dell Precision M6300 64 bit architecture uses EM64T instruction
161. uch as libpthread so 0 cannot load shared obj If this occurs simply compile the program without lefence before loading into GDB Once bugs have been found and identified consider sending a notice to those who might have been affected by the bug 1 Identify bug symptoms so users may determine whether they were affected by it It is also helpful to identify versions and or dates of the code releases known to be affected by the bug 9 58 Valgrind 107 2 Identify the bug cause in plain English i e passed wrong pointer transposed two arguments error in equation etc 3 Describe extent of side effects which bug may cause Estimates of magnitude of bug whether results were randomly or systematically biased which particular regions were more or less affected etc 4 Complete the classification of the bug s damage by mentioning what processes routines regions or versions are not affected by the bug 5 Determine and report on what future changes if any should be made to software manage ment to ensure this type of bug does not occur again 6 Acknowledge whether or not the bug fix is known to be solid 7 Provide actual code patch to fix bug Linux Journal 87 July 2001 p 82 gives helpful debugging tips The MALLOC_CHECK_ environment variable is one such method Setting this variable and then running a faulty program will cause the program to print some verbose error messages when the fault is triggered See the man page f
162. uci edu 110 mavericks ps uci edu 110 moon 87 nco cvs sf net 113 nco sf net 113 ntp ucsd edu 41 pbs ess uci edu 97 sand ess uci edu 77 swamis ps uci edu 110 tek850 ess uci edu 95 time nist gov 41 triolet obs ujf grenoble fr 88 virga 93 www ess uci edu 110 YYYY 34 ZZZZ 34 2D 13 3D 13 absolute path 17 ACPI 93 Acroread 103 Address Resolution Protocol 92 Advanced Configuration and Power Interface 93 Apache 109 INDEX APT 101 ARM 26 ARP 90 92 ATA 23 Atmospheric Radiation Measurement 26 Autoconf 103 Autoheader 103 Automake 103 backups 36 bad blocks 25 Bash 32 103 Bison 103 bpp 17 burning 77 C 29 C language 40 C library 105 CDs 77 CentOS 97 cgd ucar edu 27 CGI 109 110 command line 28 Compact Disks 77 CompactFlash 8 37 coordinated universal time 40 Cox net 27 Cron 36 CUPS 95 curses 21 CVS 103 113 daemon 23 68 92 daemons 26 DDD 103 106 Debian 17 18 28 36 38 90 96 101 103 DeCSS 77 deleting user accounts 111 DHCP 90 display manager 18 DNS 96 DODS 103 DSA 112 DVDs 77 Dynamic Host Configuration Protocol 90 INDEX Electric Fence 106 Emacs 27 103 email gateway 95 encoding 69 Ethernet 92 ethernet 90 ext2 25 filename expansion 32 filesystem 8 Fink 28 firewall 96 Flex 103 FlexLM 65 formatting disks 21 FQDN 112 FreeBSD 28 112 FTP 69 96 G95 109 GCC 66
163. uild nano nano 1 2 tar gz rpmbuild nano nano spec Then you can build your rpm with rm rf TMP x BUILD rpmbuild ba spec 2 gt amp 1 tee rpmbuild log For more information see www iki fi karvinen de de SESE de Se de dh de de de Se e HE 9 51 4 RPM commands The RedHat Package Manager RPM is used to maintain sources and binaries on a wide variety of Linux systems The packages so called RPMs are manipulated with the rpm command rpm ga grep foo List all installed packages and search for foo rom Uhv x rpm Upgrade packages even if not installed 9 51 RPM packages in usr that were installed and may need to be uninstalled or reinstalled by hand 101 rom Fhv x rpm Freshen packages only if already installed rpm q whatprovides foo Which installed package provides file foo rpm qf foo Which installed package provides file foo rpm ql foo less Which files does installed package foo own rpm qpl foo rpm less Which files will package foo rpm install rpm e foo rpm Uninstall package rpm info foo rpm Print descriptive information about package rpm qR foo rpm Upon what packages does foo depend rpm nodeps foo rpm Uninstall package regardless of dependencies rpm F replacefiles nodeps foox rpm Do not check dependencies allow 9 51 5 APT commands The Debian package manager is called APT Advanced Package Tool Debian p
