diff --git a/dev-tools/airavata-python-sdk/airavata_auth/device_auth.py b/dev-tools/airavata-python-sdk/airavata_auth/device_auth.py
index 3037ab1702..944055ad26 100644
--- a/dev-tools/airavata-python-sdk/airavata_auth/device_auth.py
+++ b/dev-tools/airavata-python-sdk/airavata_auth/device_auth.py
@@ -10,6 +10,13 @@
 
 
 class AuthContext:
+    
+    @staticmethod
+    def get_access_token():
+        if os.environ.get("CS_ACCESS_TOKEN", None) is None:
+            context = AuthContext()
+            context.login()
+        return os.environ["CS_ACCESS_TOKEN"]
 
     def __init__(self):
         self.settings = Settings()
@@ -21,6 +28,8 @@ def __init__(self):
         self.console = Console()
 
     def login(self):
+        if os.environ.get('CS_ACCESS_TOKEN', None) is not None:
+            return
         # Step 1: Request device and user code
         auth_device_url = f"{self.settings.AUTH_SERVER_URL}/realms/{self.settings.AUTH_REALM}/protocol/openid-connect/auth/device"
         response = requests.post(auth_device_url, data={
diff --git a/dev-tools/airavata-python-sdk/airavata_experiments/__init__.py b/dev-tools/airavata-python-sdk/airavata_experiments/__init__.py
index dd391c07c4..bb5e33a0dd 100644
--- a/dev-tools/airavata-python-sdk/airavata_experiments/__init__.py
+++ b/dev-tools/airavata-python-sdk/airavata_experiments/__init__.py
@@ -18,8 +18,9 @@
 
 from . import base, plan
 from airavata_auth.device_auth import AuthContext
-from .runtime import list_runtimes, Runtime
+from .runtime import find_runtimes, Runtime
 from typing import Any
+from . import md, neuro
 
 
 context = AuthContext()
@@ -27,7 +28,7 @@
 def login():
   context.login()
 
-__all__ = ["list_runtimes", "base", "plan", "login"]
+__all__ = ["find_runtimes", "base", "plan", "login", "md", "neuro"]
 
 
 def display_runtimes(runtimes: list[Runtime]) -> None:
diff --git a/dev-tools/airavata-python-sdk/airavata_experiments/airavata.py b/dev-tools/airavata-python-sdk/airavata_experiments/airavata.py
index e6d7b10385..f5ca757de1 100644
--- a/dev-tools/airavata-python-sdk/airavata_experiments/airavata.py
+++ b/dev-tools/airavata-python-sdk/airavata_experiments/airavata.py
@@ -35,7 +35,9 @@
 from airavata.model.experiment.ttypes import ExperimentModel, ExperimentType, UserConfigurationDataModel
 from airavata.model.scheduling.ttypes import ComputationalResourceSchedulingModel
 from airavata.model.data.replica.ttypes import DataProductModel, DataProductType, DataReplicaLocationModel, ReplicaLocationCategory
-from airavata.model.appcatalog.groupresourceprofile.ttypes import GroupResourceProfile
+from airavata.model.appcatalog.groupresourceprofile.ttypes import GroupResourceProfile, ResourceType
+from airavata.model.appcatalog.computeresource.ttypes import ComputeResourceDescription
+from airavata.model.status.ttypes import JobStatus, JobState, ExperimentStatus, ExperimentState
 
 warnings.filterwarnings("ignore", category=DeprecationWarning)
 logger = logging.getLogger("airavata_sdk.clients")
@@ -100,8 +102,10 @@ def create_experiment_model(
     )
   
   def get_resource_host_id(self, resource_name):
-        resources: dict = self.api_server_client.get_all_compute_resource_names(self.airavata_token) # type: ignore
-        return next((str(k) for k, v in resources.items() if v == resource_name))
+    resources = self.api_server_client.get_all_compute_resource_names(self.airavata_token)
+    resource_id = next((k for k in resources if k.startswith(resource_name)), None)
+    assert resource_id is not None, f"Compute resource {resource_name} not found"
+    return resource_id
   
   def configure_computation_resource_scheduling(
       self,
@@ -188,7 +192,7 @@ def get_process_id(self, experiment_id: str) -> str:
     """
     tree = self.api_server_client.get_detailed_experiment_tree(self.airavata_token, experiment_id) # type: ignore
     processModels = tree.processes
-    assert processModels is not None
+    assert processModels is not None, f"No process models found for experiment {experiment_id}"
     assert len(processModels) == 1, f"Expected 1 process model, got {len(processModels)}"
     return processModels[0].processId
 
