10x Genomics Support/Xenium Ranger/Downloads/

System Requirements

Xenium Ranger pipelines run on Linux systems that meet these minimum requirements:

  • 8-core Intel or AMD processor (32 cores recommended) with avx2
  • 64GB RAM (128GB recommended)
  • 1TB free disk space
  • 64-bit CentOS 7 and later/RedHat 7.4 or Ubuntu 16.04 and later; See the 10x Genomics OS Support page for details.

Running xeniumranger import-segmentation with the following tissue area and input data have higher minimum memory requirements:

Tissue areaInputMinimum memory
1cm2 dataset (e.g., full coronal mouse brain)Nucleus and cell label mask (e.g., from Cellpose)64GB RAM
Entire wellNucleus and cell label mask256GB RAM
Entire wellNucleus and cell boundary (e.g., GeoJSON from QuPath)128GB RAM

The pipeline can also run on clusters that meet these additional minimum requirements:

  • Shared filesystem (e.g. NFS)
  • Slurm batch scheduling system
  • Xenium Ranger runs with --jobmode=local by default, using 90% of available memory and all available cores. To restrict resource usage, please see the --localcores and --localmem arguments for xeniumranger subcommands.
  • Many Linux systems have default user limits (ulimits) for maximum open files and maximum user processes as low as 1024 or 4096. Because Xenium Ranger spawns multiple processes per core, jobs that use a large number of cores can exceed these limits. 10x Genomics recommends higher limits.
LimitRecommendation
user open files16k
system max files10k per GB RAM available to Xenium Ranger
user processes64 per core available to Xenium Ranger

There are three primary ways to run Xenium Ranger:

  1. Single server: Xenium Ranger can run directly on a dedicated server. This is the most straightforward approach and the easiest to troubleshoot. The majority of the information on this website uses the single server approach.
  2. Job submission mode: Xenium Ranger can run using a single node on the cluster. Less cluster coordination is required since all work is done on the same node. This method works well even with job schedulers that are not officially supported.
  3. Cluster mode: Xenium Ranger can run using multiple nodes on the cluster. This method provides high performance, but is difficult to troubleshoot since cluster setup varies among institutions.

Recommendations and requirements, in order of computational speed (left to right):

Cluster ModeJob Submission ModeSingle Server
Recommended forOrganizations using an HPC with SLURM for job schedulingOrganizations using an HPCUsers without access to an HPC
Compute detailsSplits each analysis across multiple compute nodes to decrease run timeRuns each analysis on a single compute nodeRuns each analysis directly on a dedicated server
RequirementsHPC with SLURM for job schedulingHPC with most job schedulersLinux computer with minimum 8 cores & 64 GB RAM (but see above)

These plots are based on time trials using Amazon EC2 instances and Xenium Ranger v1.6.0.

The plots will be updated for subsequent releases of Xenium Ranger if pipeline performance changes significantly.

Shown below is a xeniumranger resegment analysis with --expansion-distance=0 for a 140 FOV dataset:

  • Wall time as a function of memory
  • Wall time as a function of threads