hpc-task 0.1.2__tar.gz → 0.2.0__tar.gz

{hpc_task-0.1.2 → hpc_task-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hpc_task
-Version: 0.1.2
+Version: 0.2.0
 Summary: HPC Task python library.
 Home-page: https://gitee.com/pjren/hpc_task
 Author: Renpj
@@ -61,13 +61,14 @@ hpc.close()  # 此时可以关闭 ssh 通道
 # 在运行时候再重新构造和连接 hpc
 hpc = HPCTask(jobid=jobid)  # workdir 会根据 jobid 提取得到
 hpc.connect(target_host)
-
+hpc.get_workdir()
 # 结构、计算参数设置
 atoms = ase.Atoms('N2', positions=[(0., 0., 0.), (1.4, 0., 0.)],
                   cell=[10, 10, 10], pbc=True)
 # calc 设置
 calc = hpc_Vasp(  
             xc='pbe',
+            directory=hpc.workdir,  # 必须设置, 会新建文件夹，并进入文件夹执行命令
             command='mpirun -np 8 vasp544_std',  # 必须设置，或者提供了 ASE vasp 的相关设置
             hpctask=hpc,  # 这个非常关键，必须提供
             gamma=True,

{hpc_task-0.1.2 → hpc_task-0.2.0}/README.md

@@ -1,63 +1,64 @@
-# HPC Task
- 
-Python package for easy HPC task management based on paramiko.
-
-## Installation
-
-pip install -U hpc_task
-
-**Requirements**
-* paramiko
-* ase
-
-## Usage
-
-```
-import ase
-from hpc_task.hpc import HPCTask
-from hpc_task.hpc_calculator.vasp import Vasp as hpc_Vasp  # 必须导入hpc_Vasp 而非原生的 ase 的 Vasp
-
-target_host = {
-    'hostname': "TARGET HOST IP",
-    'port': 22, 
-    'username': "YOUR_USERNAME",
-    'password': "YOUR_PASSWD", 
-}
-
-workdir = 'test_vasp_calc'
-hpc = HPCTask(workdir=workdir)
-hpc.scriptdir = '/data/bin/remote.job'  # 提交作业的脚本
-hpc.connect(target_host)
-# 启动队列，得到 jobid
-hpc.prerun()
-jobid = hpc.jobid
-hpc.close()  # 此时可以关闭 ssh 通道
-
-# 在运行时候再重新构造和连接 hpc
-hpc = HPCTask(jobid=jobid)  # workdir 会根据 jobid 提取得到
-hpc.connect(target_host)
-
-# 结构、计算参数设置
-atoms = ase.Atoms('N2', positions=[(0., 0., 0.), (1.4, 0., 0.)],
-                  cell=[10, 10, 10], pbc=True)
-# calc 设置
-calc = hpc_Vasp(  
-            xc='pbe',
-            command='mpirun -np 8 vasp544_std',  # 必须设置，或者提供了 ASE vasp 的相关设置
-            hpctask=hpc,  # 这个非常关键，必须提供
-            gamma=True,
-            encut=400,
-            lwave=False,
-            lcharg=False,
-            )
-# 计算
-atoms.calc = calc
-e = atoms.get_potential_energy()
-print(f"Energy of N2 is {e} eV.")
-# finish job，结束节点任务
-hpc.postrun()
-# 关闭通道
-hpc.close()
-```
-
-## TODO
+# HPC Task
+ 
+Python package for easy HPC task management based on paramiko.
+
+## Installation
+
+pip install -U hpc_task
+
+**Requirements**
+* paramiko
+* ase
+
+## Usage
+
+```
+import ase
+from hpc_task.hpc import HPCTask
+from hpc_task.hpc_calculator.vasp import Vasp as hpc_Vasp  # 必须导入hpc_Vasp 而非原生的 ase 的 Vasp
+
+target_host = {
+    'hostname': "TARGET HOST IP",
+    'port': 22, 
+    'username': "YOUR_USERNAME",
+    'password': "YOUR_PASSWD", 
+}
+
+workdir = 'test_vasp_calc'
+hpc = HPCTask(workdir=workdir)
+hpc.scriptdir = '/data/bin/remote.job'  # 提交作业的脚本
+hpc.connect(target_host)
+# 启动队列，得到 jobid
+hpc.prerun()
+jobid = hpc.jobid
+hpc.close()  # 此时可以关闭 ssh 通道
+
+# 在运行时候再重新构造和连接 hpc
+hpc = HPCTask(jobid=jobid)  # workdir 会根据 jobid 提取得到
+hpc.connect(target_host)
+hpc.get_workdir()
+# 结构、计算参数设置
+atoms = ase.Atoms('N2', positions=[(0., 0., 0.), (1.4, 0., 0.)],
+                  cell=[10, 10, 10], pbc=True)
+# calc 设置
+calc = hpc_Vasp(  
+            xc='pbe',
+            directory=hpc.workdir,  # 必须设置, 会新建文件夹，并进入文件夹执行命令
+            command='mpirun -np 8 vasp544_std',  # 必须设置，或者提供了 ASE vasp 的相关设置
+            hpctask=hpc,  # 这个非常关键，必须提供
+            gamma=True,
+            encut=400,
+            lwave=False,
+            lcharg=False,
+            )
+# 计算
+atoms.calc = calc
+e = atoms.get_potential_energy()
+print(f"Energy of N2 is {e} eV.")
+# finish job，结束节点任务
+hpc.postrun()
+# 关闭通道
+hpc.close()
+```
+
+## TODO

