@bgicli/bgicli 2.1.1 → 2.2.1

package/data/skills/performance-profiling/SKILL.md

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+---
+name: performance-profiling
+description: Identify computational bottlenecks, analyze scaling behavior, estimate memory requirements, and receive optimization recommendations for any computational simulation. Use when simulations are slow, investigating parallel efficiency, planning resource allocation, or seeking performance improvements through timing analysis, scaling studies, memory profiling, or bottleneck detection.
+allowed-tools: Read, Bash, Write, Grep, Glob
+---
+
+# Performance Profiling
+
+## Goal
+
+Provide tools to analyze simulation performance, identify bottlenecks, and recommend optimization strategies for computational materials science simulations.
+
+## Requirements
+
+- Python 3.8+
+- No external dependencies (uses Python standard library only)
+- Works on Linux, macOS, and Windows
+
+## Inputs to Gather
+
+Before running profiling scripts, collect from the user:
+
+| Input | Description | Example |
+|-------|-------------|---------|
+| Simulation log | Log file with timing information | `simulation.log` |
+| Scaling data | JSON with multi-run performance data | `scaling_data.json` |
+| Simulation parameters | JSON with mesh, fields, solver config | `params.json` |
+| Available memory | System memory in GB (optional) | `16.0` |
+
+## Decision Guidance
+
+### When to Use Each Script
+
+```
+Need to identify slow phases?
+├── YES → Use timing_analyzer.py
+│         └── Parse simulation logs for timing data
+│
+Need to understand parallel performance?
+├── YES → Use scaling_analyzer.py
+│         └── Analyze strong or weak scaling efficiency
+│
+Need to estimate memory requirements?
+├── YES → Use memory_profiler.py
+│         └── Estimate memory from problem parameters
+│
+Need optimization recommendations?
+└── YES → Use bottleneck_detector.py
+          └── Combine analyses and get actionable advice
+```
+
+### Choosing Analysis Thresholds
+
+| Metric | Good | Acceptable | Poor |
+|--------|------|------------|------|
+| Phase dominance | <30% | 30-50% | >50% |
+| Parallel efficiency | >0.80 | 0.70-0.80 | <0.70 |
+| Memory usage | <60% | 60-80% | >80% |
+
+## Script Outputs (JSON Fields)
+
+| Script | Key Outputs |
+|--------|-------------|
+| `timing_analyzer.py` | `timing_data.phases`, `timing_data.slowest_phase`, `timing_data.total_time` |
+| `scaling_analyzer.py` | `scaling_analysis.results`, `scaling_analysis.efficiency_threshold_processors` |
+| `memory_profiler.py` | `memory_profile.total_memory_gb`, `memory_profile.per_process_gb`, `memory_profile.warnings` |
+| `bottleneck_detector.py` | `bottlenecks`, `recommendations` |
+
+## Workflow
+
+### Complete Profiling Workflow
+
+1. **Analyze timing** from simulation logs
+2. **Analyze scaling** from multi-run data (if available)
+3. **Profile memory** from simulation parameters
+4. **Detect bottlenecks** and get recommendations
+5. **Implement optimizations** based on recommendations
+6. **Re-profile** to verify improvements
+
+### Quick Profiling (Timing Only)
+
+1. **Run timing analyzer** on simulation log
+2. **Identify dominant phases** (>50% of runtime)
+3. **Apply targeted optimizations** to dominant phases
+
+## CLI Examples
+
+### Timing Analysis
+
+```bash
+# Basic timing analysis
+python3 scripts/timing_analyzer.py \
+    --log simulation.log \
+    --json
+
+# Custom timing pattern
+python3 scripts/timing_analyzer.py \
+    --log simulation.log \
+    --pattern 'Step\s+(\w+)\s+took\s+([\d.]+)s' \
+    --json
+```
+
+### Scaling Analysis
+
+```bash
+# Strong scaling (fixed problem size)
+python3 scripts/scaling_analyzer.py \
+    --data scaling_data.json \
+    --type strong \
+    --json
+
+# Weak scaling (constant work per processor)
+python3 scripts/scaling_analyzer.py \
+    --data scaling_data.json \
+    --type weak \
+    --json
+```
+
+### Memory Profiling
+
+```bash
+# Estimate memory requirements
+python3 scripts/memory_profiler.py \
+    --params simulation_params.json \
+    --available-gb 16.0 \
+    --json
+```
+
+### Bottleneck Detection
+
+```bash
+# Detect bottlenecks from timing only
+python3 scripts/bottleneck_detector.py \
+    --timing timing_results.json \
+    --json
+
+# Comprehensive analysis with all inputs
+python3 scripts/bottleneck_detector.py \
+    --timing timing_results.json \
+    --scaling scaling_results.json \
+    --memory memory_results.json \
+    --json
+```
+
+## Conversational Workflow Example
+
+**User**: My simulation is taking too long. Can you help me identify what's slow?
