Centos7

Remote connection

  1. Get IP address of network interface (using ifconfig command)
  2. Add to /etc/hosts IP and hostname

Thunderbird

Screen resolution

1.- Find the name of the port (DP-1 in the example below):

[sevilla@pcitk01]:~$ xrandr
Screen 0: minimum 320 x 200, current 1920 x 1200, maximum 8192 x 8192
HDMI-1 disconnected (normal left inverted right x axis y axis)
DP-1 connected primary 1920x1200+0+0 (normal left inverted right x axis y axis) 527mm x 296mm
   1920x1080     60.00 +  50.00    59.94    59.99  
   1920x1080i    60.00    50.00    59.94  
   1600x1200     60.00  
   1680x1050     59.95  
   1280x1024     75.02    60.02  
   1440x900      59.89  
   1280x960      60.00  
   1366x768      59.79  
   1152x864      75.00  
   1280x720      60.00    50.00    59.94  
   1024x768      75.03    70.07    60.00  
   832x624       74.55  
   800x600       72.19    75.00    60.32    56.25  
   720x576       50.00  
   720x480       60.00    59.94  
   640x480       75.00    72.81    66.67    60.00    59.94  
   720x400       70.08  
HDMI-2 disconnected (normal left inverted right x axis y axis)
DP-2 disconnected (normal left inverted right x axis y axis)
HDMI-3 disconnected (normal left inverted right x axis y axis)
DP-3 disconnected (normal left inverted right x axis y axis)
  2560x1440 (0x287) 11.830MHz -HSync +VSync
        h: width  2560 start 2744 end 3024 total 3488 skew    0 clock   3.39KHz
        v: height 1440 start 1441 end 1444 total 1490           clock   2.28Hz

2.- find the display parameters of the new mode:

[sevilla@pcitk01]:~$ gtf 1920 1200 60 -x

  # 1920x1200 @ 60.00 Hz (GTF) hsync: 74.52 kHz; pclk: 193.16 MHz
  Modeline "1920x1200_60.00"  193.16  1920 2048 2256 2592  1200 1201 1204 1242  -HSync +Vsync

3.- Create the new mode with xrandr using the values from the gtf command:

xrandr --newmode "1920x1200" 193.16  1920 2048 2256 2592  1200 1201 1204 1242  -HSync +Vsync

4.- Tell xrandr that DP-1 understands the mode called 1920x1200:

xrandr --admode DP-1 1920x1200

5.- Switch to the new mode:

xrandr --output DP-1 --mode 1920x1200

ALERT! For 2560x1440 the output from the gtf command did not work, and had to use instead the one from cvt:

[sevilla@pcitk01]:~$ cvt -r 2560 1440 60
# 2560x1440 59.95 Hz (CVT 3.69M9-R) hsync: 88.79 kHz; pclk: 241.50 MHz
Modeline "2560x1440R"  241.50  2560 2608 2640 2720  1440 1443 1448 1481 +hsync -vsync
[sevilla@pcitk01]:~$ xrandr --newmode "2560x1440R" 241.50  2560 2608 2640 2720  1440 1443 1448 1481 +hsync -vsync
[sevilla@pcitk01]:~$ xrandr --addmode DP-1 2560x1440R
[sevilla@pcitk01]:~$ xrandr --output DP-1 --mode 2560x1200R

emacs

installing in osx

Via homebrew:

brew update
brew install emacs --with-cocoa

Optionally:

brew linkapps emacs
to start Emacs from the launchpad or from Spotlight.

Finally, within bashrc:

alias emacs="/usr/local/Cellar/emacs/25.3/Emacs.app/Contents/MacOS/Emacs"
alias e=emacs

commenting block of text

Assuming we'd like to comment a large block of text of a tex file:

  1. move cursor to beginning
  2. Set mark (on mac keyboard: CTRL + SHIFT + 2)
  3. move cursor to end (with keyboard or select lines with mouse)
  4. CTRL+X, followed by R then T (this is called the Rectangle method)
  5. write character to be used (e.g. % for tex file)

configuration file

In .emacs:
  • set font size to 10 pt: (set-face-attribute 'default nil :height 100)

Commands, useful tools

disk usage

ncdu

Very nice utility, with a non-graphical ncurses interface. Link: https://dev.yorhel.nl/ncdu

