singularity working

.clinerules

@@ -0,0 +1,115 @@
+# Cline's Memory Bank
+
+I am Cline, an expert software engineer with a unique characteristic: my memory resets completely between sessions. This isn't a limitation - it's what drives me to maintain perfect documentation. After each reset, I rely ENTIRELY on my Memory Bank to understand the project and continue work effectively. I MUST read ALL memory bank files at the start of EVERY task - this is not optional.
+
+## Memory Bank Structure
+
+The Memory Bank consists of core files and optional context files, all in Markdown format. Files build upon each other in a clear hierarchy:
+
+flowchart TD
+    PB[projectbrief.md] --> PC[productContext.md]
+    PB --> SP[systemPatterns.md]
+    PB --> TC[techContext.md]
+
+    PC --> AC[activeContext.md]
+    SP --> AC
+    TC --> AC
+
+    AC --> P[progress.md]
+
+### Core Files (Required)
+1. `projectbrief.md`
+   - Foundation document that shapes all other files
+   - Created at project start if it doesn't exist
+   - Defines core requirements and goals
+   - Source of truth for project scope
+
+2. `productContext.md`
+   - Why this project exists
+   - Problems it solves
+   - How it should work
+   - User experience goals
+
+3. `activeContext.md`
+   - Current work focus
+   - Recent changes
+   - Next steps
+   - Active decisions and considerations
+   - Important patterns and preferences
+   - Learnings and project insights
+
+4. `systemPatterns.md`
+   - System architecture
+   - Key technical decisions
+   - Design patterns in use
+   - Component relationships
+   - Critical implementation paths
+
+5. `techContext.md`
+   - Technologies used
+   - Development setup
+   - Technical constraints
+   - Dependencies
+   - Tool usage patterns
+
+6. `progress.md`
+   - What works
+   - What's left to build
+   - Current status
+   - Known issues
+   - Evolution of project decisions
+
+### Additional Context
+Create additional files/folders within memory-bank/ when they help organize:
+- Complex feature documentation
+- Integration specifications
+- API documentation
+- Testing strategies
+- Deployment procedures
+
+## Core Workflows
+
+### Plan Mode
+flowchart TD
+    Start[Start] --> ReadFiles[Read Memory Bank]
+    ReadFiles --> CheckFiles{Files Complete?}
+
+    CheckFiles -->|No| Plan[Create Plan]
+    Plan --> Document[Document in Chat]
+
+    CheckFiles -->|Yes| Verify[Verify Context]
+    Verify --> Strategy[Develop Strategy]
+    Strategy --> Present[Present Approach]
+
+### Act Mode
+flowchart TD
+    Start[Start] --> Context[Check Memory Bank]
+    Context --> Update[Update Documentation]
+    Update --> Execute[Execute Task]
+    Execute --> Document[Document Changes]
+
+## Documentation Updates
+
+Memory Bank updates occur when:
+1. Discovering new project patterns
+2. After implementing significant changes
+3. When user requests with **update memory bank** (MUST review ALL files)
+4. When context needs clarification
+
+flowchart TD
+    Start[Update Process]
+
+    subgraph Process
+        P1[Review ALL Files]
+        P2[Document Current State]
+        P3[Clarify Next Steps]
+        P4[Document Insights & Patterns]
+
+        P1 --> P2 --> P3 --> P4
+    end
+
+    Start --> Process
+
+Note: When triggered by **update memory bank**, I MUST review every memory bank file, even if some don't require updates. Focus particularly on activeContext.md and progress.md as they track current state.
+
+REMEMBER: After every memory reset, I begin completely fresh. The Memory Bank is my only link to previous work. It must be maintained with precision and clarity, as my effectiveness depends entirely on its accuracy.

.env.example

@@ -9,6 +9,20 @@
 # - atropos : Atroposlib ServerManager/ManagedServer-backed loop (training/env integration)
 HERMES_BACKEND=openai
 
+
+# =============================================================================
+# LOCAL / SELF-HOSTED OPENAI-COMPATIBLE ENDPOINTS (vLLM, SGLang, llama.cpp, etc.)
+# =============================================================================
+# For local development (matches the Atropos test env defaults):
+# ATROPOS_SERVER_BASE_URL=http://127.0.0.1:8080
+# ATROPOS_SERVER_MODEL=hermes-4-36b
+# For hosted inference (Nous Research inference API):
+ATROPOS_SERVER_BASE_URL=
+ATROPOS_SERVER_MODEL=
+ATROPOS_TOKENIZER_NAME=
+# Set this to your Nous API key (Bearer token).
+ATROPOS_SERVER_API_KEY=
+
 # Debugging (prints to stdout; use with care)
 # HERMES_DEBUG_ATROPOS_REQUEST=1
 # HERMES_DEBUG_ATROPOS_RESPONSE=1

.gitignore

@@ -40,7 +40,14 @@ agent-browser/
 privvy*
 images/
 
-# CLI config (may contain sensitive SSH paths)
-cli-config.yaml
-
-.DS_Store
+# CLI config (may contain sensitive SSH paths)
+cli-config.yaml
+
+.DS_Store
+
+# artifacts
+*.jsonl
+*.html
+*.json
+*.log
+*.csv