+
+**Agent workflow**:
+1. Ask for simulation log file
+2. Run timing analyzer:
+   ```bash
+   python3 scripts/timing_analyzer.py --log simulation.log --json
+   ```
+3. Interpret results:
+   - If solver dominates (>50%): Recommend preconditioner tuning
+   - If assembly dominates: Recommend caching or vectorization
+   - If I/O dominates: Recommend reducing output frequency
+4. If user has multi-run data, analyze scaling:
+   ```bash
+   python3 scripts/scaling_analyzer.py --data scaling.json --type strong --json
+   ```
+5. Generate comprehensive recommendations:
+   ```bash
+   python3 scripts/bottleneck_detector.py --timing timing.json --scaling scaling.json --json
+   ```
+
+## Interpretation Guidance
+
+### Timing Analysis
+
+| Scenario | Meaning | Action |
+|----------|---------|--------|
+| Solver >70% | Solver-dominated | Tune preconditioner, check tolerance |
+| Assembly >50% | Assembly-dominated | Cache matrices, vectorize, parallelize |
+| I/O >30% | I/O-dominated | Reduce frequency, use parallel I/O |
+| Balanced (<30% each) | Well-balanced | Look for algorithmic improvements |
+
+### Scaling Analysis
+
+| Efficiency | Meaning | Action |
+|------------|---------|--------|
+| >0.80 | Excellent scaling | Continue scaling up |
+| 0.70-0.80 | Good scaling | Monitor at larger scales |
+| 0.50-0.70 | Poor scaling | Investigate communication/load balance |
+| <0.50 | Very poor scaling | Reduce processor count or redesign |
+
+### Memory Profile
+
+| Usage | Meaning | Action |
+|-------|---------|--------|
+| <60% available | Safe | No action needed |
+| 60-80% available | Moderate | Monitor, consider optimization |
+| >80% available | High | Reduce resolution or increase processors |
+| >100% available | Exceeds capacity | Must reduce problem size |
+
+## Error Handling
+
+| Error | Cause | Resolution |
+|-------|-------|------------|
+| `Log file not found` | Invalid path | Verify log file path |
+| `No timing data found` | Pattern mismatch | Provide custom pattern with --pattern |
+| `At least 2 runs required` | Insufficient data | Provide more scaling runs |
+| `Missing required parameters` | Incomplete params | Add mesh and fields to params file |
+
+## Optimization Strategies by Bottleneck Type
+
+### Solver Bottlenecks
+- Use algebraic multigrid (AMG) preconditioner
+- Tighten solver tolerance if over-solving
+- Consider direct solver for small problems
+- Profile matrix assembly vs solve time
+
+### Assembly Bottlenecks
+- Cache element matrices if geometry is static
+- Use vectorized assembly routines
+- Consider matrix-free methods
+- Parallelize assembly with coloring
+
+### I/O Bottlenecks
+- Reduce output frequency
+- Use parallel I/O (HDF5, MPI-IO)
+- Write to fast scratch storage
+- Compress output data
+
+### Scaling Bottlenecks
+- Investigate communication overhead
+- Check for load imbalance
+- Reduce synchronization points
+- Use asynchronous communication
+- Consider hybrid MPI+OpenMP
+
+### Memory Bottlenecks
+- Reduce mesh resolution
+- Use iterative solver (lower memory than direct)
+- Enable out-of-core computation
+- Increase number of processors
+- Use single precision where appropriate
+
+## Limitations
+
+- **Log parsing**: Depends on pattern matching; may miss unusual formats
