From 034c9d7d4a673b2325e85075b9350fb783e407ba Mon Sep 17 00:00:00 2001
From: Thang Nguyen <46436648+thangckt@users.noreply.github.com>
Date: Wed, 27 Mar 2024 02:17:14 +0900
Subject: [PATCH 1/2] Update pbs.py

---
 dpdispatcher/machines/pbs.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/dpdispatcher/machines/pbs.py b/dpdispatcher/machines/pbs.py
index 7e49b709..ec464f65 100644
--- a/dpdispatcher/machines/pbs.py
+++ b/dpdispatcher/machines/pbs.py
@@ -4,6 +4,7 @@
 from dpdispatcher.machine import Machine
 from dpdispatcher.utils.job_status import JobStatus
 from dpdispatcher.utils.utils import customized_script_header_template
+from pathlib import Path
 
 pbs_script_header_template = """
 #!/bin/bash -l
@@ -219,9 +220,8 @@ def gen_script_header(self, job):
 
         if (resources["strategy"].get("customized_script_header_template_file")
                 is not None):
-            sge_script_header = customized_script_header_template(
-                resources["strategy"]["customized_script_header_template_file"],
-                resources,)
+            filename = self.context.remote_root / Path(resources["strategy"]["customized_script_header_template_file"])
+            sge_script_header = customized_script_header_template(str(filename.as_posix()), resources)
         else:
             sge_script_header = sge_script_header_template.format(
                 **sge_script_header_dict)
@@ -230,9 +230,11 @@ def gen_script_header(self, job):
     def do_submit(self, job):
         script_file_name = job.script_file_name
         script_str = self.gen_script(job)
-        script_str = script_str.replace(f"source $REMOTE_ROOT/{job.script_file_name}.run", f"source $REMOTE_ROOT/{job.script_file_name}")
         job_id_name = job.job_hash + "_job_id"
         self.context.write_file(fname=script_file_name, write_str=script_str)
+        script_run_str = self.gen_script_command(job)
+        script_run_file_name = f"{job.script_file_name}.run"
+        self.context.write_file(fname=script_run_file_name, write_str=script_run_str)
         script_file_dir = self.context.remote_root
         stdin, stdout, stderr = self.context.block_checkcall(
             "cd {} && {} {}".format(script_file_dir, "qsub", script_file_name)

From 3f07742f58c974c43f9069d4606e59e1830e9bb2 Mon Sep 17 00:00:00 2001
From: Thang Nguyen <46436648+thangckt@users.noreply.github.com>
Date: Wed, 27 Mar 2024 02:25:05 +0900
Subject: [PATCH 2/2] Update pbs.py

---
 dpdispatcher/machines/pbs.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/dpdispatcher/machines/pbs.py b/dpdispatcher/machines/pbs.py
index ec464f65..2a78c74e 100644
--- a/dpdispatcher/machines/pbs.py
+++ b/dpdispatcher/machines/pbs.py
@@ -4,7 +4,6 @@
 from dpdispatcher.machine import Machine
 from dpdispatcher.utils.job_status import JobStatus
 from dpdispatcher.utils.utils import customized_script_header_template
-from pathlib import Path
 
 pbs_script_header_template = """
 #!/bin/bash -l
@@ -220,8 +219,8 @@ def gen_script_header(self, job):
 
         if (resources["strategy"].get("customized_script_header_template_file")
                 is not None):
-            filename = self.context.remote_root / Path(resources["strategy"]["customized_script_header_template_file"])
-            sge_script_header = customized_script_header_template(str(filename.as_posix()), resources)
+            filename = resources["strategy"]["customized_script_header_template_file"]
+            sge_script_header = customized_script_header_template(filename, resources)
         else:
             sge_script_header = sge_script_header_template.format(
                 **sge_script_header_dict)