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Docs pages organized by tag.
- (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
- Conditional statements
- Expansion
- Linux Command Line for Beginners I
- Linux Command Line for Beginners II
- Loops
- Regular expressions
- Variables I
- Variables II
- (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 installaion with Conda and Mamba
- (2022-10-08) Lab Notebook: Praat installation and execution using Singularity Overlays on CentOS8
- (2022-10-19) Lab Notebook: OpenVDB installaion with Conda
- (2022-10-19) Lab Notebook: TractSeg installation with Conda
- (2022-12-20) Lab Notebook: Conda --- Cleanning out your cache on HPCC
- Installing TensorFlow using anaconda
- Installing TF using conda
- Installing Pytorch with Anaconda
- Migrating Conda environments
- Replacing an existing Conda installation
- Using Conda
- (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
- (2024-08-28) Lab Notebook: cuQuantum Installation and Usage
- (2024-09-17) Lab Notebook: Common Machine Learning Tools on OnDemand
- (2023-02-07) Lab Notebook: WRF installation with EasyBuild
- (2023-05-18) Lab Notebook: EasyBuild PostgreSQL Installation
- EasyBuild Reference
- EasyBuild Tutorial
- Overview
- Data Machine overview
- File permissions
- HPCC layout
- Home space
- Overview
- Overview
- Python on HPCC
- Research space
- Overview
- Scratch space
- Singularity Advanced Topics
- Migrating from Torque
- Using BLAS and FlexiBLAS to speed up linear algebra operations
- (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 count
- File permissions
- Guidelines for choosing file systems and I/O
- Home space
- Managing file permissions
- Research space
- Scratch space
- Sensitive data storage
- (2022-09-28) Lab Notebook: HPCC via RStudio and GitHub
- (2023-11-21) Lab Notebook: Git in Research Spaces
- SSH tunneling to directly access development nodes
- Backwards compatibility scripts
- Buy-in and account management
- Change primary group
- SSH connection via VS Code
- Connect to the HPCC
- Connections to compute nodes
- Editing text with nano
- File transfer
- Installing TensorFlow using anaconda
- Installing TF using conda
- Installing Pytorch with Anaconda
- Jupyter Notebooks in VS Code
- Managing file permissions
- Migrating Conda environments
- Migrating Python virtual environments
- Migrating R packages
- Migrating to the new operating system
- Migrating to the upgraded module system
- Cloud storage file transfer
- Replacing an existing Conda installation
- SLURM resource request guide
- SSH keys
- Scavenger Queue
- Tensorflow Model Training Code Examples
- Overview
- Using Conda
- (2023-08-30) Lab Notebooks: Incident Report on System Slowdown due to I/O
- Guidelines for choosing file systems and I/O
- Example job scripts
- Writing and submitting job scripts
- List of job specifications
- SLURM environment variables
- (2023-06-30) Lab Notebooks: Jupyter --- Port-Forwarding Servers
- (2023-08-11) Lab Notebooks: Jupyter and MobaXterm--- Port-Forwarding Servers
- Jupyter Notebooks in VS Code
- Python on HPCC
- (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 installaion 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 installaion 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 --- Cleanning out your cache on HPCC
- (2022-12-20) Lab Notebook: SSHFS mapping on Windows
- (2023-02-07) Lab Notebook: NAMD --- Running on Multile 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
- (2023-06-30) Lab Notebooks: Jupyter --- Port-Forwarding Servers
- (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
- (2023-07-13) 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: Running ggplot in R without X11
- (2024-08-07) Lab Notebook: RStudio Server Shows Blank or Gray Screen
- (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)
- 10-23-2024 Lab Notebook: Architecture specific compilation
- (2024-08-28) Lab Notebook: Change to modules in SLURM jobs
- (2024-09-24) Lab Notebook: Ollama Module
- User created modules
- (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
- File transfer
- Quick start - Open OnDemand
- Accessing nodes running Ubuntu
- Backwards compatibility scripts
- Migrating Conda environments
- Migrating Python virtual environments
