added slurm command and proper setting of variuables

jarvis_util/shell/slurm_exec.py

@@ -9,58 +9,87 @@
 from jarvis_util.shell.local_exec import LocalExec
 from .exec_info import ExecInfo, ExecType
 
+
 class SlurmExec(LocalExec):
     """
-    This class contains methods for executing a command in parallel
-    using MPI.
+    This class contains methods for executing a command
+    through the Slurm scheduler
     """
 
     def __init__(self, cmd, exec_info):
         """
         Execute a command through sbatch
 
         :param cmd: A command (string) to execute
-        :param exec_info: Information needed by MPI
+        :param exec_info: Information needed by sbatch
         """
 
         self.cmd = cmd
-        self.job_name = exec_info
+        self.job_name = exec_info.job_name
         self.num_nodes = exec_info.num_noodes
-        self.nprocs = exec_info.nprocs
         self.ppn = exec_info.ppn
-        self.hostfile = exec_info.hostfile
-        self.mpi_env = exec_info.env
+        self.cpus_per_task = exec_info.cpus_per_task
+        self.time = exec_info.time
+        self.partition = exec_info.partition
+        self.mail_type = exec_info.mail_type
+        self.output = exec_info.pipe_stdout
+        self.error = exec_info.pipe_stderr
+        self.memory = exec_info.memory
+        self.gres  = exec_info.gres
+        self.exclusive = exec_info.exclusive
+
         super().__init__(self.slurmcmd(),
                          exec_info.mod(env=exec_info.basic_env))
 
+    def generate_sbatch_command(self):
+        cmd = "sbatch"
+
+        # Mapping of attribute names to their corresponding sbatch option names
+        options_map = {
+            'job_name': 'job-name',
+            'num_nodes': 'nodes',
+            'ppn': 'ntasks',
+            'cpus_per_task': 'cpus-per-task',
+            'time': 'time',
+            'partition': 'partition',
+            'mail_type': 'mail-type',
+            'output': 'output',
+            'error': 'error',
+            'memory': 'mem',
+            'gres': 'gres',
+            'exclusive': 'exclusive'
+        }
+
+        for attr, option in options_map.items():
+            value = getattr(self, attr)
+            if value is not None:
+                if value is True:  # For options like 'exclusive' that don't take a value
+                    cmd += f" --{option}"
+                else:
+                    cmd += f" --{option}={value}"
+
+        cmd += f" {self.cmd}"
+        return cmd
+
     def slurmcmd(self):
-        params = [f'mpirun -n {self.nprocs}']
-        params.append('--oversubscribe')
-        if self.ppn is not None:
-            params.append(f'-ppn {self.ppn}')
-        if len(self.hostfile):
-            if self.hostfile.is_subset() or self.hostfile.path is None:
-                params.append(f'--host {",".join(self.hostfile.hosts)}')
-            else:
-                params.append(f'--hostfile {self.hostfile.path}')
-        params += [f'-x {key}=\"{val}\"'
-                   for key, val in self.mpi_env.items()]
-        params.append(self.cmd)
-        cmd = ' '.join(params)
+        cmd = self.generate_sbatch_command()
         jutil = JutilManager.get_instance()
-        if jutil.debug_mpi_exec:
+        if jutil.debug_slurm:
             print(cmd)
         return cmd
 
 
 class SlurmExecInfo(ExecInfo):
     def __init__(self, job_name=None, num_nodes=1, **kwargs):
         super().__init__(exec_type=ExecType.SLURM, **kwargs)
-        allowed_options = ['cpus_per_task', 'time', 'partition', 'mail_type', 'mail_user', 'mem', 'gres', 'exclusive', 'pipeline_file']
+        allowed_options = ['job_name', 'num_nodes', 'cpus_per_task', 'time', 'partition', 'mail_type',
+                           'mail_user', 'mem', 'gres', 'exclusive']
+        self.keys += allowed_options
+        # We use ppn, and the output and error file from the base Exec Info
         self.job_name = job_name
         self.num_nodes = num_nodes
-        self.keys.append(['job_name', 'num_nodes'])
-        for key, value in kwargs.items():
-            if key in allowed_options:
-                setattr(self, key, value)
-                self.keys.append(key)
+        for key in allowed_options:
+            if key in kwargs:
+                setattr(self, key, kwargs[key])
+            else:
+                setattr(self, key, None)