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AlphaFold is an AI program developed by DeepMind that predicts protein structures from amino acid sequences. Databases The necessary databases are pre-mounted on GPU nodes at /alphafold_storage/alphafold_db — no download needed. Required Parameters Parameter ...

AlphaFold3 runs via Singularity/Apptainer container on GPU nodes with the af3 GRES constraint. Loading the Module module load alphafold3 This automatically loads Apptainer and sets the following environment variables: Variable Description $AF3_CONTAINER Path ...

Conda and Mamba let you create isolated software environments with specific package versions. Use Mamba for faster dependency resolution. Loading the Module module load mamba/mamba-2.1.1 Listing Available Environments Before creating your own, check if an envi...

Run JupyterLab interactively on a compute node via SSH port forwarding. For a simpler browser-based experience, see PowerIDE. Step 1: Start an Interactive Job srun -p <partition-name> -A <account-name> --pty bash Replace <partition-name> and <account-name> w...

PowerIDE provides interactive access to the HPC cluster through a web browser. Run Jupyter notebooks, VS Code, and RStudio directly on compute nodes without needing SSH access. Access PowerIDE at: https://poweride.tau.ac.il/jupyter Getting Started Log in with ...

RELION is a cryo-EM structure determination package. On the TAU HPC cluster it runs on the dedicated gpu-relion partition with X11 forwarding. Requirements Access to the gpu-relion-users_v2 account — contact HPC support if you don't have it SSH connection wi...

Quick reference for the most common Slurm commands on the TAU HPC cluster. Submitting Jobs Command Description sbatch job.sh Submit a batch job script srun --pty bash Start an interactive session sbatch --depend=afterok:JOBID job.sh Submit job after another co...

Quick reference for users migrating from the old PBS/Torque system to Slurm. Command Equivalents PBS/Torque Slurm Description qsub job.sh sbatch job.sh Submit a job qsub -I srun --pty bash Interactive session qstat squeue View jobs qstat -u username squeue -u ...

Common errors and solutions for job submission and cluster usage. Job Submission Errors No partition specified srun: error: Unable to allocate resources: No partition specified or system default partition Always specify a partition. Run check_my_partitions to...

Required security software for TAU workstations and servers. NAC — Forescout Network Access Control client required for connecting to the TAU network. ForeScoutSecureConnector_64_visible_daemon.tar.gz Installation tar -zxvf ForeScoutSecureConnector_64_visible_...

External tools and resources to help with TAU HPC usage. HPC Helper Toolkit An AI-powered toolkit to help with common HPC tasks including QOS configuration, job submission, and more. HPC Helper Toolkit for TAU