singler process, singler gpu

runner.py

@@ -18,6 +18,8 @@ import multiprocessing
 import shutil
 import os
 
+if Path('simulation_log.log').exists():
+    Path('simulation_log.log').unlink()
 # 设置日志记录
 logging.basicConfig(level=logging.INFO, filename='simulation_log.log', filemode='a',
                     format='%(asctime)s - %(levelname)s - %(message)s')
@@ -116,8 +118,7 @@ class SimulationRunner:
                 "PATH": os.environ.get("PATH", ""),
                 "LD_LIBRARY_PATH": os.environ.get("LD_LIBRARY_PATH", ""),
                 "HOME": os.environ["HOME"],
-                "CUDA_VISIBLE_DEVICES": str(self.gpu_id) if self.gpu_id is not None else "",
-                'OMP_NUM_THREADS': str(num_cores)
+                "CUDA_VISIBLE_DEVICES": str(self.gpu_id) if self.gpu_id is not None else ""
             }
             logger.info(f"pdb_file: {self.pdb_file.name}")
             logger.info(f"Executing script at: {self.bash_script}")
@@ -178,11 +179,18 @@ def main(simulation_steps, time_step, pdb_folder_path, bash_script_path, gmxrc_p
         logger.error("No GPUs detected, exiting.")
         return
 
-    # 创建一个进程池，每个GPU运行两个任务
-    with multiprocessing.Pool(processes=num_gpus * 2) as pool: # num_gpus * 1
+    # 创建一个进程池，每个GPU运行1个任务
+    # with multiprocessing.Pool(processes=num_gpus * 1) as pool: # num_gpus * 1
+    #     for i, pdb_file in enumerate(pdb_files):
+    #         gpu_id = i % num_gpus  # 分配GPU
+    #         pool.apply_async(run_simulation_task, (pdb_file, simulation_steps, time_step, pdb_folder, bash_script_path, gmxrc_path, gpu_id))
+        
+    #     pool.close()
+    #     pool.join()
+    with multiprocessing.Pool(processes=1) as pool: # num_gpus * 1
         for i, pdb_file in enumerate(pdb_files):
             gpu_id = i % num_gpus  # 分配GPU
-            pool.apply_async(run_simulation_task, (pdb_file, simulation_steps, time_step, pdb_folder, bash_script_path, gmxrc_path, gpu_id))
+            pool.apply_async(run_simulation_task, (pdb_file, simulation_steps, time_step, pdb_folder, bash_script_path, gmxrc_path, '0'))
         
         pool.close()
         pool.join()
@@ -190,7 +198,7 @@ def main(simulation_steps, time_step, pdb_folder_path, bash_script_path, gmxrc_p
 if __name__ == "__main__":
     NSTEPS = 50000000  # Example: 50000000 steps
     DT = 0.002  # Example: 2 fs time step
-    PDB_FOLDER_PATH = Path("./pdb_testb")  # Assuming the PDB files are in a folder named 'pdb_files' in the current directory
+    PDB_FOLDER_PATH = Path("./pdb_test")  # Assuming the PDB files are in a folder named 'pdb_files' in the current directory
     # 传入自定义的bash脚本路径
     CUSTOM_BASH_SCRIPT_PATH = Path('md_gromacs.sh')
     # 传入 GMXRC 文件的路径