Usage: https://lintut.com/ncdu-check-disk-usage/

du ordered by size

du -hs * | sort -h

For MAC:

brew install coreutils
du -hs * | gsort -h

analyzing a core dump file

sevilla@lxplus100 :/afs/cern.ch/work/s/sevilla/atlas/pixel/dq/batch$ gdb program core.117935
GNU gdb (GDB) Red Hat Enterprise Linux (7.2-92.el6)
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
program: No such file or directory.
Missing separate debuginfo for the main executable file
Try: yum --enablerepo='*-debug*' install /usr/lib/debug/.build-id/93/87c8ee7e5c79270b9787a2a371a76880a04cf2
[New Thread 117935]
Core was generated by `/bin/sh /pool/spool/1510245892.117842032'.
Program terminated with signal 24, CPU time limit exceeded.
#0  0x00002b504627082e in ?? ()
(gdb)

chmod

Numeric mode

# Permission rwx
7 read, write and execute rwx
6 read and write rw-
5 read and execute r-x
4 read only r--
3 write and execute -wx
2 write only -w-
1 execute only --x
0 none ---

chmod -R 755 .

Symbolic mode

Reference Class Description
u owner file's owner
g group users who are members of the file's group
o others users who are neither the file's owner nor members of the file's group
a all all three of the above, same as ugo

ls colors

With
ls --colors=auto
ls emits color codes only when standard output is connected to a terminal. The LS_COLORS environment variable can change the settings. Use the dircolors command to set it.

From dircolors --print-database:

# Below are the color init strings for the basic file types. A color init string consists of one or more of the following numeric codes:             
# Attribute codes:                                                           
# 00=none 01=bold 04=underscore 05=blink 07=reverse 08=concealed             
# Text color codes:                                                          
# 30=black 31=red 32=green 33=yellow 34=blue 35=magenta 36=cyan 37=white     
# Background color codes:                                                    
# 40=black 41=red 42=green 43=yellow 44=blue 45=magenta 46=cyan 47=white     

dircolors -b

LS_COLORS='rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lz=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:';
export LS_COLORS

terminal color scheme

Color scheme and background: black on yellow
  • yellow:
    • Hue: 52
    • Sat: 73
    • Val: 255
    • Red: 255
    • Green: 246
    • Blue: 182

HTML: #FFF6B6

yum

Individual packages

  • yum list *Firefox* list matching packages
  • yum install firefox: install package
  • yum update: update packages to latest versions

Groups:

  • yum grouplist: see list of groups
  • yum groupinstall 'Office/Productivity': install a software group

Repositories

list only the symbolic links in directory

prefered solution (assuming current directory):

ls -l `find * -maxdepth 1 -type l -print`
ALERT! Problem is that there are no symbolic links, above corresponds to ls -l.

by recursively traversing /path/to/folder directory:

ls -lR /path/to/folder | grep ^l

rsync

useful options
  • -a: archive mode; same as -rlptgoD (no -H)
  • -v: increase verbosity
  • -z: compress file data during the transfer
  • -h: output numbers in a human-readable format
  • --progress: show progress during transfer
  • --exclude=PATTERN: exclude files / directories that match PATTERN
  • --exclude-from=FILE: read exclude patterns from FILE
  • --dry-run: show what would have been transferred

copy from local to server

rsync -avz rpmpkgs/ root@192.168.0.101:/home/

update remote only if a newer version exists in local

rsync --update -raz --progress /aLocalDir 128-141-141-161.cern.ch:/aRemoteDir

same as above but checking before what will be copied

rsync --dry-run --update -raz --progress /aLocalDir 128-141-141-161.cern.ch:/aRemoteDir

Demangling undefined symbol in libray

  • Example: dyld: Symbol not found: __ZN6MiniSL8finalizeEv

c++filt __ZN6MiniSL8finalizeEv

  • It happens often to me when I forget the namespace before a function defintion in the src file...

Replace commas by tabs in a ascii file

tr ',' '\t' < infile.txt > outfile.txt

find and remove

find * -name "*converted*" -exec rm {} \;

find and grep

find * -name "*.tex" -print0 | xargs -0 grep "spread"

Remove "last login" message when starting a new shell

touch ~/.hushlogin

ssh tunneling

SLC6

pdf viewers

  • evince
  • xpdf (had to install sudoyum install xpdf)
  • gv

keyboard shortcut to switch workspaces in KDE

Kmenu -> System settings -> Keyboard & Mouse -> Global Settings Shortcuts, then for KDE component select KWin and set custom shortcut to each Swith Desktop X.

installing latest chrome

https://chrome.richardlloyd.org.uk/

wget http://chrome.richardlloyd.org.uk/install_chrome.sh
chmod u+x install_chrome.sh
./install_chrome.sh

Libraries and binary are put in /opt/google/chrome. The executable google-chrome is also copied into /usr/bin.

