Pegasus

University of Tsukuba · OSS CHFS · Fully Reproducible

System Purpose

Question asked

Please describe the purpose and general usage of the submitted system.  This would include the types of typical applications it supports (e.g., defense applications, molecular dynamics, benchmarking, system test, systems research), and the general use and purpose of the data generated by the applications running on it.

Pegasus supercomputer is operated by the Center for Computational Sciences, University of Tsukuba.  It is available to users around the world through various research programs such as Interdisciplinary Collaborative Research, HPCI Collaborative Research, and General Research, thereby contributing to the further development of computational science.

Availability

Question asked

Please provide the deployment timeframe of the submitted system, or for on-demand cloud systems, the general period over which it is deployed and destroyed.

Please describe the availability of the system to users and who are its set of most regular users.

Pegasus was installed in December 2022, and provided to users since April 2023.  It will be operated until 2028.  Users who are granted by research programs can ues the supercomputer.

Storage System Software

Question asked

How is this storage software available? (e.g., commercially, open-source, not publicly available) Note that if the storage software is not open-source or commercially available, then a general description would be requested, but this would limit the submission’s reproducibility score.

Can anyone download/purchase this software?

List either product webpage or open-source repo of the exact software used in IO500.

Give any and all additional details of this specific storage deployment: (e.g., type of storage server product such IBM ESS or DDN SFA400X2, use of Ext4 or some other file system on each storage node, dual connected storage media to storage servers).

The storage software is CHFS/Cache, which supports various type of applications.  It is an open-source software and available at https://github.com/otatebe/chfs.  Anyone can download the software.  CHFS/Cache is deployed on compute nodes using node-local persistent memory on Pegasus.  It is a caching file system and the backend file system is Lustre.

Runtime Environment

Question asked

State here that you provided all scripts/documentation that would allow someone else to reproduce your environment and attempt to achieve a similar IO500 score as the submitted system.

NOTE: provide all files/documentation/scripts that would enable a user to build your environment and deploy the custom scripts, software, or config files once they have obtained the appropriate storage system hardware and software. These may be included into the io500.tgz or into the extraCodes upload on the submission form.

Several examples include:

  • Commands used to set striping information (either for the entire system or for particular directories)
  • File system config and tuning information (or a reason why this is not available due to lack of root access, etc) on each node type (e.g., non-default config parameters on all three types of Lustre nodes: MDS, OSS, and client)
  • Any additional scripts utilized that impact IO500 execution beyond the io500 config file. For example, with IBM Spectrum Scale, the output of mmlsconfig, mmlscluster, mmlsfs, and mmlsfileset commands (and possibly even a dump of the configuration if possible). Each file system probably has similar type of config/tuning information that would need to be shared for a user to fully reproduce the environment.

All information is included in the submitted user script and zip file.  we uses 10 compute nodes for clients, 100 compute nodes for a CHFS/Cache caching file system, and the Lustre as a backend file system.

Fault Tolerance Mechanisms

Question asked

Does your system have a single point of failure as defined by “Definition 7” of a Production System? Please describe all mechanisms that provide fault tolerance for the submitted storage system. Be specific to your submission, not general storage system capabilities.

  • Power (For example, can power failure of a node or rack bring down the storage system?)
  • Networking (For example, can failure of a single NIC bring down the storage system? Remember that any networking failure that brings down multiple nodes is acceptable)
  • Inter storage data and metadata server (For example, what type of data protection mechanism does the storage system use to keep operating during node failures, e.g., active-active servers, client-directed RAID, declustered RAID, erasure-coding, 3-way replication)
  • Intra storage data and metadata server storage media (For example, how does the storage eysstem protect against fiailure of a single storage device within a node, e.g., raid5)

Please list any additional information needed to determine whether this system has a single point of failure.

CHFS/Cache is a fully distributed peer-to-peer system.  It does not have a single point of failure.  For the cached files, all data is persistent stored in persistent memory.  On the other hand, the cached data does not have redundancy.  If one of servers fails, the data stored on the server is not available until the server is returned unless the data is flushed yet to the backend file system.

Execution

Question asked

Please provide a description of how the IO500 benchmark was executed, e.g., via system scheduler (e.g., SLURM) to run a job on the compute cluster, which initially ran a setup process to configure the client and file system, and then started the full benchmark.

During the IO500 benchmark execution was the system entirely dedicated to running the benchmark or were there other jobs running in the same cluster and storage system?

The IO500 benchmark was executed via the system scheduler NQSV provided by NEC.  The number of nodes required are provided by the command line like 'qsub -b 110 user_script'.  The benchmark was executed in the normal operation time.  Because the system is not dedicated to running the benchmark, there are some interferences in the system.  However, because the total number of nodes is 120, the system is mostly ocupied by the benchmark execution.

Caching

Question asked

Please describe all caching mechanisms in client/server that were utilized during the IO500 run. This could include caching in any storage medium (e.g., SSD, RAM).

A few examples would include:

  • Client data/metadata caching (in Linux page cache or in other memory cache)
  • Client side NVMe read-only data cache
  • Storage server metadata/data caching in RAM
  • Storage controller caching
  • RAID card caching

There is no client side caching in the CHFS/Cache.  Because the client library is a user-level, there is no benefit of Linux page cache.  All file data and metadata are stored on remote nodes comprising the CHFS/Cache.

Data Source

Question asked

Is the submitted system a stand-alone storage system or an acceleration layer in front of another storage system that is the source of truth for all application data? This question relates to whether the submitted system is a burst buffer layered on primary storage or primary storage itself.

The created data is stored on the CHFS/Cache caching file system that consists of persistent memory of 100 compute nodes.  Because the all data are deleted during the benchmark, the data are not flushed to the backend file system.  Actually, although the data created by IOR are not deleted, it is not flushed intentionally because it is not required.

Trust

Question asked

Please describe any steps taken to ensure that the results are trustworthy.

  • Did you run the benchmark multiple times and get similar scores?
  • Did you validate the score is below the physical capabilities of the deployed hardware?
  • How did you validate that the storage system follows the IO500 rules regarding persistence, which states, "All data must be written to persistent storage within the measured time for the individual benchmark, e.g. if a file system caches data, it must ensure that data is persistently stored before acknowledging the close"?

We executed the benchmark changing the number of compute nodes and the results are consistent.  The network bandwidth is 200 Gbps, which is equal to 23.3 GiB/s.  IOR easy benchmark achives 230 GiB/s that is below the physical capacities of networks 233 GiB/s.  All the data are persistent because they are stored in the persistent memory.