...
| Code Block |
|---|
for j in `bjobs | cut -f 1 -d " "`; do bkill $j; echo $j; done |
To run eclipse (see this page):
| Code Block |
|---|
unset _JAVA_OPTIONS /afs/slac.stanford.edu/g/atlas/work/a/ahaas/eclipse/eclipse |
...
| Code Block |
|---|
hadd -h #show how to use
hadd -f step.root */*step.root #for instance
|
Sometime when running over data it helps to put a link in your running directory:
| Code Block |
|---|
mkdir sqlite200; ln -s /afs/cern.ch/user/a/atlcond/coolrep/sqlite200/COMP200.db sqlite200/ALLP200.db
|
Can run these on a POOL file to see what StoreGate keys are in there:
| Code Block |
|---|
checkFile.py <file>
checkSG.py <file>
|
Can put this in a bash script near the top, to check if you have a GRID cert:
| Code Block |
|---|
voms-proxy-info
if [ $? -eq 1 ] ; then echo You need to get a GRID cert; exit; fi
|
To get a list of filenames (to load into athena) from a given dataset:
| Code Block |
|---|
dq2-ls -f -p -H $1 | sed "s%srm://osgserv04.slac.stanford.edu:8443/srm/v2/server?SFN=/xrootd/atlas/%filelist += [\"root://atl-xrdr//atlas/xrootd/%g" | sed "s%$%\"]%g" | grep xrootd
|
This gets a ROOT file with info on a given data run (mag field configuration, #events, streams, etc.):
| Code Block |
|---|
#!/bin/bash
#gets a ROOT file with info on a run (takes run number as argument)
wget http://atlas-runquery.cern.ch/query.py?q=find+run+${1}+%2F+show+all+%2F+nodef
sleep 3
wget http://atlas-runquery.cern.ch/data/atlrunquery.root
rm -v query.py\?q\=find+run*
|
There's a few athena options (I like the -s and -c etc.):
| Code Block |
|---|
athena -h #show athena help
|
Sometimes my JiveXML files get messed up and can't be read, due to a binary character in the trigger string. Fix it with:
| Code Block |
|---|
#!/bin/bash
for f in JiveXML*; do sed -i '/Obeys/d' $f ; done
for f in JiveXML*; do sed -i 's/<trigInfoStreamTag>/<trigInfoStreamTag>fixJive/' $f ; done
|
If a script is expecting a particular ATLAS release version, you can check it with:
| Code Block |
|---|
#!/bin/bash
if [ $AtlasVersion != "15.3.1" ]; then echo "Go to a cmthome and do . setup.sh -tag=15.3.1"; exit; fi
|
Check out all the CSC transforms:
| Code Block |
|---|
csc_<tab> #will show them all... look at csc_atlasG4_trf.py, csc_digi_trf.py, csc_reco_trf.py, etc...
|
This will actually put your files into the catalog, so you don't get annoying warnings:
| Code Block |
|---|
pool_insertFileToCatalog <file>
|
When running on the batch farm, you really should write things out into the /scratch area on the batch node during the job, and then cp it all back at the end of the job, to prevent hammering on NFS. Here's an example script:
| Code Block |
|---|
#!/bin/bash
. /u/at/ahaas/cmthome/setup.sh -tag=15.3.0 #setup the ATLAS release
export d=`date +%s`; echo $d #make a variable name for the directory which is the number of seconds since 1975
mkdir /scratch/ahaas; mkdir /scratch/ahaas/${d}; mkdir /scratch/ahaas/${d}/temp; cd /scratch/ahaas/${d}; pwd;
athena.py -c "TIMESHIFT=0" -c "DECAY=False" /u/at/ahaas/reldirs/15.3.0/Generators/Pythia_i/share/jobOptions.pythiaRhad.py > temp/pyth.log.txt
#all outputs of the athena job that are important should get put into the temp directory too...
echo copying back results
pwd; ls -lh temp
mv -v /scratch/ahaas/${d}/temp /nfs/slac/g/atlas/u01/users/ahaas/temp/rh_production_stripped_files/temp_${d}
cd; rm -rfv /scratch/ahaas/${d}; echo done
|
You could run this batch script above (put in a file called myjob.sh) with the following.
(The xlong queue will kill your job after 177.6 hours of CPU time in "SLAC units"... which is about ~15 hours of real CPU time.)
(See all queues with "bqueues". You can see the the details of a queue with "bqueues -l xlong".)
| Code Block |
|---|
bsub -q xlong -R rhel40 -J SG${n}_${s} time myjob.sh
|