Bridges-2 EM

Bridges-2 EM is the extreme-memory tier of Bridges-2: 4 nodes with 96 cores each (four Intel Xeon Platinum 8260M) and up to 4 TB of RAM. It suits problems that need very large shared memory and cannot be split across nodes, and is often used for genome sequence assembly, graph analytics, and large in-memory statistics. Its software base is strongest in memory-bound genomics and statistical or data-analysis work.

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Submitting Jobs Documentation

You can run jobs at different sizes and durations on Bridges-2 EM. The following lists the different queues that you can submit to, describing how many nodes you get, how long you can run, the type of resources you get, and the average wait time.

Jobs are submitted through Slurm in batch mode. EM does not support interactive jobs or OnDemand, so connect over SSH and submit from a Bridges-2 login node with sbatch. A job uses at most one EM node, and you request cores in multiples of 24 (24, 48, 72, or 96); memory scales with the cores you request, at about 1 TB per 24 cores. The default walltime is 1 hour and the maximum is 120 hours.

For submission commands, a sample batch script, and more detail, see the [Bridges-2 Extreme Memory] section of the user guide, or the [Bridges-2 Batch Jobs] guide.

Queue specifications Documentation

Metrics updated 2026-09-29

Queue CPU cores / node Num nodes Node RAM Max wallclock Wait time
30-day trend
 Wall time
30-day trend
 Number of jobs run
30 days
EM
Extreme Memory jobs requiring very large shared memory. Designed for applications that require terabytes of memory and cannot use distributed-memory approaches.
 4x Intel Xeon Platinum 8260M (96 cores) 4 4 TB 120h
EM wait time: average 3.4 hours, range 0 to 14 hours over 30 days
EM wall time: average 4.4 hours, range 0.2 to 24 hours over 30 days, wall-time limit 120h
402

Software Documentation

The following software packages are among the most frequently used on Bridges-2 EM, based on job data from XDMoD.

Most Frequently Used

Application Description Research Discipline Jobs
python Python is a high-level, interpreted programming language known for its simplicity and readability. It supports multiple programming paradigms and has a vast ecosystem of libraries and frameworks. Computer & Information Sciences, Software Engineering, Systems & Development 412
r R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows, and MacOS. Computer Science 39
q-espresso Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. Condensed Matter Physics 18
lammps LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics code designed for simulating large-scale atomistic systems. It is highly versatile and can be used to model a wide range of materials and complex molecular structures. Chemical Sciences 8
dl_poly 7
cp2k CP2K is an open-source quantum chemistry and solid state physics software package designed to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It can be used to study a wide range of properties, including electronic structures, molecular dynamics, and vibrational spectra. Physical Sciences 6
samtools Samtools is a suite of programs for interacting with high-throughput sequencing data generated in sequence alignment/map (SAM) format, such as those produced by the Short Read Mapping (SHRiMP) or Burrows-Wheeler Aligner (BWA) aligners. It allows various operations on SAM/BAM files, including indexing, sorting, merging, and manipulating sequence alignments. Biological Sciences 6
gromacs GROMACS (GROningen MAssive Parallel MD for Molecular Dynamics) is a versatile package for molecular dynamics simulations with a strong emphasis on high-performance computing capabilities. Biological Sciences 5

SEE ALL SOFTWARE AVAILABLE ON BRIDGES-2 EM

Storage Documentation

Bridges-2 has two persistent spaces: a small Home for code and configuration, and the Ocean project space for active data and results. There is no separate scratch tier; node-local disk and RAM disk last only for the duration of a job. Ocean is shared across all of Bridges-2. See the File Spaces section of the user guide for more information.

File System

Directory Path Quota Purge Backup Notes
Home $HOME 25 GB Purged 3 months after allocation expires Backed up daily
Projects $PROJECT See notes Purged 3 months after allocation expires Not backed up Quota size depends on allocation
Node-local $LOCAL See notes Purged at job end Not backed up Quota varies by node type
Node memory $RAMDISK See notes Purged at job end Not backed up Quota varies by node type

File Transfer Documentation

Globus is recommended for large or many-file transfers, since it retries and resumes automatically. Use rsync, scp, or sftp for command-line transfers. Run all transfers through the Data Transfer Node (data.bridges2.psc.edu), not the login nodes.

For more information, please visit the Transferring Files section of the user guide.

Supported Methods Data Transfer Node / Globus Collection Notes
GLOBUS | RECOMMENDED PSC Bridges-2 /ocean and /jet filesystems https://app.globus.org
RSYNC data.bridges2.psc.edu
SCP data.bridges2.psc.edu
SFTP data.bridges2.psc.edu

Datasets Documentation

Name Description
2019nCoVR

COVID-19 genomic surveillance data and metadata (hosted by NGDC).

2019nCoVR Webpage
AlphaFold

Predicted protein structures for the human proteome and other key proteins.

AlphaFold Webpage
Path in Bridges-2: /ocean/datasets/community/alphafold
CIFAR-10

60,000 labeled images across 10 classes; standard image-classification benchmark.

CIFAR-10 Webpage

Path in Bridges-2: /ocean/datasets/community/cifar
COCO

Large-scale image dataset for object detection, segmentation, and captioning.

COCO Dataset Webpage
Path in Bridges-2: /ocean/datasets/community/COCO
CosmoFlow

~10,000 cosmological dark-matter simulations. Access requires a request via the CosmoFlow request form.

CosmoFlow Webpage
Path in Bridges-2: /ocean/datasets/community/cosmoflow
ImageNet

Image dataset organized by WordNet hierarchy.

ImageNet Webpage
Path in Bridges-2: /ocean/datasets/community/imagenet
MNIST

Classic handwritten-digit dataset for image-processing benchmarks.

Path in Bridges-2: /ocean/datasets/community/mnist
Natural Language Tool Kit Data

Corpora, grammars, and trained models for NLP.

NLTK Data Webpage
Path in Bridges-2: /ocean/datasets/community/nltk
OpenWebText

Path in Bridges-2: /ocean/datasets/community/openwebtext
PREVENT-AD

Longitudinal multimodal data from cognitively healthy older adults at risk for Alzheimer's, from two prevention trials.

Path in Bridges-2: /ocean/datasets/community/prevent_ad
TCGA Images

Path in Bridges-2: /ocean/datasets/community/tcga_images
Genomics datasets

These datasets are available to anyone with an allocation on Bridges-2. They are stored under /ocean/datasets/community/genomics.

AUGUSTUS, BLAST, CheckM, Dammit, Homer, Kraken2, Pfam, Prokka, Repbase