Overview
This example shows how to run jobs and especially SLIC, the Simulator for the Linear Collider, on the FermiGrid which is part of the Open Science Grid. SLIC is a Geant4-based simulations package that uses an XML geometry input format called LCDD to describe geometry, sensitive detectors and readout geometry.
Note! The examples are written in a way that one can just cut and paste from your browser window to the terminal session on ILCSIM. Do not cut and paste into an editor (It wouldn't work unless you remove a lot of back slashes: \ ). Instead copy and edit the files that are created and modify them to to fit your own needs.
Prerequisites
- Obtain a DOE grid certificate from http://security.fnal.gov/pki/Get-Personal-DOEGrids-Cert.html, which also explains how to export the certificate from the browser and how to deal with directory permissions, etc.
- Register with the ILC VO (Virtual organization) at http://cd-amr.fnal.gov/ilc/ilcsim/ilcvo-registration.shtml that will guide you to: https://voms.fnal.gov:8443/vomrs/ilc/vomrs
- Get an account on ILCSIM and ILCSIM2, using the following form http://cd-amr.fnal.gov/ilc/ilcsim/ilcsim.shtml. This machines serve as a portals to the grid.
Setting up your own gateway to the grid is beyond the scope of this write-up. It involves installing and configuring the Virtual Data Toolkit (VDT) , installing a host certificate for the gateway machine, etc. For an administrative guide see the Fermi Grid web page.
Connecting from an External Site
Kerberos Configuration
Fermilab uses Kerberos for external authentication. This section assumes that you have a Fermilab Kerberos principal. Follow these instructions if you need an account at Fermilab and are authorized to obtain one.
Assuming that your machine has recent versions of SSH and Kerberos and you will not be using a Cryptocard, download Fermilab's official Kerberos configuration file.
Download the file.
wget http://security.fnal.gov/krb5.conf
Set the environment variable KRB5_CONFIG to point to the Fermilab configuration file.
export KRB5_CONFIG=`pwd`/krb5.conf
This variable can be added to your shell profile or setup in a script and the configuration file it points to will override the one in /etc.
Logging In
Logging in to a Fermilab gateway machine should now work provided that Kerberos has been configured correctly.
Initialize the Kerberos session.
kinit -f USERNAME@FNAL.GOV
Now ssh to a gateway machine at Fermilab.
ssh USERNAME@flxi02.fnal.gov
You may need to use ssh_config as your SSH configuration file for the Kerberos ticket forwarding to work correctly.
ssh -F ssh_config USERNAME@flxi02.fnal.gov
Now you should be able to connect to the ilcsim node.
ssh ilcsim
Grid Authentication from an External Site Outside Fermilab
If you want to use a grid-enabled node outside Fermilab, you may only need to add a single configuration file containing the ilc VOMS server information.
The following should be put into a file that we will call ilc-fermilab-voms.
"ilc" "fermigrid2.fnal.gov" "15023" "/DC=org/DC=doegrids/OU=Services/CN=host/fermigrid2.fnal.gov" "ilc"
Now a certificate can be obtained by referencing this configuration when running voms-proxy-init.
voms-proxy-init ilc:/ilc -userconf ./ilc-fermilab-voms
The file ilc-fermilab-voms must be owned by your account. The command will fail if this file has some other owner.
Provided that your local node is configured correctly, this should allow you to start a grid session on an external node outside Fermilab.
Setting up the Environment at Fermilab
To set up the environment and to get the necessary grid proxy certificate, log onto ILCSIM and issue the following commands:
source /fnal/ups/grid/setup.sh voms-proxy-init -voms ilc:/ilc/detector # give passwd etc.
To check the status of the proxy:
voms-proxy-info -all
Submitting the First Example Jobs
Now you should be all setup to submit a test job to make sure that everything is working. Cut and paste the following lines into your terminal window. This will submit a grid job which starts 5 separate processes. The processes will just execute sleep for 10 seconds before terminating. Since no output is created the sleep_grid.out.$(Cluster).$(Process) and sleep_grid.err.$(Cluster).$(Process) files should be empty.