+- **Scaling analysis**: Requires at least 2 runs for meaningful results
+- **Memory estimation**: Approximate; actual usage may vary
+- **Recommendations**: General guidance; may need domain-specific tuning
+
+## References
+
+- `references/profiling_guide.md` - Profiling concepts and interpretation
+- `references/optimization_strategies.md` - Detailed optimization approaches
+
+## Version History
+
+- **v1.0.0** (2025-01-22): Initial release with 4 profiling scripts
+

package/data/skills/perplexity-search/SKILL.md

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+---
+name: perplexity-search
+description: Perform AI-powered web searches with real-time information using Perplexity models via LiteLLM and OpenRouter. This skill should be used when conducting web searches for current information, finding recent scientific literature, getting grounded answers with source citations, or accessing information beyond the model's knowledge cutoff. Provides access to multiple Perplexity models including Sonar Pro, Sonar Pro Search (advanced agentic search), and Sonar Reasoning Pro through a single OpenRouter API key.
+---
+
+# Perplexity Search
+
+## Overview
+
+Perform AI-powered web searches using Perplexity models through LiteLLM and OpenRouter. Perplexity provides real-time, web-grounded answers with source citations, making it ideal for finding current information, recent scientific literature, and facts beyond the model's training data cutoff.
+
+This skill provides access to all Perplexity models through OpenRouter, requiring only a single API key (no separate Perplexity account needed).
+
+## When to Use This Skill
+
+Use this skill when:
+- Searching for current information or recent developments (2024 and beyond)
+- Finding latest scientific publications and research
+- Getting real-time answers grounded in web sources
+- Verifying facts with source citations
+- Conducting literature searches across multiple domains
+- Accessing information beyond the model's knowledge cutoff
+- Performing domain-specific research (biomedical, technical, clinical)
+- Comparing current approaches or technologies
+
+**Do not use** for:
+- Simple calculations or logic problems (use directly)
+- Tasks requiring code execution (use standard tools)
+- Questions well within the model's training data (unless verification needed)
+
+## Quick Start
+
+### Setup (One-time)
+
+1. **Get OpenRouter API key**:
+   - Visit https://openrouter.ai/keys
+   - Create account and generate API key
+   - Add credits to account (minimum $5 recommended)
+
+2. **Configure environment**:
+   ```bash
+   # Set API key
+   export OPENROUTER_API_KEY='sk-or-v1-your-key-here'
+
+   # Or use setup script
+   python scripts/setup_env.py --api-key sk-or-v1-your-key-here
+   ```
+
+3. **Install dependencies**:
+   ```bash
+   uv pip install litellm
+   ```
+
+4. **Verify setup**:
+   ```bash
+   python scripts/perplexity_search.py --check-setup
+   ```
+
+See `references/openrouter_setup.md` for detailed setup instructions, troubleshooting, and security best practices.
+
+### Basic Usage
+
+**Simple search:**
+```bash
+python scripts/perplexity_search.py "What are the latest developments in CRISPR gene editing?"