@@ -213,7 +217,8 @@ def get_preferred_storage(self, gateway_id: str | None = None, sr_hostname: str
     sr_hostname = sr_hostname or self.default_sr_hostname()
     # logic
     sr_names: dict[str, str] = self.api_server_client.get_all_storage_resource_names(self.airavata_token) # type: ignore
-    sr_id = next((str(k) for k, v in sr_names.items() if v == sr_hostname))
+    sr_id = next((str(k) for k, v in sr_names.items() if v == sr_hostname), None)
+    assert sr_id is not None, f"Storage resource {sr_hostname} not found"
     return self.api_server_client.get_gateway_storage_preference(self.airavata_token, gateway_id, sr_id)
 
   def get_storage(self, storage_name: str | None = None) -> any:  # type: ignore
@@ -225,7 +230,8 @@ def get_storage(self, storage_name: str | None = None) -> any:  # type: ignore
     storage_name = storage_name or self.default_sr_hostname()
     # logic
     sr_names: dict[str, str] = self.api_server_client.get_all_storage_resource_names(self.airavata_token) # type: ignore
-    sr_id = next((str(k) for k, v in sr_names.items() if v == storage_name))
+    sr_id = next((str(k) for k, v in sr_names.items() if v == storage_name), None)
+    assert sr_id is not None, f"Storage resource {storage_name} not found"
     storage = self.api_server_client.get_storage_resource(self.airavata_token, sr_id)
     return storage
 
@@ -236,11 +242,9 @@ def get_group_resource_profile_id(self, group: str) -> str:
     """
     # logic
     grps: list[GroupResourceProfile] = self.api_server_client.get_group_resource_list(self.airavata_token, self.default_gateway_id()) # type: ignore
-    try:
-      grp_id = next((grp.groupResourceProfileId for grp in grps if grp.groupResourceProfileName == group))
-      return str(grp_id)
-    except StopIteration:
-      raise Exception(f"Group resource profile {group} not found")
+    grp_id = next((grp.groupResourceProfileId for grp in grps if grp.groupResourceProfileName == group), None)
+    assert grp_id is not None, f"Group resource profile {group} not found"
+    return str(grp_id)
   
   def get_group_resource_profile(self, group_id: str):
     grp = self.api_server_client.get_group_resource_profile(self.airavata_token, group_id) # type: ignore
@@ -253,7 +257,8 @@ def get_compatible_deployments(self, app_interface_id: str, group: str):
     """
     # logic
     grps: list = self.api_server_client.get_group_resource_list(self.airavata_token, self.default_gateway_id()) # type: ignore
-    grp_id = next((grp.groupResourceProfileId for grp in grps if grp.groupResourceProfileName == group))
+    grp_id = next((grp.groupResourceProfileId for grp in grps if grp.groupResourceProfileName == group), None)
+    assert grp_id is not None, f"Group resource profile {group} not found"
     deployments = self.api_server_client.get_application_deployments_for_app_module_and_group_resource_profile(self.airavata_token, app_interface_id, grp_id)
     return deployments
 