To start chrome: google-chrome

To uninstall Google Chrome and its dependencies added by this script, run:

yum remove google-chrome-stable chrome-deps-stable
or
./install_chrome.sh -u

%W% The forthcoming Google Chrome 59 release - expected in early June 2017 - will not work on RHEL/CentOS 6 because it is switching (like Mozilla Firefox already has) to using GTK+3, which isn't available on RHEL/CentOS 6.

update gcc by installation of Developer Toolset Collection

http://linux.web.cern.ch/linux/scientific6/docs/softwarecollections.shtml

In the example below, I will install the devtools-6 collection, providing gcc-6.2.1

su
yum install sl-release-scl
yum install devtoolset-6
ln -s /opt/rh/devtoolset-6/root/usr/bin/gcc /usr/bin/gcc6.2
ln -s /opt/rh/devtoolset-6/root/usr/bin/g++ /usr/bin/g++6.2
export CC=gcc62 
export CXX=g++62

To switch to devtools environment in bash-shell:

scl enable devtoolset-6 bash

Ubuntu

CernVM-FS and Docker

Followed AthenaUbuntuDockerSetup

1.-Install CE Docker for ubuntu (16.04)

  • Followed step-by-step instructions from https://docs.docker.com/engine/installation/linux/ubuntu/
    • installation using the repository
  • I then follow the post-install instructions to manage Docker as a non-root user:
    1. add sevilla to the docker group
               sudo groupadd docker
               sudo usermod -aG docker sevilla
               
    2. logout and log back so that group membership is re-evaluated.
    3. Verify that you can docker commands without sudo
               docker run hello-world
               
  • Docker is then configured to start on boot: sudo systemctl enable docker
    • to disable this behaviour: sudo systemctl disable docker

2.- Install cvmfs

  • Followed step-by-step instructions from https://cernvm.cern.ch/portal/filesystem/quickstart, which worked out of the box.
  • my /etc/cvmfs/default.local is:
       CVMFS_REPOSITORIES=atlas.cern.ch,atlas-condb.cern.ch,atlas-nightlies.cern.ch,sft.cern.ch
       CVMFS_QUOTA_LIMIT=10000
       CVMFS_HTTP_PROXY="DIRECT"
       
    ALERT! Note that I did not create a specific partition in /var/lib/cvmfs and that CVMFS_HTTP_PROXY does not point to any squid server (which AFAIK, squid is only needed if many computers are accessing cvmfs)

adding repository for apt

example for CernVM-FS Package Repository (http://cvmrepo.web.cern.ch/cvmrepo/apt)
wget https://ecsft.cern.ch/dist/cvmfs/cvmfs-release/cvmfs-release-latest_all.deb
sudo dpkg -i cvmfs-release-latest_all.deb
rm -f cvmfs-release-latest_all.deb
sudo apt-get update

partitions, mount, fstab and such

  • sudo blkid: locate/print block device attributes (useful to get UUID of partition to be used in fstab)
  • mount -t ntfs-3g /dev/sdb1 /mnt/win/: mount NTFS partition /dev/sdb1 at mount point /mnt/win
  • entry in fstab to mount second internal hdd (partitioned as ext4): /dev/sdc1 /data   ext4  user,exec,rw 0  2
    • do not forget to do chmod 777 /data to give write access to all users

Checking version

 
lsb_release -a

afs

Taken as is from here. Another interesing link is this one,

  1. - download required packages: sudo apt-get install openafs-client openafs-modules-dkms openafs-krb5 krb5-user krb5-config
  2. - .keytab file
    • if already existing, delete .keytab file.
    • generate a new file:
               $ ktutil
               ktutil: addent -password -p sevilla@CERN.CH -k 1 -e aes256-cts
               ktutil: addent -password -p sevilla@CERN.CH -k 1 -e arcfour-hmac-md5
               ktutil: wkt .keytab
               ktutil: q
               
    • if kinit -kt .keytab sevilla produces nothing, then it worked. Move the .keytab file to /etc/krb5.keytab.
  3. - edit /etc/openafs/ThisCell and add cern.ch.
  4. - edit /etc/krb5.conf:
; AD  : This Kerberos configuration is for CERN's Active Directory realm.
;
; /etc/krb5.conf
; On SLC nodes this file is maintained via ncm-krb5clt(1), local changes may be lost.
; If you need to add your realm, look at the "template" file 
; in /usr/lib/ncm/config/krb5clt/etc_krb5.conf.tpl
; or get in touch with project-elfms@cern.ch
;
; Created on 1-Apr-2011
;