164. upported software for Linux not the free evaluation software The Intel compilers are OpenMP compliant The Fortran and C compiler work fine on RedHat 7 2 Only the OpenMP features of the C compiler seems not to work Serial numbers of icc and ifc are 1110 19809410 and 1130 7084 6464 respectively Intel compiler support questions go to pto support intel com We bought Lahey 6 1 Pro fortran compiler serial number LP072528 Technical support is support lahey con My PGI PINs are 109584 dust 502421 seasalt and 508553 sand Download releases from PGI website at http www pgroup com downloads Generate permanent licenses keys using personalized account on the PGI website at http www pgroup com pgilogin htm Username pn109584 and Password Ma11 21 dust Username pn502421 and Password Teen 28 seasalt Username pn508553 and Password Jane 40 sand Updating PGI license keys To learn the FLEXIm style hostid of the system execute From the Ubuntu website Ubuntu is an ancient African word meaning humanity to others Ubuntu also means I am what I am because of who we all are Ubuntu means towards humanity in Bemba 64 9 RSYNC S PGI 1linux86 bin lmutil lmhostid S PGI 1linux86 64 6 0 bin lmutil lmhostid For lanina this results in 0010a4081231 For seasalt this results in 0001031c5c7f For seasalt this results in 00d0680399a4 PGI style hostids do not require a license daemon but a
165. ups There is an rsync cron job in etc crond daily rsync home2data that will rsync the home dir where the web site is the local dir tree an all user dirs as well as some additional stuff to the data home dir It s stored uncompressed so we can sgueeze a bit more data out of it if we want The rsync is initiallized and tested and will write an entry into the syslog excluded dirs files can be entered in the file etc rsync sand home2data exclude one per line 6 7 05 also rsyncing the web site to soot so it can be used as a backup server in case sand explodes again Note that it is being owned as hjm so it may have to be recursively chowned on soot tho I think it will work fine There is a etc init d local file that is responsible for starting a variety of local services the license manager the nco bm benchmark server makeing sure apache starts mounting the data dir etc It should be updated on a change with update rc d local defaults 80 hjm 9 20 05 sand s syslog and dmesg ring was filling up with ethernet errors degree of control by editing etc syslog conf the easiest way to of such errors like Sep 20 10 14 56 sand kernel DROPPED IN eth0 OUT MAC ff ff ff ff Sep 20 10 14 56 sand kernel DROPPED IN eth0 OUT MAC ff ff ff ff Sep 20 10 14 57 sand kernel DROPPED IN eth0 OUT MAC ff ff ff ff UO While you stop the EEEE OOs TESEDUDS s PEE yl O D is to stop the logging u
166. vidia com object linux html Integrate the NVidia drivers into these kernels by hand 14 3 X AND XFREES6 wget http download nvidia com XFree86 Linux x86 1 0 7174 NVIDIA Linux x86 cd usr src sh NVIDIA Linux x86 1 0 4496 pkg2 run cd usr src sh NVIDIA Linux x86 1 0 5336 pkg2 run cd usr src sh NVIDIA Linux x86 1 0 6111 pkgl run cd usr src sh NVIDIA Linux x86 1 0 7174 pkgl run When using the closed source NVidia module driver make sure that XF86Config 4 references nvidia not the open source XFree86 driver nv The X org and XFree86 X servers write output from the initialization process to var log Xorg 0 log and var log XFree86 0 log respectively Ubuntu Breezy Badger packages for NVIDIA cards sudo aptitude install linux restricted modules 2 6 15 16 686 Non free Lin sudo aptitude install nvidia glx nvidia settings avm fritz firmware NV D 3 3 Performance Profiling Clay is set up to do performance profiling by both oprofile and PAPI with HPCToolkit This required a kernel patch and recompile There is one module for each approach oprofile for oprofile and perfctr for any software that requires the PAPI modifications specifically hpcrun from the HPCToolkit There are other performance tools that use the PAPI API Tau for one but so far we only have HPCToolkit installed As a side note most Ubuntu kernels have the
