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Docs pages organized by tag.
- (2024-06-19) Lab Notebook: LM Studio Installation
- (2025-05-13) Lab Notebook: AI Models Available on the HPCC
- (2025-08-19) Lab Notebook: LLM Embeddings
- LM Studio
- OpenWebUI
- (2023-07-18) Lab Notebook: AlphaFold 2.3.1 DEPRECATED
- (2023-11-10) Lab Notebook: AlphaFold 2.3.2 WorkInProgress
- AlphaFold on HPCC
- AlphaFold via Singularity
- AlphaFold3
- (2024-08-28) Lab Notebook: cuQuantum Installation and Usage
- (2024-09-17) Lab Notebook: Common Machine Learning Tools on OnDemand
- (2022-06-27) Lab Notebook: AntiSMASH installation with Conda
- (2022-09-20) Lab Notebook: PyMesh installation with Conda
- (2022-09-24) Lab Notebook: Singularity Overlays
- (2022-10-03) Lab Notebook: Bactopia installation with Conda and Mamba
- (2022-10-08) Lab Notebook: Praat installation and execution using Singularity Overlays on CentOS8
- (2022-10-19) Lab Notebook: OpenVDB installation with Conda
- (2022-10-19) Lab Notebook: TractSeg installation with Conda
- (2022-12-20) Lab Notebook: Conda --- Cleaning out your cache on HPCC
- (2024-08-28) Lab Notebook: cuQuantum Installation and Usage
- (2024-09-16) Lab Notebook: PyTorch OnDemand Usage
- (2024-09-17) Lab Notebook: Common Machine Learning Tools on OnDemand
- (2024-09-25) Lab Notebook: Transitioning from Anaconda to Miniforge
- Installing Pytorch with pip
- Installing Software on the HPCC
- Installing Tensorflow
- Package management
- Replacing an existing Conda installation
- Using Conda
- Using Conda in a research space
- Checkpointing with DMTCP
- Checkpointing with DMTCP in batch jobs
- Template for a General Purpose Checkpointing Script
- (2023-02-07) Lab Notebook: WRF installation with EasyBuild
- (2023-05-18) Lab Notebook: EasyBuild PostgreSQL Installation
- EasyBuild reference
- EasyBuild tutorial
- Installing Software on the HPCC
- (2026-09-15) Lab Notebook: GPU Scheduling
- Compiling for GPUs
- GPU programming tools
- GPU resources
- Requesting GPUs
- Tensorflow GPU usage
- (2023-08-30) Lab Notebooks: Incident Report on System Slowdown due to I/O
- Guidelines for choosing file systems and I/O
- (2023-06-30) Lab Notebooks: Jupyter --- Port-Forwarding Servers
- (2023-08-11) Lab Notebooks: Jupyter and MobaXterm--- Port-Forwarding Servers
- Jupyter
- Jupyter Notebooks in VS Code
- Loading modules in a Jupyter notebook
- Python on HPCC
- (2025-01-13) Lab Notebook: How to use LLMs on the HPCC
- (2025-01-31) Lab Notebook: How to run RAG on the HPCC
- (2025-02-07) Lab Notebook: Load Custom Models in Ollama
- (2025-03-05) Lab Notebook: Update: How to run RAG in OpenWebUI
- (2025-05-13) Lab Notebook: AI Models Available on the HPCC
- (2025-08-19) Lab Notebook: LLM Embeddings
- LM Studio
- OpenWebUI
- (2023-04-04) Lab Notebook: OnDemand RunningMPIJobs
- (2026-01-13) Lab Notebook: Using OpenMPI versions >= 5.0.0 with srun
- (2022-10-04) Lab Notebook: OnDemand --- Unable to click icons on the Interactive Desktop
- (2022-10-08) Lab Notebook: Praat installation and execution using Singularity Overlays on CentOS8
- (2022-10-10) Lab Notebook: OnDemand Interactive Desktop Error
- (2022-12-07) Lab Notebook: OnDemand --- Bad Request from browser
- (2023-04-04) Lab Notebook: OnDemand RunningMPIJobs
- (2024-07-01) Lab Notebook: NewOS and OnDemand Workarounds
- (2024-08-07) Lab Notebook: RStudio Server Shows Blank or Gray Screen
- (2026-09-15) Lab Notebook: GPU Scheduling
- Code Server
- File transfer
- Interactive Desktop
- Jupyter
- LM Studio
- MATLAB
- OpenWebUI
- ParaView
- Quick start - Login to HPCC via Web portal
- RStudio Server
- STATA
- Tensorboard
