ATLAS Environment at SLAC

This page describes how to have your environment configured to run ATLAS jobs at SLAC. It also tries to explain where you may need to do something different.

For first time SLAC computing users, you need to first register as a SLAC user and obtain a SLAC computing account. The initial account setup related info can be found on the US Western Tier-2 page under the link "SLAC UNIX users", which also contains links to info on batch system and printing etc. Other general computing services and information provided by the SLAC Scientific Computing and Computing Services (SCCS) can be found at the general "SLAC computing environment" page. There is also some information on configuring ssh to avoid using passwords multiple times. Among the various Public Machines at SLAC, the recommended interactive machines to login are yakut's (yakut@slac.stanford.edu), which are Linux nodes running SL3. If you use tcsh then you should email unix-admin@slac.stanford.edu to request /usr/etc/tcsh as your shell.

Some essential background to the ATLAS software setup at SLAC:

The ATLAS software installation at SLAC is the 'Pacman kits' which includes the sharable libraries, but not the full release tree with code of all packages. However, the code can be easily browsed on the web throught LXR or go to more detail viewcvs (what you most likely need should be in the offline folder). See `Default release' section below for further details on the SLAC local release setup.
For code development on working packages, the default operating setup is to use the CERN CVS repository over AFS. The Kerberos setup is not yet established at SLAC so that you need to make a simple manual environment definition for CVSROOT (see the `CVSROOT' section below) in your login. This also implies that you must have a CERN account setup already. In case you have not yet done so, some orientations about setting up CERN account may help.
The current SLAC site installation script restricts the user private release setup to a fixed location of ~username/reldirs at present which must be followed in order to get the right library path. You can make different release directories under reldirs with their independent InstallArea. However, there is a file ATLCURRENT in your home directory (~username) which determines your choice of working release.

If you have any questions please post them to the Non-Grid Jobs at SLAC Forum in the ATLAS Hypernews system, where all local ATLAS computing issues at SLAC are discussed.

Activate ATLAS Login

To turn on the ATLAS login you can do it one of two ways, below. Next time you login the ATLAS commands should be in your path. You need to use the HEPiX login to get the general SLAC setup (so things like LSF can be used).

Make ATLAS you HEPiX preferred login

In this case there are three steps required to get it working correctly. If you've already set your account up for HEPiX login (because you use to work on BaBar for instance) then you only need to do that last step.

Add the following lines to your .cshrc if they are not already there;

#####################################################
# Do HEPiX login
if ( -r /usr/local/lib/hepix/central_env.csh ) then
    source /usr/local/lib/hepix/central_env.csh
endif
#####################################################

or (if you use a bourne based shell) the following to your .bashrc;

#####################################################
# Do HEPiX login
if [ -r /usr/local/lib/hepix/central_env.sh ]; then
    source /usr/local/lib/hepix/central_env.sh
fi
#####################################################

Add the following to your .login file;

###########################################################
# Do HEPiX login
if ( -r /usr/local/lib/hepix/central_login.csh ) then
         source /usr/local/lib/hepix/central_login.csh
endif
###########################################################

or (if you use a bourne based shell) the following to your .profile;

###########################################################
# Do HEPiX login
if [ -r /usr/local/lib/hepix/central_login.sh ]; then
         source /usr/local/lib/hepix/central_login.sh
fi
###########################################################

Then create a file like the following one;

[noric06] ~ > cat .hepix/preferred-group
atlas

Without changing your HEPiX preferred-group

For this to work you add the following line to your .login file if you use a c based shell:

source /afs/slac.stanford.edu/g/atlas/etc/atlas_env.csh

or the following for a bourne based shell;

. /afs/slac.stanford.edu/g/atlas/etc/atlas_env.sh

Differences at SLAC

atlsetup

This command can be used to switch releases. The only argument it takes is the release you want to use (eg "atlsetup 12.2.0").

atladdpkg

Amir Farbin wrote a script he called addpkg (to mimic a BaBar script of the same name) to allow you to check out a package without knowing the tag if you wanted the same version as was in the release. I've created a new version that works using a cmt command (suggested by Zach Marshal).

Default Release

The default release is the "current" released (defined by a symlink in $ATLROOT/b/AtlasOffline). If someone wants to choose a different release by default they should create a file in their home directory called ATLCURRENT with the release number in it (or "latest" to use the latest symlink in $ATLROOT/b/AtlasOffline). You can in principle also do "atlsetup " to change releases after logging in (currently this doesn't seem to work, SJG 20060216, so to change releases you should update ATLCURRENT, log out and then log in again). There had been a major recent change (Sep/06) to the way the environment is configured at SLAC such that only more limited range of older releases are supported.

Disk Space

Information on this is available on another page now.

CVSROOT

If your user name is different between SLAC and CERN you'll need to set CVSROOT to include your CERN user name. By default it is set to :ext:atlas-sw.cern.ch:/atlascvs. You should set it with a command like;

setenv CVSROOT :ext:<CERNusername>@atlas-sw.cern.ch:/atlascvs

if you use a c-shell or;

CVSROOT=:ext:<CERNusername>@atlas-sw.cern.ch:/atlascvs
export CVSROOT

if your use a bourne based shell. You should of course replace <CERNusername> with your CERN username.

dq2_*

As not all machines have grid certificates installed so you need to edit your .srmconfig/config.xml file after it gets created. In there you'll find an entry for x509_user_trusted_certificates which will point to a non-existent directory in /etc. You should instead change it to point to /afs/slac.stanford.edu/package/globustools/vdtclient/curr/globus/TRUSTED_CA.

Stephen J. Gowdy <gowdy@slac.stanford.edu>