README.md

@@ -610,3 +610,248 @@ All environment variables can be configured in the `.env` file (copy from `.env.
 | `skills/` | On-demand knowledge documents |
 | `docs/` | Documentation |
 | `configs/` | Example batch run scripts |
+
+# Atropos Integrations & RL Training
+
+Atropos is an RL training framework that uses Hermes-Agent for agent-based environments. This section covers setting up the sandbox infrastructure with either Docker or Singularity backends.
+
+## Prerequisites
+
+### 1. Install Nomad
+Nomad is a workload orchestrator that manages the sandbox containers:
+
+```bash
+# Install Nomad (Linux)
+curl -fsSL https://apt.releases.hashicorp.com/gpg | sudo gpg --dearmor -o /usr/share/keyrings/hashicorp-archive-keyring.gpg
+echo "deb [signed-by=/usr/share/keyrings/hashicorp-archive-keyring.gpg] https://apt.releases.hashicorp.com $(lsb_release -cs) main" | sudo tee /etc/apt/sources.list.d/hashicorp.list
+sudo apt update && sudo apt install nomad
+
+# Verify installation
+nomad --version
+```
+
+For other platforms, see: https://developer.hashicorp.com/nomad/docs/install
+
+### 2. Install Atropos Dependencies
+
+```bash
+python3 -m venv .venv
+source .venv/bin/activate
+pip install -e '.[atropos]'
+```
+
+## Backend Options
+
+Atropos supports two container backends for the sandbox environment:
+
+| Backend | Use Case | Requirements |
+|---------|----------|--------------|
+| **Docker** | Development, servers with Docker | Docker installed, user in `docker` group |
+| **Singularity** | HPC clusters, rootless environments | Apptainer/Singularity installed (no root needed) |
+
+---
+
+## Docker Backend (Default)
+
+### 1. Build the Sandbox Image
+
+```bash
+cd atropos
+docker build -t atropos-sandbox:local .
+```
+
+### 2. Start Nomad (Development Mode)
+
+```bash
+# Start Nomad with Docker driver
+nomad agent -dev -config=nomad-dev.hcl
+```
+
+Or create `nomad-dev.hcl`:
+```hcl
+client {
+  enabled = true
+  options {
+    "driver.allowlist" = "docker"
+  }
+}
+```
+
+### 3. Run with Docker Backend
+
+```bash
+source .venv/bin/activate
+
+# Test the environment
+python -m atropos.envs.swe_smith_oracle_env process \
+    --env.use_wandb false \
+    --env.total_steps 1 \
+    --env.max_items 1 \
+    --env.driver docker
+```
+
+---
+
+## Singularity Backend (HPC/Rootless)
+
+Singularity/Apptainer is ideal for HPC clusters where Docker requires root privileges.
+
+### 1. Build the Singularity Image
+
+```bash
+cd atropos
+
+# Option A: Convert from Docker image (if Docker is available)
+docker build -t atropos-sandbox:local .
+apptainer build atropos-sandbox.sif docker-daemon://atropos-sandbox:local
+
+# Option B: Build directly from Dockerfile (requires root or fakeroot)
+apptainer build atropos-sandbox.sif docker://ghcr.io/nousresearch/atropos-sandbox:latest
+```
+
+### 2. Start Nomad with raw_exec Driver
+
+Singularity uses Nomad's `raw_exec` driver. Create `nomad-singularity.hcl`:
+
+```hcl
+client {
+  enabled = true
+  options {
+    "driver.allowlist" = "raw_exec,docker"
+  }
+}
+
+plugin "raw_exec" {
+  config {
+    enabled = true
+  }
+}
+```
+
+Start Nomad:
+```bash
+nomad agent -dev -config=nomad-singularity.hcl
+```
+
+### 3. Run with Singularity Backend
+
+```bash
+source .venv/bin/activate
+
+# Basic test
+python -m atropos.envs.swe_smith_oracle_env process \
+    --env.use_wandb false \
+    --env.total_steps 1 \
+    --env.max_items 1 \
+    --env.driver singularity \
+    --env.singularity_image /path/to/atropos-sandbox.sif
+
+# Full example with all options
+python -m atropos.envs.swe_smith_oracle_env process \
+    --env.use_wandb false \
+    --env.total_steps 10 \
+    --env.group_size 4 \
+    --env.max_items 100 \
+    --env.driver singularity \
+    --env.singularity_image /path/to/atropos-sandbox.sif \
+    --env.slots_per_container 10 \
+    --env.min_containers 1 \
+    --env.max_containers 5
+```
+
+---
+
+## CLI Arguments Reference
+
+### Environment Configuration (`--env.*`)
+
+| Argument | Default | Description |
+|----------|---------|-------------|
+| `--env.driver` | `docker` | Container backend: `docker` or `singularity` |
+| `--env.singularity_image` | - | Path to `.sif` file (required for singularity driver) |
+| `--env.sandbox_image` | `atropos-sandbox:local` | Docker image name (for docker driver) |
+| `--env.slots_per_container` | `10` | Number of parallel slots per container |
+| `--env.min_containers` | `1` | Minimum number of containers to run |
+| `--env.max_containers` | `10` | Maximum containers for auto-scaling |
+| `--env.nomad_address` | `http://localhost:4646` | Nomad server address |
+| `--env.privileged` | `false` | Run containers in privileged mode (Docker only) |
+
+### Processing Configuration
+
+| Argument | Default | Description |
+|----------|---------|-------------|
+| `--env.total_steps` | `1` | Number of processing steps |
+| `--env.group_size` | `1` | Items per processing group |
+| `--env.max_items` | `0` | Max dataset items (0 = all) |
+| `--env.use_wandb` | `true` | Enable Weights & Biases logging |
+| `--env.agent_max_steps` | `50` | Max agent steps per trajectory |
+
+---
+
+## Troubleshooting
+
+### Port Already in Use
+```bash
+# Find and kill process on port 8080
+lsof -ti :8080 | xargs kill
+
+# Or use a different port
+--env.port 8081
+```
+
+### Singularity: Permission Denied
+```bash
+# Check Apptainer is installed
+apptainer --version
+
+# Ensure the .sif file is readable
+ls -la /path/to/atropos-sandbox.sif
+```
+
+### Nomad: Job Not Starting
+```bash
+# Check Nomad status
+nomad status
+
+# View job logs
+nomad alloc logs -job atropos-sandbox-agent-env
+
+# Check stderr for errors
+nomad alloc logs -stderr -job atropos-sandbox-agent-env
+```
+
+### OpenAI API Token Error
+If you see `NotImplementedError: OpenAI endpoints do not support token IDs`:
+```bash
+# For testing/evaluation only (not training)
+export ATROPOS_ALLOW_DUMMY_MANAGED_SERVER=1
+```
+
+---
+
+## Example: Full HPC Workflow
+
+```bash
+# 1. Setup environment
+python3 -m venv .venv
+source .venv/bin/activate
+pip install -e '.[atropos]'
+
+# 2. Build Singularity image (on a machine with Docker)
+cd atropos
+docker build -t atropos-sandbox:local .
+apptainer build atropos-sandbox.sif docker-daemon://atropos-sandbox:local
+
+# 3. Transfer .sif to HPC cluster
+scp atropos-sandbox.sif user@hpc-cluster:/scratch/user/
+
+# 4. On HPC cluster: Start Nomad
+nomad agent -dev -config=nomad-singularity.hcl &
+
+# 5. Run training
+python -m atropos.envs.swe_smith_oracle_env process \
+    --env.driver singularity \
+    --env.singularity_image /scratch/user/atropos-sandbox.sif \
+    --env.total_steps 100 \
+    --env.max_items 1000
+```

atropos/backends/nomad_backend.py

@@ -26,6 +26,10 @@ class NomadBackendConfig:
     privileged: bool
     acquire_timeout_s: float
     purge_job_on_start: bool
+    # Driver selection: "docker" or "singularity"
+    driver: str = "docker"
+    # Path to .sif file for singularity driver (required if driver="singularity")
+    singularity_image: Optional[str] = None
 
     @classmethod
     def from_agent_env_config(cls, cfg: Any) -> "NomadBackendConfig":
@@ -39,6 +43,8 @@ class NomadBackendConfig:
             privileged=bool(getattr(cfg, "privileged")),
             acquire_timeout_s=float(getattr(cfg, "acquire_timeout_s")),
             purge_job_on_start=bool(getattr(cfg, "purge_job_on_start", False)),
+            driver=str(getattr(cfg, "driver", "docker")),
+            singularity_image=getattr(cfg, "singularity_image", None),
         )
 
 
@@ -56,6 +62,8 @@ class NomadToolBackend(ToolBackend):
                 privileged=config.privileged,
                 acquire_timeout=config.acquire_timeout_s,
                 purge_job_on_start=bool(config.purge_job_on_start),
+                driver=config.driver,
+                singularity_image=config.singularity_image,
             )
         )
 

atropos/envs/agent_env.py

@@ -60,6 +60,16 @@ class AgentEnvConfig(BaseEnvConfig):
         ),
     )
     purge_job_on_shutdown: bool = Field(default=True, description="Nomad mode: stop/purge job on shutdown")
+    
+    # Nomad driver selection (docker or singularity)
+    driver: str = Field(
+        default="docker",
+        description="Nomad task driver: 'docker' (default) or 'singularity' (for HPC without sudo Docker)",
+    )
+    singularity_image: Optional[str] = Field(
+        default=None,
+        description="Path to .sif file for Singularity driver (required if driver='singularity')",
+    )
 
