OpenStack and High Performance Data

OpenStack and High Performance Data

What can data requirements mean an HPC context? The range of use cases is almost boundless. With considerable generalisation we can consider some broad criteria for requirements, which expose the inherent tensions between HPC-centric and cloud-centric storage offerings:

  • The data access model: data objects could be stored and retrieved using file-based, block-based, object-based or stream-based access. HPC storage tends to focus on a model of file-based shared data storage (with an emerging trend for object-based storage proposed for achieving new pinnacles of scalability). Conversely cloud infrastructure favours block-based storage models, often backed with and extended by object-based storage. Support for data storage through shared filesystems is still maturing in OpenStack.
  • The data sharing model: applications may request the same data from many clients, or the clients may make data accesses that are segregated from one another. This distinction can have significant consequences for storage architecture. Cloud storage and HPC storage are both highly distributed, but often differ in the way in which data access is parallelised. Providing high-performance access for many clients to a shared dataset can be a niche requirement specific to HPC. Cloud-centric storage architectures typically focus on delivering high aggregate throughput on many discrete data accesses.
  • The level of data persistence. An HPC-style tiered data storage architecture does not need to incorporate data redundancy at every level of the hierarchy. This can improve performance for tiers caching data closer to the processor.

The cloud model offers capabilities that enable new possibilities for HPC:

  • Automated provisioning. Software-defined infrastructure automates the provisioning and configuration of compute resources, including storage. Users and group administrators are able to create and configure storage resources to their specific requirements at the exact time they are needed.
  • Multi-tenancy. HPC storage does not offer multi-tenancy with the level of segregation that cloud can provide. A virtualised storage resource can be reserved for the private use of a single user, or could be shared between a controlled group of collaborating users, or could even be accessible by all users.
  • Data isolation. Sensitive data requires careful data management. Medical informatics workloads may contain patient genomes. Engineering simulations may contain data that is trade secret. OpenStack’s segregation model is stronger than ownership and permissions on a POSIX-compliant shared filesystem, and also provides finer-grained access control.

There is clear value in increased flexibility - but at what cost in performance? In more demanding environments, HPC storage tends to focus on and be tuned for delivering the requirements of a confined subset of workloads. This is the opposite approach to the conventional cloud model, in which assumptions may not be possible about the storage access patterns of the supported workloads.

This study will describe some of these divergences in greater detail, and demonstrate how OpenStack can integrate with HPC storage infrastructure. Finally some methods of achieving high performance data management on cloud-native storage infrastructure will be discussed.

File-based Data: HPC Parallel Filesystems in OpenStack

Conventionally in HPC, file-based data services are delivered by parallel filesystems such as Lustre and Spectrum Scale (GPFS). A parallel filesystem is a shared resource. Typically it is mounted on all compute nodes in a system and available to all users of a system. Parallel filesystems excel at providing low-latency, high-bandwidth access to data.

Parallel filesystems can be integrated into an OpenStack environment in a variety of configuration models.

Provisioned Client Model

Access to an external parallel filesystem is provided through an OpenStack provider network. OpenStack compute instances - virtualised or bare metal - mount the site filesystem as clients.

This use case is fairly well established. In the virtualised use case, performance is achieved through use of SR-IOV (with only a moderate level of overhead). In the case of Lustre, with a layer-2 VLAN provider network the o2ib client drivers can use RoCE to perform Lustre data transport using RDMA.

Cloud-hosted clients on a parallel filesystem raise issues with root in a cloud compute context. On cloud infrastructure, privileged accesses from a client do not have the same degree of trust as on conventional HPC infrastructure. Lustre approaches this issue by introducing Kerberos authentication for filesystem mounts and subsequent file accesses. Kerberos credentials for Lustre filesystems can be supplied to OpenStack instances upon creation as instance metadata.

Provisioned Filesystem Model

There are use cases where the dynamic provisioning of software-defined parallel filesystems has considerable appeal. There have been proof-of-concept demonstrations of provisioning Lustre filesystems from scratch using OpenStack compute, storage and network resources.

The OpenStack Manila project aims to provision and manage shared filesystems as an OpenStack service. IBM’s Spectrum Scale integrates with Manila to re-export GPFS parallel filesystems using the user-space Ganesha NFS server.

Currently these projects demonstrate functionality over performance. In future evolutions the overhead of dynamically provisioned parallel filesystems on OpenStack infrastructure may improve.

A Parallel Data Substrate for OpenStack Services

IBM positions Spectrum Scale as a distributed data service for underpinning OpenStack services such as Cinder, Glance, Swift and Manila. More information about using Spectrum Scale in this manner can be found in IBM Research’s red paper on the subject (listed in the Further Reading section).

