Knowledge Base
Accounts
Cannot Connect to Hoffman2
10
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Connection refused jupyter notebook or JupyterLab on Hoffman2
Tuesday, March 5, 2024 h2jupynb jupyter jupyter lab jupyter nb jupyter notebooks on h2
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VSCode
Monday, February 5, 2024 code vscode
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SSH connection breaks - packet_write_wait/Broken pipe
Updated: Tuesday, March 10, 2020 broken pipe ipqos packet_write_wait ssh
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Why can't I connect to the Hoffman2 cluster from mednet or UCLAHealthSecure?
Updated: Monday, October 28, 2019 mednet virtual private network vpn
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Connecting to the campus VPN
Updated: Monday, October 28, 2019 virtual private network vpn
User Accounts
3
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New Account Request Sponsor Approval
Friday, February 24, 2023 account management gim sim
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Hoffman2 Account Management
Updated: Friday, February 24, 2023 account management gim sim
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I forgot my password - how do I change or reset it?
Updated: Monday, February 27, 2023
Other
1
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Registering as a new sponsor on the Hoffman2 Cluster
Updated: Monday, October 28, 2019
Applications, Compilers, and Libraries
Adapting an App for Use on Hoffman2
5
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Running Seurat version 5 on the Hoffman2 Cluster
Updated: Tuesday, March 12, 2024 r seurat tutorial
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Running CrystalExplorer on the Hoffman2 Cluster
Updated: Tuesday, February 20, 2024 chemistry crystal crystalexplorer
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Using AlphaFold on Hoffman2
Updated: Wednesday, December 20, 2023
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Guide for Installing TensorFlow and PyTorch
Updated: Tuesday, September 3, 2024 code
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How to run BIOBAKERY on the Hoffman2 Cluster
Friday, May 5, 2023
Code/Programming/Scripts
2
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After loading Intel 13.cs module, why is mpicc/mpicxx/mpif90 still not using Intel compiler?
Updated: Monday, October 28, 2019
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How to load in your environment the previously used Intel compiler
Updated: Monday, October 28, 2019
Jupyter on Hoffman2
3
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Cannot open Jupyter notebook files with 500 : Internal Server Error
Tuesday, April 9, 2024 jupyter jupyter lab jupyter nb jupyter notebooks on h2
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Running Seurat v5 via Jupyter
Updated: Tuesday, March 12, 2024
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Troubleshooting jupyter notebooks session not starting
Updated: Tuesday, July 9, 2024 jupyter jupyter nb jupyter notebooks on h2
Licensed Software
2
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Running Ansys on a local Widows machine while checking out a license on the Hoffman2 cluster (YOU NEED A VALID LICENSE INSTALLED ON THE CLUSTER - WE HAVE NO PUBLIC LICENSES FOR ANSYS)
Updated: Thursday, March 10, 2022
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ssh port forwarding from windows computers
Updated: Monday, October 28, 2019
Software Installation Help (Project/Home directory)
9
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Installation of package igraph in R
Friday, September 13, 2024 igraph r r igraph
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Cellbender on the Hoffman2 Cluster
Updated: Wednesday, July 10, 2024
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NGLview on the Hoffman2 Cluster
Updated: Wednesday, January 31, 2024 h2jupynb jupyter lab jupyter nb jupyter notebooks on h2 nlgview quantum chemistry
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Installing Gossamer bioinformatics suite in your $HOME
Thursday, December 5, 2019 cmake electus goss gossamer gossple xenome
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Installing HTSeq in python 2
Updated: Monday, October 28, 2019
Remote Desktop (NX/X2Go)
1
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NoMachine: Verify host identification message always appears when connecting to remote host
Thursday, August 15, 2024
Other
1
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Qiime2 on the Hoffman2 Cluster
Updated: Monday, September 26, 2022
Job Errors/Job Scheduler
How to Submit a Job
6
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qsub command not found
Updated: Monday, October 28, 2019
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Requesting the appropriate amount of resources for jobs on the Hoffman2 cluster
Updated: Monday, October 28, 2019
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Why cannot I submit too many individual jobs?
Updated: Monday, October 28, 2019
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How do I request large memory to run multi-threaded (single node) program?
Updated: Monday, October 28, 2019
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How do I request large memory to run sequential (1-core) program?
Updated: Monday, October 28, 2019
Job Not Starting
2
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Why is my job still waiting in the queue?
Updated: Monday, October 28, 2019 job scheduler sge uge wait
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Why my highp job did not start in 24 hours?
Updated: Monday, October 28, 2019
Job Status
2
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I have a lot of jobs in error state E. How do I find out what the problem is?
Updated: Monday, October 28, 2019
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An OIT/IDRE consultant sent me an email about a lot of left over jobs running under my userid. How do I delete them?
Updated: Monday, October 28, 2019
Other
2
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$TMPDIR for interactive job on Hoffman2
Updated: Monday, October 28, 2019
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How many cores does my job get with "exclusive"?
Updated: Monday, October 28, 2019
Node and Storage Purchases
Node and Storage Purchases
4
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What is the lifetime of a compute node?
Monday, May 1, 2023
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Purchasing HPC Storage on the Hoffman2 Cluster
Updated: Thursday, April 14, 2022
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Purchasing nodes on the Hoffman2 Cluster
Updated: Thursday, April 14, 2022
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Buying HPC storage on the Hoffman2 cluster
Updated: Wednesday, November 10, 2021
Other
1
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Hoffman2 HPC Storage: Home, project and nobackup directories
Updated: Monday, October 28, 2019 directories directory home hpc nobackup project storage
Storage and Filesystems
Access / Permissions / Quotas
1
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Data Sharing on Hoffman2
Updated: Friday, May 1, 2020
Cloud Storage (AWS, Box, etc.)
1
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Can I use Dropbox on Hoffman2?
Updated: Monday, October 28, 2019
File Transfer and Globus
5
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Moving data from Google Drive to the Hoffman2 Cluster
Wednesday, April 3, 2024
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Instructions on how to install the aspera connect tool on Hoffman2
Updated: Monday, November 13, 2023
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What endpoint do I use with Globus?
Friday, October 15, 2021
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High-speed file transfer with Globus
Updated: Monday, October 28, 2019
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Globus: Your task is currently receiving the error: ENDPOINT_TOO_BUSY
Updated: Monday, October 28, 2019
General Requests
3
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I deleted a file in my home directory. How can I recover it?
Updated: Monday, October 28, 2019
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/u/scratch file retention policy
Updated: Monday, October 28, 2019
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Hoffman2 Cluster Filesystem Classifications
Updated: Monday, October 28, 2019
Other
Policies
1
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How can I acknowledge Hoffman2 Shared Cluster in my presentations or publications?
Updated: Monday, October 28, 2019