docker run -d \
  --name simstack-mongo \
  -p 27017:27017 \
  -e MONGO_INITDB_ROOT_USERNAME=admin \
  -e MONGO_INITDB_ROOT_PASSWORD=yourpassword \
  mongo:latest

# activate the (simstack) env
python -m pip install --upgrade pip
pip install simstack

Just type `tree` in the terminal, if the **installation** succeeds, you should see a directory structure like the folder tree shown below.

### Step 3 — Clone subrepos for existing simstack packages 📦

```bash
# activate the (simstack) env
python -m pip install --upgrade pip
pip install simstack

Just type `tree` in the terminal, if the **installation** succeeds, you should see a directory structure like the folder tree shown below.



### Step 2 — Install dependencies 📦

```bash
# activate the (simstack) env
python -m pip install --upgrade pip
pip install simstack

Just type `tree` in the terminal, if the **installation** succeeds, you should see a directory structure like the folder tree shown below.





## 2. Configure Simstack II with `simstack.toml` ⚙️

Simstack II reads a single **TOML** file (`simstack.toml`) to learn

* which **resources** (local & remote) exist,
* how to reach your **MongoDB** backend,
* and where each host should place logs / artifacts.

> **Where should the file live?**
> Save it next in the folder simstack-model in both your local and HPC accounts.
> The CLI searches those paths automatically.

### 2.1 Minimal template

```toml
#######################################
# Global / shared parameters
#######################################
[parameters.common]
resources        = ["local", "int-nano", "horeka", "justus", "self", "exchange", "uploads"]
database         = "celso_data"                    # default DB
test_database    = "celso_test_data"               # used by `simstack selftest`
connection_string = "mongodb://<user>:<pass>@<host>:27017/"  # ⬚ change!

#######################################
# Host-specific overrides
#######################################
# 1) Your own machine --------------------------------
[parameters.local]
ssh-key     = "~/.ssh/id_rsa"                      # private key
resource    = "local"                              # → maps to runners.local
workdir     = "~/simstack/workflows"               # absolute path
python_path = ["~/simstack/simstack-model",
               "~/simstack/simstack-model/src"]

# 2) Remote upload node -----------------------------
[parameters.uploads]
ssh-key     = "~/.ssh/id_rsa"
resource    = "self"
workdir     = "~/simstack/workflows"
python_path = ["~/simstack/simstack-model",
               "~/simstack/simstack-model/src"]

# 3) Example HPC login node -------------------------
[parameters.int-nano]
ssh-key            = "~/.ssh/id_rsa"
workdir            = "/home/<user>/simstack"
python_path        = ["/home/<user>/simstack/simstack-model",
                      "/home/<user>/simstack/simstack-model/src"]
environment_start  = "mamba activate simstack"  # run before each task

#######################################
# Internal web-server (rarely touched)
#######################################
[server]
port        = 8000
SECRET_KEY  = "<32-byte hex or env-var>"           # ⬚ never commit real keys
upload_dir  = "/srv/simstack/uploads"              # Windows paths OK too

#######################################
# Canonical DNS names for hosts
#######################################
[hosts]
local    = "localhost"
int-nano = "int-nano.int.kit.edu"
justus   = "justus.int.kit.edu"
horeka   = "horeka.int.kit.edu"

#######################################
# Directed data routes
#######################################
[[routes]]
source = "local"     # where the artifact lives
target = "int-nano"  # where you want it
host   = "local"     # node that **pushes** the data

[[routes]]
source = "int-nano"
target = "local"
host   = "local"

# …repeat as needed

#!/usr/bin/env bash
# -----------------------------
# Adds the current repo + src/ to PYTHONPATH
# Call with:  source set_pythonpath.sh
# -----------------------------
this_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
export PYTHONPATH="$this_dir:$this_dir/src${PYTHONPATH+:$PYTHONPATH}"
echo "PYTHONPATH = $PYTHONPATH"

chmod +x set_pythonpath.sh        # one-time
source /path/to/set_pythonpath.sh # every session, or add to ~/.bashrc

scp set_pythonpath.sh [email protected]:~/simstack/