[libdefaults]
 default_realm = CERN.CH
 ticket_lifetime = 25h
 renew_lifetime = 120h
 forwardable = true
 proxiable = true
 default_tkt_enctypes = arcfour-hmac-md5 aes256-cts aes128-cts des3-cbc-sha1 des-cbc-md5 des-cbc-crc
 allow_weak_crypto = true

[realms]
 CERN.CH = {
  default_domain = cern.ch
  kpasswd_server = afskrb5m.cern.ch
  admin_server = afskrb5m.cern.ch
  kdc = cerndc.cern.ch:88

  v4_name_convert = {
     host = {
         rcmd = host
     }
  }
 }
; the external institutes info is completely static for now and comes
; straight from the NCM template
 FNAL.GOV = {
  default_domain = fnal.gov
  admin_server = krb-fnal-admin.fnal.gov
  kdc = krb-fnal-1.fnal.gov:88 
  kdc = krb-fnal-2.fnal.gov:88 
  kdc = krb-fnal-3.fnal.gov:88 
 }
 KFKI.HU = {
  kdc = kerberos.kfki.hu
  admin_server = kerberos.kfki.hu
 } 
 HEP.MAN.AC.UK = {
  kdc = afs4.hep.man.ac.uk
  kdc = afs1.hep.man.ac.uk
  kdc = afs2.hep.man.ac.uk
  kdc = afs3.hep.man.ac.uk
  admin_server = afs4.hep.man.ac.uk
  kpasswd_server = afs4.hep.man.ac.uk
  default_domain = hep.man.ac.uk
 }
[domain_realm]
 .cern.ch = CERN.CH
 .fnal.gov = FNAL.GOV
 .kfki.hu = KFKI.HU
 .hep.man.ac.uk = HEP.MAN.AC.UK
[appdefaults]
   pkinit_pool =  DIR:/etc/pki/tls/certs/
   pkinit_anchors = DIR:/etc/pki/tls/certs/
; options for Red Hat pam_krb5-2
 pam = {
   external = true
   ticket_lifetime = 25h
 }
; AD  : This Kerberos configuration is for CERN's Active Directory realm.
;
; /etc/krb5.conf
; On SLC nodes this file is maintained via ncm-krb5clt(1), local changes may be lost.
; If you need to add your realm, look at the "template" file 
; in /usr/lib/ncm/config/krb5clt/etc_krb5.conf.tpl
; or get in touch with project-elfms@cern.ch
;
; Created   1-Apr-2011
; Modified  3-Mar-2014
;

[libdefaults]
 default_realm = CERN.CH
 ticket_lifetime = 25h
 renew_lifetime = 120h
 forwardable = true
 proxiable = true
 default_tkt_enctypes = arcfour-hmac-md5 aes256-cts aes128-cts des3-cbc-sha1 des-cbc-md5 des-cbc-crc
 allow_weak_crypto = true

[realms]
 CERN.CH = {
  default_domain = cern.ch
  kpasswd_server = cerndc.cern.ch
  admin_server = cerndc.cern.ch
  kdc = cerndc.cern.ch

  v4_name_convert = {
     host = {
         rcmd = host
     }
  }
 }
; the external institutes info is completely static for now and comes
; straight from the NCM template
 FNAL.GOV = {
  default_domain = fnal.gov
  admin_server = krb-fnal-admin.fnal.gov
  kdc = krb-fnal-1.fnal.gov:88 
  kdc = krb-fnal-2.fnal.gov:88 
  kdc = krb-fnal-3.fnal.gov:88 
 }
 KFKI.HU = {
  kdc = kerberos.kfki.hu
  admin_server = kerberos.kfki.hu
 } 
 HEP.MAN.AC.UK = {
  kdc = afs4.hep.man.ac.uk
  kdc = afs1.hep.man.ac.uk
  kdc = afs2.hep.man.ac.uk
  kdc = afs3.hep.man.ac.uk
  admin_server = afs4.hep.man.ac.uk
  kpasswd_server = afs4.hep.man.ac.uk
  default_domain = hep.man.ac.uk
 }
[domain_realm]
 .cern.ch = CERN.CH
 .fnal.gov = FNAL.GOV
 .kfki.hu = KFKI.HU
 .hep.man.ac.uk = HEP.MAN.AC.UK
[appdefaults]
   pkinit_pool =  DIR:/etc/pki/tls/certs/
   pkinit_anchors = DIR:/etc/pki/tls/certs/
; options for Red Hat pam_krb5-2
 pam = {
   external = true
   krb4_convert =  false 
   krb4_convert_524 =  false 
   krb4_use_as_req =  false 
   ticket_lifetime = 25h
 }
  • config ssh connection: edit /etc/ssh/ssh_config and make it look like this:
HOST lxplus*
    ForwardX11 yes
    ForwardX11Trusted no
    GSSAPITrustDNS yes
    HashKnownHosts yes
    GSSAPIAuthentication yes
    GSSAPIDelegateCredentials yes
  1. - renew your token automatically: edit /etc/crontab and add the following line:
@daily ID=afstoken kinit --renew
  1. time synchronization
    • sudo apt-get install ntp
    • edit /etc/ntp.conf, erase or comment all lines refering to ubuntu servers and add the cern servers:
# CERN Client

