Added support for PBS scheduler

jarvis_util/jutil_manager.py

@@ -27,4 +27,5 @@ def __init__(self):
  self.debug_local_exec = False
  self.debug_scp = False
  self.debug_slurm = False
+ self.debug_pbs = True
 

jarvis_util/shell/exec.py

@@ -2,6 +2,7 @@
 This module provides mechanisms to execute binaries either locally or
 remotely.
 """
+from jarvis_util.shell.pbs_exec import PbsExec
 from jarvis_util.shell.slurm_exec import SlurmExec
 from .local_exec import LocalExec
 from .pssh_exec import PsshExec
@@ -37,6 +38,8 @@ def __init__(self, cmd, exec_info=None):
  exec_type = MpiVersion(exec_info).version
  elif exec_type == ExecType.SLURM:
  exec_type = SlurmExec(cmd, exec_info)
+ elif exec_type == ExecType.PBS:
+ exec_type = PbsExec(cmd, exec_info)
 
  if exec_type == ExecType.MPICH:
  self.exec_ = MpichExec(cmd, exec_info)

jarvis_util/shell/exec_info.py

@@ -24,6 +24,7 @@ class ExecType(Enum):
  OPENMPI = 'OPENMPI'
  INTEL_MPI = 'INTEL_MPI'
  SLURM = 'SLURM'
+ PBS = 'PBS'
 
 
 class ExecInfo:

jarvis_util/shell/pbs_exec.py

@@ -0,0 +1,82 @@
+"""
+This module provides methods to execute a process in parallel using the
+Message Passing Interface (MPI). This module assumes MPI is installed
+on the system. This class is intended to be called from Exec,
+not by general users.
+"""
+
+from jarvis_util.jutil_manager import JutilManager
+from jarvis_util.shell.local_exec import LocalExec
+from .exec_info import ExecInfo, ExecType
+
+
+class PbsExec(LocalExec):
+ """
+ This class contains methods for executing a command
+ through the PBS scheduler
+ """
+
+ def __init__(self, cmd, exec_info):
+ """
+ Execute a command through qsub
+ :param cmd: A command (string) to execute
+ :param exec_info: Information needed by qsub
+ """
+ self.cmd = cmd
+ self.interactive = exec_info.interactive
+ self.nnodes = exec_info.nnodes
+ self.system = exec_info.system
+ self.filesystems = exec_info.filesystems
+ self.walltime = exec_info.walltime
+ self.account = exec_info.account
+ self.queue = exec_info.queue
+ super().__init__(self.pbscmd(),
+ exec_info.mod(env=exec_info.basic_env))
+
+ def generate_qsub_command(self):
+ cmd = 'qsub'
+
+ if self.interactive:
+ cmd += ' -I'
+
+ options_map = {
+ 'filesystems': 'l filesystems',
+ 'walltime': 'l walltime',
+ 'account': 'A',
+ 'queue': 'q'
+ }
+
+ if self.nnodes and self.system:
+ cmd += f' -l select={self.nnodes}:system={self.system}'
+ elif self.nnodes:
+ cmd += f' -l select={self.nnodes}'
+ else:
+ raise ValueError("System defined without select value.")
+
+ for attr, option in options_map.items():
+ value = getattr(self, attr)
+ if value is not None:
+ cmd += f' -{option}={value}'
+
+ cmd += f' {self.cmd}'
+ return cmd
+
+ def pbscmd(self):
+ cmd = self.generate_qsub_command()
+ jutil = JutilManager.get_instance()
+ if jutil.debug_pbs:
+ print(cmd)
+ return cmd
+
+
+class PbsExecInfo(ExecInfo):
+ def __init__(self, **kwargs):
+ super().__init__(exec_type=ExecType.PBS, **kwargs)
+ allowed_options = ['interactive', 'nnodes', 'system', 'filesystems', 'walltime', 'account', 'queue']
+ self.keys += allowed_options
+ # We use output and error file from the base Exec Info
+ for key in allowed_options:
+ if key in kwargs:
+ setattr(self, key, kwargs[key])
+ else:
+ setattr(self, key, None)