+```
+
+**Save results:**
+```bash
+python scripts/perplexity_search.py "Recent CAR-T therapy clinical trials" --output results.json
+```
+
+**Use specific model:**
+```bash
+python scripts/perplexity_search.py "Compare mRNA and viral vector vaccines" --model sonar-pro-search
+```
+
+**Verbose output:**
+```bash
+python scripts/perplexity_search.py "Quantum computing for drug discovery" --verbose
+```
+
+## Available Models
+
+Access models via `--model` parameter:
+
+- **sonar-pro** (default): General-purpose search, best balance of cost and quality
+- **sonar-pro-search**: Most advanced agentic search with multi-step reasoning
+- **sonar**: Basic model, most cost-effective for simple queries
+- **sonar-reasoning-pro**: Advanced reasoning with step-by-step analysis
+- **sonar-reasoning**: Basic reasoning capabilities
+
+**Model selection guide:**
+- Default queries → `sonar-pro`
+- Complex multi-step analysis → `sonar-pro-search`
+- Explicit reasoning needed → `sonar-reasoning-pro`
+- Simple fact lookups → `sonar`
+- Cost-sensitive bulk queries → `sonar`
+
+See `references/model_comparison.md` for detailed comparison, use cases, pricing, and performance characteristics.
+
+## Crafting Effective Queries
+
+### Be Specific and Detailed
+
+**Good examples:**
+- "What are the latest clinical trial results for CAR-T cell therapy in treating B-cell lymphoma published in 2024?"
+- "Compare the efficacy and safety profiles of mRNA vaccines versus viral vector vaccines for COVID-19"
+- "Explain AlphaFold3 improvements over AlphaFold2 with specific accuracy metrics from 2023-2024 research"
+
+**Bad examples:**
+- "Tell me about cancer treatment" (too broad)
+- "CRISPR" (too vague)
+- "vaccines" (lacks specificity)
+
+### Include Time Constraints
+
+Perplexity searches real-time web data:
+- "What papers were published in Nature Medicine in 2024 about long COVID?"
+- "What are the latest developments (past 6 months) in large language model efficiency?"
+- "What was announced at NeurIPS 2023 regarding AI safety?"
+
+### Specify Domain and Sources
+
+For high-quality results, mention source preferences:
+- "According to peer-reviewed publications in high-impact journals..."
+- "Based on FDA-approved treatments..."
+- "From clinical trial registries like clinicaltrials.gov..."
+
+### Structure Complex Queries
+
+Break complex questions into clear components:
+1. **Topic**: Main subject
+2. **Scope**: Specific aspect of interest
+3. **Context**: Time frame, domain, constraints
+4. **Output**: Desired format or type of answer
+
+**Example:**
+"What improvements does AlphaFold3 offer over AlphaFold2 for protein structure prediction, according to research published between 2023 and 2024? Include specific accuracy metrics and benchmarks."
+
+See `references/search_strategies.md` for comprehensive guidance on query design, domain-specific patterns, and advanced techniques.
+
+## Common Use Cases
+
+### Scientific Literature Search
+
+```bash
+python scripts/perplexity_search.py \
+  "What does recent research (2023-2024) say about the role of gut microbiome in Parkinson's disease? Focus on peer-reviewed studies and include specific bacterial species identified." \
+  --model sonar-pro
+```
+
+### Technical Documentation
+
+```bash
+python scripts/perplexity_search.py \
+  "How to implement real-time data streaming from Kafka to PostgreSQL using Python? Include considerations for handling backpressure and ensuring exactly-once semantics." \
+  --model sonar-reasoning-pro
