HPC_pulsar

Pipeline with scripts for running pulsar search software (PRESTO and custom Python routines) on HPC nodes.

Dependencies

HPC_pulsar is written in Python 3, tested on Python 3.7.4 and has the following package dependencies.

• psrdynspec
• PRESTO

The above packages have several underlying dependencies that are listed in their respective repositories.

Note: To avoid the hassle of installing PRESTO and its several dependencies, you can pull a Singularity container encasing a full PRESTO installation here via the following command line call.

singularity pull shub://federatedcloud/singularity-PRESTO

Alternately, for a Singularity container with both PRESTO and [psrdynspec](https://github.com/akshaysuresh1/psrdynspec) installed, run the below command line code.

singularity pull shub://federatedcloud/ pulsar-pipeline-container

Batch scripts found the batch_HPC directory provide example command line calls run within a singularity container.

Organization

1. batch_HPC: Batch scripts for non-interactive execution via Slurm.
2. cmd_files: Command line calls invoked by batch scripts for non-interactive program run.
3. config: Configuration script of inputs to different modules.
4. executables: Executable scripts that perform the computation. NOTE: Do not tamper with these scripts.

Installation

1. Clone this repository to your local machine.
2. Edit relevant files in the batch_HPC, cmd_files and config folders.
3. Pass relevant batch script to Slurm. You can now wait and relax while your code execution progresses non-interactively.

Example

Say that you want to dedisperse some data using MPI-enabled prepsubband of PRESTO.

1. Edit inputs in the configuration script config/dedisp.cfg.
2. Verify that the paths to the relavant executable file and config script are correctly provided in the Shell script cmd_files/dedispersion.cmd.
3. Supply appropriate parameters to Slurm in batch_HPC/dedispersion.sh.
4. Type sbatch batch_HPC/dedispersion.sh and hit Enter.

Troubleshooting

Please submit an issue to voice any problems or requests.

Improvements to the code are always welcome.