(Note!: $(Cluster) represents the job number and $(Process) represents the (5) process numbers)
The condor log files are: sleep_grid.log.\$(Cluster).\$(Process)
cat > sleep_grid << +EOF universe = grid type = gt2 globusscheduler = fngp-osg.fnal.gov/jobmanager-condor executable = /bin/sleep transfer_output = true transfer_error = true transfer_executable = true log = sleep_grid.log.\$(Cluster).\$(Process) notification = NEVER output = sleep_grid.out.\$(Cluster).\$(Process) error = sleep_grid.err.\$(Cluster).\$(Process) stream_output = false stream_error = false ShouldTransferFiles = YES WhenToTransferOutput = ON_EXIT globusrsl = (jobtype=single)(maxwalltime=999) Arguments = 10 queue 5 +EOF condor_submit sleep_grid
The second example is an exploration job where the job reports the run time environment it encounters and the file systems that are mounted. This is very often useful to find out what is available on the worker nodes . So have a look at env_grid.out.$(Cluster).$(Process).
Note!: The grid job doesn't inherit the run time environment from your interactive session!
rm -f env_grid.sh cat > env_grid.sh << +EOF #!/bin/sh -f printenv cd \${_CONDOR_SCRATCH_DIR} pwd # # This sets up the environment for osg in case we want to # use grid services like srmcp # . $OSG_GRID/setup.sh source \${VDT_LOCATION}/setup.sh printenv /bin/df +EOF chmod +x env_grid.sh rm -f env_grid.run cat > env_grid.run << +EOF universe = grid type = gt2 globusscheduler = fngp-osg.fnal.gov/jobmanager-condor executable = ./env_grid.sh transfer_output = true transfer_error = true transfer_executable = true log = env_grid.log.\$(Cluster).\$(Process) notification = NEVER output = env_grid.out.\$(Cluster).\$(Process) error = env_grid.err.\$(Cluster).\$(Process) stream_output = false stream_error = false ShouldTransferFiles = YES WhenToTransferOutput = ON_EXIT globusrsl = (jobtype=single)(maxwalltime=999) queue +EOF condor_submit env_grid.run
Submitting a Job running SLIC
Now finally let's run SLIC . We will use the SLIC installation and a data set that are available on the GRID worker nodes. As in the previous examples cut and paste the contends below:
rm -f slic_grid.csh cat > slic_grid.csh << +EOF #!/bin/csh echo start /bin/date setenv LABELRUN slic_grid-\${ClusterProcess} setenv TARFILE \${LABELRUN}-results.tar echo \${TARFILE} echo start /bin/date mkdir results /grid/app/ilc/detector/SimDist/Oct-31-2007/SimDist/scripts/slic.sh -r 5 \ -g /grid/app/ilc/detector/SimDist/detectors/sid01/sid01.lcdd \ -i /grid/data/ilc/detector/LDC/stdhep/ZZ_run10.stdhep -o ./results/ZZ_run10\${LABELRUN} >& \ ./results/ZZ_run10\${LABELRUN}.lis ls -lh results /bin/date echo "build output tarball: " \${TARFILE} tar -cf \${TARFILE} results echo done +EOF chmod +x slic_grid.csh rm -f slic_grid.run cat > slic_grid.run << +EOF universe = grid type = gt2 globusscheduler = fngp-osg.fnal.gov/jobmanager-condor executable = ./slic_grid.csh transfer_output = true transfer_error = true transfer_executable = true environment = "ClusterProcess=\$(Cluster)-\$(Process)" transfer_output_files = slic_grid-\$(Cluster)-\$(Process)-results.tar log = slic_grid.log.\$(Cluster).\$(Process) notification = NEVER output = slic_grid.out.\$(Cluster).\$(Process) error = slic_grid.err.\$(Cluster).\$(Process) stream_output = false stream_error = false ShouldTransferFiles = YES WhenToTransferOutput = ON_EXIT globusrsl = (jobtype=single)(maxwalltime=999) queue +EOF condor_submit slic_grid.run
Running Commands directly on the Head Node
To run some commands directly on the grid head nodes use a syntax like this:
globus-job-run fngp-osg.fnal.gov/jobmanager-condor /bin/ls /grid/app globus-job-run fngp-osg.fnal.gov/jobmanager-condor /usr/bin/printenv globus-job-run fngp-osg.fnal.gov/jobmanager-condor /bin/df
The examples above show how to check what grid applications are installed, the runtime environment of a job and what file systems are mounted. To check for available SLIC/SimDist distributions type:
globus-job-run fngp-osg.fnal.gov/jobmanager-condor /bin/ls /grid/app/ilc/detector/SimDist/
Checking and Killing your Jobs
You can see the status of all jobs using the following command:
condor_q or condor_q -globus
Or to check the jobs submitted by user <username>:
condor_q -submitter <username>
You can view information about all requests with the following command:
condor_status -submitters
To cancel a job type condor_rm followed by the job number:
condor_rm <job number>