WORK is a Lustre filesystem with metadata servers and object storage servers managing the user data. WORK is a single, shared resource, and as such some user jobs may impact with their I/O patterns the performance of other jobs running concurrently using the WORK resources. We want to achieve that this resource is used fairly across the wide spectrum of applications and users.
If jobs request hundreds of thousands metadata operations like open, close and stat per job, this can cause a "slow" filesystem (unresponsiveness) even when the metadata are stored on SSDs in our Lustre configuration.
Therefore, we provide here some general advice to avoid critical conditions of WORK including unresponsiveness:
- Write intermediate results and checkpoints as seldom as possible.
- Try to write/read larger data volumes (>1 MiB) and reduce the number of files concurrently managed in WORK.
- For inter-process communication use proper protocols (e.g. MPI) instead of files in WORK.
- If you want to control your jobs externally, consider to use POSIX signals, instead of using files frequently opened/read/closed by your program. You can send signals e.g. to batch jobs via "scancel --signal..."
- Use MPI-IO to coordinate your I/O instead of each MPI task doing individual POSIX I/O (HDF5 and netCDF may help you with this).
For some of the codes we are aware of certain issues:
- OpenFOAM: always set ‘runTimeModifiable false’ and fileHandler collated with a sensible value for purgeWrite and writeInterval (see: https://www.hlrn.de/doc/display/PUB/OpenFOAM)
- NAMD: special considerations during replica-exchange runs: https://www.hlrn.de/doc/display/PUB/NAMD
If you have questions or you are unsure regarding your individual scenario, please get in contact with your consultant.