This page covers some best practices related to data processing on UMIACS Compute resources.
It is recommended to store data that is actively being worked on as close to the processing source as possible. In the context of a cluster job, the data being processed, as well as any generated results, should be stored on a disk physically installed in the compute node itself. We'll cover how to identify local disk space later on this page.
The following is a suggested workflow for a computational job:
- Copy the data to be processed to the local compute node.
- Process the data, storing results on local disk space.
- Once processing is finished, transfer results to permanent storage location. (i.e. a network file share)
- Clean up data and results from compute node local disk space.
Why this matters
Similar to how too many processes on a single machine can slow it down, too many users accessing a network file server can impact performance. This issue is further compounded in the context of cluster jobs, as a single user can generate hundreds if not thousands of jobs all trying to access the same network fileserver. By utilizing the local disks on the compute nodes, you effectively distribute the data access load and reduce the load on the central fileserver.
Following these best practices isn't just about being a good neighbor however, they will also improve the performance of your jobs.
To further illustrate this issue, consider a service like Netflix. While Netflix invests heavily in their data storage and supporting network, if they allowed their customers to access it directly it would quickly reach capacity resulting in performance degradation for all users. In order to accommodate this Netflix distributes it's data into various caching tiers, which are much closer to the end user. This distribution evens the load across multiple different devices, increasing the performance and availability for all users.
While UMIACS obviously does not operate at the same scale as Netflix, the same issues are still present within the compute infrastructure. Processing data that resides on local disk space reduces the load on the central file server and improves the performance of the process.
When possible, it is recommended that data be stored in an archive file.
Utilizing archive files provide the following benefits:
- Faster data transfers
- Reduced data size
- Easier data management.
Practically every filesystem in existence has limitations in it's ability to handle large numbers of small files. By grouping large collections of small files into a single archive file we reduce the impact of this limitation, as well as improve the efficiency of data storage when combined with techniques such as compression. Another advantage manifests when transferring data over the network. In order to transfer a file a connection to the remote location has to be established and closed for each file, which can add significant overhead when dealing with large numbers of files. When the files are collected into a single archive file we reduce the number of connections that are created and destroyed, and focus more on streaming data.
Common utilities for creating archive files are
Identifying Local Disk Space
Local disk storage at UMIACS typically conforms to the following guidelines:
- Directory name starts with
- Almost every UMIACS supported machine has a
- Machines with multiple local disks will have multiple
/scratchXdirectories, where X is a number that increases with the number of disks.
# Output shortened for brevity. -bash-4.2$ lsblk NAME MAJ:MIN RM SIZE RO TYPE MOUNTPOINT sda 8:0 0 931.5G 0 disk └─sda2 8:2 0 930.5G 0 part ├─vol00-scratch0 253:3 0 838G 0 lvm /scratch0 sdb 8:16 0 477G 0 disk └─sdb1 8:17 0 477G 0 part /scratch1 sdc 8:32 0 953.9G 0 disk └─sdc1-scratch2 253:2 0 953.9G 0 lvm /scratch2
As shown above, common utilities such as
lsblk can be used to identify the specific configuration on a given node.
|Local data storage is considered transitory and as such is not backed up. It is not intended for long-term storage of critical/sensitive data|
If you have any questions about the available local disk storage on a given cluster please refer to the documentation specific for that cluster, or contact the UMIACS Help Desk