add SGE class in pbs.py (#323)

This SGE class inherit from PBS machine class. I have tested with a
vanilla python print job and it works. I can continue working on testing
with more complex tasks.

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

Author: 3 people

dpdispatcher/machines/pbs.py

@@ -177,3 +177,107 @@ def gen_script_header(self, job):
                 **pbs_script_header_dict
             )
         return pbs_script_header
+
+
+sge_script_header_template = """
+#!/bin/bash
+#$ -N dpdispatcher_submit
+{select_node_line}
+#$ -cwd
+
+"""
+
+
+class SGE(PBS):
+    def __init__(
+        self,
+        batch_type=None,
+        context_type=None,
+        local_root=None,
+        remote_root=None,
+        remote_profile={},
+        *,
+        context=None,
+    ):
+        super(PBS, self).__init__(
+            batch_type,
+            context_type,
+            local_root,
+            remote_root,
+            remote_profile,
+            context=context,
+        )
+
+    def gen_script_header(self, job):
+        resources = job.resources
+        sge_script_header_dict = {}
+        # resources.number_node is not used
+        sge_script_header_dict[
+            "select_node_line"
+        ] = f"#$ -pe mpi {resources.cpu_per_node} "
+        # resources.queue_name is not necessary
+        sge_script_header = sge_script_header_template.format(**sge_script_header_dict)
+        return sge_script_header
+
+    def do_submit(self, job):
+        script_file_name = job.script_file_name
+        script_str = self.gen_script(job)
+        job_id_name = job.job_hash + "_job_id"
+        self.context.write_file(fname=script_file_name, write_str=script_str)
+        script_file_dir = self.context.remote_root
+        stdin, stdout, stderr = self.context.block_checkcall(
+            "cd {} && {} {}".format(script_file_dir, "qsub", script_file_name)
+        )
+        subret = stdout.readlines()
+        job_id = subret[0].split()[2]
+        self.context.write_file(job_id_name, job_id)
+        return job_id
+
+    def default_resources(self, resources):
+        pass
+
+    def check_status(self, job):
+        job_id = job.job_id
+        status_line = None
+        if job_id == "":
+            return JobStatus.unsubmitted
+        ret, stdin, stdout, stderr = self.context.block_call("qstat")
+        err_str = stderr.read().decode("utf-8")
+        if ret != 0:
+            raise RuntimeError(
+                "status command qstat fails to execute. erro info: %s return code %d"
+                % (err_str, ret)
+            )
+        status_text_list = stdout.read().decode("utf-8").split("\n")
+        for txt in status_text_list:
+            if job_id in txt:
+                status_line = txt
+
+        if status_line is None:
+            count = 0
+            while count <= 6:
+                if self.check_finish_tag(job=job):
+                    return JobStatus.finished
+                dlog.info(
+                    "not tag_finished detected, execute sync command and wait. count "
+                    + str(count)
+                )
+                self.context.block_call("sync")
+                import time
+
+                time.sleep(10)
+                count += 1
+            return JobStatus.terminated
+        else:
+            status_word = status_line.split()[4]
+            # dlog.info (status_word)
+            if status_word in ["qw"]:
+                return JobStatus.waiting
+            elif status_word in ["r"]:
+                return JobStatus.running
+            else:
+                return JobStatus.unknown
+
+    def check_finish_tag(self, job):
+        job_tag_finished = job.job_hash + "_job_tag_finished"
+        return self.context.check_file_exists(job_tag_finished)