167. wed 9 67 Security It happens Passwords get compromised When this occurs the security environment of all com puters logically connected to the compromised account should be rebuilt First disable password less logins from the affected account by removing the authorized_keys files from all machines This firewalls the machines while the passwords are changed Then search the systems for evi dence of compromises Two packages that check for installation of root kits are rkhunter and chkrootkit Theese may help get discover eliminate spyware and malware as well Login individually to all machines and change the passwords with usermod 1 Remove password less authorization mch_lst biogenic ess uci edu dust ess uci edu esmf ess uci edu goldhill cg for mch in S mch_lst do printf Removing authorized keys from mch ssh S mch bin rm HOME ssh authorized_keys printf done n done 2 Change passwords for mch in S mch_lst do ssh mch sudo usermod p S1SsaltShashedpassword zender done 3 Check for compromises rkhunter 4 Change keys 9 68 GCC The GNU Compiler Collection GCC is the default compiler on Linux systems To report a GCC bug send following compile command g v save temps OPTIONS PROGRAM and its text output in plain text to bug gcec gnu org Attach with MIME the resulting fully preprocessed file ix It is OK to compress the file before attaching it Do not attach the asse
168. works perfectly with suspend sh Hibernate on virga works per fectly after modifying xorg conf to allow session restores Only checked virga with NVidia driver not sure if suspend and hibernate work on virga with nv driver The i8kutils package provides a number of Inspiron specific control commands including i8kmon i8kctl i8kbuttons These appear to work when the kernel has loaded the i 8k kernel module e g with insmod lib modules 2 6 15 23 686 kernel drivers char i8k ko The gkrellm utility will graphically display output from the i8kut i ls package sudo aptitude install xosview hddtemp gkrellm i8kutils gkrellm i8k To load module automatically add i8k force 1 to end of etc modules sudo emacs nw etc modules sudo modprobe i8k Restart or modprobe to load module See here for more details Thisthreadhttps launchpad net distros ubuntu rsource util linux bug 66637 describes how to fix broken swap partitions with Ubuntu Edgy 1 Determine your swap with fdisk 1 94 9 RSYNC 2 Run mk swap on your swap partition and record the output UUID Put this UUID into fstab Put RESUME UUID lt the swap partition uuid from vol_ID into etc initramfs tools conf d resume Runupdate initramfs u Reboot normally after this finishes Run swapon s to check if your swap is active Runls la dev disk by uuid AU oo N o on Do not change any symlinks Just try these instructions 9
