A first batch job

With the knowledge on how to submit an interactive job, submitting a batch job is straightforward. The main difference is that you need to specify an Executable to run, and should specify where to store output and logs. In our first simple example, we will go with a batch script which shows some information about the environment inside the job.

We need two files:

Save the following into a file of your choosing or use the file CentOS7_simple.jdl from the repository.

Executable = environment-info.sh
Arguments  = some Arguments for our program $(ClusterId) $(Process)
Universe   = vanilla

# Specify files to be transferred (please note that files on a shared filesystem should not be transferred!!!)
# Should executable be transferred from the submit node to the job working directory on the worker node?
Transfer_executable     = True

Error                   = logs/err.$(ClusterId).$(Process)
#Input                  = input/in.$(ClusterId).$(Process)
Output                  = logs/out.$(ClusterId).$(Process)
Log                     = logs/log.$(ClusterId).$(Process)

+ContainerOS="CentOS7"

Request_cpus = 2
Request_memory = 2 GB
Request_disk = 100 MB

Queue

Save the following into a file of your choosing or use the file environment-info.sh from the repository.

#!/bin/bash
source /etc/profile

echo "Called with arguments:"
echo "$@"

echo "PATH variable:"
echo $PATH

echo "OS release:"
cat /etc/os-release

echo "Running in Condor Slot:"
echo ${_CONDOR_SLOT_NAME}

echo "Kernel version:"
uname -a

echo "Full environment:"
env

echo "Running processes:"
ps faux

echo "Directory content:"
ls

echo "Sleeping a bit..."
for num in {1..10}; do
  echo "Sleep iteration ${num}/10..."
  sleep 60;
done

Please check that the shell script is executable - if not, run chmod +x environment-info.sh.

Usually, you should test your code before. If a special environment is needed, you can do that in an interactive job, before firing off many jobs. In our case, just test the script on the submit node by running ./environment-info.sh and check what happens.

Now, you can finally submit the job:

$ condor_submit CentOS7_simple.jdl
Submitting job(s)
ERROR: Invalid log file: "/home/student00/gridka-school-2019-htcondor/files/logs/log.44.0" (No such file or directory)

Please note that this fails! HTCondor usually performs a check whether the log files and other output files can be written before submitting the job. You can turn this off by adding -disable to the call to condor_submit, which speeds up submission - but then the jobs will go into HOLD state in case the files can not be written on the submit node.

So you will want to fix the problem:

mkdir logs

Now, please try again:

$ condor_submit CentOS7_simple.jdl
Submitting job(s).
1 job(s) submitted to cluster 46.

Now, you can investigate the job a bit. Some examples follow.

Use condor_q.
Check out some more details with condor_q -long clusterid.process.
Check out the files inside the logs directory.
Try to follow along the job output using condor_tail -f clusterid.process.

Especially at this point, you are invited to ask questions about what you find!

Removing jobs

Take note of the possibility to remove jobs, for example when you are finished with your investigations or have found a bug and want to re-submit!

To remove a full cluster of jobs:

condor_rm clusterid

To remove a single job:

condor_rm clusterid.process

To remove all your jobs:

condor_rm username

Submit another one of your test jobs and remove it. How long does it take? Check the status with condor_q during the process.

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