加强 log

2024-01-11 11:04:38 +08:00
parent 660f741274
commit e23905ce84
2 changed files with 83 additions and 95 deletions
--- a/md_gromacs.sh
+++ b/md_gromacs.sh
@@ -52,12 +52,29 @@ echo "OUTPUT_FOLDER: $OUTPUT_FOLDER"
 echo "EXTRACT_EVERY_PS: $EXTRACT_EVERY_PS"
 echo "NUM_CORES: $NUM_CORES"

+# 函数：打印步骤信息和运行命令
+run_command() {
+    local step_description=$1
+    local command=$2
+
+    echo "Starting: $step_description"
+    echo "Command: $command"
+    eval $command
+    local status=$?
+
+    if [ $status -ne 0 ]; then
+        echo "Error in $step_description. Command: $command"
+        exit $status
+    fi
+    echo "Completed: \n $step_description"
+}
+
 # generate GROMACS .gro file
-mpirun -np $NUM_CORES gmx_mpi pdb2gmx -f $NAME.pdb -o $NAME.gro -ff $FORCEFIELD -water $WATERMODEL -ignh -p topol.top
+run_command "Generating GROMACS .gro file" "mpirun -np $NUM_CORES gmx_mpi pdb2gmx -f $NAME.pdb -o $NAME.gro -ff $FORCEFIELD -water $WATERMODEL -ignh -p topol.top"
 # define the box
-mpirun -np $NUM_CORES gmx_mpi editconf -f $NAME.gro -o $NAME-box.gro -bt $BOXTYPE -c -d $BOXORIENTATION
+run_command "Defining the box" "mpirun -np $NUM_CORES gmx_mpi editconf -f $NAME.gro -o $NAME-box.gro -bt $BOXTYPE -c -d $BOXORIENTATION"
 # add solvate
-mpirun -np $NUM_CORES gmx_mpi solvate -cp $NAME-box.gro -cs $WATERTOPFILE -o $NAME-solv.gro -p topol.top
+run_command "Adding solvate" "mpirun -np $NUM_CORES gmx_mpi solvate -cp $NAME-box.gro -cs $WATERTOPFILE -o $NAME-solv.gro -p topol.top"
 # add icons # ! ions.mdp add by manual
 # --- ions.mdp file content --- #
 cat << EOF > ions.mdp
@@ -76,9 +93,10 @@ rcoulomb        = 1.0       ; Short-range electrostatic cut-off
 rvdw            = 1.0       ; Short-range Van der Waals cut-off
 pbc             = xyz       ; Periodic Boundary Conditions in all 3 dimensions
 EOF
-mpirun -np $NUM_CORES gmx_mpi grompp -f ions.mdp -c $NAME-solv.gro -p topol.top -o ions.tpr -maxwarn 1
-echo "SOL" > ions_input.txt
-mpirun -np $NUM_CORES gmx_mpi genion -s ions.tpr -o $NAME-solv-ions.gro -p topol.top -pname NA -nname CL -conc 0.125 -neutral < ions_input.txt
+run_command "Adding ions" "mpirun -np $NUM_CORES gmx_mpi grompp -f ions.mdp -c $NAME-solv.gro -p topol.top -o ions.tpr -maxwarn 1"
+# echo "SOL" > ions_input.txt
+# mpirun -np $NUM_CORES gmx_mpi genion -s ions.tpr -o $NAME-solv-ions.gro -p topol.top -pname NA -nname CL -conc 0.125 -neutral < ions_input.txt
+run_command "Generating ions" "echo 'SOL' | mpirun -np $NUM_CORES gmx_mpi genion -s ions.tpr -o $NAME-solv-ions.gro -p topol.top -pname NA -nname CL -conc 0.125 -neutral"
 # energy minimization of the structure in solvate # ! minim.mdp add by manual
 # --- minim.mdp file content --- #
 cat << EOF > minim.mdp
@@ -97,8 +115,8 @@ rcoulomb        = 1.0       ; Short-range electrostatic cut-off
 rvdw            = 1.0       ; Short-range Van der Waals cut-off
 pbc             = xyz       ; Periodic Boundary Conditions in all 3 dimensions
 EOF
-mpirun -np $NUM_CORES gmx_mpi grompp -f minim.mdp -c $NAME-solv-ions.gro -p topol.top -o em.tpr
-mpirun -np $NUM_CORES gmx_mpi mdrun -v -deffnm em 
+run_command "Energy minimization" "mpirun -np $NUM_CORES gmx_mpi grompp -f minim.mdp -c $NAME-solv-ions.gro -p topol.top -o em.tpr"
+run_command "Running energy minimization" "mpirun -np $NUM_CORES gmx_mpi mdrun -v -deffnm em"
 # optional em, you will need the Xmgrace plotting too
 #gmx_mpi energy -f em.edr -o potential.xvg
 #position restrain
@@ -150,8 +168,8 @@ gen_vel                 = yes       ; assign velocities from Maxwell distributio
 gen_temp                = 300       ; temperature for Maxwell distribution
 gen_seed                = -1        ; generate a random seed
 EOF
-mpirun -np $NUM_CORES gmx_mpi grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr
-mpirun -np $NUM_CORES gmx_mpi mdrun -v -deffnm nvt
+run_command "Preparing NVT simulation" "mpirun -np $NUM_CORES gmx_mpi grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr"
+run_command "Running NVT simulation" "mpirun -np $NUM_CORES gmx_mpi mdrun -v -deffnm nvt"
 # optional : Let's analyze the temperature progression, again using energy:
 # gmx_mpi energy -f nvt.edr -o temperature.xvg
 # npt
@@ -203,8 +221,8 @@ pbc                     = xyz       ; 3-D PBC
 ; Velocity generation
 gen_vel                 = no        ; Velocity generation is off 
 EOF
-mpirun -np $NUM_CORES gmx_mpi grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
-mpirun -np $NUM_CORES gmx_mpi mdrun -v -deffnm npt
+run_command "Preparing NPT simulation" "mpirun -np $NUM_CORES gmx_mpi grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr"
+run_command "Running NPT simulation" "mpirun -np $NUM_CORES gmx_mpi mdrun -v -deffnm npt"
 # Optional: Let's analyze the pressure progression, again using energy: type 18 0
 # gmx energy -f npt.edr -o pressure.xvg
 # Optional: Let's take a look at density as well, this time using energy and entering "24 0" at the prompt.
@@ -261,8 +279,7 @@ gen_vel                 = no        ; Velocity generation is off
 EOF

