Managing Large Numbers of Jobs with DAGMan
Using DAGMan is recommended when submitting large numbers of jobs. The recommendation holds whether the jobs are represented by a DAG due to dependencies, or all the jobs are independent of each other, such as they might be in a parameter sweep. DAGMan offers:
Throttling limits the number of submitted jobs at any point in time.
- Retry of jobs that fail
This is a useful tool when an intermittent error may cause a job to fail or may cause a job to fail to run to completion when attempted at one point in time, but not at another point in time. The conditions under which retry occurs are user-defined. In addition, the administrative support that facilitates the rerunning of only those jobs that fail is automatically generated.
- Scripts associated with node jobs
PRE and POST scripts run on the submit host before and/or after the execution of specified node jobs.
Each of these capabilities is described in detail within this manual section about DAGMan. To make effective use of DAGMan, there is no way around reading the appropriate subsections.
To run DAGMan with large numbers of independent jobs, there are generally two ways of organizing and specifying the files that control the jobs. Both ways presume that programs or scripts will generate needed files, because the file contents are either large and repetitive, or because there are a large number of similar files to be generated representing the large numbers of jobs. The two file types needed are the DAG input file and the submit description file(s) for the HTCondor jobs represented. Each of the two ways is presented separately:
- A unique submit description file for each of the many jobs.
A single DAG input file lists each of the jobs and specifies a distinct submit description file for each job. The DAG input file is simple to generate, as it chooses an identifier for each job and names the submit description file. For example, the simplest DAG input file for a set of 1000 independent jobs, as might be part of a parameter sweep, appears as
# file sweep.dag JOB job0 job0.sub JOB job1 job1.sub JOB job2 job2.sub ... JOB job999 job999.sub
There are 1000 submit description files, with a unique one for each of the job<N> jobs. Assuming that all files associated with this set of jobs are in the same directory, and that files continue the same naming and numbering scheme, the submit description file for
job6.submight appear as
# file job6.sub universe = vanilla executable = /path/to/executable log = job6.log input = job6.in output = job6.out arguments = "-file job6.out" request_cpus = 1 request_memory = 1024M request_disk = 10240K queue
Submission of the entire set of jobs uses the command line:
$ condor_submit_dag sweep.dag
A benefit to having unique submit description files for each of the jobs is that they are available if one of the jobs needs to be submitted individually. A drawback to having unique submit description files for each of the jobs is that there are lots of submit description files.
- Single submit description file.
A single HTCondor submit description file might be used for all the many jobs of the parameter sweep. To distinguish the jobs and their associated distinct input and output files, the DAG input file assigns a unique identifier with the VARS command.
# file sweep.dag JOB job0 common.sub VARS job0 runnumber="0" JOB job1 common.sub VARS job1 runnumber="1" JOB job2 common.sub VARS job2 runnumber="2" ... JOB job999 common.sub VARS job999 runnumber="999"
The single submit description file for all these jobs utilizes the
runnumbervariable value in its identification of the job’s files. This submit description file might appear as
# file common.sub universe = vanilla executable = /path/to/executable log = wholeDAG.log input = job$(runnumber).in output = job$(runnumber).out arguments = "-$(runnumber)" request_cpus = 1 request_memory = 1024M request_disk = 10240K queue
The job with
runnumber="8"expects to find its input file
job8.inin the single, common directory, and it sends its output to
job8.out. The single log for all job events of the entire DAG is
wholeDAG.log. Using one file for the entire DAG meets the limitation that no macro substitution may be specified for the job log file, and it is likely more efficient as well. This node’s executable is invoked with
These examples work well with respect to file naming and file location when there are less than several thousand jobs submitted as part of a DAG. The large numbers of files per directory becomes an issue when there are greater than several thousand jobs submitted as part of a DAG. In this case, consider a more hierarchical structure for the files instead of a single directory. Introduce a separate directory for each run. For example, if there were 10,000 jobs, there would be 10,000 directories, one for each of these jobs. The directories are presumed to be generated and populated by programs or scripts that, like the previous examples, utilize a run number. Each of these directories named utilizing the run number will be used for the input, output, and log files for one of the many jobs.
As an example, for this set of 10,000 jobs and directories, assume that
there is a run number of 600. The directory will be named
and it will hold the 3 files called
representing the input, output, and HTCondor job log files associated
with run number 600.
The DAG input file sets a variable representing the run number, as in the previous example:
# file biggersweep.dag JOB job0 bigger.sub VARS job0 runnumber="0" JOB job1 bigger.sub VARS job1 runnumber="1" JOB job2 bigger.sub VARS job2 runnumber="2" ... JOB job9999 bigger.sub VARS job9999 runnumber="9999"
A single HTCondor submit description file may be written. It resides in the same directory as the DAG input file.
# file bigger.sub universe = vanilla executable = /path/to/executable log = log input = in output = out arguments = "-$(runnumber)" initialdir = dir$(runnumber) request_cpus = 1 request_memory = 1024M request_disk = 10240K queue
One item to care about with this set up is the underlying file system for the pool. The transfer of files (or not) when using initialdir differs based upon the job universe and whether or not there is a shared file system. See the condor_submit manual page for the details on the submit command.
Submission of this set of jobs is no different than the previous examples. With the current working directory the same as the one containing the submit description file, the DAG input file, and the subdirectories:
$ condor_submit_dag biggersweep.dag