Building a scalable data storage for scientific computing

Research can require enormous amounts of data. Such data needs to be accessed by multiple people at the same time, and is used across a diverse range of computations or research questions. The size of the dataset, the need for simultaneous access and transformation of this data by multiple people, and the subsequent storing of multiple copies or derivatives of the data constitutes a challenge for computational clusters and requires state-of-the-art data management solutions. This use case details a model implementation for a scalable data storage solution, suitable to serve the computational and logistic demands of data science in big (scientific) institutions, while keeping workflows for users as simple as possible. It elaborates on

  1. How to implement a scalable, remote data store so that data are stored in a different place than where people work with it,

  2. How to configure the data store and general cluster setup for easy and fast accessibility of data, and

  3. How to reduce technical complexities for users and encourage reproducible, version-controlled scientific workflows.

Note

This section is technical in nature and aimed at IT/data management personnel seeking insights into the technical implementation and configuration of a scalable data storage. It is not meant for users of such a data store. A use case about user-facing interactions and workflows with such a data storage is detailed in

Todo

write and link HAMMERPANTS usecase

The Challenge

The data science institute XYZ consists of dozens of people: Principle investigators, PhD students, general research staff, system administration, and IT support. It does research on important global issues, and prides itself with ground-breaking insights obtained from elaborate and complex computations run on a large scientific computing cluster. The data sets used in the institute are big both in size and number of files, and expensive to collect. Therefore, datasets are used for various different research questions, by multiple researchers.

Every member of the institute has an account on an expensive and large compute cluster, and all of the data exists in dedicated directories on this server. In order to work on their research questions without modifying original data, every user creates their own copies of the full data in their user account on the cluster – even if it contains many files that are not necessary for their analysis. In addition, they add all computed derivatives and outputs, even old versions, out of fear of losing work that may become relevant again. This is because version control is not a standard skill in the institute, and especially PhD students and other trainees struggle with the technical overhead of data management and data science. Thus, an excess of data copies and derivatives exists in addition to the already substantial amount of original data. At the same time, the compute cluster is both the data storage and the analysis playground for the institute. With data directories of several TB in size, and computationally heavy analyses, the compute cluster is quickly brought to its knees: Insufficient memory and IOPS starvation make computations painstakingly slow, and hinder scientific progress, despite the elaborate and expensive cluster setup.

The DataLad approach

The compute cluster is refurbished to a state-of-the-art data management system. Unlike traditional solutions, both because of the size of the large amounts of data, and for more efficient use of compute power for calculations instead of data storage, the cluster gets a remote data store: Data lives as DataLad datasets on a different machine than the one the scientific analyses are computed on. For access to the annexed data in datasets, the data store is configured as a git-annex RIA-remote. In case of filesystem inode limitations on the machine serving as the data store (e.g., HPC storage systems), full datasets can be (compressed) 7-zip archives, without losing the ability to query available files. Regardless of the number of file and size of them, such datasets thus use only few inodes. Using DataLad’s run-procedures, an institute-wide configuration is distributed among users. Applying the procedure is done in a single datalad run-procedure command, and users subsequently face minimal technical overhead to interact with the data store.

The infrastructural changes are accompanied by changes in the mindset and workflows of the researchers that perform analyses on the cluster. By using the data store, the institute’s work routines are adjusted around DataLad datasets: Analyses are set-up inside of DataLad datasets, and for every analysis, an associated project is created under the namespace of the institute on the institute’s GitLab instance automatically. This has the advantage of vastly simplified version control and simplified access to projects for collaborators and supervisors. Data from the data store is installed as subdatasets. This comes with several benefits: Analyses are automatically linked to data, no unused file copies waste disk space on the compute cluster as data can be retrieved on-demand, and files that are easily re-obtained or recomputed can safely be dropped locally to save even more disk-space. Moreover, upon creation of an analysis project, the associated GitLab project it is automatically configured as a remote with a publication dependency on the data store, thus enabling vastly simplified data publication routines and backups of pristine results.

