Lustre

Cori uses Lustre as its $SCRATCH file system. For many applications a technique called file striping will increase I/O performance. File striping will primarily improve performance for codes doing serial I/O from a single node or parallel I/O from multiple nodes writing to a single shared file as with MPI-I/O, parallel HDF5 or parallel NetCDF.

Lustre File Striping

The Lustre file system is made up of an underlying set of I/O servers and disks called Object Storage Targets (OSTs). A file is said to be striped when its data is on multiple OSTs. Read and write operations on striped files will access multiple OST's concurrently. File striping is a way to increase I/O performance since writing or reading from multiple OST's simultaneously increases the available I/O bandwidth. Selecting the best striping can be complicated since striping a file over too few OSTs will not take advantage of the system's available bandwidth but striping over too many will cause unnecessary overhead and lead to a loss in performance. The default striping is set to 1 on Cori's $SCRATCH. This means that each file is written to 1 OSTs on Cori by default.

NERSC File Striping Recommendations

NERSC has provided striping command shortcuts based on file size and I/O pattern to simplify optimization on Cori.

  • Shared file I/O: Either one processor does all the I/O for a simulation in serial or multiple processors write to a single shared file as with MPI-IO and parallel HDF5 or NetCDF
  • File per process: Each process writes to its own file resulting in as many files as number of processes
Single Shared-File I/O File per Process
File size (GB) command
< 1 keep default striping keep default striping
1 - 10 stripe_small keep default striping
10 - 100 stripe_medium keep default striping
> 100 stripe_large keep default striping
> 1000 stripe_large stripe_large

These helper scripts will set the number of OSTs to stripe across to 8, 24, and 72 for stripe_small, stripe_medium and stripe_large, respectively. In all cases, the stripe size is 1MB.

Warn

Files larger than 1 TB should be striped with the stripe_large script.

Striping must be set on a file before is written. For example, one could simultaneously create an empty file which will later be 10-100 GB in size and set its striping appropriately with the command:

nersc$ stripe_medium output_file

This could be done before running a job which will later populate this file. Striping of a file cannot be changed once the file has been written to, aside from copying the existing file into a newly created (empty) file with the desired striping.

Files inherit the striping configuration of the directory in which they are created. Again, the desired striping must be set on the directory before creating the files (later changes of the directory striping are not inherited). When copying an existing striped file into a striped directory, the new copy will inherit the directory's striping configuration. This provides another approach to changing the striping of an existing file.

Inheritance of striping provides a convenient way to set the striping on multiple output files at once, if all such files are written to the same output directory. For example, if a job will produce multiple 10-100 GB output files in a known output directory, the striping of the latter can be configured before job submission:

nersc$ mkdir output_directory 
nersc$ stripe_medium output_directory

Restriping an Existing File

Currently the only way to restripe an existing file is to make a copy of it.

nersc$ stripe_large tmp_my_big_file
nersc$ cp my_big_file tmp_my_big_file
nersc$ mv tmp_my_big_file my_big_file
If there are multiple files, you could create a directory with the desired striping and copy the files into it to avoid doing the above procedure multiple times.

Custom Lustre Striping

To set striping for a file or directory use the command lfs setstripe.

Each file and directory can have a separate striping pattern and a directory's striping setting can be overridden for a particular file by issuing the lfs setstripe command for individual files within that directory. However, as noted above, striping settings for a file must be set before it is created. If the settings for an existing file are changed, it will only get the new striping setting if the file is recreated. If the settings for an existing directory are changed, the files need to be copied elsewhere and then copied back to the directory in order to inherit the new settings. The lfs setstripe syntax is:

nersc$ lfs setstripe --size [stripe-size] --index [OST-start-index]
--count [stripe-count] filename
Option Description Default
stripe-size Number of bytes write on one OST before cycling to the next. Use multiples of 1MB. Default has been most successful. 1MB
stripe-count Number of OSTs a file exists on 1 on Cori
OST-start-index Starting OST. Default highly recommended -1 (System follows a round robin procedure to optimize creation of files by all users.)