From 966b0aded8b9021a55f7b7a4d2e14caf48f21fd8 Mon Sep 17 00:00:00 2001
From: Charles Cowart <ccowart@ucsd.edu>
Date: Mon, 11 Mar 2024 16:54:24 -0700
Subject: [PATCH] incorporates the latest changes from production testing.

---
 sequence_processing_pipeline/Job.py                | 13 ++++++++++---
 sequence_processing_pipeline/templates/nuqc_job.sh |  2 ++
 setup.py                                           |  2 +-
 3 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/sequence_processing_pipeline/Job.py b/sequence_processing_pipeline/Job.py
index 6c15a0e..92caf0f 100644
--- a/sequence_processing_pipeline/Job.py
+++ b/sequence_processing_pipeline/Job.py
@@ -232,8 +232,11 @@ def submit_job(self, script_path, job_parameters=None,
 
         job_info = {'job_id': None, 'job_name': None, 'job_state': None,
                     'elapsed_time': None}
-        # Just to give sometime for everything to be set up properly
-        sleep(5)
+        # Just to give some time for everything to be set up properly
+        sleep(10)
+
+        exit_count = 0
+
         while wait:
             result = self._system_call(f"sacct -P -n --job {job_id} --format "
                                        "JobID,JobName,State,Elapsed,ExitCode")
@@ -276,9 +279,13 @@ def submit_job(self, script_path, job_parameters=None,
             # if job is completed after having run or exited after having
             # run, then stop waiting.
             if not set(states) - {'COMPLETED', 'FAILED', 'CANCELLED'}:
+                # break
+                exit_count += 1
+
+            if exit_count > 4:
                 break
 
-            sleep(5)
+            sleep(10)
 
         if job_info['job_id'] is not None:
             # job was once in the queue
diff --git a/sequence_processing_pipeline/templates/nuqc_job.sh b/sequence_processing_pipeline/templates/nuqc_job.sh
index 9451956..12586d9 100644
--- a/sequence_processing_pipeline/templates/nuqc_job.sh
+++ b/sequence_processing_pipeline/templates/nuqc_job.sh
@@ -9,6 +9,8 @@
 ### as well as sbatch -c. demux threads remains fixed at 1.
 ### Note -c set to 4 and thread counts set to 7 during testing.
 #SBATCH -c {{cores_per_task}}
+#SBATCH --gres=node_jobs:4
+
 
 echo "---------------"
 echo "Run details:"
diff --git a/setup.py b/setup.py
index 9daf65e..5ab23cc 100644
--- a/setup.py
+++ b/setup.py
@@ -48,4 +48,4 @@
         ],
       entry_points={
           'console_scripts': ['demux=sequence_processing_pipeline.scripts.cli'
-                              ':demux',], })
+                              ':demux', ], })