It is useful to run the ATLAS
workbook at CERN first to get
familiarized with the general ATLAS software setup, then try the
workbook from the SLAC environment. You also need to take note of
the SLAC ATLAS computing environment
info to recognize the differences between the current SLAC
setup and CERN, including disk space for ATLAS work at SLAC. First some
general points about using Atlas software at SLAC:
We recommend ignoring all GRID related setup/examples in the
workbook at the first pass and only get back to them later if you wish.
The releases currently available at SLAC can be seen by checking
"ls /afs/slac.stanford.edu/g/atlas/b/AtlasProduction/".
Be sure to log into rhel4-32.slac.stanford.edu machines,
not generic noric or yakut nodes. That way you will get
a machine that certainly can run ATLAS software.
Explicit
Instructions for Running Athena at SLAC
First Time Only Set Up
This should be very similar to the setup in the CERN ATLAS workbook.
Create a folder in your home directory for keeping your ATLAS
work area.
mkdir ~/testarea
Follow these instructions to setup remote
CERN ssh keys (or you have to type a password eight times
for each checkout).
Make a directory for your cmt setup scripts.
mkdir ~/cmthome
Put a requirements file into the new cmt directory. These are
fairly standard ones. You can see a full list in the AtlasLogin
documentation.
set CMTSITE STANDALONE
set SITEROOT /afs/slac/g/atlas/b
macro ATLAS_DIST_AREA ${SITEROOT}
macro ATLAS_TEST_AREA ${HOME}/testarea
macro SITE_PROJECT_AREA ${SITEROOT}
macro EXTERNAL_PROJECT_AREA ${SITEROOT}
apply_tag opt
apply_tag setup
apply_tag simpleTest
use AtlasLogin AtlasLogin-* $(ATLAS_DIST_AREA)
Move into the new cmt directory and source the cmt setup script.
Create a new release folder within your work area (if necessary)
mkdir ~/testarea/14.4.0
Make a run directory to use in the package.
cd ~/testarea/14.4.0
mkdir run
cd run
Now set up the release, and you're ready to go! In the setup line
below, 14.4.0 is the release to be used, and 32 requests a 32-bit
executable (whether the machine is 64-bit or 32-bit). The latter tag
should always be used - 64-bit executables have not yet been completely
validated by ATLAS.
source ~/cmthome/setup.sh -tag=14.4.0,32
If this is NOT your first release and you wish to copy over
old files, you should check out the newest
versions of all scripts from the workbook (e.g.
jobOptions.G4Atlas_Sim.py) to check for changes in the structure of
job options.
To check out additional packages
Check the tag collector to see what the relevant tag is for your
package here,
or do
cmt show versions ThisIsWhere/MyPackageSits/MyPackage
cd ~/testarea/14.4.0
cmt co -r MyPackage-xx-yy-zz
ThisIsWhere/MyPackageSits/MyPackage
You can now make your package. Once this is done and the
libraries appear in your InstallArea, all scripts will
use your copy of the package by default.
cd ThisIsWhere/MyPackageSits/MyPackage/cmt
gmake
Disk space
You should claim yourself some space in the ATLAS scratch space
at SLAC
cd
~/testarea/14.4.0/PhysicsAnalysis/AnalysisCommon/UserAnalysis/run
The ATLAS
workbook at CERN should
now run without any additional
modifications, just as it does at CERN.
To setup a release each time you log in
Simply do:
source ~/cmthome/setup.sh -tag=14.4.0,32
To Simulate Events on the Batch System at SLAC
To save time, you can create a little bash script for running
your simulation on the batch system at SLAC. If you don't run on the
batch system, expect to wait 15 minutes per Z to ee event.
Now you can run your job on the batch system. Very few simulation
jobs will
run in the time allowed by the long queue, so you
should almost certainly use the xlong cue. Many simple evgen, digi, and
reco tasks will run in the long queue, though.
bsub -q xlong -J MyAtlasSim myjob.sh
Troubleshooting
If you get any of the below problems while working at SLAC, please post
them to the Non-Grid
Jobs at SLAC forum in ATLAS Hypernews. They should have all been
resolved, so these fixes should be unnecessary.
If on log in you get an error like
AtlasLogin: Configuration problem - CMTCONFIG
(i686-slc4-gcc345-opt) not available for
/afs/slac.stanford.edu/g/atlas/b/AtlasOffline/12.0.3
or something similar upon login, please check that you have logged into
the correct machines (rhel4-32.slac.stanford.edu).
If during installation you see something like "/include:
permission denied", then you will have to set two variables by hand for
your first package installation (and never again, we hope)