 # Generate GROMACS .tpr file for the simulation
-mpirun -np $NUM_CORES gmx_mpi grompp -f ${MDRUN_NAME}.mdp -c npt.gro -t npt.cpt -p topol.top -o ${TPR_FILE}
-
+run_command "Preparing MD simulation" "mpirun -np $NUM_CORES gmx_mpi grompp -f ${MDRUN_NAME}.mdp -c npt.gro -t npt.cpt -p topol.top -o ${TPR_FILE}"
 # Run the simulation
 mpirun -np $NUM_CORES gmx_mpi mdrun -deffnm ${MDRUN_NAME}
 # mpirun -np $(ls | egrep "Scaled[0-9]+$" | wc -l) gmx_mpi mdrun -v --deffnm md -cpi Scaled.cpt -multidir $(ls -v | egrep "Scaled[0-9]+$") -plumed plumed.dat -hrex -replex 1000 >& run_$(date "+%H%M%S_%d%m%Y").log || { echo "mdrun failed at line ${LINENO} "; exit -1; }
@@ -270,44 +287,15 @@ mpirun -np $NUM_CORES gmx_mpi mdrun -deffnm ${MDRUN_NAME}
 echo -e "1\nq" | gmx_mpi make_ndx -f ${MDRUN_NAME}.gro -o ${NDX_FILE}
 # echo -e "1\nq" | gmx_mpi make_ndx -f md.gro -o index.ndx

-# Create extraction output directory
-mkdir -p ${OUTPUT_FOLDER}
+# Create extraction output directory Create temp output directory
+run_command "Creating output directories" "mkdir -p ${OUTPUT_FOLDER} && mkdir -p ${TEMP_FOLDER}"