     # modal mode settings (stub; implementation pending)
     modal_app_name: str = Field(default="atropos-sandbox", description="Modal app name (stub)")

atropos/nomad/client.py

@@ -241,9 +241,10 @@ class NomadClient:
             if networks:
                 network = networks[0]
                 address = network.get("IP")
-                # Look for dynamic ports
+                # Look for dynamic ports OR reserved ports (Singularity/raw_exec uses reserved)
                 dyn_ports = network.get("DynamicPorts") or []
-                for dp in dyn_ports:
+                reserved_ports = network.get("ReservedPorts") or []
+                for dp in dyn_ports + reserved_ports:
                     if dp.get("Label") == "http":
                         port = dp.get("Value")
                         break
@@ -353,16 +354,18 @@ def create_sandbox_job(
     memory: int = 512,
     port: int = 8080,
     datacenter: str = "dc1",
+    driver: str = "docker",  # "docker" or "singularity"
+    singularity_image: str = None,  # Path to .sif file for singularity driver
 ) -> Dict[str, Any]:
     """
     Create a sandbox job specification.
     
-    This job runs the sandbox_server.py inside a Python container,
+    This job runs the sandbox_server.py inside a container,
     with the specified number of slots for agent workspaces.
     
     Args:
         job_id: Unique job identifier
-        image: Docker image to use
+        image: Docker image to use (for docker driver)
         count: Number of container instances
         slots_per_container: Number of slots per container
         privileged: Run container in privileged mode (recommended for bubblewrap)
@@ -370,10 +373,81 @@ def create_sandbox_job(
         memory: Memory allocation in MB
         port: HTTP port for sandbox server
         datacenter: Nomad datacenter
+        driver: Container driver - "docker" or "singularity"
+        singularity_image: Path to .sif file (required if driver="singularity")
         
     Returns:
         Job specification dict
     """
+    # Build task config based on driver
+    if driver == "singularity":
+        if not singularity_image:
+            raise ValueError("singularity_image path required when driver='singularity'")
+        
+        # Use raw_exec driver to run apptainer via shell for variable expansion
+        # The container binds the allocation directory for workspace persistence
+        # For raw_exec, we use static port since Nomad's dynamic port mapping doesn't
+        # work the same as Docker - the process runs directly on the host.
+        shell_cmd = (
+            f'apptainer run '
+            f'--bind "$NOMAD_ALLOC_DIR/data:/data" '
+            f'--pwd /app '
+            f'--env PYTHONUNBUFFERED=1 '
+            f'{singularity_image} '
+            f'python sandbox_server.py '
+            f'--port {port} '
+            f'--slots {slots_per_container} '
+            f'--data-dir /data'
+        )
+        task_config = {
+            "command": "/bin/sh",
+            "args": ["-c", shell_cmd],
+        }
+        task_driver = "raw_exec"
+    else:
+        # Docker driver (default)
+        task_config = {
+            "image": image,
+            "force_pull": False,  # Use local image, don't try to pull
+            "ports": ["http"],
+            "privileged": privileged,
+            "command": "python",
+            "args": [
+                "sandbox_server.py",
+                "--port", str(port),
+                "--slots", str(slots_per_container),
+                "--data-dir", "/data",
+            ],
+            # Note: On Linux, you can mount persistent storage:
+            # "volumes": ["${NOMAD_ALLOC_DIR}/data:/data"],
+            # On macOS/Docker Desktop, skip volumes for PoC
+            # (container /data is ephemeral but works for testing)
+        }
+        task_driver = "docker"
+    
+    # For Singularity/raw_exec, use static ports since the process runs directly on host.
+    # For Docker, use dynamic ports with port mapping.
+    if driver == "singularity":
+        network_config = {
+            "Mode": "host",
+            "ReservedPorts": [
+                {
+                    "Label": "http",
+                    "Value": port,
+                }
+            ],
+        }
+    else:
+        network_config = {
+            "Mode": "host",
+            "DynamicPorts": [
+                {
+                    "Label": "http",
+                    "To": port,
+                }
+            ],
+        }
+    
     return {
         "ID": job_id,
         "Name": job_id,
@@ -390,38 +464,12 @@ def create_sandbox_job(
                     "HealthCheck": "task_states",
                     "MinHealthyTime": 0,
                 },
-                "Networks": [
-                    {
-                        "Mode": "host",
-                        "DynamicPorts": [
-                            {
-                                "Label": "http",
-                                "To": port,
-                            }
-                        ],
-                    }
-                ],
+                "Networks": [network_config],
                 "Tasks": [
                     {
                         "Name": "sandbox-server",
-                        "Driver": "docker",
-                        "Config": {
-                            "image": image,
-                            "force_pull": False,  # Use local image, don't try to pull
-                            "ports": ["http"],
-                            "privileged": privileged,
-                            "command": "python",
-                            "args": [
-                                "sandbox_server.py",
-                                "--port", str(port),
-                                "--slots", str(slots_per_container),
-                                "--data-dir", "/data",
-                            ],
-                            # Note: On Linux, you can mount persistent storage:
-                            # "volumes": ["${NOMAD_ALLOC_DIR}/data:/data"],
-                            # On macOS/Docker Desktop, skip volumes for PoC
-                            # (container /data is ephemeral but works for testing)
-                        },
+                        "Driver": task_driver,
+                        "Config": task_config,
                         "Env": {
                             "PYTHONUNBUFFERED": "1",
                             "NOMAD_ALLOC_DIR": "${NOMAD_ALLOC_DIR}",

atropos/slots/pool.py

@@ -44,6 +44,11 @@ class SlotPoolConfig:
     cpu: int = 500  # MHz
     memory: int = 512  # MB
     
