cryoSPARC System Architecture Overview

CryoSPARC is a backend and frontend high performance computing software system that provides data processing and image analysis capabilities for single particle cryo-EM, along with a rich browser-based user interface and command line tools.

Master-worker pattern

The system is based on a master-worker pattern.

• The master processes (web application, core application and MongoDB database) run together on one node (master node). The master node requires relatively lightweight resources (2+ CPUs, 16GB+ RAM)

• Worker processes can be spawned on any available/configured node that has GPUs (worker node). The worker is responsible for all actual computation and data handling, and is dispatched by the master node. Note: The same node can function as both master and worker.

The master-worker architecture allows cryoSPARC to be installed and scaled up in a flexible manner, on a variety of hardware, including a single workstation, groups of workstations, cluster nodes, HPC clusters, cloud nodes, etc.

Typical cryoSPARC System Setups

Single Workstation

Both the cryoSPARC master and cryoSPARC worker processes can be run on the same machine. The only requirement is that GPU resources are available for the cryoSPARC worker processes. This is the simplest setup.

Master-Worker

In the master-worker setup, the cryoSPARC master is installed on a lightweight machine, and the worker processes are installed on one or more GPU servers. This is the most flexible setup for installing cryoSPARC. There are three main requirements for this setup, which are also explained in greater detail in the Installation sections of this document:

Clusters

The master node can also spawn or submit jobs to a cluster scheduler system (e.g., Slurm Workload Manager). This integration is transparent, and works in a similar fashion to the master-worker setup explained above, except all resource scheduling is handled by the cluster scheduler, and cryoSPARC's scheduler is only used for orchestration and management of jobs. Similar requirements are present:

Supported cluster schedulers

CryoSPARC supports most cluster schedulers, including SLURM, SGE and PBS. Please see here for example cluster configurations for popular schedulers.

cryoSPARC System Requirements

The following are requirements for every master and worker node in the system unless otherwise specified. The user account cryosparcuser is a service account for hosting the cryoSPARC master process and running cryoSPARC jobs on worker nodes. You can in fact use any user account or name (other than root) but we recommend the creation of a user account specifically to be the cryoSPARC service account.

A 10Gbps connection is recommended to the storage servers as raw cryo-EM movies can be several TB in size, and I/O bottlenecks may be more of a concern than processing power for pre-processing jobs in cryoSPARC. Also, even though a CPU with a higher core count is recommended, having a CPU with a faster clock rate would be more advantageous due to the way the master processes are built.

Worker Node/Cluster Worker Minimum Requirements

System RAM is very important for worker nodes, and should scale proportionately to the number of GPUs available for processing on the system. Fast local storage is also necessary as reconstruction jobs require random access to particle images. SSDs can provide high throughput in this context.

Disks and compression

Fast disks are a necessity for processing cryo-EM data efficiently. Fast sequential read/write throughput is needed during pre-processing stages (e.g., motion correction) where the volume of data is very large (tens of TB) while the amount of computation is relatively low (sequential processing for motion correction, CTF estimation, particle picking, etc.)

Spinning disk arrays in a RAID configuration are used to store large raw data files, and often cluster file systems are used for larger systems. As a rule of thumb, to saturate a 4-GPU machine during pre-processing, sustained sequential read of 1000MB/s is required.

Compression can greatly reduce the amount of data stored in movie files, and also greatly speeds up preprocessing because decompression is actually faster than reading uncompressed data straight from disk. Typically, counting-mode movie files are stored in LZW compressed TIFF format without gain correction, so that the gain reference file is stored separately and must be applied on-the-fly during processing (which is supported by cryoSPARC). Compressing gain corrected movies can often result in much worse compression ratios than compressing pre-gain corrected (integer count) data.

CryoSPARC supports LZW compressed TIFF format and BZ2 compressed MRC format natively. In either case, the gain reference must be supplied as an MRC file. Both TIFF and BZ2 compression are implemented as multi-core decompression streams on-the-fly.

