Cern Web Service (Personal Website)
This twiki stoped updating since June 2018.
A personal website was build up following this tutorial:
https://cernbox.web.cern.ch/cernbox/en/web/personal_website_content.html
The new website is :
https://cern.ch/shhan
1.DESY computer resources
DESY hosts
Hosts working with Qsub:
nafhh-atlas01.desy.de ~ nafhh-atlas02.desy.de
Hosts working with HTCondor:
naf-atlas11.desy.de ~ naf-atlas16.desy.de
.
submit HTCondor jobs:
Since Dec. 2017, the DESY local computing system has been updated to HTcondor
https://confluence.desy.de/pages/viewpage.action?pageId=67639562
The following commands is the cheat list from qsub to HTcondor
QSub (SGE) |
HTCondor |
qsub 123.job |
echo "executable = 123.job" > 123.sub condor_submit 123.sub (more details below) |
qstat |
condor_q |
qdel |
condor_rm |
condor_rm [username]: kill all your jobs
While submitting jobs, it has to be changed from
qsub -q short.q,default.q -l os=sld6 -l site=hh -l h_vmem=8G -o ${base_dir}/out/${jobname}_"$ijob".out -e ${base_dir}/err/{jobname}_"$ijob".err ${jobfilename}
To
rm -fr ${submitfilename}
echo "executable = ${jobfilename}" > ${submitfilename}
echo "should_transfer_files = Yes" >> ${submitfilename}
echo "when_to_transfer_output = ON_EXIT" >> ${submitfilename}
echo "input = ${base_dir}/input/${jobname}_"$ijob".txt" >> ${submitfilename}
echo "output = ${base_dir}/out/${jobname}_"$ijob".out2" >> ${submitfilename}
echo "error = ${base_dir}/err/${jobname}_"$ijob".err2" >> ${submitfilename}
echo "log = ${base_dir}/log/${jobname}_"$ijob".log2" >> ${submitfilename}
echo "+RequestRuntime = 43200" >> ${submitfilename}
echo "universe = vanilla" >> ${submitfilename}
echo "RequestMemory = 4G" >> ${submitfilename}
echo "queue" >> ${submitfilename}
condor_submit ${submitfilename}
The example scripts are in this path:
/afs/desy.de/user/h/hans/public/condor_example
DESY HTCondor queue :
On 25th May 2018 there are ~7500 cpus, HTCondor can distribute cpus for jobs itself
HTCondor is going to have more and more cpus, please always check
http://bird.desy.de/stats/day.html
On 25th May 2018 there are still ~500 cpus for Qsub (SGE), please always check
http://bird.desy.de/status/day.html
DESY disks
Login
https://amfora.desy.de to check AFS and NAF quota
AFS is usually 16G, NAF is 1T (default)
DESY Tire2
The quota on DESY-HH_LOCALGROUPDISK will be 20T (default) after applying for atlas/de VO
The transferred files on this disk can be found under /pnfs path
2. IHEP computer resources
http://afsapply.ihep.ac.cn:86/quick/
IHEP hosts:
SLC6 hosts:
lxslc6.ihep.ac.cn
atlasui01.ihep.ac.cn
atlasui04.ihep.ac.cn ~ atlasui06.ihep.ac.cn (IHEP inner hosts)
SLC5 hosts:
atlasui03.ihep.ac.cn
lxslc5.ihep.ac.cn
submit HTCondor jobs:
before doing anything, use the command:
export PATH=/afs/ihep.ac.cn/soft/common/sysgroup/hep_job/bin5:$PATH # SLC5
export PATH=/afs/ihep.ac.cn/soft/common/sysgroup/hep_job/bin:$PATH # SLC6
Then you use the following cheat table
Qsub |
HTCondor |
qsub |
hep_sub |
qstat |
hep_q |
qdel |
hep_rm |
hep_rm -a: kill all the jobs
hep_q -u yourIhepUserName: check your jobs status
normally it is very similar as using Qsub, we just need use the command:
hep_sub job.sh -o out -e err -mem 4800 -g atlas
other optional arguments:
-os OPERATINGSYSTEM, --OperatingSystem OPERATINGSYSTEM
# set the system version of resource you want.
-prio PRIORITY, --priority PRIORITY
# set the inner job priority of your own jobs.
-np NUMBERPROCESS, --numberprocess NUMBERPROCESS
# set the total cores required by your job.
The example scripts are in this path (do not submit in /workfs or /afs):
/publicfs/atlas/atlasnew/higgs/hgg/ShuoHan/ATLAS/job1_data2016
IHEP HTCondor queue :
one universal queue sharing 4300 cpus, the working time is infinite, HTCondor can distribute cpus for jobs itself
IHEP disks :
disk name |
disk path |
size |
backup |
Can submit HTCondor jobs |
afs |
/afs/ihep.ac.cn/users/ |
500MB |
unknown |
no |
workfs |
/workfs/atlas/ |
10GB |
yes |
no |
scratchfs |
/scratchfs/atlas/ |
500GB |
delete every 2 weeks |
yes |
publicfs atlasnew |
/publicfs/atlas/atlasnew/higgs/hgg/ |
320TB shared |
no |
yes |
publicfs codesbackup |
/publicfs/atlas/codesbackup/ |
320TB shared |
yes |
yes |
IHEP Tier2
The quota on BEIJING-LCG2_LOCALGROUPDISK will be 8T after applying for atlas/cn VO
But those files (on disk /dpm) should be downloaded to Tier3 anyway by command "dpns-ls -l" and "rfcp" , they cannot be directly read
3. ATLAS environment
Setup ATLAS environment:
Setup ATLAS Environment:
export ATLAS_LOCAL_ROOT_BASE=/cvmfs/atlas.cern.ch/repo/ATLASLocalRootBase
alias setupATLAS='source ${ATLAS_LOCAL_ROOT_BASE}/user/atlasLocalSetup.sh'
setupATLAS
Then, setup Root:
lsetup root
Certificate, ATLAS VO, Rucio, AMI
Certificate: "New Grid User Certificate" in
https://ca.cern.ch/ca/
Setup certificate on DESY/IHEP/Lxplus:
openssl pkcs12 -in usercert.p12 -nokeys -clcerts -out ~/.globus/usercert.pem
openssl pkcs12 -in usercert.p12 -nocerts -out ~/.globus/userkey.pem
chmod 400 ~/.globus/userkey.pem
chmod 444 ~/.globus/usercert.pem
voms-proxy-init voms atlas
ATLAS VO page (request here):
https://voms2.cern.ch:8443/voms/atlas/user/home.action
Rucio transfer request page:
https://rucio-ui.cern.ch/r2d2/request
Rucio commands:
voms-proxy-init -voms atlas
lsetup rucio
rucio list-dids DATASETNAME
rucio list-file-replicas DATASETNAME
rucio get DATASETNAME
rucio list-rules --file FILETYPE(e.g. data16_13TeV):FILEPATH
AMI page:
https://ami.in2p3.fr/
pyAMI commands:
https://ami.in2p3.fr/pyAMI/
voms-proxy-init -voms atlas
lsetup pyami
ami show dataset info DATASETNAME
How to read Ntuple from CERN eos disk (see
https://confluence.desy.de/display/IS/How+to+use+Grid+resources+in+batch+jobs)
voms-proxy-init -voms atlas
lsetup xrootd rucio root
root -l
root [0] TFile *mytuple =TFile::Open("root://eosatlas.cern.ch//eos/atlas/atlascerngroupdisk/phys-higgs/*/myntuple.root")
While submitting jobs in condor, in the job-file, one should type
export X509_USER_PROXY=${PATHTOPROXY}
echo "#!/bin/expect" > voms.sh
echo "spawn voms-proxy-init -voms atlas" >> voms.sh
echo "expect 'Enter GRID pass phrase for this identity:'" >> voms.sh
echo "send 'your_proxy_passwd\r'" >> voms.sh
echo "interact" >> voms.sh
expect voms.sh
lsetup xrootd rucio root
and in condor submit-file, type
transfer_input_files = ${PATHTOPROXY}
Where the $PATHTOPROXY is default to be $X509_USER_PROXY in host, but need to be copied to a readable path, e.g. cp /tmp/x509up_u2xxxx ${HOME}/nfs/proxyfile/
ATLAS Configs/Tools
Truth Type and Truth origin :
https://gitlab.cern.ch/atlas/athena/blob/master/PhysicsAnalysis/MCTruthClassifier/MCTruthClassifier/MCTruthClassifierDefs.h
Electron / Photon ID config:
http://atlas.web.cern.ch/Atlas/GROUPS/DATABASE/GroupData/ElectronPhotonSelectorTools/offline/
Binary location of e/gamma ID:
https://gitlab.cern.ch/atlas/athena/blob/master/PhysicsAnalysis/ElectronPhotonID/ElectronPhotonSelectorTools/ElectronPhotonSelectorTools/egammaPIDdefs.h
e/gamma Author definitions:
https://gitlab.cern.ch/atlas/athena/blob/master/Event/xAOD/xAODEgamma/xAODEgamma/EgammaDefs.h
e/gamma Enum (
ConversionType,
EgammaType,
ShowerShapeType):
https://gitlab.cern.ch/atlas/athena/blob/master/Event/xAOD/xAODEgamma/xAODEgamma/EgammaEnums.h
Tracking Enum :
