misc

Author: pabloprf

src/mitim_tools/gacode_tools/CGYROtools.py

@@ -178,7 +178,7 @@ def run_full(
         minutes = 5,
         n = 16,
         nomp = 1,
-        submit_via_qsub=True,
+        submit_via_qsub=True, #TODO fix this, works only at NERSC? no scans?
         clean_folder_going_in=True, # Make sure the scratch folder is removed before running (unless I want a restart!)
     ):
 
@@ -205,13 +205,31 @@ def run_full(
                 launchSlurm=False,
             )
 
-            CGYROcommand = f'gacode_qsub -e . -n {n} -nomp {nomp} -queue {self.cgyro_job.machineSettings['slurm']['partition']} -w 0:{minutes}:00 -s'
+            subfolder = "scan0"
+
+            CGYROcommand = f'gacode_qsub -e {subfolder} -n {n} -nomp {nomp} -queue {self.cgyro_job.machineSettings['slurm']['partition']} -w 0:{minutes}:00 -s'
 
             if "account" in self.cgyro_job.machineSettings["slurm"] and self.cgyro_job.machineSettings["slurm"]["account"] is not None:
                 CGYROcommand += f" -repo {self.cgyro_job.machineSettings['slurm']['account']}"
 
             self.slurm_output = "batch.out"
 
+            # ---
+            folder_run = self.folderCGYRO / subfolder
+            folder_run.mkdir(parents=True, exist_ok=True)
+
+            # Copy the input.cgyro in the subfolder
+            input_cgyro_file_this = folder_run / "input.cgyro"
+            shutil.copy2(input_cgyro_file, input_cgyro_file_this)
+
+            # Copy the input.gacode file in the subfolder
+            inputgacode_file_this = folder_run / "input.gacode"
+            shutil.copy2(self.inputgacode_file, inputgacode_file_this)
+
+            # Prepare the input and output folders
+            input_folders = [folder_run]
+            output_folders = [subfolder]
+
         else:
 
             if scan_param is None:

tests/CGYRO_workflow.py

@@ -5,7 +5,7 @@
 cold_start = True
 
 gacode_file = __mitimroot__ / "tests" / "data" / "input.gacode"
-folder = __mitimroot__ / "tests" / "scratch" / "cgyro_test"
+folder = __mitimroot__ / "tests" / "scratch" / "cgyro_test2"
 
 if cold_start and folder.exists():
     os.system(f"rm -r {folder}")
@@ -21,28 +21,17 @@
     roa = 0.55,
     CGYROsettings=0,
     extraOptions={
-        'KY':0.3
-    })
-cgyro.read(label="cgyro1")
+        'KY':0.3,
+        'MAX_TIME': 1E1, # Short, I just want to test the run
+    },
+    submit_via_qsub=True # NERSC: True #TODO change this
+    )
 
-cgyro.run(
-    'linear',
-    roa = 0.55,
-    CGYROsettings=0,
-    extraOptions={
-        'KY':0.5
-    })
-cgyro.read(label="cgyro2")
-
-cgyro.run(
-    'linear',
-    roa = 0.55,
-    CGYROsettings=0,
-    extraOptions={
-        'KY':0.7
-    })
-cgyro.read(label="cgyro3")
+cgyro.check(every_n_minutes=1)
+cgyro.fetch()
+cgyro.delete()
 
+cgyro.read(label="cgyro1")
 
 cgyro.plotLS()
-cgyro.fnLS.show()
+cgyro.fn.show()