New User Resource Guide | Ohio Supercomputer Center

New User Resource Guide | Ohio Supercomputer Center
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Getting Started
New User Resource Guide
New User Resource Guide
Getting Started at OSC
This guide was created for new users of OSC.
It explains how to use OSC from the very beginning of the process, from creating an account right up to using resources at OSC.
OSC account setup
The first step is to make sure that you have an OSC username.
There are multiple ways to start this process.
You can sign up at
MyOSC
or be invited to use OSC via email.
Make sure to select the PI checkbox if you are a PI at your institution and want to start your own project at OSC.
After creating an account at MyOSC, you may not be able to log into OSC using OnDemand or an SSH client. If you do not have access to a project, you would get an "invalid credentials" message, although the credentials are correct. Sometimes OSC administrators need to approve your username if your institution is not recognized in our database.
Contact
OSC Help
with questions.
Email notifications from OSC
As soon as you register for an account with OSC, you will start receiving automated emails from MyOSC. These include password expiration emails, access to project(s), etc. These are sent from "
no-reply@osc.edu
."  All folders should be checked, including spam/junk. If you did not receive this email, please
contact OSC Help
OSC will also add you to our mailing list within a month of your account being opened. Emails will be sent from
oschelp@osc.edu
for system notices, monthly newsletters, event updates, etc. This information can also be found on our
events page
and
known issues page
Finally, we may notify clients through ServiceNow, our internal ticketing and monitoring system. These notices will come from the OH-TECH Service Desk,
support@oh-tech.org
Project and user management
Creating a project
Only users with PI status are able to create a project. See how to request PI status in
manage profile information
. Follow the instructions in
creating projects and budgets
to create a new project.
Adding new or existing users to a project
Once a project is created, the PI should add themselves to it and any others that they want to permit to use OSC resources under their project.
Refer to
adding/inviting users to a project
for details on how to do this.
Reuse an existing project
If there was already a project that you would like to reuse, follow the same instructions as found in
creating projects and budget
, but skip to the budget creation section.
These instructions are the same for projects which are restricted. Creating a new budget and getting it activated or approved will set the project to active.
Costs of OSC resources
If there are questions about the cost, refer to
service costs
Generally, an Ohio academic PI can create a budget for $1,000 on a project and use the annual $1,000 credit offered to Ohio academic PIs. Review
service cost terms
for explanations of budgets and credits at OSC.
See the complete MyOSC documentation in our Client Portal
here
. The
OSCusage command
can also provide useful details.
Classroom project support
OSC supports classrooms by making it simpler for students to use OSC resources through a customizable OnDemand interface at
class.osc.edu
Visit the
OSC classroom resource guide
and contact
oschelp@osc.edu
if you want to discuss the options there.
There will be no charges for classroom projects.
Transfer files to/from OSC systems
There are a few options for transferring files between OSC and other systems.
OnDemand file explorer
Using the OnDemand file explorer is the quickest option to get started. Just log into
ondemand.osc.edu
and click "File Explorer" from the navigation bar at the top of the page. From there you can upload/download files and directories.
Users cannot access ondemand.osc.edu unless they have an active OSC account and have been added to at least one project. Refer to the above sections which cover this.
This is a simple option, but for files or directories that are very large, it may not be best. See other options below in this case.
SFTP client software
Local software can be used to connect to OSC for downloading and uploading files.
There are quite a few options for this, and OSC does not have a preference for which one you use.
The general guidance for all of them is to connect to host sftp.osc.edu using port 22.
Globus
Using Globus is recommended for users that frequently need to transfer many large files/dirs.
We have documentation detailing
how to connect to our OSC endpoint in Globus
and
how to set up a local endpoint on your machine with Globus
Request extra storage for a project
Storage can be requested for a project that is larger than the standard offered by home directories.
On the project details page, submit a "Request Storage Change" and a ticket will be created for OSC staff to create the project space quota.
Make sure that the cost of storage is understood prior to sending the request.
See
service costs
for details.