Applying HPC Technologies to Enhance Data IO

A recurring theme throughout this study has been the use of remote DMA for efficient data transfer in HPC environments. The advantages of this technology are especially pertinent in data intensive environments. OpenStack’s flexibility enables the introduction of RDMA protocols for many cloud infrastructure operations to reduce latency, increase bandwidth and enhance processor efficiency:

Cinder block data IO can be performed using iSER (iSCSI extensions for RDMA). iSER is a drop-in replacement for iSCSI that is easy to configure and set up. Through providing tightly-coupled IO resources using RDMA technologies, the functional equivalent of HPC-style burst buffers can be added to the storage tiers of cloud infrastructure.

Ceph data transfers can be performed using the Accelio RMDA transport. This technology was demonstrated some years ago but does not appear to have achieved production levels of stability or gained significant mainstream adoption.

The NOWLAB group at Ohio State University have developed extensions to data analytics platforms such as HBase, Hadoop, Spark and Memcached to optimise data movements using RDMA.

Optimising Ceph Storage for Data-Intensive Workloads

The versatility of Ceph embodies the cloud-native approach to storage, and consequently Ceph has become a popular choice of storage technology for OpenStack infrastructure. A single Ceph deployment can support various protocols and data access models.

Ceph is capable of delivering strong read bandwidth. For large reads from OpenStack block devices, Ceph is able to parallelise the delivery of the read data across multiple OSDs.

Ceph’s data consistency model commits writes to multiple OSDs before a write transaction is completed. By default a write is replicated three times. This can result in higher latency and lower performance on write bandwidth.

Ceph can run on clusters of commodity hardware configurations. However, in order to maximise the performance (or price performance) of a Ceph cluster some design rules of thumb can be applied:

Use separate physical network interfaces for external storage network and internal storage management. On the NICs and switches, enable Ethernet flow control and raise the MTU to support jumbo frames.

Each drive used for Ceph storage is managed by an OSD process. A Ceph storage node usually contains multiple drives (and multiple OSD processes).

The best price/performance and highest density is achieved using fat storage nodes, typically containing 72 HDDs. These work well for large scale deployments, but can lead to very costly units of failure in smaller deployments. Node configurations of 12-32 HDDs are usually found in deployments of intermediate scale.

Ceph storage nodes usually contain a higher-speed write journal, which is dedicated to service of a number of HDDs. An SSD journal can typically feed 6 HDDs while an NVMe flash device can typically feed up to 20 HDDs.

About 10G of external storage network bandwidth balances the read bandwidth of up to 15 HDDs. The internal storage management network should be similarly scaled.

A rule of thumb for RAM is to provide 0.5GB-1GB of RAM per TB per OSD daemon.

On multi-socket storage nodes, close attention should be paid to NUMA considerations. The PCI storage devices attached to each socket should be working together. Journal devices should be connected with HDDs attached to HBAs on the same socket. IRQ affinity should be confined to cores on the same socket. Associated OSD processes should be pinned to the same cores.

For tiered storage applications in which data can be regenerated from other storage, the replication count can safely be reduced from 3 to 2 copies.

The Cancer Genome Collaboratory: Large-scale Genomics on OpenStack

Genome datasets can be hundreds of terabytes in size, sometimes requiring weeks or months to download and significant resources to store and process.

OICR logo

The Ontario Institute for Cancer Research built the Cancer Genome Collaboratory (or simply The Collaboratory) as a biomedical research resource built upon OpenStack infrastructure. The Collaboratory aims to facilitate research on the world’s largest and most comprehensive cancer genome dataset, currently produced by the International Cancer Genome Consortium (ICGC).

By making the ICGC data available in cloud compute form in the Collaboratory, researchers can bring their analysis methods to the cloud, yielding benefits from the high availability, scalability and economy offered by OpenStack, and avoiding the large investment in compute resources and the time needed to download the data.

An OpenStack Architecture for Genomics

The Collaboratory’s requirements for the project were to build a cloud computing environment providing 3000 compute cores and 10-15 PB of raw data stored in a scalable and highly-available storage. The project has also met constraints of budget, data security, confined data centre space, power and connectivity. In selecting the storage architecture, capacity was considered to be more important than latency and performance.

Each rack hosts 16 compute nodes using 2U high-density chassis, and between 6 and 8 Ceph storage nodes. Hosting a mix of compute and storage nodes in each rack keeps some of the Nova-Ceph traffic in the same rack, while also lowering the power requirement for these high density racks (2 x 60A circuits are provided to each rack).

As of September 2016, Collaboratory has 72 compute nodes (2600 CPU cores, Hyper-Threaded) with a physical configuration optimized for large data-intensive workflows: 32 or 40 CPU cores and a large amount of RAM (256 GB per node). The workloads make extensive use of high performance local disk, incorporating hardware RAID10 across 6 x 2TB SAS drives.

