Bridges-2 RM

Bridges-2 RM is the regular-memory, CPU-only tier of Bridges-2: 128-core nodes (dual AMD EPYC 7742) with 256 GB RAM, plus a 512 GB subset for memory-heavy work. It is well suited to large multi-node parallel jobs, and is often used for simulation and data-analysis workloads. Its software base is strongest in computational chemistry, molecular dynamics, and materials science, with additional support for bioinformatics and statistical computing.

Submitting Jobs Documentation

You can run jobs at different sizes and durations on Bridges-2 RM. 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. Unless you set otherwise, a job runs on one node with a one-hour walltime. Pick a queue by how much of a node you need:

  • RM: whole 256 GB nodes. Request the number of nodes with -N; each node gives you all 128 cores. Up to 64 nodes per job, 72-hour maximum walltime.
  • RM-shared: part of a single 256 GB node, shared with other jobs. Request up to 64 cores with --ntasks-per-node, and you are charged only for the cores you request. Each core comes with about 2 GB of memory, and a job cannot span nodes. Use RM-shared when you do not need a full node; it usually shortens your wait.
  • RM-512: like RM, but on the 15 larger 512 GB nodes for memory-intensive work. These are always allocated whole, up to 2 nodes per job, 72-hour maximum walltime.
  • RM-small: for interactive and small or quick jobs. Check its current limits with sinfo.

For submission commands, sample scripts, and node-sharing details, see the Bridges-2 Batch Jobs guide. Partition-specific information is on the Bridges-2 Regular Memory section of the user guide.

Queue specifications

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
RM
Jobs using one or more full 256 GB
2x AMD EPYC 7742 (128 cores) 484 256 GB 72h
RM wait time: average 19.2 hours, range 4 to 94.2 hours over 30 days
RM wall time: average 2.9 hours, range 0.3 to 6.5 hours over 30 days, wall-time limit 72h
34,373
RM-shared
Jobs using part of a single 256 GB node (up to 64 cores), sharing the node with other jobs.
2x AMD EPYC 7742 (128 cores) 396 256 GB 72h
RM-shared wait time: average 16.9 hours, range 3.3 to 45.1 hours over 30 days
RM-shared wall time: average 0.4 hours, range 0.2 to 1.5 hours over 30 days, wall-time limit 72h
2,244,661
RM-512
Jobs using one or more full 512 GB Regular Memory nodes for memory-intensive workloads; these nodes cannot be shared.
2x AMD EPYC 7742 (128 cores) 15 512 GB 72h
RM-512 wait time: average 28.9 hours, range 0 to 70.8 hours over 30 days
RM-512 wall time: average 12.7 hours, range 0 to 18.9 hours over 30 days, wall-time limit 72h
570
RM-small
Used for interactive and small/quick jobs
2x AMD EPYC 7742 (128 cores) 4 256 GB N/A
RM-small wait time: average 0.1 hours, range 0 to 0.5 hours over 30 days
RM-small wall time: average 0.8 hours, range 0.3 to 1.2 hours over 30 days
7,480

Software Documentation

The following software packages are among the most frequently used on Bridges-2 RM, 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 996,297
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 329,042
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 95,728
orca Orca is a flexible, efficient, and powerful quantum chemistry software written by Frank Neese and co-workers. It provides accurate and reliable computational simulations of molecular structures and properties based on quantum mechanical methods. Chemical Sciences 39,293
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 27,740
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 18,137
q-espresso Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. Condensed Matter Physics 17,573
ncbi-blast BLAST+ is a suite of programs designed to allow researchers to compare nucleotide or protein sequences to sequence databases and identify similarities. Genomics 9,236
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 8,578
abinit Abinit is a first-principles simulation software for materials science, condensed matter physics, and related fields. It performs electronic structure calculations based on density functional theory (DFT) and many-body perturbation theory. Physical Sciences 2,148

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