+    # Driver selection: "docker" or "singularity"
+    driver: str = "docker"
+    # Path to .sif file for singularity driver (required if driver="singularity")
+    singularity_image: Optional[str] = None
+    
     # Scaling settings
     min_containers: int = 1
     max_containers: int = 10
@@ -238,7 +243,7 @@ class SlotPool:
 
             if job is None:
                 # Deploy new job
-                logger.info(f"Deploying sandbox job: {self.config.job_id}")
+                logger.info(f"Deploying sandbox job: {self.config.job_id} (driver={self.config.driver})")
                 job_spec = create_sandbox_job(
                     job_id=self.config.job_id,
                     image=self.config.image,
@@ -248,6 +253,8 @@ class SlotPool:
                     cpu=self.config.cpu,
                     memory=self.config.memory,
                     datacenter=self.config.datacenter,
+                    driver=self.config.driver,
+                    singularity_image=self.config.singularity_image,
                 )
                 result = await self.nomad.submit_job(job_spec)
                 if "error" in result:

hermes_agent.egg-info/PKG-INFO

@@ -647,3 +647,13 @@ All environment variables can be configured in the `.env` file (copy from `.env.
 | `skills/` | On-demand knowledge documents |
 | `docs/` | Documentation |
 | `configs/` | Example batch run scripts |
+
+# Atropos Integrations & RL Training
+
+## Nomad Setup
+Follow this: https://developer.hashicorp.com/nomad/docs/deploy
+
+## Atropos dependencies
+python3 -m venv .venv
+source .venv/bin/activate
+pip install -e '.[atropos]'

hermes_agent.egg-info/SOURCES.txt

@@ -15,8 +15,13 @@ atropos/agent/atropos_agent.py
 atropos/api/__init__.py
 atropos/api/tool_executor_server.py
 atropos/api/tool_server.py
+atropos/backends/__init__.py
+atropos/backends/base.py
+atropos/backends/modal_backend.py
+atropos/backends/nomad_backend.py
 atropos/envs/__init__.py
 atropos/envs/agent_env.py
+atropos/envs/hermes_compat_test_env.py
 atropos/envs/sandbox_terminal_smoke_env.py
 atropos/envs/swe_smith_oracle_env.py
 atropos/envs/test_env.py
@@ -50,6 +55,7 @@ tests/test_modal_terminal.py
 tests/test_nous_api_limits.py
 tests/test_nous_api_pattern.py
 tests/test_temperature_fix.py
+tests/test_tool_call_parsing.py
 tests/test_web_tools.py
 tools/__init__.py
 tools/browser_tool.py

memory-bank/activeContext.md

@@ -0,0 +1,62 @@
+# Active Context
+
+## Current Focus
+Singularity/Apptainer integration for HPC environments has been **COMPLETED AND TESTED**.
+
+## Recently Completed (Feb 6, 2026)
+
+### Singularity/Apptainer Sandbox Integration - FULLY WORKING
+Successfully adapted the Atropos implementation from Docker to Singularity/Apptainer for HPC clusters where Docker cannot run without sudo permissions.
+
+**Files Modified:**
+1. `atropos/nomad/client.py` - Added `driver` and `singularity_image` parameters to `create_sandbox_job()`; Fixed port detection to check both `DynamicPorts` and `ReservedPorts` in `get_job_allocations()`
+2. `atropos/slots/pool.py` - Added `driver` and `singularity_image` to `SlotPoolConfig`
+3. `atropos/backends/nomad_backend.py` - Added driver options to `NomadBackendConfig`
+4. `atropos/envs/agent_env.py` - Added CLI arguments `--env.driver` and `--env.singularity_image` to `AgentEnvConfig`
+
+**Files Created:**
+1. `nomad-singularity.hcl` - Nomad config with raw_exec driver enabled
+2. `atropos/atropos-sandbox.sif` - Singularity image (80MB) built from Docker image
+3. `test_singularity_job.py` - Test script for Singularity integration
+
+**Key Implementation Details:**
+- Uses Nomad's `raw_exec` driver to run `apptainer` commands
+- Shell wrapper (`/bin/sh -c`) ensures Nomad environment variables expand correctly
+- Binds Nomad allocation directory to `/data` for workspace persistence
+- Uses **static ports** (`ReservedPorts`) instead of dynamic ports since raw_exec runs directly on host
+- `get_job_allocations()` now checks both `DynamicPorts` (Docker) and `ReservedPorts` (Singularity)
+
+**Test Results (All Passing):**
+- Health check: ✅ Server responding with 5 slots
+- Bash execution: ✅ Commands execute inside Singularity container
+- Write file: ✅ File written to slot workspace
+- Read file: ✅ File read back successfully
+
+## Usage
+
+### For Docker (default):
+```python
+config = SlotPoolConfig(
+    driver="docker",
+    image="atropos-sandbox:local",
+)
+```
+
+### For Singularity/Apptainer:
+```python
+config = SlotPoolConfig(
+    driver="singularity",
+    singularity_image="/path/to/atropos-sandbox.sif",
+)
+```
+
+### Nomad Configuration:
+```bash
+# Start Nomad with Singularity support
+nomad agent -dev -config=nomad-singularity.hcl
+```
+
+## Next Steps
+- Deploy to HPC cluster for production testing
+- Consider adding bubblewrap (bwrap) support inside Singularity for additional sandboxing
+- Document HPC-specific deployment procedures in skills/mlops/

memory-bank/productContext.md

@@ -0,0 +1,55 @@
+# Product Context: Hermes-Agent
+
+## Why This Project Exists
+
+Hermes-Agent addresses several key challenges in the AI agent space:
+
+1. **Unified Tool Interface** - Provides a clean, consistent interface for LLMs to use various tools (web, terminal, browser, vision, etc.) without requiring custom integration for each model provider.
+
+2. **Training Data Generation** - Enables efficient generation of high-quality tool-calling trajectories for fine-tuning LLMs, with features like batch processing, checkpointing, and trajectory compression.
+
+3. **Flexible Deployment** - Supports multiple execution environments (local, Docker, Singularity, Modal, SSH) to accommodate different security and isolation requirements.
+
+4. **Developer Experience** - Offers a beautiful, interactive CLI with kawaii-style feedback that makes working with AI agents enjoyable.
+
+## Problems It Solves
+
+### For AI Researchers
+- **Data Generation at Scale**: Parallel batch processing with content-based checkpointing for fault tolerance
+- **Clean Trajectories**: Trajectory compression to fit token budgets while preserving important information
+- **Toolset Distributions**: Probability-based tool selection for varied training data
+
+### For Developers
+- **Tool Orchestration**: Logical grouping of tools into toolsets (research, development, debugging, etc.)
+- **Session Persistence**: Conversation history and session logging for debugging
+- **Multi-Model Support**: Works with any OpenAI-compatible API (OpenRouter, local models, etc.)
+
+### For MLOps
+- **Skills System**: On-demand knowledge documents for specific tools/frameworks (Axolotl, vLLM, TRL, etc.)
+- **Sandboxed Execution**: Terminal commands can run in isolated environments (Docker, Singularity, Modal)
+- **Configurable Backends**: Easy switching between local and cloud execution
+
+## How It Should Work
+
+### User Flow (CLI)
+1. User launches `./hermes` 
+2. Beautiful welcome banner displays with caduceus logo, model info, and available tools
+3. User types a natural language request
+4. Agent processes request, potentially calling tools with animated feedback
+5. Agent responds with results, conversation continues
+6. Session is automatically logged for debugging
+
+### User Flow (Batch Processing)
+1. User prepares JSONL file with prompts
+2. Runs `batch_runner.py` with distribution and worker count
+3. System processes prompts in parallel, saves checkpoints
+4. Completed trajectories saved to `data/<run_name>/trajectories.jsonl`
+5. Optional: compress trajectories with `trajectory_compressor.py`
+
+## User Experience Goals
+
+- **Delightful Interaction**: Kawaii ASCII faces, animated spinners, cute messages
+- **Informative Feedback**: Clear progress indication during tool execution
+- **Configurable Personalities**: From "helpful" to "pirate" to "Shakespeare"
+- **Easy Configuration**: YAML config file + environment variables + CLI flags
+- **Graceful Degradation**: Missing tools/APIs don't break the system, just disable features