@@ -264,13 +269,15 @@ def get_app_interface_id(self, app_name: str, gateway_id: str | None = None):
     """
     gateway_id = str(gateway_id or self.default_gateway_id())
     apps: list = self.api_server_client.get_all_application_interfaces(self.airavata_token, gateway_id) # type: ignore
-    app_id = next((app.applicationInterfaceId for app in apps if app.applicationName == app_name))
+    app_id = next((app.applicationInterfaceId for app in apps if app.applicationName == app_name), None)
+    assert app_id is not None, f"Application interface {app_name} not found"
     return str(app_id)
 
   def get_project_id(self, project_name: str, gateway_id: str | None = None):
     gateway_id = str(gateway_id or self.default_gateway_id())
     projects: list = self.api_server_client.get_user_projects(self.airavata_token, gateway_id, self.user_id, 10, 0) # type: ignore
-    project_id = next((p.projectID for p in projects if p.name == project_name and p.owner == self.user_id))
+    project_id = next((p.projectID for p in projects if p.name == project_name and p.owner == self.user_id), None)
+    assert project_id is not None, f"Project {project_name} not found"
     return str(project_id)
 
   def get_application_inputs(self, app_interface_id: str) -> list:
@@ -323,14 +330,14 @@ def upload_files(self, process_id: str | None, agent_ref: str | None, sr_host: s
     elif process_id is not None and agent_ref is not None:
       assert len(local_files) == 1, f"Expected 1 file, got {len(local_files)}"
       file = local_files[0]
-      fp = os.path.join("/data", file.name)
+      fp = os.path.join(".", file.name)
       rawdata = file.read_bytes()
       b64data = base64.b64encode(rawdata).decode()
       res = requests.post(f"{self.connection_svc_url()}/agent/execute/shell", json={
           "agentId": agent_ref,
           "envName": agent_ref,
           "workingDir": ".",
-          "arguments": ["sh", "-c", f"echo {b64data} | base64 -d > {fp}"]
+          "arguments": [f"echo {b64data} | base64 -d > {fp}"]
       })
       data = res.json()
       if data["error"] is not None:
@@ -372,7 +379,7 @@ def list_files(self, process_id: str, agent_ref: str, sr_host: str, remote_dir:
         "agentId": agent_ref,
         "envName": agent_ref,
         "workingDir": ".",
-        "arguments": ["sh", "-c", r"find /data -type d -name 'venv' -prune -o -type f -printf '%P\n' | sort"]
+        "arguments": [r"find . -type f -printf '%P\n' | sort"]
     })
     data = res.json()
     if data["error"] is not None:
@@ -405,12 +412,12 @@ def download_file(self, process_id: str, agent_ref: str, sr_host: str, remote_fi
 
     """
     import os
-    fp = os.path.join("/data", remote_file)
+    fp = os.path.join(".", remote_file)
     res = requests.post(f"{self.connection_svc_url()}/agent/execute/shell", json={
         "agentId": agent_ref,
         "envName": agent_ref,
         "workingDir": ".",
-        "arguments": ["sh", "-c", f"cat {fp} | base64 -w0"]
+        "arguments": [f"cat {fp} | base64 -w0"]
     })
     data = res.json()
     if data["error"] is not None:
@@ -441,7 +448,36 @@ def download_file(self, process_id: str, agent_ref: str, sr_host: str, remote_fi
     assert process_id is not None, f"Expected process_id, got {process_id}"
     url_path = os.path.join(process_id, remote_file)
     filemgr_svc_download_url = f"{self.filemgr_svc_url()}/download/live/{url_path}"
-  
+
+  def execute_cmd(self, agent_ref: str, cmd: str) -> bytes:
+    """
+    Execute a command on a remote directory of a storage resource
+    TODO add data_svc fallback
+
+    Return Path: /{project_name}/{experiment_name}
+
+    """
+    res = requests.post(f"{self.connection_svc_url()}/agent/execute/shell", json={
+        "agentId": agent_ref,
+        "envName": agent_ref,
+        "workingDir": ".",
+        "arguments": [f"{cmd} | base64 -w0"]
+    })
+    data = res.json()
+    if data["error"] is not None:
+      raise Exception(data["error"])
+    else:
+      exc_id = data["executionId"]
+      while True:
+        res = requests.get(f"{self.connection_svc_url()}/agent/execute/shell/{exc_id}")
+        data = res.json()
+        if data["executed"]:
+          content = data["responseString"]
+          import base64
+          content = base64.b64decode(content)
+          return content
+        time.sleep(1)
+
   def cat_file(self, process_id: str, agent_ref: str, sr_host: str, remote_file: str, remote_dir: str) -> bytes:
     """
     Download files from a remote directory of a storage resource to a local directory
@@ -451,12 +487,12 @@ def cat_file(self, process_id: str, agent_ref: str, sr_host: str, remote_file: s
 
