Configuration

Oris uses a TOML configuration file to control its execution environment, HPC scheduling, and simulation parameters. Oris will use the configuration file specified via the optional --config argument. If no file is provided, Oris falls back to an internal default configuration.

The configuration file is organized into three sections:

1. [slurm] - HPC scheduling directives (SLURM-specific)

2. [env] - Software environment setup

3. [oris] - Oris-specific simulation parameters

Below is the default configuration used by Oris:

# ==========================================
# ORIS - CLUSTER CONFIGURATION / PIPELINE
# ==========================================

# 🖥️ CLUSTER (Slurm)
[slurm]
partition           = "CPUQ"          # Cluster queue
account             = "myuser"      # Project (if applies)
time                = "24:00:00"      # Time limit ⏳

nodes               = 18              # Number of nodes 🧩
ntasks_per_node     = 14              # MPI tasks per node 🚀

output              = "oris_%j.out"  # Standard log 📄
error               = "oris_%j.err"  # Error log ❗
auto_submit         = true            # Automatic sbatch launch 🧚

# 🧬 ENVIRONMENT
[env]
preamble = """
module load intel/2024a
module load SciPy-bundle/2024.05-gfbf-2024a
module load Python/3.12.3-GCCcore-13.3.0
"""

# 🧠 ORIS configuration
[oris]
default_sampling     = 10                       # When no --sampling 🧮
media_targets        = ["EGFR", "IGF1R", "MET"] # Media nodes 🌐
timeout_sampling     = 300                      # Sampling threshold (seconds) ⏱️
timeout_paths        = 600                      # CountPaths threshold (seconds) ⏱️

🖥️ [slurm] - HPC Scheduling Section

This section controls how Oris interacts with SLURM when submitting jobs.

Parameter	Type	Description
partition	string	SLURM partition/queue to submit jobs to
account	string	Project/account for billing (cluster-dependent)
time	string	Wall-time limit in HH:MM:SS format
nodes	int	Number of SLURM nodes requested
ntasks_per_node	int	MPI tasks spawned per node
output	string	Path for standard output logs (%j = JobID)
error	string	Path for error logs
auto_submit	bool	If true, Oris submits via sbatch

📝 If auto_submit = false, Oris witll instead generate the .sbatch script and print instructions for manual submission.

🧬 [env] - Software Environment Section

This section defines the runtime software environment, typically using module load, conda activate, or similar commands.

Parameter	Type	Description
preamble	multiline string	Shell commands executed before job execution

Common uses include:

• loading compiler toolchains

• activating conda environments

• loading MPI implementations

• loading Python modules

🧠 [oris] - Simulation Parameters Section

This section controls Oris-specific runtime behavior:

Parameter	Type	Description
default_sampling	int	Default number of sampled models if --sampling is not provided
media_targets	array[string]	Input/media nodes forced ON during initial condition filtering
timeout_sampling	int (seconds)	Max time for CountPaths during model sampling
timeout_paths	int (seconds)	Max time for CountPaths during full simulation

📝 Notes:

• media_targets defines culture medium context, enforcing media nodes as inputs during initial condition selection.

• timeout_sampling applies only to sampling mode, i.e. selecting fast-running models.

• timeout_paths applies to CountPaths runs under all modes.

💡 Example Usage

To run Oris with a custom configuration:

oris --zips /path/to/zips --mode full --sampling 20 --config /path/to/oris_config.toml

If --config is omitted, Oris will load its internal default.

📝 Depending on your HPC system you may need to modify:

• partition

• account

• module load lines

• MPI versions

• Python versions (always 3.10+)

Oris does not validate environment modules, so incorrect module names will result in SLURM job failures at runtime.