Getting started using OSC
Finally, after the above setup, you can start using OSC resources. Usually you have some setup that needs to be performed before you can really start using OSC, like creating a custom environment, gaining access to preinstalled software or installing software to your home directory that is not already available.
Interactive desktop session
The best place to start is by visiting
ondemand.osc.edu
, logging in and starting an interactive desktop session.
Look for the navigation bar at the top of the page and select Interactive Apps, then choose a Desktop.
Notice that there are a lot of fields, but the most important ones, for now, are cores and the number of hours.
Try using only a single core at first, until you are more familiar with the system and can decide when more cores will be needed.
Other interactive apps
If there is specific software in the Interactive Apps list that you want to use, then go ahead and start a session with it. Just remember to change the cores to one until you understand what you need.
Getting to a terminal without starting a desktop session
A terminal session can also be started in OnDemand by clicking Clusters, then selecting a Shell Access.
In this terminal you can perform the needed commands in the below sections on environment setup and software use/installation.
You can choose to log into OSC with any ssh client available. Make sure to use either cardinal.osc.edu or pitzer.osc.edu as the hostname to connect to.
Environment setup to install packages for different programming languages
Some of the common programming languages for which users need an environment set up are python and R.
See add
python packages with conda
or
R software
for details.
There are other options, so please browse the
OSC software listing
OSC managed software
All the software already available at OSC can be found in the
software listing
Each page has some information on how to use the software from a command line. If you are unfamiliar with the command line in Linux, then try reviewing some
Linux tutorials
For now, try to get comfortable with moving to different directories on the filesystem, creating and editing files, and using the module commands from the software pages.
Install software not provided by OSC
Software not already installed on OSC systems can be installed locally to one's home directory without admin privileges. Try reviewing
locally installing software at OSC
This may be difficult for new users to accomplish; please contact
SC Help
with questions.
Batch system basics
After getting set up at OSC and understanding the use of interactive sessions, you should start looking into how to utilize the batch system to have your software run programmatically.
The benefits of the batch system are that a user can submit what we call a job (a request to reserve resources) and have the job execute from start to finish without any interaction by the user.
A good place to start is by reviewing
job scripts
OnDemand job composer
OnDemand provides a convenient method for editing and submitting jobs in the job composer.
It can be used by logging into ondemand.osc.edu and clicking Jobs at the top and then Job Composer. A short help message should be shown on basic usage.
Training
OSC offers periodic training both at our facility and at universities across the state on a variety of topics. Additionally, we will partner with other organizations to enable our users to access additional training resources.
We are currently in the process of
updating our training strategy and documents
. If you are interested in having us come to your campus to provide training, please
contact OSC Help
. You can also contact us if there is a specific training need you would like to see us address.
To get an introduction to HPC, see our
HPC Basics page
To learn more about using the command line, see our
UNIX Basics page
For detailed instructions on how to perform tasks on our systems, check out
HOWTO articles
Still Need Help?
Before contacting OSC Help, please check to see if your question is answered in either the
FAQ
or the
Knowledge Base
. Many of the questions asked by both new and experienced OSC users are answered on these web pages.
If you still cannot solve your problem, please do not hesitate to contact OSC Help:
Phone:
(614) 292-1800
Email:
oschelp@osc.edu
Submit your issue online
Schedule virtual consultation
Basic and advanced support is available Monday through Friday, 9 a.m.– 5 p.m.,
except for these listed holidays
We recommend following
HPCNotices on X
to get up-to-the-minute information on system outages and important operations-related updates.