server 137.138.18.69 version 4 #IP-TIME-0
server 137.138.16.69 version 4 #IP-TIME-1
server 137.138.17.69 version 4 #IP-TIME-2

# Disable remote access, but trust sources of time restrict default nomodify #noquery
restrict default nomodify noquery

# Allow hosts to query stats and ask for the time.
# eg restrict 123.123.123.123 nomodify

# Allow localhost to do everything.
restrict 127.0.0.1

#logconfig=all
    • retart ntp service: sudo service ntp restart
  1. - automatize identification: alias afs="kdestroy && kinit -kt /etc/krb5.keytab sevilla -l 7d -r 1d ; aklog CERN.CH"
  2. - test everyting
    • open new terminal
    • restart afs client: sudo service openafs-client restart
    • % afs; then check afs token: klist

Installing a CERN printer

  • install the following packages:
   sudo apt-get install libnet-ldap-perl; 
   sudo apt-get install cups;
  • Download lpadmincern from http://ftp.riken.jp/Linux/cern/slc60beta/x86_64/updates/SRPMS/repoview/lpadmincern.html
  • This downloads an rpm file, which you should unpack as follows (replacing the version number as appropriate).
   rpm2cpio lpadmincern-1.3.13-1.slc6.src.rpm | cpio -idmv;
   tar -zxvf lpadmincern-1.3.13.tar.gz;
  • Now we need to edit the file lpadmincern.pl to replace
   $cupsc='/sbin/service cups reload';
with
   $cupsc='/usr/bin/service cups reload';
   sudo perl /usr/share/lpadmincern/lpadmincern.pl --add 32-1B03-HPC
Note that the final step requires root because that is necessary to add/remove/update/set default printers.

Live CD

  • set root password: sudo passwd root
  • partioning: gparted

Mesa and OpenGL

sudo apt-get install libgl1-mesa-dev
sudo apt-get install libegl1-mesa-dev
sudo apt-get install libgles2-mesa
sudo apt-get install libgles2-mesa-dev
sudo apt-get install freeglut3
sudo apt-get install freeglut3-dev
sudo apt-get install libglew-dev
sudo apt-get install mesa-utils
  • I think with just libglew-dev it should be enough (once dependencies have been resolved), but not bother checking...
  • mesa=utils provides the binary glxinfo, so it is not needed strictly speaking, but worth having it. For example, to get information about the openGL and GLX implementations running in a given X-display:
sevilla@unigehp01:~$ glxinfo | grep OpenGL
OpenGL vendor string: Intel Open Source Technology Center
OpenGL renderer string: Mesa DRI Intel(R) Q45/Q43 
OpenGL version string: 2.1 Mesa 10.1.3
OpenGL shading language version string: 1.20
OpenGL extensions:

kubuntu

  • multiple desktops: "System settings -> Workspace Appearance and Behavior -> Workspace Behavior"

show partitions and volumes in konsole

[sevilla@unigehp02]:~$ sudo lsblk -o NAME,TYPE,FSTYPE,MOUNTPOINT
[sudo] password for sevilla: 
NAME   TYPE FSTYPE      MOUNTPOINT
sda    disk             
&#9500;&#9472;sda1 part ntfs        
&#9500;&#9472;sda5 part swap        [SWAP]
&#9500;&#9472;sda6 part ext4        
&#9492;&#9472;sda7 part ext4        /
sdb    disk             
&#9500;&#9472;sdb1 part ntfs        
&#9492;&#9472;sdb2 part ext4        /mnt/data
sdc    disk             
&#9500;&#9472;sdc1 part ext4        /mnt/slc6
&#9492;&#9472;sdc2 part LVM2_member 
sr0    rom              

-- SergioGonzalez - 2016-08-26

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Topic revision: r29 - 2019-11-01 - SergioGonzalez
 
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