memory-bank/progress.md

@@ -0,0 +1,67 @@
+# Progress
+
+## Completed Features
+
+### ✅ Singularity/Apptainer Sandbox Integration (Feb 6, 2026 - FULLY TESTED)
+Adapted the Atropos sandbox environment from Docker to Singularity/Apptainer for HPC clusters.
+
+**What Works:**
+- `create_sandbox_job()` supports both `driver="docker"` and `driver="singularity"`
+- SlotPoolConfig and NomadBackendConfig propagate driver settings
+- Singularity container runs sandbox_server.py via Nomad's raw_exec driver
+- All sandbox operations work: bash execution, file read/write
+- Nomad environment variables properly expanded via shell wrapper
+- **CLI arguments** `--env.driver` and `--env.singularity_image` for AgentEnvConfig
+- **Static port binding** for Singularity (ReservedPorts vs DynamicPorts)
+- **Port detection** works for both Docker and Singularity allocations
+
+**CLI Usage:**
+```bash
+python -m atropos.envs.swe_smith_oracle_env process \
+    --env.driver singularity \
+    --env.singularity_image /path/to/atropos-sandbox.sif
+```
+
+**Created Files:**
+- `nomad-singularity.hcl` - Nomad config with raw_exec enabled
+- `atropos/atropos-sandbox.sif` - 80MB Singularity image
+- `test_singularity_job.py` - Integration test script
+
+**Modified Files:**
+- `atropos/nomad/client.py` - driver support + ReservedPorts detection
+- `atropos/slots/pool.py` - driver config fields
+- `atropos/backends/nomad_backend.py` - driver config fields
+- `atropos/envs/agent_env.py` - CLI arguments for driver selection
+
+### ✅ Memory Bank Initialized (Feb 5, 2026)
+Set up project documentation structure for context persistence.
+
+## In Progress
+None currently.
+
+## Known Issues
+- `bwrap_available: false` in Singularity containers - bubblewrap sandboxing not available inside the container (kernel namespaces already in use)
+- Health check timing - may need longer wait for container startup on slower systems
+
+## What's Left to Build
+
+### HPC Deployment
+- [ ] Test on actual HPC cluster with Slurm/PBS integration
+- [ ] Document cluster-specific deployment procedures
+- [ ] Add support for shared filesystem workspace binding
+
+### Enhanced Sandboxing
+- [ ] Investigate alternative sandboxing inside Singularity (seccomp, etc.)
+- [ ] Add network isolation options for Singularity
+
+### Documentation
+- [ ] Add Singularity deployment to README
+- [ ] Create HPC deployment skill in skills/mlops/
+
+## Evolution of Decisions
+
+### Container Runtime Selection
+- **Initial**: Docker-only via Nomad docker driver
+- **Problem**: HPC clusters don't allow Docker without sudo
+- **Solution**: Added Singularity/Apptainer support via raw_exec driver
+- **Result**: Both runtimes now supported with same API

memory-bank/projectbrief.md

@@ -0,0 +1,44 @@
+# Project Brief: Hermes-Agent
+
+## Overview
+Hermes-Agent is an AI agent harness for LLMs with advanced tool-calling capabilities, featuring a flexible toolsets system for organizing and managing tools. Named after Hermes, the Greek messenger god, it serves as a bridge between human intent and AI-powered task execution.
+
+## Core Requirements
+
+### Primary Goals
+1. **Interactive CLI Experience** - Beautiful terminal interface with animated feedback, personalities, and session management
+2. **Flexible Tool System** - Modular tools organized into logical toolsets for different use cases
+3. **Batch Processing** - Process multiple prompts in parallel with checkpointing and statistics
+4. **Multi-Backend Support** - Support for local, Docker, Singularity, Modal, and SSH terminal backends
+5. **Training Data Generation** - Save conversation trajectories in formats suitable for LLM fine-tuning
+
+### Target Users
+- AI researchers generating training data
+- Developers needing an AI assistant with tool access
+- MLOps practitioners automating workflows
+- Anyone needing a powerful CLI-based AI agent
+
+## Scope
+
+### In Scope
+- Interactive CLI with rich formatting and kawaii-style feedback
+- Web tools (search, extract, crawl via Firecrawl)
+- Terminal tools (command execution across multiple backends)
+- Browser automation (via agent-browser + Browserbase)
+- Vision tools (image analysis)
+- Image generation (FLUX via FAL.ai)
+- Mixture-of-Agents reasoning
+- Skills system for on-demand knowledge
+- Batch processing with parallel workers
+- Trajectory compression for training
+
+### Out of Scope (Current)
+- Proactive suggestions (agent only runs on request)
+- Clipboard integration (no local system access)
+- Real-time streaming of thinking/reasoning (deferred)
+
+## Success Metrics
+- Clean, maintainable tool architecture
+- Reliable tool execution with proper error handling
+- Efficient context management for long conversations
+- High-quality trajectory data for training