Solid State Storage (SSDs)

SSD space is optional on a per-worker node basis, but is highly recommended for worker nodes that will be running refinements and reconstructions using particle images. Nodes reserved for pre-processing (motion correction, particle picking, CTF estimation, etc) do not need to have an SSD.

CryoSPARC particle processing algorithms rely on random-access patterns and multiple passes through the data, rather than sequentially reading the data at once. Using a storage medium that allows for fast random reads will speed up processing dramatically.

CryoSPARC manages the SSD cache on each worker node transparently. Files are automatically cached, re-used across the same project and deleted if more space is needed. Please see the SSD Caching tutorial for more information.​

Graphical Processing Units (GPUs)

At least one worker node must have GPUs available to be able to run the complete set of cryoSPARC jobs, but non-GPU workers can also be connected to run CPU-only jobs. The worker nodes connected to a cryoSPARC instance can be running different CUDA versions. This can be useful if machines with older GPUs (that require older versions of CUDA) are still being used. To keep installation simple, it's best to connect worker nodes that all use the same version of the CUDA Toolkit.

The GPU memory (VRAM) in each GPU limits the maximum particle box size able to be reconstructed. Typically, a GPU with 12GB VRAM can handle a box size of up to 700^3, and up to 1024^3 in some job types.

Notable GPUS

Browser Requirements

The cryoSPARC web interface works best on the latest version of Google Chrome. Firefox and Safari are also an option, although some features may not work as intended. Internet Explorer is not supported.

Additional Configuration Notes

Root Access

The cryoSPARC system is specifically designed not to require root access to install or use. The reason for this is to avoid security vulnerabilities that can occur when a network application (web interface, database, etc.,) is hosted as the root user. For this reason, the cryoSPARC system must be installed and run as a regular UNIX user (cryosparcuser), and all input and output file locations must be readable and writable as this user. In particular, this means that project input and output directories that are stored within a regular user's home directory need to be accessible by cryosparcuser, or else (more commonly) another location on a shared file system must be used for cryoSPARC project directories.

Multi-user environment

If you are installing the cryoSPARC system for use by a number of users (for example within a lab), there are two options:

Using UNIX Groups

Create a new regular user (cryosparcuser) and install and run cryoSPARC as this user. Create a cryoSPARC project directory (on a shared file system) where project data will be stored, and create sub-directories for each lab member. If extra security is necessary, use UNIX group privileges to make each sub-directory read/writeable only by cryosparcuser and the appropriate lab member's UNIX account. Within the cryoSPARC command-line interface, create a cryoSPARC user account for each lab member, and have each lab member create their projects within their respective project directories. This method relies on the cryoSPARC web application for security to limit each user to seeing only their own projects. This is not guaranteed security, and malicious users who try hard enough will be able to modify the system to be able to see the projects and results of other users.

Using Separate cryoSPARC Instances

If each user must be guaranteed complete isolation and security of their projects, each user must install cryoSPARC independently within their own home directories. Projects can be kept private within user home directories as well, using UNIX permissions. Multiple single-user cryoSPARC master processes can be run on the same master node, and they can all submit jobs to the same cluster scheduler system. This method relies on the UNIX system for security and is more tedious to manage but provides stronger access restrictions. Each user will need to have their own cryoSPARC license ID in this case.

Hardware Vendors and Example Systems

We do not currently partner with any specific hardware vendors to sell machines with cryoSPARC pre-installed, but if you email info@structura.bio we can point you to a number of vendors we have worked with and who offer compatible turnkey systems.

Example Hardware Systems

We have provided details for example workstations which meet or exceed the minimum requirements specified above, including those we use internally for development and testing.

The "medium" workstation example is a great starting point for processing cryo-EM data using cryoSPARC, whereas the "large" workstation example details an ideal hardware setup.