From ddddc7907ad7ea2cadf93f9fd31f098032532ffc Mon Sep 17 00:00:00 2001
From: Xylar Asay-Davis <xylarstorm@gmail.com>
Date: Fri, 19 Jul 2024 02:27:11 -0700
Subject: [PATCH 1/2] Fix --copy_executable

---
 polaris/model_step.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/polaris/model_step.py b/polaris/model_step.py
index b0a6dc2a1..2819dadc1 100644
--- a/polaris/model_step.py
+++ b/polaris/model_step.py
@@ -465,12 +465,12 @@ def _process_model(config, base_work_dir):
         copy_executable = config.getboolean('setup', 'copy_executable')
         if copy_executable:
             # make a copy of the model executable, then link to that
-            mpas_subdir = os.path.basename(
-                config.get('paths', 'mpas_model'))
-            mpas_workdir = os.path.join(base_work_dir, mpas_subdir)
-            target = os.path.join(mpas_workdir, filename)
+            component_subdir = os.path.basename(
+                config.get('paths', 'component_path'))
+            component_workdir = os.path.join(base_work_dir, component_subdir)
+            target = os.path.join(component_workdir, filename)
             try:
-                os.makedirs(mpas_workdir)
+                os.makedirs(component_workdir)
             except FileExistsError:
                 pass
 

From 477a0f43874b7802cab40db603400707c26523d3 Mon Sep 17 00:00:00 2001
From: Xylar Asay-Davis <xylarstorm@gmail.com>
Date: Fri, 19 Jul 2024 02:54:48 -0700
Subject: [PATCH 2/2] Fix submodule checkout in bisect utility

---
 utils/bisect/bisect_step.py | 16 +++++++++++-----
 utils/bisect/example.cfg    |  2 +-
 2 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/utils/bisect/bisect_step.py b/utils/bisect/bisect_step.py
index 68dff6271..465e6977d 100755
--- a/utils/bisect/bisect_step.py
+++ b/utils/bisect/bisect_step.py
@@ -6,8 +6,8 @@
 import subprocess
 
 
-def run(launch_path, mpas_path, work_base, load_script, make_command,
-        setup_command, run_command):
+def run(launch_path, e3sm_path, mpas_path, work_base, load_script,
+        make_command, setup_command, run_command):
     """
     This function runs a single step in the bisection process.  It is typically
     called through ``git bisect run`` within the ``utils/bisect/bisect.py`` but
@@ -19,6 +19,8 @@ def run(launch_path, mpas_path, work_base, load_script, make_command,
         The path from which relative paths in the config file are defined,
         typically the root of the polaris branch where the config file
         resides and where ``utils/bisect/bisect.py`` was called.
+    e3sm_path : str
+        The relative or absolute path to the e3sm branch to build from.
     mpas_path : str
         The relative or absolute path to the mpas component to be built.
     work_base : str
@@ -38,6 +40,7 @@ def run(launch_path, mpas_path, work_base, load_script, make_command,
         test case(s)
     """
 
+    e3sm_path = to_abs(e3sm_path, launch_path)
     mpas_path = to_abs(mpas_path, launch_path)
     work_base = to_abs(work_base, launch_path)
     load_script = to_abs(load_script, launch_path)
@@ -55,10 +58,12 @@ def run(launch_path, mpas_path, work_base, load_script, make_command,
     except FileExistsError:
         pass
 
-    os.chdir(mpas_path)
     commands = f'source {load_script} && ' \
+               f'cd {e3sm_path} && ' \
+               f'rm -rf * && ' \
+               f'git reset --hard HEAD && ' \
                f'git submodule update --init --recursive && ' \
-               f'make clean >& {work_path}/clean.log && ' \
+               f'cd {mpas_path} && ' \
                f'{make_command} >& {work_path}/make.log && ' \
                f'{setup_command} -p {mpas_path} -w {work_path} && ' \
                f'cd {work_path} && ' \
@@ -112,7 +117,8 @@ def main():
     launch_path = os.path.dirname(args.config_file)
 
     section = config['bisect']
-    run(launch_path=launch_path, mpas_path=section['mpas_path'],
+    run(launch_path=launch_path, e3sm_path=section['e3sm_path'],
+        mpas_path=section['mpas_path'],
         work_base=section['work_base'], load_script=section['load_script'],
         make_command=section['make_command'],
         setup_command=section['setup_command'],
diff --git a/utils/bisect/example.cfg b/utils/bisect/example.cfg
index bcb6eb331..4c4a484bf 100644
--- a/utils/bisect/example.cfg
+++ b/utils/bisect/example.cfg
@@ -27,4 +27,4 @@ setup_command = polaris setup --copy_executable -n 39 -b /lcrc/group/e3sm/ac.xyl
 # polaris environment
 load_script = load_polaris_bisect_anvil_intel_impi.sh
 # the command to run polaris within the work directory
-run_command = polaris run
+run_command = polaris serial