{hpc_task-0.1.2 → hpc_task-0.2.0}/hpc_task/hpc.py

@@ -79,7 +79,7 @@ class HPCTask:
             abs_workdir = stdout.read().decode('utf-8').strip().split()[-1]
             workdir = Path(abs_workdir).relative_to(Path(self._remote_parent_workdir))
             if self.workdir is None:
-                self.workdir = str(workdir)
+                self.workdir = workdir.as_posix()
         return self.workdir
 
     @property
@@ -292,7 +292,6 @@ class HPCTask:
                 print(f"Waiting for the queue 10 seconds...")
                 sleep(10)
                 status = self.status
-                need_sync = False
             elif status in ('SUSPENDED', 'DONE'):
                 output = ''
                 err = f"Job {self.jobid} status: {status}"
@@ -327,12 +326,12 @@ class HPCTask:
             rel_path = Path(root).relative_to(local_path)
             remote_dir = remote_path / rel_path
             if str(rel_path) != ".":
-                _ensure_remote_dir_exists(sftp_client, str(remote_dir))
+                _ensure_remote_dir_exists(sftp_client, remote_dir.as_posix())
             # 上传文件
             for file in files:
                 local_file = Path(root) / file
                 remote_file = remote_dir / file
-                sftp_client.put(str(local_file), str(remote_file), confirm=False)
+                sftp_client.put(local_file.as_posix(), remote_file.as_posix(), confirm=False)
 
         return None
 
@@ -365,13 +364,14 @@ def _ensure_remote_dir_exists(sftp, remote_dir):
     except FileNotFoundError:
         # 递归创建目录
         parts = Path(remote_dir).parts
-        current_path = parts[0]
+        current_path = Path(parts[0])
         for part in parts[1:]:  # 跳过根目录
-            current_path = os.path.join(current_path, part)
+            # current_path = os.path.join(current_path, part)
+            current_path = current_path / part
             try:
-                sftp.stat(current_path)
+                sftp.stat(current_path.as_posix())
             except FileNotFoundError:
-                sftp.mkdir(current_path)
+                sftp.mkdir(current_path.as_posix())
 
 def _download_dir(sftp, remote, local):
     os.makedirs(local, exist_ok=True)

hpc_task-0.2.0/hpc_task/hpc_calculator/vasp.py

@@ -0,0 +1,88 @@
+import os
+import subprocess
+from pathlib import Path
+
+from ase.calculators import calculator
+from ase.calculators.vasp import Vasp as ase_Vasp
+import ase.io
+from hpc_task.hpc import HPCTask
+
+
+class Vasp(ase_Vasp):
+    def __init__(self,
+                 atoms=None,
+                 restart=None,
+                 directory='.',
+                 label='vasp',
+                 command=None,
+                 hpctask:HPCTask=None,
+                 **kwargs):
+        super().__init__(
+            atoms=atoms,
+            restart=restart,
+            directory=directory,
+            label=label,
+            command=command,
+            **kwargs
+        )
+        self.hpctask = hpctask
+
+    def _run(self, command=None, out=None, directory=None):
+        """Method to explicitly execute VASP"""
+        if command is None:
+            command = self.command
+
+        if self.hpctask is not None:
+            remote_cmd = f"gosh-remote -vv client run '{command}'"
+            returncode, stderr, stdout = self.hpctask.execute(remote_cmd)
+
+        else:
+            result = subprocess.run(command,
+                                    shell=True,
+                                    cwd=directory,
+                                    capture_output=True,
+                                    text=True)
+            stdout = result.stdout
+            returncode = result.returncode
+            stderr = result.stderr
+        if out is not None:
+            out.write(stdout)
+        return returncode, stderr
+
+    def execute_only(self):
+        """
+        仅仅执行 command 命令，从文件夹中读取 INCAR、POTCAR、POSCAR、KPOINTS
+        """
+        self.read_potcar(filename=self._indir('POTCAR'))
+        self.read_incar(filename=self._indir('INCAR'))
+        self.read_kpoints(filename=self._indir('KPOINTS'))
+        atoms = ase.io.read(filename=self._indir('POSCAR'))
+        # 需要读进去ase-sort.dat，否则结果会报错
+        sortfile = self._indir('ase-sort.dat')
+        if os.path.isfile(sortfile):
+            self.sort = []
+            self.resort = []
+            with open(sortfile) as fd:
+                for line in fd:
+                    sort, resort = line.split()
+                    self.sort.append(int(sort))
+                    self.resort.append(int(resort))
+        else:
+            # Redo the sorting
+            self.initialize(atoms)
+
+        command = self.make_command(self.command)
+        with self._txt_outstream() as out:
+            errorcode, stderr = self._run(command=command,
+                                          out=out,
+                                          directory=self.directory)
+
+        if errorcode:
+            raise calculator.CalculationFailed(
+                '{} in {} returned an error: {:d} stderr {}'.format(
+                    self.name, Path(self.directory).resolve(), errorcode,
+                    stderr))
+
+        # Read results from calculation
+        self.update_atoms(atoms)
+        self.read_results()