memory-bank/systemPatterns.md

@@ -0,0 +1,149 @@
+# System Patterns: Hermes-Agent
+
+## Architecture Overview
+
+```
+┌─────────────────────────────────────────────────────────────────┐
+│                           CLI (cli.py)                          │
+│  - Rich welcome banner with caduceus                            │
+│  - prompt_toolkit for input with history                        │
+│  - Kawaii-style feedback and personalities                      │
+└────────────────────────────┬────────────────────────────────────┘
+                             │
+                             ▼
+┌─────────────────────────────────────────────────────────────────┐
+│                     AIAgent (run_agent.py)                      │
+│  - Conversation loop with tool calling                          │
+│  - KawaiiSpinner for animated feedback                          │
+│  - Retry logic with exponential backoff                         │
+│  - Session logging to logs/ directory                           │
+└────────────────────────────┬────────────────────────────────────┘
+                             │
+                             ▼
+┌─────────────────────────────────────────────────────────────────┐
+│                   Tool Routing (model_tools.py)                 │
+│  - get_tool_definitions() - returns tools for API calls         │
+│  - handle_function_call() - dispatches to tool handlers         │
+│  - Toolset filtering (enabled/disabled)                         │
+└────────────────────────────┬────────────────────────────────────┘
+                             │
+           ┌─────────────────┼─────────────────┐
+           ▼                 ▼                 ▼
+    ┌───────────┐     ┌───────────┐     ┌───────────┐
+    │ Web Tools │     │ Terminal  │     │ Browser   │
+    │ (Firecrawl)│    │ (mini-swe)│     │(agent-brw)│
+    └───────────┘     └───────────┘     └───────────┘
+           │                 │                 │
+           └─────────────────┼─────────────────┘
+                             ▼
+                    ┌───────────────┐
+                    │  Toolsets     │
+                    │  (toolsets.py)│
+                    │  Composition  │
+                    └───────────────┘
+```
+
+## Key Design Patterns
+
+### 1. Toolset Composition Pattern
+Toolsets can include other toolsets, allowing flexible composition:
+
+```python
+TOOLSETS = {
+    "web": {"tools": ["web_search", "web_extract"], "includes": []},
+    "debugging": {"tools": ["terminal"], "includes": ["web"]},
+    "full_stack": {"tools": [], "includes": ["web", "terminal", "vision", "browser"]}
+}
+```
+
+Resolution is recursive with cycle detection.
+
+### 2. Graceful Degradation Pattern
+Each tool module has a `check_*_requirements()` function:
+- Tools are only loaded if requirements are met
+- Missing API keys disable tools, not crash the system
+- Import errors are caught and tools marked unavailable
+
+```python
+try:
+    from tools.web_tools import web_search_tool, check_firecrawl_api_key
+except ModuleNotFoundError:
+    web_search_tool = None
+    def check_firecrawl_api_key(): return False
+```
+
+### 3. Session Isolation Pattern (task_id)
+Stateful tools (terminal, browser) use `task_id` to isolate concurrent sessions:
+- Each batch worker gets unique task_id
+- VMs and browser sessions are tracked per task_id
+- Cleanup functions release resources: `cleanup_vm(task_id)`, `cleanup_browser(task_id)`
+
+### 4. Trajectory Format Pattern
+Conversations are saved in ShareGPT format for training:
+
+```json
+{"from": "system", "value": "System prompt with <tools>...</tools>"}
+{"from": "human", "value": "User message"}
+{"from": "gpt", "value": "<think>reasoning</think>\n<tool_call>{...}</tool_call>"}
+{"from": "tool", "value": "<tool_response>{...}</tool_response>"}
+{"from": "gpt", "value": "Final response"}
+```
+
+### 5. Ephemeral System Prompt Pattern
+Guide model behavior during data collection without saving to trajectories:
+- `ephemeral_system_prompt` influences execution
+- Only standard tool-calling system prompt saved to trajectories
+- Keeps training data clean
+
+### 6. Retry with Validation Pattern
+The agent validates responses before accepting:
+- Check tool names against `valid_tool_names` set
+- Validate JSON arguments can be parsed
+- Check for content after `<think>` blocks
+- Roll back to last valid state on persistent failures
+
+## Component Relationships
+
+### AIAgent Class
+- Central orchestrator for conversations
+- Manages conversation history
+- Calls OpenAI-compatible API
+- Routes tool calls to handlers
+- Provides animated feedback (KawaiiSpinner)
+
+### Tool Modules (tools/*.py)
+- Self-contained tool implementations
+- Export: handler function + check function + schema
+- Return JSON strings (never raw dicts)
+- Accept optional `task_id` for stateful tools
+
+### Toolsets System (toolsets.py)
+- Defines logical groupings of tools
+- Supports composition via `includes`
+- `resolve_toolset()` recursively resolves all tools
+- `validate_toolset()` checks if name is valid
+
+### Model Tools (model_tools.py)
+- Aggregates all tool definitions
+- Routes function calls to correct handlers
+- Filters tools based on enabled/disabled toolsets
+- Bridge between agent and tool implementations
+
+## Critical Implementation Paths
+
+### Tool Execution Flow
+1. AIAgent receives tool_calls from API response
+2. Validates tool names against `valid_tool_names`
+3. Validates JSON arguments can be parsed
+4. Calls `handle_function_call()` with tool name, args, task_id
+5. `handle_function_call()` routes to appropriate handler
+6. Tool executes, returns JSON string
+7. Result added to conversation as tool message
+8. Loop continues until natural language response
+
+### Configuration Loading Flow
+1. `cli.py` calls `load_cli_config()`
+2. Loads `cli-config.yaml`, merges with defaults
+3. Sets environment variables for terminal config
+4. `AIAgent` reads env vars when initializing terminal tool
+5. Terminal tool creates appropriate backend based on `TERMINAL_ENV`

memory-bank/techContext.md

@@ -0,0 +1,113 @@
+# Technical Context: Hermes-Agent
+
+## Technologies Used
+
+### Core Stack
+- **Python 3.11+** - Primary language
+- **OpenAI SDK** - For LLM API interactions (OpenAI-compatible)
+- **OpenRouter** - Default LLM provider (supports multiple models)
+- **Rich** - Terminal formatting and panels
+- **prompt_toolkit** - Interactive input with history
+- **Fire** - CLI argument parsing
+- **PyYAML** - Configuration files
+- **python-dotenv** - Environment variable management
+
+### Tool Dependencies
+- **Firecrawl** - Web search and extraction (`FIRECRAWL_API_KEY`)
+- **mini-swe-agent** - Terminal tool backend (local/docker/singularity/modal/ssh)
+- **agent-browser** - Browser automation (npm package)
+- **Browserbase** - Cloud browser execution (`BROWSERBASE_API_KEY`)
+- **FAL.ai** - Image generation with FLUX (`FAL_KEY`)
+- **Nous API** - Vision and MoA tools (`NOUS_API_KEY`)
+
+### Optional Dependencies
+- **Modal** - Cloud compute for sandboxed environments
+- **Singularity/Apptainer** - Rootless containers (HPC environments)
+- **Docker** - Container isolation
+
+## Development Setup
+
+### Quick Start
+```bash
+# Clone with submodules
+git clone --recurse-submodules https://github.com/NousResearch/Hermes-Agent.git
+cd Hermes-Agent
+
+# Create virtual environment
+python3 -m venv venv
+source venv/bin/activate
+
+# Install dependencies
+pip install -r requirements.txt
+pip install -e ./mini-swe-agent
+
+# Install browser tools (optional)
+npm install
+
+# Configure environment
+cp .env.example .env
+# Edit .env with your API keys
+```
+
+### Key Configuration Files
+- `.env` - API keys and secrets
+- `cli-config.yaml` - CLI configuration (model, terminal, toolsets, personalities)
+- `configs/` - Batch run scripts and configuration
+
+### Environment Variables
+
+**Required for Full Functionality:**
+- `OPENROUTER_API_KEY` - Primary LLM access
+- `FIRECRAWL_API_KEY` - Web tools
+- `NOUS_API_KEY` - Vision and reasoning tools
+- `FAL_KEY` - Image generation
+
+**Terminal Backend:**
+- `TERMINAL_ENV` - Backend type: `local`, `docker`, `singularity`, `modal`, `ssh`
+- `TERMINAL_CWD` - Working directory
+- `TERMINAL_DOCKER_IMAGE` / `TERMINAL_SINGULARITY_IMAGE` - Container images
+- `TERMINAL_SSH_HOST/USER/KEY` - SSH backend config
+- `SUDO_PASSWORD` - Optional sudo support
+
+**Browser:**
+- `BROWSERBASE_API_KEY` - Browser automation
+- `BROWSERBASE_PROJECT_ID` - Browserbase project
+
+## Technical Constraints
+
+1. **Context Window Limits** - Long tool outputs can exhaust context; trajectory compression helps
+2. **API Rate Limits** - OpenRouter and tool APIs have rate limits; exponential backoff implemented
+3. **Tool Availability** - Tools gracefully degrade if dependencies/keys missing
+4. **Async Compatibility** - Some tools are async, handled via `asyncio.run()` in sync context
+
+## Dependency Graph
+
+```
+tools/*.py → tools/__init__.py → model_tools.py → toolsets.py → toolset_distributions.py
+                                       ↑
+run_agent.py ──────────────────────────┘
+cli.py → run_agent.py (uses AIAgent with quiet_mode=True)
+batch_runner.py → run_agent.py + toolset_distributions.py
+```
+
+## Tool Usage Patterns
+
+### Adding a New Tool
+1. Create `tools/your_tool.py` with handler + requirements check
+2. Export in `tools/__init__.py`
+3. Register in `model_tools.py` (definitions + handler routing)
+4. Add to toolset in `toolsets.py`
+5. Optionally add to `toolset_distributions.py` for batch processing
+
+### Tool Handler Pattern
+```python
+def your_tool(param: str, task_id: str = None) -> str:
+    """Execute tool and return JSON string result."""
+    try:
+        result = {"success": True, "data": "..."}
+        return json.dumps(result, ensure_ascii=False)
+    except Exception as e:
+        return json.dumps({"error": str(e)}, ensure_ascii=False)
+```
+
+All tool handlers MUST return a JSON string, never raw dicts.

