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This method is preferred over multiple submissions (e.g. with a for loop) because:
The environment variables defined by PBS during their execution are:
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| Name | Description |
|---|---|
| PBS_JOBID | Job identifier provided by PBS when a job is submitted. Created after executing the qsub command |
| PBS_JOBNAME | The name of the job provided by the user. The default name is the name of the submitted script |
| PBS_NODEFILE | List of work nodes, or processor cores on which the job is executed |
| PBS_O_WORKDIR | The working directory in which the job was submitted, i.e. in which qsub command was called |
| OMP_NUM_THREADS | An OpenMP variable that PBS exports to the environment, which is equal to the value of the ncpus option from the PBS script header |
| NCPUS | Number of cores requested. Matches the value from the ncpus option from the PBS script header |
| TMPDIR | Path to temporary directory |
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| Tip | ||
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While in PBS the path for the output and error files is specified in the directory in which they are executed, the input and output files of the program itself are loaded/saved in the $HOME directory by default. PBS does not have an option to specify the job execution in the current directory we are in, so it is necessary to change the directory manually. If you want to switch to the directory where the script was started, after the header you have to write:
If you want to run jobs with high storage load (I/O intensive) job execution is not recommended to run from $PBS_O_WORKDIR-a but from $TMPDIR location, which will use fast storage. Read more about using fast storage and temporary results below. |
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PBS makes it possible to define the necessary resources in several ways. The main unit for resource allocation is the so-called "Chunk" or piece of node. A chunk is defined with the select option. The number of processor cores per chunk can be defined with ncpus, the number of mpi processes with mpiprocs and the amount of working memory with mem. It is also possible to define walltime (maximum job execution time) and place (chunk allocation method by nodes).
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In this case, the user gets 4 processor cores and a total of 14GB of memory on one chunk. When jobs are described without the select option, it is not possible to "chain resources" (separate the required resources with a colon, it is necessary to put the -l option on a new line for each resource)
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OpenMP applications require the variable The value of the variable |
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qsub -W depend=<type>:<job_ID>[:<job_ID>] ... |
Where <type> can can be:
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after*- starting the current one with respect to the others-
after- execution of the current one after the start of execution of the specified ones -
afterok- execution of the current one after the successful completion of the specified ones -
afternotok-execution of the current after an error in the completion of the specified -
afterany- execution of the current one after the end of the specified ones
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before*- starting the others with respect to the current one-
before- execution of the specified ones after the start of the current one -
beforeok- execution of the specified ones after the successful completion of the current one -
beforenotok- execution of the specified ones after the an error in the completion of the current one -
beforeany- execution of the specified ones after the end of the current one
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on:<number>- execution of a job that will depend on the subsequently specified number ofbefore*types
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A job with a directive -W depend=... will not be submitted if the specified job IDs do not exist (or if they are not in a queue) |
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