+```
+
+### Comparative Analysis
+
+```bash
+python scripts/perplexity_search.py \
+  "Compare PyTorch versus TensorFlow for implementing transformer models in terms of ease of use, performance, and ecosystem support. Include benchmarks from recent studies." \
+  --model sonar-pro-search
+```
+
+### Clinical Research
+
+```bash
+python scripts/perplexity_search.py \
+  "What is the evidence for intermittent fasting in managing type 2 diabetes in adults? Focus on randomized controlled trials and report HbA1c changes and weight loss outcomes." \
+  --model sonar-pro
+```
+
+### Trend Analysis
+
+```bash
+python scripts/perplexity_search.py \
+  "What are the key trends in single-cell RNA sequencing technology over the past 5 years? Highlight improvements in throughput, cost, and resolution, with specific examples." \
+  --model sonar-pro
+```
+
+## Working with Results
+
+### Programmatic Access
+
+Use `perplexity_search.py` as a module:
+
+```python
+from scripts.perplexity_search import search_with_perplexity
+
+result = search_with_perplexity(
+    query="What are the latest CRISPR developments?",
+    model="openrouter/perplexity/sonar-pro",
+    max_tokens=4000,
+    temperature=0.2,
+    verbose=False
+)
+
+if result["success"]:
+    print(result["answer"])
+    print(f"Tokens used: {result['usage']['total_tokens']}")
+else:
+    print(f"Error: {result['error']}")
+```
+
+### Save and Process Results
+
+```bash
+# Save to JSON
+python scripts/perplexity_search.py "query" --output results.json
+
+# Process with jq
+cat results.json | jq '.answer'
+cat results.json | jq '.usage'
+```
+
+### Batch Processing
+
+Create a script for multiple queries:
+
+```bash
+#!/bin/bash
+queries=(
+  "CRISPR developments 2024"
+  "mRNA vaccine technology advances"
+  "AlphaFold3 accuracy improvements"
+)
+
+for query in "${queries[@]}"; do
+  echo "Searching: $query"
+  python scripts/perplexity_search.py "$query" --output "results_$(echo $query | tr ' ' '_').json"
+  sleep 2  # Rate limiting
+done
+```
+
+## Cost Management
+
+Perplexity models have different pricing tiers:
+
+**Approximate costs per query:**
+- Sonar: $0.001-0.002 (most cost-effective)
+- Sonar Pro: $0.002-0.005 (recommended default)
+- Sonar Reasoning Pro: $0.005-0.010
+- Sonar Pro Search: $0.020-0.050+ (most comprehensive)
+
+**Cost optimization strategies:**
+1. Use `sonar` for simple fact lookups
+2. Default to `sonar-pro` for most queries
+3. Reserve `sonar-pro-search` for complex analysis
+4. Set `--max-tokens` to limit response length
+5. Monitor usage at https://openrouter.ai/activity
+6. Set spending limits in OpenRouter dashboard
+
+## Troubleshooting
+
+### API Key Not Set
+
+**Error**: "OpenRouter API key not configured"
+
+**Solution**:
+```bash
+export OPENROUTER_API_KEY='sk-or-v1-your-key-here'
+# Or run setup script
+python scripts/setup_env.py --api-key sk-or-v1-your-key-here
+```
+
+### LiteLLM Not Installed
+
+**Error**: "LiteLLM not installed"
+
+**Solution**:
+```bash
+uv pip install litellm
+```
+
+### Rate Limiting
+
+**Error**: "Rate limit exceeded"
+
+**Solutions**:
+- Wait a few seconds before retrying
+- Increase rate limit at https://openrouter.ai/keys
+- Add delays between requests in batch processing
+
+### Insufficient Credits
+
+**Error**: "Insufficient credits"
+
+**Solution**:
+- Add credits at https://openrouter.ai/account
+- Enable auto-recharge to prevent interruptions
+
+See `references/openrouter_setup.md` for comprehensive troubleshooting guide.