- (2024-09-16) Lab Notebook: PyTorch OnDemand Usage
- (2024-09-17) Lab Notebook: Common Machine Learning Tools on OnDemand
- Installing Pytorch with pip
- (2023-07-13) Lab Notebook: Ignoring Local Python Libraries
- (2024-08-28) Lab Notebook: cuQuantum Installation and Usage
- (2024-09-16) Lab Notebook: PyTorch OnDemand Usage
- (2024-09-17) Lab Notebook: Common Machine Learning Tools on OnDemand
- (2024-09-25) Lab Notebook: Transitioning from Anaconda to Miniforge
- BLAS and FlexiBLAS
- Jupyter
- Loading modules in a Jupyter notebook
- Package management
- Python on HPCC
- Replacing an existing Conda installation
- Using Conda
- Using Conda in a research space
- Using virtual environments
- (2023-05-18) Lab Notebook: EasyBuild PostgreSQL Installation
- (2024-08-07) Lab Notebook: RStudio Server Shows Blank or Gray Screen
- (2024-08-07) Lab Notebook: Running ggplot in R without X11
- BLAS and FlexiBLAS
- Getting started
- R workshop tutorial
- RStudio Server
- Some packages and other information
- (2022-09-28) Lab Notebook: HPCC via RStudio and GitHub
- (2024-08-07) Lab Notebook: RStudio Server Shows Blank or Gray Screen
- RStudio Server
- (2022-09-23) Lab Notebook: Singularity --- Using an alternate OS
- (2022-09-24) Lab Notebook: Singularity Overlays
- (2022-10-08) Lab Notebook: Praat installation and execution using Singularity Overlays on CentOS8
- (2023-07-13) Lab Notebook: Ignoring Local Python Libraries
- (2023-07-18) Lab Notebook: AlphaFold 2.3.1 DEPRECATED
- (2023-11-03) Lab Notebook: Connecting to a Singularity container with VS Code
- (2023-11-10) Lab Notebook: AlphaFold 2.3.2 WorkInProgress
- AlphaFold via Singularity
- Containers (Singularity and Docker)
- Singularity Advanced Topics
- Singularity Introduction
- Singularity Overlays
- (2024-09-17) Lab Notebook: Common Machine Learning Tools on OnDemand
- Installing Tensorflow
- Some packages and other information
- Submitting a Tensorflow job
- Tensorflow GPU usage
- Tensorflow Model Training Code Examples
- (2023-11-03) Lab Notebook: Connecting to a Singularity container with VS Code
- (2024-09-05) Lab Notebook: Setting up a terminal with VS Code to connect to the HPCC
- Jupyter Notebooks in VS Code
- SSH connection via VS Code
- (2023-11-03) Lab Notebook: Connecting to a Singularity container with VS Code
- (2024-09-05) Lab Notebook: Setting up a terminal with VS Code to connect to the HPCC
- Jupyter Notebooks in VS Code
- SSH connection via VS Code
- Acceptable Use Policy and Guidelines
- Buy-in and account management
- Find My Account Sponsor
- Obtaining an HPCC account
- Obtaining and Managing HPCC accounts
- OnDemand Could Not Find User Account
- (2025-05-14) Scavenger Queue and Checkpointing
- Checkpointing jobs
- Checkpointing overview
- Checkpointing with DMTCP
- Checkpointing with DMTCP in batch jobs
- Powertools `longjob` by DMTCP
- Template for a General Purpose Checkpointing Script
- Compilers and Libraries
- Compiling for GPUs
- Optimizing for AMD CPUs
- Targeting Cluster Architectures
- Using different cluster architectures
- make
- Containers (Singularity and Docker)
- Docker
- Singularity Advanced Topics
- Singularity Introduction
- Singularity Overlays
- (2022-12-07) Lab Notebook: OnDemand --- Bad Request from browser
- (2025-09-11) Data Display Debugger
- TotalView
- Acceptable Use Policy and Guidelines
- BLAS and FlexiBLAS
- Checkpointing jobs
- Checkpointing overview
- Containers (Singularity and Docker)
- Data Machine overview
- File backups
- File permissions
- Getting started
- HPCC layout
- High Speed Research Network
- Home space
- Maintenance
- Migrating from Torque
