Tags

Docs pages organized by tag.

accounts

• Buy-in and account management
• Obtaining an HPCC account

AlphaFold

• (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

AntiSMASH

• (2022-06-27) Lab Notebook: AntiSMASH installation with Conda

Bactopia

• (2022-10-03) Lab Notebook: Bactopia installaion with Conda and Mamba

bioinformatics

• Mothur
• QIIME 2

buyin

• Buy-in and account management
• SLURM queueing and partitions

CentOS 8

• (2022-09-23) Lab Notebook: Singularity --- Using an alternate OS

checkpointing

• Checkpoint with DMTCP
• Overview
• Powertools longjob by DMTCP

clean up

• (2022-12-20) Lab Notebook: Anaconda --- Cleanning out your cache on HPCC

cloud

• Cloud storage file transfer

command line

• Conditional statements
• Expansion
• Linux Command Line for Beginners I
• Linux Command Line for Beginners II
• Loops
• Regular expressions
• Variables I
• Variables II

compilers

• Compilers and Libraries
• Compiling for GPUs
• make

Conda

• (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: Anaconda --- Cleanning out your cache on HPCC
• Installing TF using anaconda
• Installing Pytorch with Anaconda
• Using Conda

containers

• Overview
• Docker
• Singularity Advanced Topics
• Singularity Introduction

CryoSPARC

• (2023-02-16) Lab Notebook: CryoSPARC Installation on HPCC

Crystal

• (2023-03-14) Lab Notebook: CRYSTAL23 --- Parallel submission script on the MSU HPCC

csh

• (2023-08-02) Lab Notebook: Alternative Linux Shells on HPCC

dashboard

• Dashboard

data machine

• Data Machine overview
• Using the Data Machine

DDD

• Data Display Debugger

Debugging

• (2022-12-07) Lab Notebook: OnDemand --- Bad Request from browser
• Data Display Debugger

Docker

• Overview
• Docker
• Singularity Advanced Topics

drive mapping

• Mapping drives using SSHFS
• Mapping drives using Samba

EasyBuild

• (2023-02-07) Lab Notebook: WRF installation with EasyBuild
• (2023-05-18) Lab Notebook: EasyBuild PostgreSQL Installation
• EasyBuild Reference
• EasyBuild Tutorial

explanation

• Overview
• Data Machine overview
• File permissions
• HPCC layout
• Home space
• Overview
• Python on HPCC
• Research space
• Overview
• Scratch space
• Singularity Advanced Topics
• Migrating from Torque

FAQ

• FAQ

files

• (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

git

• (2022-09-28) Lab Notebook: HPCC via RStudio and GitHub
• (2023-11-21) Lab Notebook: Git in Research Spaces

globus

• Overview

GPU

• Compiling for GPUs
• GPU resources
• Requesting GPUs
• TF GPU usage

groups

• Change primary group
• File permissions
• Managing file permissions

how-to guide

• SSH tunneling to directly access development nodes
• 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 TF using anaconda
• Installing Pytorch with Anaconda
• Jupyter Notebooks in VS Code
• Managing file permissions
• Cloud storage file transfer
• SLURM resource request guide
• SSH keys
• Scavenger Queue
• Tensorflow Model Training Code Examples
• Overview
• Using Conda

HRLDAS

• (2023-02-27) Lab Notebook: HRLDAS

I/O

• (2023-08-30) Lab Notebooks: Incident Report on System Slowdown due to I/O
• Guidelines for choosing file systems and I/O

incident report

• (2023-08-30) Lab Notebooks: Incident Report on System Slowdown due to I/O

interactive desktop

• (2022-10-04) Lab Notebook: OnDemand --- Unable to click icons on the Interactive Desktop

JAGS

• Some packages and other information

job script

• Example job scripts
• Writing and submitting job scripts
• List of job specifications
• SLURM environment variables

Jupyter

• (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

lab notebook

• (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: Anaconda --- 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

Linux

• (2023-08-02) Lab Notebook: Alternative Linux Shells on HPCC

make

• make

many files

• (2022-12-20) Lab Notebook: Anaconda --- Cleanning out your cache on HPCC

Mathematica

• (2023-03-27) Lab Notebook: Mathematica --- Fixing Startup Errors

MATLAB

• (2023-07-18) Lab Notebook: MATLAB offload from localPC to HPCC
• Matlab

MobaXterm

• (2023-08-11) Lab Notebooks: Jupyter and MobaXterm--- Port-Forwarding Servers

modules

• User created modules

Molpro

• (2023-11-09) Lab Notebook: Molpro Parallel

Mothur

• Mothur

MPI

• (2023-04-04) Lab Notebook: OnDemand RunningMPIJobs

NAMD

• (2023-02-07) Lab Notebook: NAMD --- Running on Multile Nodes

nano

• Editing text with nano

OnDemand

• (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
• File transfer
• OnDemand overview