The networking is provided by Brocade ICX 7750-48C top-of-rack switches that use 6x40Gb cables to interconnect the racks in a ring stack topology, providing 240 Gbps non-blocking redundant inter-rack connectivity, at a 2:1 oversubscription ratio.

The Collaboratory is deployed using entirely community-supported free software. The OpenStack control plane is Ubuntu 14.04 and deployment configuration is based on Ansible. The Collaboratory was initially deployed using OpenStack Juno and a year later upgraded to Kilo and then Liberty.

Collaboratory deploys a standard HA stack based on Haproxy/Keepalived and Mariadb-Galera using three controller nodes. The controller nodes also perform the role of Ceph-mon and Neutron L3-agents, using three separate RAID1 sets of SSD drives for MySQL, Ceph-mon and Mongodb processes.

The compute nodes have 10G Ethernet with GRE and SDN capabilities for virtualized networking. The Ceph nodes use 2x10G NICs bonded for client traffic and 2x10G NICs bonded for storage replication traffic. The Controller nodes have 4x10G NICs in an active-active bond (802.3ad) using layer3+4 hashing for better link utilisation. The Openstack tenant routers are highly-available with two routers distributed across the three controllers. The configuration does not use Neutron DVR out of concern for limiting the number of servers directly attached to the Internet. The public VLAN is carried only on the trunk ports facing the controllers and the monitoring server.

Optimising Ceph for Genomics Workloads

Upon workload start, the instances usually download data stored in Ceph's object storage. OICR developed a download client that controls access to sensitive ICGC protected data through managed tokens. Downloading a 100GB file stored in Ceph takes around 18 minutes, with another 10-12 minutes used to automatically check its integrity (md5sum), and is mostly limited by the instance’s local disk.

The ICGC storage system adds a layer of control on top of Ceph’s object storage. Currently this is a 2-node cluster behind an Haproxy instance serving the ICGC storage client. The server component uses OICR’s authorization and metadata systems to provide secure access to related objects stored in Ceph. By using OAuth-based access tokens, researchers can be given access to the Ceph data without having to configure Ceph permissions. Access to individual project groups can also be implemented in this layer.

Each Ceph storage node consists of 36 OSD drives (4, 6 or 8 TB) in a large Ceph cluster currently providing 4 PB of raw storage, using three replica pools. The radosgw pool has 90% of the Ceph space being reserved for storing protected ICGC datasets, including the very large whole genome aligned reads for almost 2000 donors. The remaining 10% of Ceph space is used as a scalable and highly-available backend for Glance and Cinder. Ceph radosgw was tuned for the specific genomic workloads, mostly by increasing read-ahead on the OSD nodes, 65 MB as rados object stripe for Radosgw and 8 MB for RBD.

Further Considerations and Future Directions

In the course of the development of the OpenStack infrastructure at the Collaboratory, several issues have been encountered and addressed:

The instances used in cancer research are usually short lived (hours/days/weeks), but with high resource requirements in terms of CPU cores, memory and disk allocation. As a consequence of this pattern of usage the Collaboratory OpenStack infrastructure does not support live migration as a standard operating procedure.

The Collaboratory have encountered a few problems caused by Radosgw bugs involving overlapping multipart uploads. However, these were detected by the Collaboratory’s monitoring system, and did not result in data loss. The Collaboratory created a monitoring system that uses automated Rally tests to monitor end-to-end functionality, and also download a random large S3 object (around 100 GB) to confirm data integrity and monitor object storage performance.

Because of the mix of very large (BAM), medium (VCF) and very small (XML, JSON) files, the Ceph OSD nodes have imbalanced load and we have to regularly monitor and rebalance data.

Currently, the Collaboratory is hosting 500TB of data from 2,000 donors. Over the next 2 years, OICR will increase the number of ICGC genomes available in the Collaboratory, with the goal of having the entire ICGC data set of 25,000 donors estimated to be 5PB when the project completes in 2018.

Although in a closed beta phase with only a few research labs having accounts, there were more than 19,000 instances started in the last 18 months, with almost 7,000 in the last three months. One project that uses the Collaboratory heavily is the PanCancer Analysis of Whole Genomes (PCAWG), which characterizes the somatic, and germline variants from over 2,800 ICGC cancer whole genomes in 20 primary tumour sites.

In conclusion, the Collaboratory environment has been running well for OICR and its partners. George Mihaiescu, senior cloud architect at OICR, has many future plans for OpenStack and the Collaboratory:

“We hope to add new Openstack projects to the Collaboratory’s offering of services, with Ironic and Heat being the first candidates. We would also like to provide new compute node configurations with RAID0 instead of RAID10, or even SSD based local storage for improved IO performance.”