- Python on HPCC
- Research space
- SLURM overview
- Scratch space
- Singularity Advanced Topics
- Site and service accessibility
- Using different cluster architectures
- Using parallel file systems
- (2023-02-09) Lab Notebooks: Rclone --- Example of copying folder from HPCC to MSU OneDrive
- (2024-01-13) Lab Notebook: Sharing directories with other HPCC users
- File backups
- File count
- File permissions
- Guidelines for choosing file systems and I/O
- Home space
- Managing file permissions
- Research space
- Scratch space
- Sensitive data storage
- Using parallel file systems
- (2022-09-28) Lab Notebook: HPCC via RStudio and GitHub
- (2023-11-21) Lab Notebook: Git in Research Spaces
- High Speed Research Network
- Transferring data with Globus
- Transferring data with Google using Globus
- Transferring data with OneDrive using Globus
- ABySS
- ANSYS
- Application Icons on Desktop
- Aspera bulk file transfer
- Buy-in and account management
- COMSOL
- CentOS Backwards compatibility container
- Change primary group
- Cloud storage file transfer
- Connections to compute nodes
- Controlling jobs
- Editing text with nano
- File transfer
- Find My Account Sponsor
- How to connect to HPCC using an SSH client
- Installing Pytorch with pip
- Installing Tensorflow
- Intro to MobaXterm
- Jupyter Notebooks in VS Code
- Managing file permissions
- NVIDIA Grace nodes
- OrthoMCL: load module
- Replacing an existing Conda installation
- Resetting SSH Host Keys
- Running multiple jobs sequentially
- SLURM resource request guide
- SSH connection via VS Code
- SSH key based authentication
- SSH tunneling to directly access development nodes
- Scavenger Queue
- Singularity Overlays
- Stata
- Submitting Multiple Jobs Simultaneously
- Submitting a Tensorflow job
- Tensorflow Model Training Code Examples
- TotalView
- Transferring data with Globus
- Trimmomatic
- Trinity for RNA-seq de novo assembly
- Using Conda
- Using Conda in a research space
- Virtual Terminals
- elbencho
- (2022-10-04) Lab Notebook: OnDemand --- Unable to click icons on the Interactive Desktop
- Application Icons on Desktop
- Interactive Desktop
- Example job scripts
- Job constraints
- List of job specifications
- SLURM environment variables
- Writing and submitting job scripts
- (2022-06-27) Lab Notebook: AntiSMASH installation with Conda
- (2022-09-20) Lab Notebook: PyMesh installation with Conda
- (2022-09-21) Lab Notebook: VisIt on HPCC
- (2022-09-23) Lab Notebook: Singularity --- Using an alternate OS
- (2022-09-24) Lab Notebook: Singularity Overlays
- (2022-09-28) Lab Notebook: HPCC via RStudio and GitHub
- (2022-09-30) Lab Notebook: ROS on HPCC
- (2022-10-03) Lab Notebook: Bactopia installation with Conda and Mamba
- (2022-10-04) Lab Notebook: OnDemand --- Unable to click icons on the Interactive Desktop
- (2022-10-08) Lab Notebook: Praat installation and execution using Singularity Overlays on CentOS8
- (2022-10-10) Lab Notebook: OnDemand Interactive Desktop Error
- (2022-10-19) Lab Notebook: OpenVDB installation with Conda
- (2022-10-19) Lab Notebook: TractSeg installation with Conda
- (2022-10-27) Lab Notebook: SFTP Mapping on HPCC File Systems
- (2022-12-07) Lab Notebook: OnDemand --- Bad Request from browser
- (2022-12-20) Lab Notebook: Conda --- Cleaning out your cache on HPCC
- (2022-12-20) Lab Notebook: SSHFS mapping on Windows
- (2023-02-07) Lab Notebook: NAMD --- Running on Multiple Nodes
- (2023-02-07) Lab Notebook: WRF installation with EasyBuild
- (2023-02-09) Lab Notebooks: Rclone --- Example of copying folder from HPCC to MSU OneDrive
- (2023-02-16) Lab Notebook: CryoSPARC Installation on HPCC
