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# Software

# AmberTools 24 and 25 (Conda-based installation)

The AmberTools 24 and AmberTools 25 packages are installed via Conda environments, not as standard modules. This is because the module system cannot handle the source command required to activate Conda environments.

# AmberTools 24 – Activation

To activate AmberTools 24, use the following commands:

source /opt/exp_soft/rocky_9/amber/24/conda/etc/profile.d/conda.sh
conda activate AmberTools24
source $CONDA_PREFIX/amber.sh

# AmberTools 25 – Activation

To activate AmberTools 25, use the following:

source /opt/exp_soft/rocky_9/amber/25/conda/etc/profile.d/conda.sh
conda activate AmberTools25
source $CONDA_PREFIX/amber.sh

Notes

  • Make sure no other Conda environment is active before running these commands.
  • Each AmberTools version has a separate environment; activate only the one you need.
  • You can create a helper script (e.g. run_ambertools24.sh) to simplify repeated use.

# Helper Script Example

You can create a helper script to simplify activation:

For AmberTools 24:

#!/bin/bash
# run_ambertools24.sh
source /opt/exp_soft/rocky_9/amber/24/conda/etc/profile.d/conda.sh
conda activate AmberTools24
source $CONDA_PREFIX/amber.sh
echo "AmberTools 24 activated successfully!"

For AmberTools 25:

#!/bin/bash
# run_ambertools25.sh
source /opt/exp_soft/rocky_9/amber/25/conda/etc/profile.d/conda.sh
conda activate AmberTools25
source $CONDA_PREFIX/amber.sh
echo "AmberTools 25 activated successfully!"

Make the scripts executable:

chmod +x run_ambertools24.sh
chmod +x run_ambertools25.sh

Important

Ensure that no other Conda environment is active before switching between AmberTools versions to avoid conflicts.

# Ollama

# Go to https://qcg.pcss.plcloud.pl

# First launch of Ollama

Click "Submit Task"

Find the Ollama template

Submit using the template

Set the appropriate General options (you can leave them by default)

Set the resource options as needed

When all options are set, click "Submit"


When the environment is ready, go to the Overview tab and click VNC

You will be redirected to the OpenWebui interface, where you need to create an account

Use it

# Deleting a task


For the appropriate task, click Cancel Task



Delete it

# Using an Environment from a Pre-Existing Job

Click "Submit Task"

Find the Ollama template

Submit using the template

Set the appropriate General options

Change the Model Environment to Use Existing

Go to home@altair

Find a similar path to the model environment and confirm



In the Webui environment similarly select use existing





Set the resource options as needed

When all options are set, click "Submit"


When the environment is ready, go to the Overview tab and click VNC

You will be redirected to the OpenWebui interface, where you need to create an account

Use it

# Searching the web with OpenWebui

Go to admin panel


Go to settings

Go to web search

Make sure web search is allowed

Expand the list of search engines

And choose the right one for you

Configure based on the appropriate tutorial

https://docs.openwebui.com/category/-web-search/

Configure the rest of the parameters (you can leave it default)

Go to chat

Indicate that you want to search the internet

Type a query.

# Ollama command line

Symbolic linking of 2 directories: ~/.singularity and ~/.ollama

ln -s <grant_id>/project_data/ollama/ ~/.ollama  
ln -s <grant_id>/project_data/singularity/ ~/.singularity

Log in to a GPU node and select the number of available GPUs

srun --mem 100G --gpus-per-node 4 -p proxima --pty bash

Create a definition file ollama.def

Bootstrap: docker  
From: ollama/ollama  

%startscript  
   ollama serve

Build the image

sudo singularity build ollama.sif ollama.def

Run the container

# ollama runs on port 11434
singularity instance start --nv --bind /mnt/:/mnt/ ollama.sif ollama

Enter the container

singularity shell instance://ollama

Test the selected model

ollama run deepseek-r1:7b

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