{hpc_task-0.1.2 → hpc_task-0.2.0}/hpc_task.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hpc_task
-Version: 0.1.2
+Version: 0.2.0
 Summary: HPC Task python library.
 Home-page: https://gitee.com/pjren/hpc_task
 Author: Renpj
@@ -61,13 +61,14 @@ hpc.close()  # 此时可以关闭 ssh 通道
 # 在运行时候再重新构造和连接 hpc
 hpc = HPCTask(jobid=jobid)  # workdir 会根据 jobid 提取得到
 hpc.connect(target_host)
-
+hpc.get_workdir()
 # 结构、计算参数设置
 atoms = ase.Atoms('N2', positions=[(0., 0., 0.), (1.4, 0., 0.)],
                   cell=[10, 10, 10], pbc=True)
 # calc 设置
 calc = hpc_Vasp(  
             xc='pbe',
+            directory=hpc.workdir,  # 必须设置, 会新建文件夹，并进入文件夹执行命令
             command='mpirun -np 8 vasp544_std',  # 必须设置，或者提供了 ASE vasp 的相关设置
             hpctask=hpc,  # 这个非常关键，必须提供
             gamma=True,

{hpc_task-0.1.2 → hpc_task-0.2.0}/setup.py

@@ -10,7 +10,7 @@ install_requires = [
 
 setup(
     name='hpc_task',
-    version='0.1.2',
+    version='0.2.0',
     url='https://gitee.com/pjren/hpc_task',
     license='MIT',
     author='Renpj',

{hpc_task-0.1.2 → hpc_task-0.2.0}/tests/test_task.py

@@ -153,3 +153,31 @@ class TestHPCTask:
         # finish job
         hpc.postrun()
         hpc.close()
+
+    def test_hpc_vasp_execute_only(self):
+        workdir = 'test_hpc_vasp_execute_only'
+        Path(workdir).mkdir(parents=True, exist_ok=True)
+        shutil.copyfile('test_files/INCAR', Path(workdir)/'INCAR')
+        shutil.copyfile('test_files/POSCAR', Path(workdir)/'POSCAR')
+        shutil.copyfile('test_files/POTCAR', Path(workdir)/'POTCAR')
+        shutil.copyfile('test_files/KPOINTS', Path(workdir)/'KPOINTS')
+
+        # 队列占据
+        hpc = HPCTask(workdir=workdir)
+        hpc.scriptdir = '/data/bin/remote.job'
+        hpc.connect(target_host, jump_host)
+        hpc.prerun()
+        calc = hpc_Vasp(
+                    directory=workdir,
+                    command='mpirun -np 2 vasp_gam',
+                    hpctask=hpc,  # 这个非常关键
+                    )
+        # 计算
+        calc.execute_only()
+        atoms = calc.atoms
+        atoms.calc = calc
+        e = atoms.get_potential_energy()
+        print(f"Energy of N2 is {e} eV.")
+        # finish job
+        hpc.postrun()
+        hpc.close()

hpc_task-0.1.2/hpc_task/hpc_calculator/vasp.py

@@ -1,46 +0,0 @@
-import subprocess
-
-from ase.calculators.vasp import Vasp as ase_Vasp
-from hpc_task.hpc import HPCTask
-
-
-class Vasp(ase_Vasp):
-    def __init__(self,
-                 atoms=None,
-                 restart=None,
-                 directory='.',
-                 label='vasp',
-                 command=None,
-                 hpctask:HPCTask=None,
-                 **kwargs):
-        super().__init__(
-            atoms=atoms,
-            restart=restart,
-            directory=directory,
-            label=label,
-            command=command,
-            **kwargs
-        )
-        self.hpctask = hpctask
-
-    def _run(self, command=None, out=None, directory=None):
-        """Method to explicitly execute VASP"""
-        if command is None:
-            command = self.command
-
-        if self.hpctask is not None:
-            remote_cmd = f"gosh-remote -vv client run '{command}'"
-            returncode, stderr, stdout = self.hpctask.execute(remote_cmd)
-
-        else:
-            result = subprocess.run(command,
-                                    shell=True,
-                                    cwd=directory,
-                                    capture_output=True,
-                                    text=True)
-            stdout = result.stdout
-            returncode = result.returncode
-            stderr = result.stderr
-        if out is not None:
-            out.write(stdout)
-        return returncode, stderr