Step-by-step

Note

This use case describes the data storage implementation as done in INM-7, research centre Juelich, Germany.

To create a data store, parts of the old compute cluster and parts of the super computer at the Juelich supercomputing centre (JSC) are used to store large amounts of data. Thus, multiple different, independent machines take care of warehousing the data. While this is unconventional, it is convenient: The data does not strain the compute cluster, and with DataLad, it is irrelevant where the data are located.

A simple, local version control workflow with datalad.

Fig. 10 Trinity of research data handling: The data store ($DATA) is managed and backed-up. The compute cluster ($COMPUTE) has an analysis-appropriate structure with adequate resources, but just as users workstations/laptops ($HOME), it is not concerned with data hosting.

On their own machines ($HOME), researchers are free to do whatever they want as long as it is within the limits of their machines. The cluster ($COMPUTE) pulls the data exclusively from the data store ($DATA). Thus, within $HOME, researchers are free to explore data from $DATA as they wish, but scaling requires them to use $COMPUTE. Results from $COMPUTE are pushed back to $DATA, and hence anything that is relevant for a computation is tracked (and backed-up) there.

The data store as a git-annex RIA remote

The remote data store exists thanks to git-annex (which DataLad builds upon): Large files in datasets are stored as values in git-annex’s object tree. A key generated from their contents is checked into Git and used to reference the location of the value in the object tree1. The object tree (or keystore) with the data contents can be located anywhere – its location only needs to be encoded using a special remote. This configuration is done on an administrative, system-wide level, and users do not need to care or know about where data are stored, as they can access it just as easily as before.

Find out more: What is a special remote?

A special-remote is an extension to Git’s concept of remotes, and can enable git-annex to transfer data to and from places that are not Git repositories (e.g., cloud services or external machines such as an HPC system). Don’t envision a special-remote as a physical place or location – a special-remote is just a protocol that defines the underlying transport of your files to and from a specific location.

The machines in question, parts of an old compute cluster, and parts of the supercomputer at the JSC are configured to receive and store data using the git-annex remote for indexed file archives (RIA) special remote. The git-annex RIA-remote is similar to git-annex’s built-in directory special remote, but distinct in certain aspects:

  • It allows read access to (compressed) 7z archives, which is a useful feature on systems where light quotas on filesystem inodes are imposed on users, or where one wants to have compression gains. This way, the entire keystore (i.e., all data contents) of the remote that serves as the data store can be put into an archive that uses only a handful of inodes, while remaining fully accessible.

  • It provides access to configurable directories via SSH. This makes it easier to accommodate infrastructural changes, especially when dealing with large numbers of repositories, as moving from local to remote operations, or switching target paths can be done by simply changing the configuration.

  • It allows a multi-repository directory structure, in which keystore directories of multiple repositories can be organized in to a homogeneous archive directory structure. Importantly, the keystore location in an archive is defined using the datasets UUID (in case of DataLad datasets) or the annex remote UUID (in case of any non DataLad dataset). This aids handling of large numbers of repositories in a data store use case, because locations are derived from repository properties rather than having to re-configure them explicitly.

The structure under which data is stored in the data store looks like this:

 082
 ├── 8ac72-f7c8-11e9-917f-a81e84238a11
 │   ├── annex
 │   │   ├── objects
 │   │   │   ├── ff4
 │   │   │   │   └── c57
 │   │   │   │       └── MD5E-s4--ba1f2511fc30423bdbb183fe33f3dd0f
 │   │   │   ├── abc
 │   │   │   │   └── def
 │   │   │   │       └── MD5E-s4--ba1f2511fc30423bdbb183fe33f3dd0f
 │   │   │   ├── [...]
 │   │   └── archives
 │   │       └── archive.7z
 │   ├── branches
 │   ├── config
 │   ├── description
 │   ├── HEAD
 │   ├── hooks
 │   │   ├── [...]
 │   ├── info
 │   │   └── exclude
 │   ├── objects
 │   │   ├── 04
 │   │   │   └── 49b485d128818ff039b4fa88ef57be0cb5b184
 │   │   ├── 06
 │   │   │   └── 4e5deab57592a54e4e9a495cde70cd6da7605a
 │   │   ├── [...]
 │   │   ├── info
 │   │   └── pack
 │   ├── refs
 │   │   ├── heads
 │   │   │   ├── git-annex
 │   │   │   └── master
 │   │   └── tags
 │   └── ria-layout-version
 └── c9d36-f733-11e9-917f-a81e84238a11
     ├── [...]