Documentation Attachment:
OSC New User Training Slides
Supercomputer:
Pitzer
‹ Getting Started
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HPC Basics ›
Client Resources
Getting Started
New User Resource Guide
HPC Basics
Getting Connected
Budgets and Accounts
Applying for Academic Accounts
UNIX Basics
Linux Command Line Fundamentals
Linux Tutorial
Tar Tutorial
Unix Shortcuts
Classroom Project Resource Guide
Classroom Guide for Students
Using Jupyter for Classroom
Using Rstudio for classroom
Using nbgrader for Classroom
HOWTO
Using Software on Pitzer RHEL 7
HOW TO: Look at requested time accuracy using XDMoD
HOWTO: Add and Use DUO MFA
HOWTO: Collect performance data for your program
HOWTO: Create and Manage Python Environments
HOWTO: Install Tensorflow locally
HOWTO: Install Python packages from source
HOWTO: Use GPU with Tensorflow and PyTorch
HOWTO: Debugging Tips
HOWTO: Establish durable SSH connections
HOWTO: Estimating and Profiling GPU Memory Usage for Generative AI
HOWTO: Identify users on a project account and check status
HOWTO: Install a MATLAB toolbox
HOWTO: Install your own Perl modules
HOWTO: Locally Installing Software
HOWTO: Manage Access Control List (ACLs)
HOWTO: Use NFSv4 ACL
HOWTO: Use POSIX ACL
HOWTO: PyTorch Distributed Data Parallel (DDP)
HOWTO: PyTorch Fully Sharded Data Parallel (FSDP2)
HOWTO: Reduce Disk Space Usage
HOWTO: Reduce GPU memory usage during ANN training and inference
HOWTO: Run Python in Parallel
HOWTO: Submit Homework to Repository at OSC
HOWTO: Submit multiple jobs using parameters
HOWTO: Tune Performance
HOWTO: Tune VASP Memory Usage
HOWTO: Use 'rclone' to Upload Data
HOWTO: Use 'rclone' to Upload Data from Google Drive
HOWTO: Use Address Sanitizer
HOWTO: Use Cron and OSCusage for Regular Emailed Reports
HOWTO: Use Docker and Singularity Containers at OSC
HOWTO: Use Extensions with JupyterLab
HOWTO: Use GPU in Python
HOWTO: Use Globus (Overview)
HOWTO: Use AWS S3 in Globus
HOWTO: Use OneDrive in Globus
HOWTO: Deploy your own endpoint on a server
HOWTO: Use Jupyter on OnDemand
HOWTO: Use VNC in a batch job
HOWTO: Use a Conda/Virtual Environment With Jupyter
HOWTO: Use an Externally Hosted License
HOWTO: Use ulimit command to set soft limits
HOWTO: Using MLFlow to track ML training and models
HOWTO: test data transfer speed
Citation
New User Training
OSC Custom Commands
OSCfinger
OSCgetent
OSCprojects
OSCusage
gpu-seff
osc-seff
OSC User Code of Ethics
Supercomputing FAQ
Supercomputing Terms
Available Software
Browse Software
Community Software
License Server Status
OnDemand Application List
Scientific Database List
BLAST Database
Software List
Abaqus
AFNI
AMBER
ANSYS
ANSYS Mechanical
CFX
FLUENT
Workbench Platform
AlphaFold 3
AlphaFold
Altair HyperWorks
Apptainer
AutoDock
BCFtools
BLAS
BLAST
BWA
Blender
Boost
Bowtie
Bowtie2
CMake
COMSOL
Interactive Parallel COMSOL Job
CP2K
CUDA
Cell Ranger
Code Server
ComfyUI
Connectome Workbench
Cufflinks
DS9
DSI Studio
Darshan
Desmond
FFTW
FSL
FastQC
FreeSurfer
GAMESS
GATK
GNU Compilers
GROMACS
GSL
Gaussian
Git
Gurobi
HDF5
HDF5-Serial
HISAT2
HPC Toolkit
HTSlib
IQmol
Intel Compilers
Intel MPI (Old)
Intel MPI
Intel Math Kernel Library
Java
Julia
LAMMPS
LAPACK
LS-DYNA
LS-OPT
LS-PrePost
User-Defined Material for LS-DYNA
Linaro HPC tools
Linaro Performance Reports
Linaro MAP
Linaro DDT
MATLAB
SPM
MRIQC
MRIcroGL
MVAPICH
MVAPICH2
Mathematica
Miniconda3
NAMD
NCCL
NVHPC
NWChem
Ncview
NetCDF
Neuropointillist