-# Create temp output directory
-mkdir -p ${TEMP_FOLDER}
-
-echo -e "1\nq" | gmx_mpi trjconv -dt ${EXTRACT_EVERY_PS} -s ${TPR_FILE} -f ${XTC_FILE} -n ${NDX_FILE} -pbc mol -o ${TEMP_FOLDER}/temp.xtc
-
-# echo -e "1\nq" | gmx_mpi trjconv -dt 100 -s md.tpr -f md.xtc -n index.ndx -pbc mol -o temp/temp.xtc
-
-echo -e "1\n1\n1" | gmx_mpi trjconv -s ${TPR_FILE} -f ${TEMP_FOLDER}/temp.xtc -n ${NDX_FILE} -center -fit rot+trans -o ${TEMP_FOLDER}/traj_show.xtc
-
-# echo -e "1\n1\n1" | gmx_mpi trjconv -s md.tpr -f temp/temp.xtc -n index.ndx -center -fit rot+trans -o temp/traj_show.xtc
-
-echo -e "1\n1\n1" | gmx_mpi trjconv -s ${TPR_FILE} -f ${TEMP_FOLDER}/temp.xtc -n ${NDX_FILE} -center -fit rot+trans -b 0 -e 0 -o ${TEMP_FOLDER}/tarj_show.pdb
-
-# echo -e "1\n1\n1" | gmx_mpi trjconv -s md.tpr -f temp/temp.xtc -n index.ndx -center -fit rot+trans -b 0 -e 0 -o temp/tarj_show.pdb
+run_command "Extracting frames" "echo -e '1\nq' | gmx_mpi trjconv -dt ${EXTRACT_EVERY_PS} -s ${TPR_FILE} -f ${XTC_FILE} -n ${NDX_FILE} -pbc mol -o ${TEMP_FOLDER}/temp.xtc"
+run_command "Centering and fitting trajectory" "echo -e '1\n1\n1' | gmx_mpi trjconv -s ${TPR_FILE} -f ${TEMP_FOLDER}/temp.xtc -n ${NDX_FILE} -center -fit rot+trans -o ${TEMP_FOLDER}/traj_show.xtc"
+run_command "Generating PDB file" "echo -e '1\n1\n1' | gmx_mpi trjconv -s ${TPR_FILE} -f ${TEMP_FOLDER}/temp.xtc -n ${NDX_FILE} -center -fit rot+trans -b 0 -e 0 -o ${TEMP_FOLDER}/tarj_show.pdb"

 # Group     1 (        Protein) 

-# ---
-# Step 1: Extract frames every 1000 ps
-gmx_mpi trjconv -s ${TPR_FILE} -f ${XTC_FILE} -o ${OUTPUT_FOLDER}/${NO_PBC_XTC_FILE} -dt ${EXTRACT_EVERY_PS} -pbc mol <<EOF
-0
-EOF
-
-# Step 2: Center and fit the trajectory
-# Centering the protein and fitting to the initial frame
-gmx_mpi trjconv -s ${TPR_FILE} -f ${OUTPUT_FOLDER}/${NO_PBC_XTC_FILE} -o ${OUTPUT_FOLDER}/${NO_PBC_XTC_FILE} -pbc mol -center <<EOF
-1
-1
-EOF
-
-# Step 3: Output PDB format file
-gmx_mpi trjconv -s ${TPR_FILE} -f ${OUTPUT_FOLDER}/${NO_PBC_XTC_FILE} -o ${OUTPUT_FOLDER}/${MDRUN_NAME}.pdb -pbc mol -center <<EOF
-1
-0
-EOF

 # Continue with further analysis like RMSD calculation...
 # ... [other analysis commands] ...
@@ -317,7 +305,7 @@ EOF
 # command reference