- (2023-02-27) Lab Notebook: HRLDAS
- (2023-03-14) Lab Notebook: CRYSTAL23 --- Parallel submission script on the MSU HPCC
- (2023-03-14) Lab Notebook: VASP
- (2023-03-27) Lab Notebook: Mathematica --- Fixing Startup Errors
- (2023-04-04) Lab Notebook: OnDemand RunningMPIJobs
- (2023-05-04) Lab Notebook: Changes to srun for jobs with multiple CPUs per task
- (2023-05-18) Lab Notebook: EasyBuild PostgreSQL Installation
- (2023-06-30) Lab Notebooks: Jupyter --- Port-Forwarding Servers
- (2023-07-13) Lab Notebook: Ignoring Local Python Libraries
- (2023-07-18) Lab Notebook: AlphaFold 2.3.1 DEPRECATED
- (2023-07-18) Lab Notebook: MATLAB offload from localPC to HPCC
- (2023-08-02) Lab Notebook: Alternative Linux Shells on HPCC
- (2023-08-11) Lab Notebooks: Jupyter and MobaXterm--- Port-Forwarding Servers
- (2023-08-30) Lab Notebooks: Incident Report on System Slowdown due to I/O
- (2023-09-21) Lab Notebooks: Example home directory software install (with links to videos)
- (2023-11-03) Lab Notebook: Connecting to a Singularity container with VS Code
- (2023-11-09) Lab Notebook: Molpro Parallel
- (2023-11-10) Lab Notebook: AlphaFold 2.3.2 WorkInProgress
- (2023-11-21) Lab Notebook: Git in Research Spaces
- (2024-01-13) Lab Notebook: Sharing directories with other HPCC users
- (2024-06-13) Lab Notebook: CTSM Installation
- (2024-06-19) Lab Notebook: LM Studio Installation
- (2024-07-01) Lab Notebook: NewOS and OnDemand Workarounds
- (2024-08-07) Lab Notebook: RStudio Server Shows Blank or Gray Screen
- (2024-08-07) Lab Notebook: Running ggplot in R without X11
- (2024-08-28) Lab Notebook: Change to modules in SLURM jobs
- (2024-08-28) Lab Notebook: cuQuantum Installation and Usage
- (2024-09-05) Lab Notebook: Setting up a terminal with VS Code to connect to the HPCC
- (2024-09-16) Lab Notebook: PyTorch OnDemand Usage
- (2024-09-17) Lab Notebook: Common Machine Learning Tools on OnDemand
- (2024-09-24) Lab Notebook: Ollama Module
- (2024-09-25) Lab Notebook: Transitioning from Anaconda to Miniforge
- (2024-10-01) Lab Notebook: New ICER User Database Testing Requested (ColdFront)
- (2024-10-23) Lab Notebook: Architecture specific compilation
- (2025-01-13) Lab Notebook: How to use LLMs on the HPCC
- (2025-01-31) Lab Notebook: How to run RAG on the HPCC
- (2025-02-07) Lab Notebook: Load Custom Models in Ollama
- (2025-02-14) Lab Notebook: Beta Access to amd24 Cluster
- (2025-03-05) Lab Notebook: Update: How to run RAG in OpenWebUI
- (2025-05-13) Lab Notebook: AI Models Available on the HPCC
- (2025-05-14) Scavenger Queue and Checkpointing
- (2025-05-14) Using AFNI Graphical User Interface
- (2025-08-06) Installing r8s on HPCC
- (2025-08-19) Lab Notebook: LLM Embeddings
- (2025-09-11) Data Display Debugger
- (2026-01-13) Lab Notebook: Using OpenMPI versions >= 5.0.0 with srun
- (2026-09-15) Lab Notebook: GPU Scheduling
- Lab Notebooks
- (2024-08-28) Lab Notebook: Change to modules in SLURM jobs
- (2024-09-24) Lab Notebook: Ollama Module
- Installing Software on the HPCC
- Loading modules in a Jupyter notebook
- User created modules
- (2023-02-09) Lab Notebooks: Rclone --- Example of copying folder from HPCC to MSU OneDrive
- Cloud storage file transfer
- AMD CPUs
- Acknowledging ICER
- Basics of parallel computing
- Classroom support
- Cluster resources
- Code Server
- Compilers and Libraries
- Compiling for GPUs
- Development nodes
- EasyBuild reference
- Example job scripts
- External Resources
- FAQ
- File count
- GPU programming tools
- GPU resources
- Gaussian access
- Gaussian workshop slides
- Get software usage examples
- Glossary