Nextflow
Nodejs
ORCA
Ollama
OpenACC
OpenAI Python
OpenCV
OpenFOAM
OpenMP
OpenMPI
ParaView
Parallel-netCDF
Perl
Picard
Podman
PyMOL
PyTorch
Python
Q-Chem
QGIS
Quantum ESPRESSO
R and Rstudio
RELION
Rosetta
Ruby
Rust
SAMtools
SRA Toolkit
STAR
STAR-CCM+
Run STAR-CCM+ to STAR-CCM+ Coupling
Schrodinger
Scipion
SnpEff
Spark
Stata
Subread
Texlive
Tinker
Trimmomatic
Trinity
TurboVNC
VASP
VCFtools
VMD
VirtualGL
VisIt
WARP3D
WCStools
XFdtd
aocc
bedtools
dcm2nii
fMRIPrep
ffmpeg
oneAPI
parallel-command-processor
vLLM
Software Refresh
Updates to Oakley Application Software - September 2015
Updates to Ruby Application Software - September 2015
Software Refresh - February 2017
Software Refresh - August/September 2018
Software Refresh - May 2020
Statewide Software Licensing
Statewide Software-Altair
Storage Documentation
Technical Support
HPC Changelog
MVAPICH2 version 2.3 modules modified on Owens
Known issues
Search Documentation
Supercomputers
Ascend
Ascend Programming Environment
Ascend Software Environment
Batch Limit Rules
Citation
Available software list on Next Gen Ascend
OSU College of Medicine Compute Service
SSH key fingerprints
Technical Specifications
Cardinal
Technical Specifications
Cardinal Programming Environment
Cardinal Software Environment
Citation
Batch Limit Rules
Cardinal SSH key fingerprints
Migrating jobs from other clusters
Pitzer
Technical Specifications
Pitzer Programming Environment
Pitzer Software Environment
Batch Limit Rules
Citation
Pitzer SSH key fingerprints
Guidance After Pitzer Upgrade to RHEL9
Guidance on Requesting Resources on Pitzer
GPU Computing
High Bandwidth Memory
Tutorials & Training
Seminar: What can OSC do for you? Services for Faculty Research and Teaching
Batch Processing at OSC
Batch System Concepts
Batch Execution Environment
Job Scripts
Job Submission
Monitoring and Managing Your Job
Scheduling Policies and Limits
Slurm Directives Summary
Batch Environment Variable Summary
Batch-Related Command Summary
License software flag usage information
Messages from sbatch
Troubleshooting Batch Problems
batch email notifications
Slurm Migration
How to Prepare Slurm Job Scripts
How to Submit, Monitor and Manage Jobs
Steps on How to Submit Jobs
Slurm Migration Issues
Knowledge Base
Account Consolidation Guide
Community Accounts
Compilation Guide
Firewall and Proxy Settings
Job and storage charging
Out-of-Memory (OOM) or Excessive Memory Usage
Thread Usage Best Practices
XDMoD Tool
Job Viewer
XDMoD - Checking Job Efficiency
Gateways
Client Portal
Self-Signup for Accounts
Change or Reset Password and Retrieve Usernames
Adding grant information
Check usage costs for current fiscal year
Invite, add, remove users
Limiting charges with budgets
Manage profile information
Multi-factor authentication
Project review and special properties
Projects, budgets and charge accounts
billing statements
HPC Job Activity tool
Interactive Reporting
OnDemand
File Transfer and Management
Job Management
Facilitation
Data Storage
Overview of File Systems
Storage Hardware
2016 Storage Service Upgrades
2020 Storage Service Upgrades
2022 Storage Service Upgrades
Protected Data Service
Manage the protected data and its access
Securely transferring files to protected data location
Security, Accessibility, and Policies
Proposed OSC Policies for Public Comments
Service Costs
FY26 budgets: Action may be required
Service Terms
Upcoming Events
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