From e0fb6970c0679a3629706aa4b5865dc044b8759d Mon Sep 17 00:00:00 2001
From: ale <ale@manalejandro.com>
Date: Mon, 13 Oct 2025 00:41:42 +0200
Subject: [PATCH] fix HDH repo

Signed-off-by: ale <ale@manalejandro.com>
---
 .gitmodules         |  4 ++++
 Dockerfile          |  5 +----
 HDH                 |  1 +
 README.md           |  4 ++--
 benchmark.py        | 36 +++++++++++++++++++++++++++++++-----
 circuit_examples.py |  3 +--
 6 files changed, 40 insertions(+), 13 deletions(-)
 create mode 100644 .gitmodules
 create mode 160000 HDH

diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..f67586e
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,4 @@
+[submodule "HDH"]
+	path = HDH
+	url = https://github.com/manalejandro/HDH
+	branch = database-branch
diff --git a/Dockerfile b/Dockerfile
index da65b35..f4d1b68 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -52,9 +52,6 @@ WORKDIR /app
 # Copy application files
 COPY . .
 
-# Copy HDH library (assuming it's in the parent directory)
-COPY ../HDH ./HDH
-
 # Install HDH library
 RUN pip install -e ./HDH
 
@@ -83,4 +80,4 @@ HEALTHCHECK --interval=30s --timeout=10s --start-period=60s --retries=3 \
 VOLUME ["/app/hdh_results", "/app/benchmark_results", "/app/logs"]
 
 # Default command
-CMD ["python", "main.py", "--demo-mode", "--output-dir", "/app/hdh_results"]
\ No newline at end of file
+CMD ["python", "main.py", "--demo-mode", "--output-dir", "/app/hdh_results"]
diff --git a/HDH b/HDH
new file mode 160000
index 0000000..e84b7d9
--- /dev/null
+++ b/HDH
@@ -0,0 +1 @@
+Subproject commit e84b7d9d8cc0438e260c23270a9a9860e96ed164
diff --git a/README.md b/README.md
index 99c089a..993da16 100644
--- a/README.md
+++ b/README.md
@@ -56,7 +56,7 @@ source hdh-env/bin/activate  # On Windows: hdh-env\Scripts\activate
 pip install -r requirements.txt
 
 # Install HDH library in development mode
-pip install -e ../HDH
+pip install -e ./HDH
 
 # Verify installation
 python main.py --help
@@ -419,4 +419,4 @@ For questions and support:
 
 *Built with ❤️ for the quantum computing community*
 
-*Thank you Maria for making quantum computation analysis more accessible through HDH! 🌟*
\ No newline at end of file
+*Thank you Maria for making quantum computation analysis more accessible through HDH! 🌟*
diff --git a/benchmark.py b/benchmark.py
index 839880a..74da33b 100644
--- a/benchmark.py
+++ b/benchmark.py
@@ -37,7 +37,8 @@ import numpy as np
 # Memory and performance monitoring
 import psutil
 import gc
-from memory_profiler import profile
+import tracemalloc
+from memory_profiler import profile, memory_usage
 
 # Add HDH to path
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'HDH')))
@@ -118,17 +119,34 @@ class HDHBenchmarkSuite:
         
         # Initial memory measurement
         gc.collect()  # Force garbage collection
+        
+        # Start memory tracking with tracemalloc
+        tracemalloc.start()
+        initial_snapshot = tracemalloc.take_snapshot()
         initial_memory = self.get_memory_usage()
         
         try:
-            # Time the conversion
+            # Time the conversion and track memory
             start_time = time.perf_counter()
             hdh = from_qiskit(circuit)
             conversion_time = time.perf_counter() - start_time
             
-            # Memory peak measurement
+            # Memory peak measurement using tracemalloc
+            current_snapshot = tracemalloc.take_snapshot()
+            top_stats = current_snapshot.compare_to(initial_snapshot, 'lineno')
+            
+            # Calculate memory difference in MB
+            tracemalloc_memory = sum(stat.size_diff for stat in top_stats) / 1024 / 1024
+            
+            # Also get psutil measurement as backup
             peak_memory = self.get_memory_usage()
-            memory_used = peak_memory - initial_memory
+            psutil_memory = peak_memory - initial_memory
+            
+            # Use the larger of the two measurements (tracemalloc is usually more accurate)
+            memory_used = max(abs(tracemalloc_memory), abs(psutil_memory))
+            
+            # Stop tracemalloc
+            tracemalloc.stop()
             
             # HDH statistics
             hdh_nodes = len(hdh.S)
@@ -142,8 +160,12 @@ class HDHBenchmarkSuite:
             if hdh_nodes > 1:
                 try:
                     num_parts = min(3, max(2, hdh_nodes // 2))
+                    # Calculate capacity: distribute qubits evenly across partitions with some buffer
+                    num_qubits = circuit.num_qubits
+                    capacity = max(1, (num_qubits + num_parts - 1) // num_parts + 1)  # Ceiling division + buffer
+                    
                     start_partition = time.perf_counter()
-                    partitions = compute_cut(hdh, num_parts)
+                    partitions, _ = compute_cut(hdh, num_parts, capacity)
                     partitioning_time = time.perf_counter() - start_partition
                     partition_cost = cost(hdh, partitions)
                 except Exception as e:
@@ -177,6 +199,10 @@ class HDHBenchmarkSuite:
             )
             
         except Exception as e:
+            # Make sure to stop tracemalloc even on error
+            if tracemalloc.is_tracing():
+                tracemalloc.stop()
+            
             self.logger.error(f"Benchmark failed for {circuit_name}: {str(e)}")
             self.logger.debug(traceback.format_exc())
             
diff --git a/circuit_examples.py b/circuit_examples.py
index 833a0f8..d9a51f3 100644
--- a/circuit_examples.py
+++ b/circuit_examples.py
@@ -28,8 +28,7 @@ sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..',
 
 from qiskit import QuantumCircuit, QuantumRegister, ClassicalRegister
 from qiskit.circuit.library import (
-    QFT, GroverOperator, DeutschJozsaOracle, 
-    TwoLocal, RealAmplitudes, EfficientSU2
+    QFT, TwoLocal, RealAmplitudes, EfficientSU2
 )
 from qiskit.circuit import Parameter
 import qiskit.circuit.library as qlib