Storage: Lustre (scratch)¶
Lustre is scalable high performance file system created for HPC. It allows MPI-IO but mainly it provides large storage capacity and high sequential throughput for cluster applications. Currently the total capacity is 2PB. The basic idea in Lustre is to spread data in each file over multiple storage servers. With large (larger than 1GB) files Lustre will significantly boost the performance.
Working with small files¶
As Lustre is meant for large files, the performance with small (smaller than 10MB) files will not be optimal.If possible, try to avoid working with multiple small files.
If small files are needed (i.e. source codes) you can tell Lustre not to spread data over all the nodes. This will help in performance.
To see the striping for any given file or directory you can use following command to check status
lfs getstripe /scratch/path/to/dir
You can not change the striping of an existing file, but you can change the striping of new files created in a directory, then copy the file to a new name in that directory.
lfs setstripe -c 1 /scratch/path/to/dir cp somefile /scratch/path/to/dir/newfile
Working with lots of small files¶
Large datasets which consist mostly of small (<1MB) files can be slow to process because of network overhead associated with individual files. If it is your case, please consult Compute node local drives page, see tar-example over there.
Working with large files¶
By default Lustre on Triton is configured to stripe a single file over a single OST. This provides the best performance for small files, serial programs, parallel programs where only one process is doing I/O, and parallel programs using a file-per-process file I/O pattern. However, when working with large files (>> 10 GB), particularly if they are accessed in parallel from multiple processes in a parallel application, it can be advantageous to stripe over several OST’s. In this case the easiest way is to create a directory for the large file(s), and set the striping parameters for any files subsequently created in that directory:
cd $WRKDIR mkdir large_file lfs setstripe -c 4 large_file
The above creates a directory “large_file” and specifies that files created inside that directory will be striped over 4 OST’s. For really really large files (hundreds of GB’s) accessed in parallel from very large MPI runs, set the stripe count to “-1” which tells the system to stripe over all the available OST’s.
To reset back to the default settings, run
lfs setstripe -d path/to/directory
Lustre: common recommendations¶
Several excellent recommendations are at
They are fully applicable to our case.
Be aware, that being a high performance filesystem Lustre still has its
own bottlenecks, and even non-proper a usage by a single user can get
whole system in stuck. See the recommendations at the link above how to
avoid those potential situations. Common Lustre troublemakers are
ls -lR, creating many small files,
rm -rf, small random i/o,
heavy bulk i/o.
For advanced user, these slides can be interesting: http://www.eofs.eu/fileadmin/lad2012/06_Daniel_Kobras_S_C_Lustre_FS_Bottleneck.pdf