 # Command 1: 提取蛋白质
-command_1 = f'echo "Protein" | gmx trjconv -dt 1000 -s {tpr_file} -f {xtc_file} -n {temp_folder}/tarj_show.ndx -pbc mol -o {temp_folder}/temp.xtc'
+# command_1 = f'echo "Protein" | gmx trjconv -dt 1000 -s {tpr_file} -f {xtc_file} -n {temp_folder}/tarj_show.ndx -pbc mol -o {temp_folder}/temp.xtc'
 # echo "Protein": 选择蛋白质组，用于告诉 gmx trjconv 要处理哪个部分。
 # -dt 1000: 指定时间间隔（这里是1000 picoseconds），用于从 .xtc 文件中抽取帧。
 # -s {tpr_file}: 指定拓扑文件（.tpr），它包含了模拟系统的完整描述。
@@ -326,12 +314,12 @@ command_1 = f'echo "Protein" | gmx trjconv -dt 1000 -s {tpr_file} -f {xtc_file}
 # -pbc mol: 处理周期性边界条件，确保分子不会被分割。
 # -o {temp_folder}/temp.xtc: 指定输出文件名和位置。
 # Command 2: 中心对齐蛋白质
-command_2 = f'echo "Protein\nProtein\nProtein" | gmx trjconv -s {tpr_file} -f {temp_folder}/temp.xtc -n {temp_folder}/tarj_show.ndx -center -fit rot+trans -o {output_folder}/traj_show.xtc'
+# command_2 = f'echo "Protein\nProtein\nProtein" | gmx trjconv -s {tpr_file} -f {temp_folder}/temp.xtc -n {temp_folder}/tarj_show.ndx -center -fit rot+trans -o {output_folder}/traj_show.xtc'
 # echo "Protein\nProtein\nProtein": 三次选择蛋白质组，分别用于中心化、拟合和输出。
 # -center: 将蛋白质移动到框架的中心。
 # -fit rot+trans: 对齐蛋白质，通过旋转和平移来最佳拟合。
 # -o {output_folder}/traj_show.xtc: 指定输出文件名和位置。
 # Command 3: 抽取帧生成 .pdb 文件
-command_3 = f'echo "Protein\nProtein\nProtein" | gmx trjconv -s {tpr_file} -f {temp_folder}/temp.xtc -n {temp_folder}/tarj_show.ndx -center -fit rot+trans -b 0 -e 0 -o {output_folder}/tarj_show.pdb'
+# command_3 = f'echo "Protein\nProtein\nProtein" | gmx trjconv -s {tpr_file} -f {temp_folder}/temp.xtc -n {temp_folder}/tarj_show.ndx -center -fit rot+trans -b 0 -e 0 -o {output_folder}/tarj_show.pdb'
 # -b 0 -e 0: 指定开始和结束时间，这里设置为0表示只取第一帧。
 # -o {output_folder}/tarj_show.pdb: 输出为 .pdb 格式，存储在指定的位置。
--- a/runner.py
+++ b/runner.py
@@ -18,12 +18,7 @@ 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')
-logger = logging.getLogger()
+

@dataclass
 class SimulationRunner:
@@ -31,13 +26,14 @@ class SimulationRunner:
    nsteps: int
    dt: float
    base_folder: Path
-    bash_script: Path = None  # Bash脚本路径作为可选参数
-    gmxrc_path: Path = None  # GMXRC文件路径作为可选参数
+    bash_script: Path = None
+    gmxrc_path: Path = None
    gpu_id: int = None
-    temp_folder: Path = field(init=False)  # 用于存储临时数据和结果数据的路径(轨迹数据处理中间数据等)
+    temp_folder: Path = field(init=False)
    runner_folder: Path = field(init=False)
    tpr_file: Path = field(init=False)
    xtc_file: Path = field(init=False)
+    logger: logging.Logger = field(init=False)

    def __post_init__(self):
        # 初始化文件夹和文件路径
@@ -50,6 +46,18 @@ class SimulationRunner:
        self.bash_script = self.bash_script.absolute() if self.bash_script else Path(__file__).resolve().parent / "md_gromacs.sh"
        # 设置 GMXRC_PATH 环境变量
        self.gmxrc_path = self.gmxrc_path
+        pdb_id = self.pdb_file.stem
+        self.logger = self.setup_logging(pdb_id, self.base_folder)
+
+    @staticmethod
+    def setup_logging(pdb_id, log_folder):
+        log_file = log_folder / f"{pdb_id}_simulation_log.log"
+        if log_file.exists():
+            log_file.unlink()
+
+        logging.basicConfig(level=logging.INFO, filename=log_file, filemode='a',
+                            format='%(asctime)s - %(levelname)s - %(message)s')
+        return logging.getLogger(pdb_id)