169. x CBEM56G bind tulip cb to 0 serial_cb to 1 9 17 Hardware description of Zender group computers 51 CBEM56G ethernet cable CABLE ETH122 CBEM56G modem cable CABLE MOD444 PCI controller Texas Instruments PCI 1225 Cardbus Airlink AWLC3026 802 11b g card purchased 20061216 from Fry s MAC 00 03 2F 36 D5 51 hda IBM DARA 225000 ATA DISK drive hdc LS 120 SLIM3 00 UHD Floppy ATAPI FLOPPY drive hdd TorISAN DVD ROM DRD U624 ATAPI CDROM drive hda IBM DARA 225000 24207MB w 418kB Cache CHS 3278 240 63 hdd ATAPI 0X DVD ROM drive 256kB Cache Video modes supported 720x400 16 colors 70 Hz text mode 1280x1024 8 16 24 32 bit 100 Hz 1400x1050 8 16 24 bit 100 Hz 1400x1050 32 bit 85 Hz 1600x1200 8 16 24 bit 100 Hz 1600x1200 32 bit 85 Hz Do horizontal and vertical refresh rates have any meaning for TFT LCD displays Installation programs ask for these variables and the following settings are reported to work for the 17500 at 1400x1050 hsync range 31 5 82 vrefresh 40 110 For haze the horizontal refresh should be set at 28 90 while the vertical should be set at 40 110 NB ATI RAGE card at 1400x1050 resolution does not work on Fedora Ubuntu unless magic option vga 792 is added to kernel boot line e g in grub conf or menu lst lanina zender org 128 200 14 80 Compaq Presario 5240 Purchased 1999
170. x Disable popup windows by adding the following line to user js user_pref dom disable_open_during_load true Do not modify prefs js directly since it is automatically overwritten on shutdown and thus custom changes are not persistent 9 18 Create krein disk structure mkdir p data zender ZENDER mkdir p dks9d2s0 BIAN match mkdir p dks9d3s0 ZENDER match n n nkdir p dks9d4s0 DSS nkdir p dks9d5s0 ZENDER csm ln s dks9d2s0 BIAN match data zender BIAN match ln s dks9d3s0 ZENDER match data zender ZENDER match ln s dks9d4s0 DSS data zender DSS ln s dks9d5s0 ZENDER csm data zender ZENDER csm 9 19 NFS export One may use the network file system NFS to mount or export directories across the network To export local disks to a host edit the exports file e g etc exports 60 9 RSYNC If remote host needs root access root on remote machine has root privilage on the disks add the hostname behind the root chain Otherwise add the host behind the access chain If not sure which one you want then add the system to access Note that the host separator is Details of managing setup are described in excellent NFS HOWTO http www linux org docs ldp howto NFS HOWTO It is easy to export the disks on an already running filesystem First make sure that the NFS daemon nfsd is running Then make sure the NFS lock daemon nfslock isrunning exportfs sudo etc init d nfs restart
171. x x usr local bin bck_var sh 37 3 x x usr bin rdate s time nist gov 38 3 x x x sbin hwclock systohc The first column is the minute of each hour for an action The second column is the hour of each day for an action The third fourth and fifth columns are the day of month month of year and year for the corresponding actions Asterisks denote all values for the corresponding field Always backup data to at least two physically separate locations My personal user specific crontab file is 30 2 x x x home zender sh bck_zender sh dly Note that the backup commands themselves are only valid when specified with fully qualified paths This security feature of Cron helps prevent malicious files from being inadvertently exe cuted Backup binaries from usr local bin e g ddd netscape The script bck pl is devoted to this and works for ZIP disks and LS120 drives too Dot files e g cshrc mailrc netscape directory should be relatively safe as they are frequently archived by CVS The most important files to backup thus become files in the mail directories 8 2 Mounting devices 37 8 2 Mounting devices Make sure CDROM is in fstab mounting it as dev cdrom is OK mounting it as dev hdc is also common ln s mnt cdrom cdrom ln s mnt floppy flp Occasionally such as when rescuing lost systems it is helpful to mount disk partitions from a command line shell e g mount dev hda7 home mount dev hda8 da