     """
     import os
-    fp = os.path.join("/data", remote_file)
+    fp = os.path.join(".", remote_file)
     res = requests.post(f"{self.connection_svc_url()}/agent/execute/shell", json={
         "agentId": agent_ref,
         "envName": agent_ref,
         "workingDir": ".",
-        "arguments": ["sh", "-c", f"cat {fp} | base64 -w0"]
+        "arguments": [f"cat {fp} | base64 -w0"]
     })
     data = res.json()
     if data["error"] is not None:
@@ -596,8 +632,8 @@ def launch_experiment(
     def register_input_file(file: Path) -> str:
       return str(self.register_input_file(file.name, sr_host, sr_id, gateway_id, file.name, abs_path))
     
-    # set up file inputs
-    print("[AV] Setting up file inputs...")
+    # set up experiment inputs
+    print("[AV] Setting up experiment inputs...")
     files_to_upload = list[Path]()
     file_refs = dict[str, str | list[str]]()
     for key, value in file_inputs.items():
@@ -610,11 +646,9 @@ def register_input_file(file: Path) -> str:
         file_refs[key] = [*map(register_input_file, value)]
       else:
         raise ValueError("Invalid file input type")
-
-    # configure experiment inputs
     experiment_inputs = []
     for exp_input in self.api_server_client.get_application_inputs(self.airavata_token, app_interface_id):  # type: ignore
-      assert exp_input.type is not None
+      assert exp_input.type is not None, f"Invalid exp_input type for {exp_input.name}: {exp_input.type}"
       if exp_input.type < 3 and exp_input.name in data_inputs:
         value = data_inputs[exp_input.name]
         if exp_input.type == 0:
@@ -623,11 +657,12 @@ def register_input_file(file: Path) -> str:
           exp_input.value = repr(value)
       elif exp_input.type == 3 and exp_input.name in file_refs:
         ref = file_refs[exp_input.name]
-        assert isinstance(ref, str)
+        assert isinstance(ref, str), f"Invalid file ref: {ref}"
         exp_input.value = ref
       elif exp_input.type == 4 and exp_input.name in file_refs:
         exp_input.value = ','.join(file_refs[exp_input.name])
       experiment_inputs.append(exp_input)
+      print(f"[AV] * {exp_input.name}={exp_input.value}")
     experiment.experimentInputs = experiment_inputs
 
     # configure experiment outputs
@@ -670,14 +705,15 @@ def register_input_file(file: Path) -> str:
     # wait until task begins, then get job id
     print(f"[AV] Experiment {experiment_name} WAITING until task begins...")
     job_id = job_state = None
-    while job_state is None:
+    while job_id in [None, "N/A"]:
       try:
         job_id, job_state = self.get_task_status(ex_id)
       except:
         time.sleep(2)
       else:
         time.sleep(2)
-    print(f"[AV] Experiment {experiment_name} - Task {job_state} with id: {job_id}")
+    assert job_state is not None, f"Job state is None for job id: {job_id}"
+    print(f"[AV] Experiment {experiment_name} - Task {job_state.name} with id: {job_id}")
 
     return LaunchState(
       experiment_id=ex_id,
@@ -688,14 +724,12 @@ def register_input_file(file: Path) -> str:
       sr_host=storage.hostName,
     )
 
