From 8e873e68f65c2328122b7b178233729a9a1f32f6 Mon Sep 17 00:00:00 2001
From: unknown <wardhsu7@gmail.com>
Date: Tue, 23 Apr 2024 21:30:02 -0500
Subject: [PATCH] update the jarvis package to support dervied quantity and
 readme

---
 .../jarvis_coeus/adios2_gray_scott/README.md  | 12 ++++++--
 .../jarvis_coeus/adios2_gray_scott/pkg.py     | 29 +++++++++++++++----
 2 files changed, 32 insertions(+), 9 deletions(-)

diff --git a/test/jarvis/jarvis_coeus/jarvis_coeus/adios2_gray_scott/README.md b/test/jarvis/jarvis_coeus/jarvis_coeus/adios2_gray_scott/README.md
index 91c939ed..2f0781e0 100644
--- a/test/jarvis/jarvis_coeus/jarvis_coeus/adios2_gray_scott/README.md
+++ b/test/jarvis/jarvis_coeus/jarvis_coeus/adios2_gray_scott/README.md
@@ -1,7 +1,7 @@
 Gray-Scott is a 3D 7-Point stencil code
 
 # Installation
-
+The gray_scott is installed along with coeus-adapter, these step can skip
 ```bash
 git clone https://github.com/pnorbert/adiosvm
 pushd adiosvm/Tutorial/gs-mpiio
@@ -21,7 +21,7 @@ popd
 Create the environment variables needed by Gray Scott
 ```bash
 spack load mpi
-export PATH="${GRAY_SCOTT_PATH}:$PATH"
+export PATH="${COEUS_Adapter/build/bin}:$PATH"
 ```````````
 
 ## 1. Create a Resource Graph
@@ -90,7 +90,7 @@ spack load hermes adios2
 # On Ares
 spack load hermes@master
 # export GRAY_SCOTT_PATH=$/coeus_adapter/build/bin
-export PATH="${GRAY_SCOTT_PATH}:$PATH"
+export PATH="${COEUS_Adapter/build/bin}:$PATH"
 ```
 
 ## 2. Create a Resource Graph
@@ -135,6 +135,12 @@ jarvis pipeline append hermes_run --sleep=10 --provider=sockets
 jarvis pipeline append adios2_gray_scott engine=hermes 
 ```
 
+For derived variable with adios2 in hermes:
+```bash
+jarvis pipeline append hermes_run --sleep=10 --provider=sockets
+jarvis pipeline append adios2_gray_scott engine=hermes_derived
+```
+
 ## 5. Run the Experiment
 
 Run the experiment
diff --git a/test/jarvis/jarvis_coeus/jarvis_coeus/adios2_gray_scott/pkg.py b/test/jarvis/jarvis_coeus/jarvis_coeus/adios2_gray_scott/pkg.py
index 74c852b7..dced2995 100644
--- a/test/jarvis/jarvis_coeus/jarvis_coeus/adios2_gray_scott/pkg.py
+++ b/test/jarvis/jarvis_coeus/jarvis_coeus/adios2_gray_scott/pkg.py
@@ -153,7 +153,7 @@ def _configure_menu(self):
             {
                 'name': 'engine',
                 'msg': 'Engine to be used',
-                'choices': ['bp5', 'hermes'],
+                'choices': ['bp5', 'hermes', 'bp5_derived', 'hermes_derived'],
                 'type': str,
                 'default': 'bp5',
             },
@@ -163,6 +163,12 @@ def _configure_menu(self):
                 'type': bool,
                 'default': True,
             },
+            {
+                'name': 'limit',
+                'msg': 'Limit the value of data to track',
+                'type': int,
+                'default': 0,
+            },
             {
                 'name': 'db_path',
                 'msg': 'Path where the DB will be stored',
@@ -215,11 +221,11 @@ def _configure(self, **kwargs):
                                        env=self.env))
 
         JsonFile(self.settings_json_path).save(settings_json)
-
-        if self.config['engine'].lower() == 'bp5':
+        print(f"Using engine {self.config['engine']}")
+        if self.config['engine'].lower() in ['bp5', 'bp5_derived']:
             self.copy_template_file(f'{self.pkg_dir}/config/adios2.xml',
                                 self.adios2_xml_path)
-        elif self.config['engine'].lower() == 'hermes':
+        elif self.config['engine'].lower() in ['hermes', 'hermes_derived']:
             self.copy_template_file(f'{self.pkg_dir}/config/hermes.xml',
                                     self.adios2_xml_path,
                                     replacements={
@@ -243,8 +249,19 @@ def start(self):
         :return: None
         """
         # print(self.env['HERMES_CLIENT_CONF'])
-        Exec(f'adios2-gray-scott {self.settings_json_path}',
-             MpiExecInfo(nprocs=self.config['nprocs'],
+        if self.config['engine'].lower() in ['bp5_derived', 'hermes_derived']:
+            derived = 1
+            Exec(f'adios2-gray-scott {self.settings_json_path} {derived}',
+                 MpiExecInfo(nprocs=self.config['nprocs'],
+                             ppn=self.config['ppn'],
+                             hostfile=self.jarvis.hostfile,
+                             env=self.mod_env,
+                             do_dbg=self.config['do_dbg'],
+                             dbg_port=self.config['dbg_port']
+                             ))
+        elif self.config['engine'].lower() in ['hermes', 'bp5']:
+            Exec(f'adios2-gray-scott {self.settings_json_path}',
+                MpiExecInfo(nprocs=self.config['nprocs'],
                          ppn=self.config['ppn'],
                          hostfile=self.jarvis.hostfile,
                          env=self.mod_env))