nomad-singularity.hcl

@@ -0,0 +1,31 @@
+# Nomad Configuration for Singularity/Apptainer Sandbox
+# Run with: nomad agent -dev -config=nomad-singularity.hcl
+#
+# This uses the raw_exec driver to run Apptainer containers.
+# Suitable for HPC environments where Docker cannot run without sudo.
+
+client {
+  enabled = true
+
+  options {
+    # Enable raw_exec driver for Singularity/Apptainer
+    "driver.raw_exec.enable" = "1"
+  }
+}
+
+# raw_exec driver plugin configuration
+plugin "raw_exec" {
+  config {
+    enabled = true
+  }
+}
+
+# Optional: If you have the nomad-driver-singularity plugin installed,
+# uncomment the following instead of using raw_exec:
+# plugin "singularity" {
+#   config {
+#     enabled = true
+#     # Allow bind mounts
+#     bind_paths = ["/tmp", "/var/tmp"]
+#   }
+# }

test_singularity_job.py

@@ -0,0 +1,126 @@
+#!/usr/bin/env python3
+"""
+Test script for Singularity sandbox job creation.
+
+This tests the create_sandbox_job function with driver="singularity".
+"""
+
+import asyncio
+import sys
+import json
+import importlib.util
+
+# Load atropos.nomad.client directly to bypass __init__.py
+spec = importlib.util.spec_from_file_location(
+    "nomad_client",
+    "/root/Hermes-Agent/atropos/nomad/client.py"
+)
+nomad_client = importlib.util.module_from_spec(spec)
+sys.modules["nomad_client"] = nomad_client
+spec.loader.exec_module(nomad_client)
+
+NomadClient = nomad_client.NomadClient
+create_sandbox_job = nomad_client.create_sandbox_job
+
+
+async def test_singularity_job():
+    """Test Singularity job creation and submission to Nomad."""
+    
+    job_id = "test-singularity-sandbox"
+    sif_path = "/root/Hermes-Agent/atropos/atropos-sandbox.sif"
+    
+    print("=== Singularity Sandbox Job Test ===\n")
+    
+    # Create job spec for Singularity
+    print("Creating Singularity job spec...")
+    job_spec = create_sandbox_job(
+        job_id=job_id,
+        driver="singularity",
+        singularity_image=sif_path,
+        slots_per_container=5,
+        count=1,
+        cpu=500,
+        memory=512,
+    )
+    
+    # Print task driver and config
+    task = job_spec["TaskGroups"][0]["Tasks"][0]
+    print(f"  Driver: {task['Driver']}")
+    print(f"  Config: {json.dumps(task['Config'], indent=4)}")
+    print()
+    
+    # Test submission to Nomad
+    print("Connecting to Nomad...")
+    client = NomadClient(address="http://localhost:4646")
+    
+    try:
+        # Check health
+        healthy = await client.is_healthy()
+        print(f"  Nomad healthy: {healthy}")
+        
+        if not healthy:
+            print("❌ Nomad is not reachable!")
+            return False
+        
+        # Purge any existing job
+        print(f"\nPurging existing job '{job_id}'...")
+        await client.stop_job(job_id, purge=True)
+        
+        # Submit job
+        print(f"Submitting Singularity job '{job_id}'...")
+        result = await client.submit_job(job_spec)
+        print(f"  Result: {result}")
+        
+        if "error" in result:
+            print(f"❌ Job submission failed: {result}")
+            return False
+        
+        # Wait for allocation
+        print("\nWaiting for allocation (10 seconds)...")
+        await asyncio.sleep(10)
+        
+        # Check allocations
+        allocs = await client.get_job_allocations(job_id)
+        print(f"Allocations: {len(allocs)}")
+        for alloc in allocs:
+            print(f"  - {alloc.id[:8]} status={alloc.status.value} http={alloc.http_address}")
+            
+            # Get detailed info
+            detail = await client.get_allocation(alloc.id)
+            if detail:
+                task_states = detail.get("TaskStates", {})
+                for task_name, state in task_states.items():
+                    events = state.get("Events", [])[-3:]
+                    print(f"    Task '{task_name}': {[e.get('Type') for e in events]}")
+        
+        # Check if any are running
+        running = [a for a in allocs if a.status.value == "running"]
+        if running:
+            print(f"\n✅ Job running! {len(running)} allocation(s)")
+            
+            # Try to reach the sandbox server
+            if running[0].http_address:
+                import aiohttp
+                try:
+                    async with aiohttp.ClientSession() as session:
+                        async with session.get(f"{running[0].http_address}/health", timeout=aiohttp.ClientTimeout(total=5)) as resp:
+                            print(f"  Health check: {resp.status} - {await resp.text()}")
+                except Exception as e:
+                    print(f"  Health check failed: {e}")
+        else:
+            print("\n⚠️ No running allocations yet (may still be starting)")
+            
+        return True
+        
+    finally:
+        # Don't cleanup - leave running for debugging
+        print(f"\n[Leaving job '{job_id}' running for debugging]")
+        print(f"  View logs: nomad alloc logs -job {job_id}")
+        print(f"  Cleanup: nomad job stop -purge {job_id}")
+        await client.close()
+        print("Done!")
+
+
+if __name__ == "__main__":
+    success = asyncio.run(test_singularity_job())
+    sys.exit(0 if success else 1)

