Checkpointing

Some recipes and tips for checkpointing on the B4F HPC

Definition

Checkpointing: Saving the program's state at a checkpoint with the aim to restart it from that point in case of (un)planned stop of failure.

It is interesting for, e.g., long jobs that could be (un)voluntary killed, or jobs running on unstable computing systems.

Two types of program

The code is accessible

Recipe

Modify the code to implement the following recipe:

1. Look for a state file that includes all imformation required to restore the state when the program was stopped.
2. If it exists, read it and restore the state. Else, create an intial state.
3. Periodically save the state to the state file.

This recipe is applicable to several languages (e.g., R, Python, Matlab, Fortran, C, shell,...). Also, the checkpointing of parallel programs is easier after a global synchronization.
The checkpointing requires some efforts:

• to write some additional code;
• some memory (e.g. for a state file). One must be careful to what is saved;
• some time (e.g., to write the state file). Therefore, checkpointing too often must be avoided. Also, SLURM and other software features can be used to checkpoint at some specific points.