Here is how the RIA-remote features look like in real life:

  • Datasets are identified via their UUID (e.g., 0828ac72-f7c8-11e9-917f-a81e84238a11). The UUID is split into the first two levels of the tree structure (as highlighted above in the first two lines), with the two-level structure to avoid exhausting file system limits on the number of files/folders within a directory.

  • This first, two-level tree structure can host keystores for any number of repositories.

  • The third level holds a directory structure that is identical to a bare git repository, and is a clone of the dataset.

    Find out more: What is a bare Git repository?

    A bare Git repository is a repository that contains the contents of the .git directory of regular DataLad datasets or Git repositories, but no worktree or checkout. This has advantages: The repository is leaner, it is easier for administrators to perform garbage collections, and it is required if you want to push to it at all times. You can find out more on what bare repositories are and how to use them here.

  • Inside of the bare Git repository, the annex directory – just as in any standard dataset or repository – contains the keystore (object tree) under annex/objects (highlighted above as well). Details on how this object tree is structured are outlined in the hidden section in Data integrity.

  • These keystores can be 7zipped if necessary to hold (additional) git-annex objects, either for compression gains, or for use on HPC-systems with inode limitations.

This implementation is fully self-contained, and is a plain file system storage, not a database. Once it is set up, in order to retrieve data from the data store, special remote access to the data store needs to be initialized.

This is done with a custom configuration (cfg_inm7) as a run-procedure2 with a datalad create command:

$ datalad create -c inm7 <PATH>

The configuration performs all the relevant setup of the dataset with a fully configured link to $DATA: It is configured as a remote to install and pull data from, but upon creation of the dataset, the dataset’s directory is also created at the remote end as a bare repository to enable pushing of results back to $DATA. At the same time, a GitLab sibling in the institute’s GitLab instance is created, with a publication dependency on the data storage.

With this setup, a dataset of any size can be installed in a matter of seconds by providing its ID as a source in a datalad install command:

$ datalad install --dataset mynewdataset \
  --source <ID/URL> \
  mynewdataset/inputs

Actual data content can be obtained on demand via datalad get. Thus, users can selectively obtain only those contents they need instead of having complete copies of datasets as before.

Todo

maybe something about caching here

Upon datalad publish, computed results can be pushed to the data store and be thus backed-up. Easy-to-reobtain input data can safely be dropped to free disk space on the compute cluster again.

With this remote data store setup, the compute cluster is efficiently used for computations instead of data storage. Researchers can not only compute their analyses faster and on larger datasets than before, but with DataLad’s version control capabilities their work also becomes more transparent, open, and reproducible.

Find out more: Software Requirements

  • git-annex version 7.20 or newer

  • DataLad version 0.12.5 (or later), or any DataLad development version more recent than May 2019 (critical feature: https://github.com/datalad/datalad/pull/3402)

  • The cfg_inm7 run procedure as provided with pip install git+https://jugit.fz-juelich.de/inm7/infrastructure/inm7-datalad.git

  • Server side: 7z needs to be in the path.

Footnotes

1

To re-read about how git-annex’s object tree works, check out section Data integrity, and pay close attention to the hidden section. Additionally, you can find much background information in git-annex’s documentation.

2

To re-read about DataLad’s run-procedures, check out section Configurations to go. You can find the source code of the procedure on GitLab.