    def copy_pdb(self):
        shutil.copy(self.pdb_file, self.runner_folder / self.pdb_file.name)
@@ -120,39 +128,29 @@ class SimulationRunner:
                "HOME": os.environ["HOME"],
                "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}")
+            self.logger.info(f"pdb_file: {self.pdb_file.name}")
+            self.logger.info(f"Executing script at: {self.bash_script}")
            result = subprocess.run(["bash", str(self.bash_script)], env=env_vars, cwd=self.runner_folder,
                                    capture_output=True, text=True, check=True)
        except subprocess.CalledProcessError as e:
-            logger.error(f"Error in simulation for {self.pdb_file.name}: {e}")
+            self.logger.error(f"Error in simulation for {self.pdb_file.name}: {e}")
            if e.stdout:
-                logger.error(f"Standard Output:\n{e.stdout}")
+                self.logger.error(f"Standard Output:\n{e.stdout}")
            if e.stderr:
-                logger.error(f"Standard Error:\n{e.stderr}")
+                self.logger.error(f"Standard Error:\n{e.stderr}")

        end_time = time.time()
        duration = end_time - start_time

        if result:
-            logger.info(f"Simulation for {self.pdb_file.name} completed successfully in {duration:.2f} seconds.")
+            self.logger.info(f"Simulation for {self.pdb_file.name} completed successfully in {duration:.2f} seconds.")
            if result.stdout:
-                logger.info(f"Shell Script Output:\n{result.stdout}")
+                self.logger.info(f"Shell Script Output:\n{result.stdout}")
            if result.stderr:
-                logger.error(f"Shell Script Error Output:\n{result.stderr}")
+                self.logger.error(f"Shell Script Error Output:\n{result.stderr}")
        else:
-            logger.error(f"Simulation for {self.pdb_file.name} failed in {duration:.2f} seconds.")
+            self.logger.error(f"Simulation for {self.pdb_file.name} failed in {duration:.2f} seconds.")

-# def main(simulation_steps, time_step, pdb_folder_path, bash_script_path, gmxrc_path):
-#     pdb_folder = Path(pdb_folder_path).resolve()
-#     for pdb_file in pdb_folder.glob("*.pdb"):
-#         runner = SimulationRunner(pdb_file, simulation_steps, time_step, pdb_folder, bash_script_path, gmxrc_path)
-#         runner.copy_pdb()
-#         logger.info(f"Running simulation for {pdb_file.name} in {runner.runner_folder}...")
-#         runner.run_simulation()
-#         logger.info(f"Finished simulation for {pdb_file.name}.")
-#         runner.process_trajectory(extract_interval=100)  # 例如，每100ps抽取一次轨迹
-#         logger.info(f"Finished processing trajectory for {pdb_file.name}. per 100ps")
 def detect_gpus():
    """检测系统上的GPU数量。"""
    try:
@@ -161,37 +159,39 @@ def detect_gpus():
    except subprocess.CalledProcessError:
        return 0

+def setup_global_logging(log_folder):
+    log_file = log_folder / "simulation_log.log"
+    if log_file.exists():
+        log_file.unlink()
+
+    logging.basicConfig(level=logging.INFO, filename=log_file, filemode='a',
+                        format='%(asctime)s - %(levelname)s - %(message)s')
+    return logging.getLogger()
+
+
 def run_simulation_task(pdb_file, simulation_steps, time_step, pdb_folder, bash_script_path, gmxrc_path, gpu_id):
-    runner = SimulationRunner(pdb_file, simulation_steps, time_step, pdb_folder, bash_script_path, gmxrc_path)
+    runner = SimulationRunner(pdb_file, simulation_steps, time_step, pdb_folder, bash_script_path, gmxrc_path, gpu_id)
    runner.set_gpu(gpu_id)  # 设置要使用的GPU
    runner.copy_pdb()
-    logger.info(f"Running simulation for {pdb_file.name} on GPU {gpu_id}...")
    runner.run_simulation()
    runner.process_trajectory(extract_interval=100)
-    logger.info(f"Finished processing trajectory for {pdb_file.name} on GPU {gpu_id}.")

 def main(simulation_steps, time_step, pdb_folder_path, bash_script_path, gmxrc_path):
-    pdb_folder = Path(pdb_folder_path).resolve()
+    pdb_folder = Path(pdb_folder_path)
+    setup_global_logging(pdb_folder)  # 设置全局日志记录器
+
    pdb_files = list(pdb_folder.glob("*.pdb"))
    num_gpus = detect_gpus()
-    
+
    if num_gpus == 0:
-        logger.error("No GPUs detected, exiting.")
+        logging.error("No GPUs detected, exiting.")
        return

-    # 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
+    with multiprocessing.Pool(processes=1) as pool:
        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, '0'))
-        
+
        pool.close()
        pool.join()