CLIMB: OpenStack, Parallel Filesystems and Microbial Bioinformatics

The Cloud Infrastructure for Microbial Bioinformatics (CLIMB) is a collaboration between four UK universities (Swansea, Warwick, Cardiff and Birmingham) and funded by the UK’s Medical Research Council. CLIMB provides compute and storage as a free service to academic microbiologists in the UK. After an extended period of testing, the CLIMB service was formally launched in July 2016.

CLIMB hardware

CLIMB is a federation of 4 sites, configured as OpenStack regions. Each site has an approximately equivalent configuration of compute nodes, network and storage.

The compute node hardware configuration is tailored to support the memory-intensive demands of bioinformatics workloads. The system as a whole comprises 7680 CPU cores, in fat 4-socket compute nodes with 512GB RAM. Each site also has three large memory nodes with 3TB of RAM and 192 hyper-threaded cores.

The infrastructure is managed and deployed using xCAT cluster management software. The system runs the Kilo release of OpenStack, with packages from the RDO distribution. Configuration management is automated using Salt.

Each site has 500 TB of GPFS storage. Every hypervisor is a GPFS client, and uses an infiniband fabric to access the GPFS filesystem. GPFS is used for scratch storage space in the hypervisors.

For longer term data storage, to share datasets and VMs, and to provide block storage for running VMs, CLIMB deploys a storage solution based on Ceph. The Ceph storage is replicated between sites. Each site has 27 Dell R730XD nodes for Ceph storage servers. Each storage server contains 16x 4TB HDDs for Ceph OSDs, giving a total raw storage capacity of 6912TB. After 3-way replication this yields a usable capacity of 2304TB.

On two sites Ceph is used as the storage back end for Swift, Cinder and Glance. At Birmingham GPFS is used for Cinder and Glance, with plans to migrate to Ceph.

In addition to the infiniband network, a Brocade 10G Ethernet fabric is used, in conjunction with dual-redundant Brocade Vyatta virtual routers to manage cross-site connectivity.

In the course of deploying and trialling the CLIMB system, a number of issues have been encountered and overcome.

  • The Vyatta software routers were initially underperforming with consequential impact on inter-site bandwidth.
  • Some performance issues have been encountered due to NUMA topology awareness not being passed through to VMs.
  • Stability problems with Broadcom 10GBaseT drivers in the controllers led to reliability issues. (Thankfully the HA failover mechanisms were found to work as required).
  • Problems with interactions between Ceph and Dell hardware RAID cards.
  • Issues with Infiniband and GPFS configuration.

CLIMB has future plans for developing their OpenStack infrastructure, including:

  • Migrating from regions to Nova cells as the federation model between sites.
  • Integrating OpenStack Manila for exporting shared filesystems from GPFS to guest VMs.

Further Reading

An IBM research study on integrating GPFS (Spectrum Scale) within OpenStack environments: http://www.redbooks.ibm.com/redpapers/pdfs/redp5331.pdf

A 2015 presentation from ATOS on using Kerberos authentication in Lustre: http://cdn.opensfs.org/wp-content/uploads/2015/04/Lustre-and-Kerberos_Buisson.pdf

Glyn Bowden of HPE and Alex Macdonald from SNIA discuss OpenStack storage (including the Provisioned Filesystem Model using Lustre): https://www.brighttalk.com/webcast/663/168821

The High-Performance Big Data team at Ohio State University: http://hibd.cse.ohio-state.edu

A useful talk from the 2016 Austin OpenStack Summit on Ceph design: https://www.openstack.org/videos/video/designing-for-high-performance-ceph-at-scale

The Ontario Institute for Cancer Research Collaboratory: http://www.cancercollaboratory.org

Further details on the International Cancer Genome Consortium: http://icgc.org/

Dr Tom Connor presented CLIMB at the 2016 Austin OpenStack summit: https://www.openstack.org/videos/video/the-cloud-infrastructure-for-microbial-bioinformatics-breaking-biological-silos-using-openstack

Acknowledgements

This document was written by Stig Telfer of StackHPC Ltd with the support of Cambridge University, with contributions, guidance and feedback from subject matter experts:

  • George Mihaiescu, Bob Tiernay, Andy Yang, Junjun Zhang, Francois Gerthoffert, Christina Yung, Vincent Ferretti from the Ontario Institute for Cancer Research. The authors wish to acknowledge the funding support from the Discovery Frontiers: Advancing Big Data Science in Genomics Research program (grant no. RGPGR/448167-2013, ‘The Cancer Genome Collaboratory’), which is jointly funded by the Natural Sciences and Engineering Research Council (NSERC) of Canada, the Canadian Institutes of Health Research (CIHR), Genome Canada, and the Canada Foundation for Innovation (CFI), and with in-kind support from the Ontario Research Fund of the Ministry of Research, Innovation and Science.
  • Dr Tom Connor from Cardiff University and the CLIMB collaboration.
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