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SSH login and batch info at BNL

You can find the main SDCC page

Interactive Connection to BNL

ssh Connection to the interactive nodes

At BNL, you need login to ssh.sdcc.bnl.gov first, then login to interactive machines attsub01, ..., attsub08 with command ssh or rterm -i without argument (please refer to the following section for the rterm usage help ). You can add the following to file $HOME/.ssh/config on your laptop or local machine, so you can login attsub* machines directly.

    host atlasgw
         hostname ssh.sdcc.bnl.gov
         user yourNameAtBNL

    host attsub*
       user yourNameAtBNL
       proxycommand ssh atlasgw nc %h %p

Replace yourNameAtBNL with your own username at BNL. So you should be able to run the following to login any machine such as attsub01 directly,

ssh attsub01

Please note that: the gateway was just changed to ssh.sdcc.bnl.gov.

These nodes should be used for debugging and testing code. To run your complete analysis code you should take advantage of the batch system.

File transfer from/to BNL machines

Connection to NX servers at BNL

If you want to use a graphical environment, you can use NoMachine client to connect to these NX servers, nx.sdcc.bnl.gov, which allows you to save/restore sessions from anywhere anytime. Please visit the NoMachine (NX) page at BNL for details. Besides the connection through NoMachine client, you can also connect to the new NX servers on web browsers, using the URL: https://nx.sdcc.bnl.gov.

Connect to the interactive nodes from NX

After you connect to the NX server, you can open a konsole terminal (depending on the Window Manager you have chosen). From NX servers, you can run rterm to ssh to other attsub machines on a separate xterm terminal. rterm will help choose the least loaded node.

Please find the detailed usage of rterm by running the command rterm -h.

    NX% rterm -h
    term, V1.502 - Written by J. Lauret 2001
    This command will open a connection to any remote node using the slogin
    command and, without node precision open a terminal on the least loaded
    node.

    Syntax is
      % rterm [Options] [NodeSpec] [UserName]

    Currently implemented options are :
      -i         interactive mode i.e. do not open an xterm but use slogin
                 directly to connect.
      -p port    use port number 'port' to connect
      -x node    Exclude 'node' from possible node to connect to. May be
                 a comma separated list of nodes.
      -funky     pick a color randomly
      -Y         use -Y option for ssh instead of -X

    The 'NodeSpec' argument may be a node name (specific login to a given node)
    or a partial node name followed by the '+' sign (wildcard). For example,
      % rterm attsub+

    will open a connection on the least loaded node amongst all batch-available
    attsub* nodes. By default, this command will determine the appropriate
    wildcarded node specification for your GroupID. However, if this help
    is displayed when the command '% rterm' is used, contact the RCF support
    team (your group ID is probably not supported by this script).

    The 'UserName' argument is also optional. If unspecified, it will revert
    to the current user ID.

    Finally, you may modify the xterminal layout by using the following
    environment variables
      TERM_BKG_COLOR     sets the xterm background color
      TERM_OPTIONS       sets any other xterm options

For example, you run define the envvar TERM_OPTIONS to pass the options the executed command xterm.

% export TERM_OPTIONS="-bg black -fg green -fn 10x20"
% rterm

which will open a xterm terminal with the black background and green text color, with the font size of 10x20.

Setup ATLAS software environment

To make ATLAS-specific commands (including setupATLAS) available immediately upon login, add the following lines to your shell startup script ($HOME/.bashrc for bash users or $HOME/.zshrc for zsh users):

# Load USAtlas group environment at BNL
group_env=/atlasgpfs01/usatlas/group/group_env.sh
if [ -r "$group_env" ]; then
    . "$group_env"
fi

After you update your startup file, either log out and log back in, or source the file manually:

source ~/.bashrc    # for bash
# or
source ~/.zshrc     # for zsh

From then on, the setupATLAS command will be available in all interactive sessions.

Please be aware that the executable or library built on Alma9 machines cannot run on CentOS7 machines because of the system glibc library difference. To use old CentOS7 releases, you can use singularity to compile your package(s) within CentOS7 container. The command setupATLAS -c CentOS7 could help set up such a container, you would get something like:

     ------------------------------------------------------------------------------
    Info: /cvmfs mounted; do 'setupATLAS -d -c ...' to skip default mounts.
    ------------------------------------------------------------------------------
    Apptainer: 1.3.4
    Host: Linux, AlmaLinux 9.5 (Teal Serval), x86_64, 5.14.0-503.19.1.el9_5.x86_64
    From: /cvmfs/atlas.cern.ch/repo/containers/sw/apptainer/x86_64-el7/1.3.4/bin/apptainer
    ContainerType: atlas-default
    apptainer  exec  -e   -H /usatlas/u/yesw2000/.alrb/container/apptainer/home.XMrLKx:/alrb -B /cvmfs:/cvmfs -B /usatlas/u:/home -B /tmp/yesw:/srv /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-centos7 /bin/zsh
    ------------------------------------------------------------------------------
    lsetup               lsetup <tool1> [ <tool2> ...] (see lsetup -h):
     lsetup agis          ATLAS Grid Information System
     lsetup asetup        (or asetup) to setup an Athena release
     lsetup atlantis      Atlantis: event display
     lsetup eiclient      Event Index
     [...]

Then it would behave like that you work on a CentOS7 machine.