https://gitlab.cern.ch/atlas/athena/blob/master/Event/xAOD/xAODTracking/xAODTracking/TrackingPrimitives.h
Isolation working points twiki:
https://twiki.cern.ch/twiki/bin/viewauth/AtlasProtected/IsolationSelectionTool
Lowest un-prescaled trigger:
https://twiki.cern.ch/twiki/bin/view/Atlas/LowestUnprescaled
Cross-Section and Branching-Ratio page:
https://twiki.cern.ch/twiki/bin/view/LHCPhysics/LHCHXSWG
Current Luminosity:
https://twiki.cern.ch/twiki/bin/view/AtlasPublic/LuminosityPublicResultsRun2
GRL page:
http://atlasdqm.web.cern.ch/atlasdqm/grlgen/All_Good/
Lumi-calculator:
https://atlas-lumicalc.cern.ch/, select "Create output plots and ntuples (--plots)" to create PRW input
Athena nightly builds:
http://atlas-nightlies-browser.cern.ch/~platinum/nightlies/globalpage
MC
JobOptions SVN:
https://svnweb.cern.ch/trac/atlasoff/browser/Generators/MC15JobOptions/trunk/share
ATLAS Twiki and Tutorials
PRW config page:
https://twiki.cern.ch/twiki/bin/viewauth/AtlasProtected/ExtendedPileupReweighting
MC Reconstruction twiki:
https://twiki.cern.ch/twiki/bin/view/AtlasComputing/RecoTf and
https://twiki.cern.ch/twiki/bin/view/Atlas/PileupMC2016
MC production twiki:
https://twiki.cern.ch/twiki/bin/viewauth/AtlasProtected/AtlasProductionGroup
Derivation twiki:
https://twiki.cern.ch/twiki/bin/viewauth/AtlasProtected/DerivationProductionTeam
HGamma twiki:
https://twiki.cern.ch/twiki/bin/viewauth/AtlasProtected/HggDerivationAnalysisFramework
MxAOD twiki:
https://twiki.cern.ch/twiki/bin/view/AtlasProtected/MxAODs
Creating Event-Loop package:
https://twiki.cern.ch/twiki/bin/viewauth/AtlasComputing/SoftwareTutorialxAODAnalysisInROOT
Analysis Base tutorial:
https://atlassoftwaredocs.web.cern.ch/ABtutorial/
ATLAS tutorial meetings:
https://indico.cern.ch/category/397/
ATLAS software tutorial twiki:
https://twiki.cern.ch/twiki/bin/view/AtlasComputing/SoftwareTutorialSoftwareBasics
PubCome Latex twiki:
https://twiki.cern.ch/twiki/bin/viewauth/AtlasProtected/PubComLaTeX
4. Softwares
Get a ssh Key here :
https://gitlab.cern.ch/help/ssh/README
Add the ssh Key here :
https://gitlab.cern.ch/profile/keys
Start a new project here :
https://gitlab.cern.ch/dashboard/projects
Basic commands here :
https://gitlab.cern.ch/help/gitlab-basics/README.md
Some basic commands:
git clone SSH_PATH
git checkout BRANCH_OR_TAG
git pull
git add --all
git commit -am "something"
git push origin BRANCH
Cmake
CmakeLists.txt of Athena based package :
https://gitlab.cern.ch/atlas-hgam-sw/HGamCore/blob/master/HGamTools/CMakeLists.txt
CmakeLists.txt of local code :
https://gitlab.cern.ch/shhan/Purity_2D/blob/master/CMakeLists.txt
Use Virtual machine (or Docker) to run Athena on your computer
Docker:
https://docs.docker.com/docker-for-mac/
Docker with Athena:
https://twiki.cern.ch/twiki/bin/viewauth/AtlasComputing/AthenaMacDockerSetup
docker pull lukasheinrich/atlas_base_fromhepsw
docker run --privileged -it -v $HOME:$HOME -e DISPLAY=${ip}:0 lukasheinrich/atlas_base_fromhepsw /bin/bash
CERNVM:
https://atlas-vp1.web.cern.ch/atlas-vp1/blog/tutorial/running-vp1-on-any-system-in-a-virtual-machine/
Follow this page until “SetupATLAS”, so you have a linux virtual machine in ATLAS environment
Administrator (in case you want to use sodo): account : atlas, password: boson
ATLAS Event Display
Latest event:
http://atlas-live.cern.ch/
Public plots:
https://twiki.cern.ch/twiki/bin/view/AtlasPublic/EventDisplayPublicResults
Event Pickup (JML and ESD):
https://twiki.cern.ch/twiki/bin/view/AtlasComputing/Atlantis
Atlantis: download latest version here (
http://atlantis.web.cern.ch/atlantis/), run in a system where Java is available
VP1:
asetup 20.7.9.2,AtlasProduction, here
vp1 DATASET.ESD.root
EUTelescrope
Home Page:
http://eutelescope.web.cern.ch
Setup on DESY NAF disk:
setupATLAS
lsetup "root 6.10.04-x86_64-slc6-gcc62-opt"
export ILCSOFT=/nfs/dust/atlas/user/hans/EUTelescrope_desy
cd $ILCSOFT
git clone -b dev-desynaf https://github.com/eutelescope/ilcinstall $ILCSOFT/ilcinstall
cd $ILCSOFT/ilcinstall
./ilcsoft-install -i examples/eutelescope/release-standalone.cfg
5. ADCoS Shift links
6. Internal Code/Packages