OpenBUGS

• Some packages and other information

OpenVDB

• (2022-10-19) Lab Notebook: OpenVDB installaion with Conda

Parallel Comuting Toolbox

• (2023-07-18) Lab Notebook: MATLAB offload from localPC to HPCC

partitions

• Buy-in and account management
• SLURM queueing and partitions
• Scavenger Queue

Perl

• Installing Local Perl Modules with CPAN

PostgreSQL

• (2023-05-18) Lab Notebook: EasyBuild PostgreSQL Installation

powertools

• Powertools longjob by DMTCP

PyMesh

• (2022-09-20) Lab Notebook: PyMesh installation with Conda

Python

• (2023-07-13) Lab Notebook: Ignoring Local Python Libraries
• Python on HPCC
• Using Conda

PyTorch

• Installing Pytorch with Anaconda

QIIME 2

• QIIME 2

queue

• SLURM resource request guide

quota

• File count
• Home space
• Research space
• Scratch space

R

• (2023-05-18) Lab Notebook: EasyBuild PostgreSQL Installation
• General information
• Some packages and other information

rclone

• (2023-02-09) Lab Notebooks: Rclone --- Example of copying folder from HPCC to MSU OneDrive
• Cloud storage file transfer

reference

• 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
• OnDemand overview
• 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

ROS

• (2022-09-30) Lab Notebook: ROS on HPCC

RStudio

• (2022-09-28) Lab Notebook: HPCC via RStudio and GitHub

rsync

• File transfer
• Cloud storage file transfer

samba

• Mapping drives using Samba

scp

• File transfer

sensitive data

• Sensitive data storage

sftp

• (2022-10-27) Lab Notebook: SFTP Mapping on HPCC File Systems

shell

• (2023-08-02) Lab Notebook: Alternative Linux Shells on HPCC

Singularity

• (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

slurm

• (2023-05-04) Lab Notebook: Changes to srun for jobs with multiple CPUs per task
• 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

software

• (2023-09-21) Lab Notebooks: Example home directory software install (with links to videos)
• Module changelog

srun

• (2023-05-04) Lab Notebook: Changes to srun for jobs with multiple CPUs per task
• Showing job steps

ssh

• (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

sshfs

• (2022-12-20) Lab Notebook: SSHFS mapping on Windows
• Mapping drives using SSHFS

tcsh

• (2023-08-02) Lab Notebook: Alternative Linux Shells on HPCC

TensorFlow

• Installing TF using anaconda
• Some packages and other information
• TF GPU usage
• Tensorflow Model Training Code Examples

text editors

• Editing text with nano

torque

• Migrating from Torque

TractSeg

• (2022-10-19) Lab Notebook: TractSeg installation with Conda

training

• External Resources

tutorial

• AlphaFold on HPCC
• AlphaFold via Singularity
• Checkpoint with DMTCP
• Data Display Debugger
• Docker
• EasyBuild Tutorial
• Expansion
• Installing Local Perl Modules with CPAN
• Introduction to the module system
• 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 longjob by DMTCP
• QIIME 2
• General information
• Some packages and other information
• Showing job steps
• Singularity Introduction
• Using Conda
• Variables I
• Variables II
• make

VASP

• (2023-03-14) Lab Notebook: VASP

VisIt

• (2022-09-21) Lab Notebook: VisIt on HPCC

VS Code

• (2023-11-03) Lab Notebook: Connecting to a Singularity container with VS Code
• SSH connection via VS Code
• Jupyter Notebooks in VS Code

VScode

• (2023-11-03) Lab Notebook: Connecting to a Singularity container with VS Code
• SSH connection via VS Code
• Jupyter Notebooks in VS Code

Windows

• (2022-12-20) Lab Notebook: SSHFS mapping on Windows

WRF

• (2023-02-07) Lab Notebook: WRF installation with EasyBuild

zsh

• (2023-08-02) Lab Notebook: Alternative Linux Shells on HPCC