- Guidelines for choosing file systems and I/O
- HTSeq
- How jobs are scheduled
- Install an SSH client
- Installing Software on the HPCC
- Interactive Desktop
- Interactive jobs
- Job constraints
- Job policies
- Jupyter
- LM Studio
- Linux shells
- List jobs using squeue and sview
- List of job specifications
- Local file system
- MATLAB
- Module changelog
- NCBI eDirect
- Office hours
- OpenWebUI
- Optimizing for AMD CPUs
- Other Computing Resources (NSF ACCESS)
- Other Computing Resources at MSU
- Overview of HPCC file systems
- Package management
- ParaView
- Powertools Listing
- Powertools overview
- Quick start - Login to HPCC via Web portal
- RNA-seq
- RStudio Server
- Requesting GPUs
- SLURM - buyin information
- SLURM - display job list
- SLURM - display job steps and their resource usages
- SLURM - node status and job partition
- SLURM commands
- SLURM environment variables
- SLURM queueing and partitions
- STATA
- Searching software modules
- Sensitive data storage
- Submitting a help ticket
- Targeting Cluster Architectures
- Template for a General Purpose Checkpointing Script
- Tensorboard
- User created modules
- Using the Data Machine
- Workshop materials
- (2023-05-04) Lab Notebook: Changes to srun for jobs with multiple CPUs per task
- (2024-08-28) Lab Notebook: Change to modules in SLURM jobs
- (2026-01-13) Lab Notebook: Using OpenMPI versions >= 5.0.0 with srun
- ABySS
- Controlling jobs
- Example job scripts
- HPCC Job Submission Workflow
- How jobs are scheduled
- Interactive jobs
- Job constraints
- Job policies
- List of job specifications
- Migrating from Torque
- Running multiple jobs sequentially
- SLURM commands
- SLURM environment variables
- SLURM overview
- SLURM resource request guide
- Scavenger Queue
- Showing job steps
- Submitting Multiple Jobs Simultaneously
- Submitting a Tensorflow job
- Writing and submitting job scripts
- (2023-09-21) Lab Notebooks: Example home directory software install (with links to videos)
- Module changelog
- Using different cluster architectures
- (2023-05-04) Lab Notebook: Changes to srun for jobs with multiple CPUs per task
- (2026-01-13) Lab Notebook: Using OpenMPI versions >= 5.0.0 with srun
- Showing job steps
- (2023-06-30) Lab Notebooks: Jupyter --- Port-Forwarding Servers
- (2023-08-11) Lab Notebooks: Jupyter and MobaXterm--- Port-Forwarding Servers
- Connections to compute nodes
- How to connect to HPCC using an SSH client
- Install an SSH client
- Resetting SSH Host Keys
- SSH connection via VS Code
- SSH key based authentication
- SSH tunneling to directly access development nodes
- (2025-09-11) Data Display Debugger
- AlphaFold on HPCC
- AlphaFold via Singularity
- AlphaFold3
- Assembly of PacBio long reads with Canu
- BLAST/BLAST+
- Bracken/KrakenTools
- Checkpointing with DMTCP
- Checkpointing with DMTCP in batch jobs
- Docker
- EasyBuild tutorial
- File Permission in Research Space
- GATK4
- Gaussian job script
- HPCC Job Submission Workflow
- Installing Local Perl Modules with CPAN
- Introduction to the module system
- Mapping drives using SSHFS
- Mapping drives using Samba
- Matlab
- Mothur
- OrthoMCL pipeline
- OrthoMCL: MySQL configuration
- Powertools `longjob` by DMTCP
- QIIME 2
- R workshop tutorial
- Replacing an existing Conda installation
- Run Multiple Similar Jobs Simultaneously Using Job-Array
- Showing job steps
- Singularity Introduction
- Some packages and other information
- Transferring data with Google using Globus
- Transferring data with OneDrive using Globus
- Using Conda
- Using Conda in a research space
- Using virtual environments
- Writing and submitting job scripts
- make