- Migrating R packages
- Migrating to the new operating system
- Migrating to the upgraded module system
- Overview
- (2023-07-13) Lab Notebook: Ignoring Local Python Libraries
- Migrating Conda environments
- Migrating Python virtual environments
- Python on HPCC
- Replacing an existing Conda installation
- Using BLAS and FlexiBLAS to speed up linear algebra operations
- Using virtual env
- Using Conda
- (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
- (2024-09-16) Lab Notebook: PyTorch OnDemand Usage
- (2024-09-17) Lab Notebook: Common Machine Learning Tools on OnDemand
- Installing Pytorch with Anaconda
- (2023-05-18) Lab Notebook: EasyBuild PostgreSQL Installation
- (2024-08-07) Lab Notebook: Running ggplot in R without X11
- (2024-08-07) Lab Notebook: RStudio Server Shows Blank or Gray Screen
- Migrating R packages
- General information
- Some packages and other information
- Using BLAS and FlexiBLAS to speed up linear algebra operations
- (2023-02-09) Lab Notebooks: Rclone --- Example of copying folder from HPCC to MSU OneDrive
- Cloud storage file transfer
- Accessing nodes running Ubuntu
- Cluster resources
- Compilers and Libraries
- Compiling for GPUs
- Conditional statements
- SLURM - node status and job partition
- EasyBuild Reference
- Example job scripts
- External Resources
- File count
- FAQ
- GPU resources
- Guidelines for choosing file systems and I/O
- How jobs are scheduled
- Searching software modules
- Classroom support
- Interactive jobs
- Linux shells
- List of job specifications
- Local file system
- Loops
- Quick start - Open OnDemand
- Regular expressions
- Requesting GPUs
- SLURM queueing and partitions
- SLURM commands
- Sensitive data storage
- SLURM environment variables
- User created modules
- Using the Data Machine
- SLURM - buyin information
- Development nodes
- Get software usage examples
- Install an SSH client
- Job policies
- SLURM - display job steps and their resource usages
- Module changelog
- SLURM - display job list
- (2022-09-28) Lab Notebook: HPCC via RStudio and GitHub
- (2024-08-07) Lab Notebook: RStudio Server Shows Blank or Gray Screen
- (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
- Overview
- Singularity Advanced Topics
- Singularity Introduction
- (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
- Example job scripts
- How jobs are scheduled
- Interactive jobs
- Writing and submitting job scripts
- List of job specifications
- SLURM commands
- Overview
- SLURM resource request guide
- Scavenger Queue
- Showing job steps
- SLURM environment variables
- Migrating from Torque
- Job policies
- (2023-09-21) Lab Notebooks: Example home directory software install (with links to videos)
- Module changelog
- (2023-06-30) Lab Notebooks: Jupyter --- Port-Forwarding Servers
- (2023-08-11) Lab Notebooks: Jupyter and MobaXterm--- Port-Forwarding Servers
- SSH tunneling to directly access development nodes
- SSH connection via VS Code
- Connect to the HPCC
- Connections to compute nodes
- SSH keys
- Install an SSH client
- (2024-09-17) Lab Notebook: Common Machine Learning Tools on OnDemand
- Installing TensorFlow using anaconda
- Installing TF using conda
- Some packages and other information
- TF GPU usage
- Tensorflow Model Training Code Examples
- AlphaFold on HPCC
- AlphaFold via Singularity
- Bracken/KrakenTools
- Checkpoint with DMTCP
- Data Display Debugger
- Docker
- EasyBuild Tutorial
- Expansion
- Installing Local Perl Modules with CPAN
- Introduction to the module system
- Run Multiple Similar Jobs Simultaneously Using Job-Array
- Writing and submitting job scripts
- Linux Command Line for Beginners I
- Linux Command Line for Beginners II
- Mapping drives using SSHFS
- Mapping drives using Samba
- Matlab
- Mothur
- Powertools
longjobby DMTCP - QIIME 2
- General information
- Some packages and other information
- Replacing an existing Conda installation
- Showing job steps
- Singularity Introduction
- Using virtual env
- Using Conda
- Variables I
- Variables II
- make
- (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
- SSH connection via VS Code
- Jupyter Notebooks in 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
- SSH connection via VS Code
- Jupyter Notebooks in VS Code