172. y because they are using SATA drivers After changing the etc fstab entry from hdc1 to sdb1 the new drive mounted again There was no data loss 4 4 Creating LVM LVM is Logical Volume Management Reference http tldp org HOWTO LVM HOWTO fdisk dev hdel fdisk dev hdil vgscan v pvcreat v dev hdel pvcreat v dev hdil vgcreate v s 16 dust_vg dev hdel dev hdil lvcreate L 305000 n dust_lv dust_vg Creats dev dust_vg dust_lv mke2fs j dev dust_vg dust_lv vgscan Creates etc lvmtab and etc lvmtab d and etc lvmconf vg commands vg_annotate vgcfgbackup vgck vgexport vgmerge vgremove vgsplit vg_cachegen vgcfgrestore vgcreate vgextend vgmknodes vgrename vga_reset vgchange vgdisplay vgimport vgreduce vgscan 22 4 DISK MANAGEMENT Entry in etc fstab dev dust_vg dust_lv data ext3 exec dev suid rw 1 2 Bootup and shutown It does not appear that any of the LVM commands appear in any of the startup or shutdown scripts However dust seems to have a perpetual problem of shutting down because it hangs on the umount command recall that all the computers mount home from dust so it is tricky for this disk not to be busy Typically upon shutdown I am forced to just power off at the point that dust gets stuck Upon boot up everything usually comes up fine after the disk is checked 4 5 LVM on ashes We installed LVM managing some partitions on ashes ess uci edu lvscan lvremove dev
173. y file Utilities kfilereplacepart k kbuildsycoca WARNING kfile_koffice desktop specifies undefined mimetype Following procedure was tested on ashes ess uci edu 20030508 neige 20080 Bring linux tex over first to revise procedure as needed scp dust ess uci edu home zender linux linux tex Upgrade base installation aptitude update aptitude dist upgrade Install packages which make installations easier aptitude install apt file cvs sudo subversion openssh server aptitude install kubuntu desktop scp dust ess uci edu etc sudoers etc sudoers sudo groupadd g 2400 cgdcsm Create group cgdcsm sudo useradd D g cgdcsm Make group cgdcsm default sudo usermod g cgdcsm u 3555 zender Change UID and default GID of user f If NFS mounting home directory from dust do this f sudo usermod d dhome zender zender Log out then log back in so UID GID will be consistent chgrp R cgdcsm home zender export CVSROOT ext zender esmf ess uci edu u zender cvs export CVSUMASK 002 export CVS_RSH ssh sudo slocate u cvs co kk dot elisp linux sh Retrieve dot files emacs Linux Cheatsheet Use KDE control center to left hand mouse auto raise xmodmap dot xmodmapre Swap ctl and caps lock export PVM_ARCH sh pvmgetarch cd mkdir p bin S PVM_ARCH include lib PVM ARCH obj PVM_ARCH crm m Ubuntu First activate universe sour
174. z Modeline 1024x768 97 40 1024 1072 1192 1416 168 768 771 809 V freq 75 00 Hz h freg 80 42 KHz Modeline 1280x1024 151 83 1280 1360 1544 1888 1024 1024 1027 1072 V freq 75 00 Hz h freg 94 24 KHz Modeline 1600x1200 242 01 1600 1728 2024 2568 1200 1200 1204 1256 sand ess uci edu 128 200 14 132 Western Scientific 4000 Chassis Serial number 1012003577 Arrived 20040221 Service Tag fxm Express Service Code fxm UCI Property 049003617 2 GB RAM Two AMD Opteron tm Processor 244s at 1 8GHz Bought without monitor Now using Dell UltraSharp monitor same as biogenic Network card sk98lin Logitech cordless mouse keyboard Navigator Duo Graphics Card ASUS V9520 Series CPU Graphics card powered by NVIDIA GeForce FX 5200 GPU Supports AGP 8x Motherboard IWILL DK8X Eight sockets for up to 16 GB RAM Use 184 pin Registered PC2700 2100 ECC DDR memory modules Two 32 bit 33 MHz PCI slots One 64 bit 66 MHz PCI slot Two PCI X slots One AGP Pro 8X slot hda DVD Plextor Model PX 708A Internal 40X ATAPI DVD R RW CD R RW drive hdc DV 516D 0106 ATAPI 48X CD DVD ROM drive Tech Support 800 443 6699 Hank Vu 800 443 6699 x 211 hank wsm com 2 28 05 mods 3 29 05 by hjm 200 gb disk from lanina moved to sand on IDE bus 1 new hoary ubuntu distro loaded on 200gb disk as Filesystem 1K blocks Used Available Use dev hdal 10482044 2048572 8433472 20tmpfs 1786416 0 1786416 0 dev hda6 105

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