+
+## Integration with Other Skills
+
+This skill complements other scientific skills:
+
+### Literature Review
+
+Use with `literature-review` skill:
+1. Use Perplexity to find recent papers and preprints
+2. Supplement PubMed searches with real-time web results
+3. Verify citations and find related work
+4. Discover latest developments post-database indexing
+
+### Scientific Writing
+
+Use with `scientific-writing` skill:
+1. Find recent references for introduction/discussion
+2. Verify current state of the art
+3. Check latest terminology and conventions
+4. Identify recent competing approaches
+
+### Hypothesis Generation
+
+Use with `hypothesis-generation` skill:
+1. Search for latest research findings
+2. Identify current gaps in knowledge
+3. Find recent methodological advances
+4. Discover emerging research directions
+
+### Critical Thinking
+
+Use with `scientific-critical-thinking` skill:
+1. Find evidence for and against hypotheses
+2. Locate methodological critiques
+3. Identify controversies in the field
+4. Verify claims with current evidence
+
+## Best Practices
+
+### Query Design
+
+1. **Be specific**: Include domain, time frame, and constraints
+2. **Use terminology**: Domain-appropriate keywords and phrases
+3. **Specify sources**: Mention preferred publication types or journals
+4. **Structure questions**: Clear components with explicit context
+5. **Iterate**: Refine based on initial results
+
+### Model Selection
+
+1. **Start with sonar-pro**: Good default for most queries
+2. **Upgrade for complexity**: Use sonar-pro-search for multi-step analysis
+3. **Downgrade for simplicity**: Use sonar for basic facts
+4. **Use reasoning models**: When step-by-step analysis needed
+
+### Cost Optimization
+
+1. **Choose appropriate models**: Match model to query complexity
+2. **Set token limits**: Use `--max-tokens` to control costs
+3. **Monitor usage**: Check OpenRouter dashboard regularly
+4. **Batch efficiently**: Combine related simple queries when possible
+5. **Cache results**: Save and reuse results for repeated queries
+
+### Security
+
+1. **Protect API keys**: Never commit to version control
+2. **Use environment variables**: Keep keys separate from code
+3. **Set spending limits**: Configure in OpenRouter dashboard
+4. **Monitor usage**: Watch for unexpected activity
+5. **Rotate keys**: Change keys periodically
+
+## Resources
+
+### Bundled Resources
+
+**Scripts:**
+- `scripts/perplexity_search.py`: Main search script with CLI interface
+- `scripts/setup_env.py`: Environment setup and validation helper
+
+**References:**
+- `references/search_strategies.md`: Comprehensive query design guide
+- `references/model_comparison.md`: Detailed model comparison and selection guide
+- `references/openrouter_setup.md`: Complete setup, troubleshooting, and security guide
+
+**Assets:**
+- `assets/.env.example`: Example environment file template
+
+### External Resources
+
+**OpenRouter:**
+- Dashboard: https://openrouter.ai/account
+- API Keys: https://openrouter.ai/keys
+- Perplexity Models: https://openrouter.ai/perplexity
+- Usage Monitoring: https://openrouter.ai/activity
+- Documentation: https://openrouter.ai/docs
+
+**LiteLLM:**
+- Documentation: https://docs.litellm.ai/
+- OpenRouter Provider: https://docs.litellm.ai/docs/providers/openrouter
+- GitHub: https://github.com/BerriAI/litellm
+
+**Perplexity:**
+- Official Docs: https://docs.perplexity.ai/
+
+## Dependencies
+
+### Required
+
+```bash
+# LiteLLM for API access
+uv pip install litellm
+```
+
+### Optional
+
+```bash
+# For .env file support
+uv pip install python-dotenv
+
+# For JSON processing (usually pre-installed)
+uv pip install jq
+```
+
+### Environment Variables
+
+Required:
+- `OPENROUTER_API_KEY`: Your OpenRouter API key
+
+Optional:
+- `DEFAULT_MODEL`: Default model to use (default: sonar-pro)
+- `DEFAULT_MAX_TOKENS`: Default max tokens (default: 4000)
+- `DEFAULT_TEMPERATURE`: Default temperature (default: 0.2)
+
+## Summary
+
+This skill provides:
+
+1. **Real-time web search**: Access current information beyond training data cutoff
+2. **Multiple models**: From cost-effective Sonar to advanced Sonar Pro Search
+3. **Simple setup**: Single OpenRouter API key, no separate Perplexity account
+4. **Comprehensive guidance**: Detailed references for query design and model selection
+5. **Cost-effective**: Pay-as-you-go pricing with usage monitoring
+6. **Scientific focus**: Optimized for research, literature search, and technical queries
+7. **Easy integration**: Works seamlessly with other scientific skills
+
+Conduct AI-powered web searches to find current information, recent research, and grounded answers with source citations.