test_singularity_sandbox.py

@@ -0,0 +1,108 @@
+#!/usr/bin/env python3
+"""
+Test script for Singularity/Apptainer sandbox integration.
+
+This tests the SlotPool with driver="singularity" using the raw_exec Nomad driver.
+"""
+
+import asyncio
+import sys
+import os
+
+# Add parent to path for imports
+sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
+
+from atropos.slots.pool import SlotPool, SlotPoolConfig
+
+
+async def test_singularity_sandbox():
+    """Test the Singularity sandbox deployment and basic execution."""
+    
+    # Configure for Singularity
+    config = SlotPoolConfig(
+        nomad_address="http://localhost:4646",
+        job_id="atropos-sandbox-singularity",
+        driver="singularity",
+        singularity_image="/root/Hermes-Agent/atropos/atropos-sandbox.sif",
+        slots_per_container=5,
+        min_containers=1,
+        max_containers=2,
+        cpu=500,
+        memory=512,
+        purge_job_on_start=True,  # Clean start for testing
+    )
+    
+    print(f"Testing Singularity sandbox with config:")
+    print(f"  driver: {config.driver}")
+    print(f"  singularity_image: {config.singularity_image}")
+    print(f"  job_id: {config.job_id}")
+    print()
+    
+    pool = SlotPool(config)
+    
+    try:
+        print("Starting SlotPool...")
+        await pool.start()
+        
+        stats = pool.get_stats()
+        print(f"Pool started! Stats: {stats}")
+        print()
+        
+        # Acquire a slot
+        print("Acquiring slot...")
+        slot = await pool.acquire("test-trajectory-001")
+        print(f"Acquired slot: {slot.slot_id} (alloc={slot.alloc_id[:8]})")
+        print()
+        
+        # Execute a simple command
+        print("Executing 'echo hello from singularity'...")
+        result = await pool.execute(
+            slot,
+            "bash",
+            {"command": "echo 'Hello from Singularity sandbox!' && uname -a"}
+        )
+        print(f"Result: {result}")
+        print()
+        
+        # Test file write
+        print("Testing file write...")
+        write_result = await pool.execute(
+            slot,
+            "write_file",
+            {"path": "test.txt", "content": "Test file from Singularity!"}
+        )
+        print(f"Write result: {write_result}")
+        
+        # Test file read
+        print("Testing file read...")
+        read_result = await pool.execute(
+            slot,
+            "read_file",
+            {"path": "test.txt"}
+        )
+        print(f"Read result: {read_result}")
+        print()
+        
+        # Release slot
+        print("Releasing slot...")
+        await pool.release(slot)
+        
+        print("✅ All tests passed!")
+        
+    except Exception as e:
+        print(f"❌ Error: {e}")
+        import traceback
+        traceback.print_exc()
+        return False
+    
+    finally:
+        print("\nStopping pool...")
+        await pool.stop(purge_job=True)
+        print("Pool stopped.")
+    
+    return True
+
+
+if __name__ == "__main__":
+    success = asyncio.run(test_singularity_sandbox())
+    sys.exit(0 if success else 1)

wandb/latest-run

@@ -0,0 +1 @@
+run-20260206_003827-82b0oahi

wandb/run-20260206_003827-82b0oahi/files/config.yaml

@@ -0,0 +1,180 @@
+_wandb:
+    value:
+        cli_version: 0.24.2
+        e:
+            2gw7xuffca69jbm2b60l3w5ymo5pb5lf:
+                args:
+                    - process
+                    - --env.driver
+                    - singularity
+                    - --env.singularity_image
+                    - /root/Hermes-Agent/atropos/atropos-sandbox.sif
+                email: shannon@nousresearch.com
+                executable: /root/Hermes-Agent/.venv/bin/python
+                git:
+                    commit: 4d619bcd21feedc9eed36c53c038585d97e7295e
+                    remote: https://github.com/NousResearch/Hermes-Agent.git
+                host: vultr
+                os: Linux-6.8.0-90-generic-x86_64-with-glibc2.39
+                program: -m atropos.envs.swe_smith_oracle_env
+                python: CPython 3.12.3
+                root: /root/Hermes-Agent
+                startedAt: "2026-02-06T00:38:27.351013Z"
+                writerId: 2gw7xuffca69jbm2b60l3w5ymo5pb5lf
+        m: []
+        python_version: 3.12.3
+        t:
+            "1":
+                - 11
+                - 49
+                - 51
+                - 95
+            "3":
+                - 13
+                - 16
+            "4": 3.12.3
+            "5": 0.24.2
+            "6": 5.0.0
+            "12": 0.24.2
+            "13": linux-x86_64
+acquire_timeout_s:
+    value: 30
+agent_max_steps:
+    value: 50
+agent_max_tokens:
+    value: null
+agent_temperature:
+    value: 0.7
+agent_tool_delay_s:
+    value: 0
+allow_network:
+    value: true
+batch_size:
+    value: 1
+custom_thinking_prompt:
+    value: null
+data_dir_to_save_evals:
+    value: null
+data_path_to_save_groups:
+    value: data/swe_smith_oracle_env_2.jsonl
+dataset_name:
+    value: NousResearch/SWE-smith-oracle
+dataset_split:
+    value: train
+disabled_toolsets:
+    value: []
+driver:
+    value: singularity
+enabled_toolsets:
+    value:
+        - terminal
+ensure_scores_are_not_same:
+    value: false
+eval_handling:
+    value: STOP_TRAIN
+eval_limit_ratio:
+    value: 0.5
+group_size:
+    value: 1
+include_messages:
+    value: true
+inference_weight:
+    value: 1
+install_timeout_s:
+    value: 600
+max_batches_offpolicy:
+    value: 3
+max_containers:
+    value: 10
+max_eval_workers:
+    value: 16
+max_items:
+    value: 0
+max_num_workers:
+    value: -1
+max_num_workers_per_node:
+    value: 8
+max_reasoning_tokens:
+    value: null
+max_token_length:
+    value: 8192
+min_batch_allocation:
+    value: null
+min_containers:
+    value: 1
+min_items_sent_before_logging:
+    value: 2
+modal_app_name:
+    value: atropos-sandbox
+modal_function_name:
+    value: sandbox_server
+modal_volume_mount_path:
+    value: /data
+modal_volume_name:
+    value: null
+nomad_address:
+    value: http://localhost:4646
+num_rollouts_per_group_for_logging:
+    value: 1
+num_rollouts_to_keep:
+    value: 32
+privileged:
+    value: false
+prompt_mode:
+    value: problem_statement
+purge_job_on_shutdown:
+    value: true
+purge_job_on_start:
+    value: true
+python_only:
+    value: true
+reasoning_effort:
+    value: null
+repo_base_url:
+    value: https://github.com
+require_sandbox:
+    value: false
+require_stateful_sandbox:
+    value: false
+rollout_server_url:
+    value: http://localhost:8000
+sandbox_image:
+    value: atropos-sandbox:local
+sandbox_job_id:
+    value: atropos-sandbox-agent-env
+score_include_fail_to_pass:
+    value: true
+seed:
+    value: 0
+shuffle:
+    value: true
+singularity_image:
+    value: /root/Hermes-Agent/atropos/atropos-sandbox.sif
+slots_per_container:
+    value: 10
+steps_per_eval:
+    value: 1
+test_timeout_s:
+    value: 600
+thinking_mode:
+    value: false
+tokenizer_name:
+    value: NousResearch/Hermes-4.3-36B
+tool_batch_window_ms:
+    value: 20
+tool_max_batch_size:
+    value: 200
+tool_pool_mode:
+    value: nomad
+tool_server_token:
+    value: null
+tool_server_url:
+    value: null
+total_steps:
+    value: 1
+use_wandb:
+    value: true
+wandb_name:
+    value: swe_smith_oracle
+worker_timeout:
+    value: 600