Created: 2014-05-19 09:51
Updated: 2017-01-17 16:53

This set of tools can be used to start and monitor jobs on LXBATCH. It will monitor every job individually and resubmit it in case of failure. There is a maximum number of trials before the monitor stops resubmitting the jobs. It consists of a python server and a python client, both running pyro (Python Remote Objects).

The server keeps track of all the batches, generates the jobs, monitor them and resubmit in case of failure.

The client connects to the server and receives informations about the batches running on the server. It has a curse interface that shows two different screens.

  • The first is the main menu, displaying the list of existing batches. The top menu gives the list of available commands. Use the arrow keys to navigate through the batches and the screen. Up and down to select a different batch. Right to see the details of the batch (second screen). The delete key will remove the batch from the server (stop monitoring only, do not actually kills or remove the jobs). Finally a capital K will stop the server (WARNING! When stopped the server forgets all the batches).
  • The second screen shows the details of the selected batch, with information about the batch itself, statistics about the jobs. It also gives access to commands to generate the jobs or re-generate them when completely failed. The left key goes back to the main screen.

To initiate the connection with the server, the client needs to know the ip address where the server runs. When starting the server writes this information in a file (.ns.cfg) in the HOME of the user. This is where the client retrieve the information. Usage [-h] [-q QUEUE] [-t] [-n NAME] [-x] [-k] [--limit N] [(-c CONFIG | -l LOAD)] [-s]

optional arguments: -h, --help show this help message and exit -q QUEUE, --queue Indicates on which LXBATCH queue the jobs will be submitted -t, --test When restarting a series of job, for each job test if the output file already exists. If yes, skip the job (do not regenerate existing output files) --limit N Limit on concurrently active (RUN or PEND) jobs (default=-1: no limit). This is not a strict limit as there is a delay between submitting and monitoring. -n NAME, --name Name of the batch -k, --keep Do not delete the LXBATCH output (LSFJOB_xxxxxxx) -c CONFIG, --config Configuration file to use (new batch) -l LOAD, --load Reload a previous batch (restart tracking the jobs, do not regenerate them) -s, --submit Submit a batch, request the job generation and exit

Specifying no option will only open the normal curse interface without creating any batch. Usage [-dn] [-t] [-h|-help|help] -dn: Print debugging information according to the debug level n: 0=No debug, 1=Error, 2=Warning, 3=Info -t: Activate tracing -h|-help|help: Print this help

Configuration file

The configuration file is parsed and defines the monitor. Several fields are mandatory: o listFile : path to a file containing the list of files to process o executable : path to the main executable to run

Others are not: o optTemplate : line to use as argument for the executable (templated) o preExecute : bash script to execute before starting the executable (templated) o postExecute : bash script to execute after the executable finished it's execution (templated) o startIndex : starting index in the input list file o maxJobs : maximum number of files to read fron the input list file o maxAttempts : maximum attempts before giving up on a job o outputDir : path to a directory where the monitor can find the output files o outputFile : name of the ouput file (templated) o requirement : specify requirement for bsub (-R flag) o finalScript : script executed when all jobs are successfully finished (can be used to create a new batch) o jobsGrouping: number of input files to group in a single job. Example: with 202 input files and jobsGrouping = 100, 3 jobs will be created. The first job run over the 100 first files, the second over the 100 next and the third over the last 2 files.

The fields marked as "templated" can use of the following placeholder that will be replaced when submitting the job: o $jobIndex : will be replaced by the index of the job (=file index in the list of files) -- not working with arrayed submitting o $fileNameArr[n] : will be replaced by the file name of the nth file in the list of input files of the job -- not working with arrayed submitting o $fileName : will be replaced by the file name of the first input file of the job o $fileList : will be replaced by a list of the input files name of the job separated by \n o $outputDir : will be replaced by the output directory as defined by the outputDir field o $outputFile : will be replaced by the filename as defined by the outputFile field

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