-  def get_experiment_status(self, experiment_id: str) -> Literal['CREATED', 'VALIDATED', 'SCHEDULED', 'LAUNCHED', 'EXECUTING', 'CANCELING', 'CANCELED', 'COMPLETED', 'FAILED']:
-    states = ["CREATED", "VALIDATED", "SCHEDULED", "LAUNCHED", "EXECUTING", "CANCELING", "CANCELED", "COMPLETED", "FAILED"]
+  def get_experiment_status(self, experiment_id: str) -> ExperimentState:
     status = self.api_server_client.get_experiment_status(self.airavata_token, experiment_id)
-    state = status.state.name
-    if state in states:
-      return state
-    else:
-      return "FAILED"
+    if status is None:
+      return ExperimentState.CREATED
+    assert isinstance(status, ExperimentStatus)
+    return status.state
 
   def stop_experiment(self, experiment_id: str):
     status = self.api_server_client.terminate_experiment(
@@ -781,23 +815,48 @@ def execute_py(self, project: str, libraries: list[str], code: str, agent_id: st
       print(f"[av] Remote execution failed! {e}")
       return None
     
-  def get_available_runtimes(self):
+  def get_available_groups(self, gateway_id: str = "default"):
+    grps: list[GroupResourceProfile] = self.api_server_client.get_group_resource_list(self.airavata_token, gatewayId=gateway_id)
+    return grps
+  
+  def get_available_runtimes(self, group: str, gateway_id: str = "default"):
+    grps = self.get_available_groups(gateway_id)
+    grp_id, gcr_prefs, gcr_policies = next(((x.groupResourceProfileId, x.computePreferences, x.computeResourcePolicies) for x in grps if str(x.groupResourceProfileName).strip() == group.strip()), (None, None, None))
+    assert grp_id is not None, f"Group {group} was not found"
+    assert gcr_prefs is not None, f"Compute preferences for group={grp_id} were not found"
+    assert gcr_policies is not None, f"Compute policies for group={grp_id} were not found" # type: ignore
     from .runtime import Remote
-    return [
-      Remote(cluster="login.expanse.sdsc.edu", category="gpu", queue_name="gpu-shared", node_count=1, cpu_count=10, gpu_count=1, walltime=30, group="Default"),
-      Remote(cluster="login.expanse.sdsc.edu", category="cpu", queue_name="shared", node_count=1, cpu_count=10, gpu_count=0, walltime=30, group="Default"),
-      Remote(cluster="anvil.rcac.purdue.edu", category="cpu", queue_name="shared", node_count=1, cpu_count=24, gpu_count=0, walltime=30, group="Default"),
-    ]
+    runtimes = []
+    for pref in gcr_prefs:
+      cr = self.api_server_client.get_compute_resource(self.airavata_token, pref.computeResourceId)
+      assert cr is not None, "Compute resource not found"
+      assert isinstance(cr, ComputeResourceDescription), "Compute resource is not a ComputeResourceDescription"
+      assert cr.batchQueues is not None, "Compute resource has no batch queues"
+      for queue in cr.batchQueues:
+        if pref.resourceType == ResourceType.SLURM:
+          policy = next((p for p in gcr_policies if p.computeResourceId == pref.computeResourceId), None)
+          assert policy is not None, f"Compute resource policy not found for {pref.computeResourceId}"
+          if queue.queueName not in (policy.allowedBatchQueues or []):
+            continue
+        runtime = Remote(
+          cluster=pref.computeResourceId.split("_")[0],
+          category="GPU" if "gpu" in queue.queueName.lower() else "CPU",
+          queue_name=queue.queueName,
+          node_count=queue.maxNodes or 1,
+          cpu_count=queue.cpuPerNode or 1,
+          gpu_count=1 if "gpu" in queue.queueName.lower() else 0,
+          walltime=queue.maxRunTime or 30,
+          group=group,
+        )
+        runtimes.append(runtime)
+    return runtimes
   
-  def get_task_status(self, experiment_id: str) -> tuple[str, Literal["SUBMITTED", "UN_SUBMITTED", "SETUP", "QUEUED", "ACTIVE", "COMPLETE", "CANCELING", "CANCELED", "FAILED", "HELD", "SUSPENDED", "UNKNOWN"] | None]:
-    states = ["SUBMITTED", "UN_SUBMITTED", "SETUP", "QUEUED", "ACTIVE", "COMPLETE", "CANCELING", "CANCELED", "FAILED", "HELD", "SUSPENDED", "UNKNOWN"]
-    job_details: dict = self.api_server_client.get_job_statuses(self.airavata_token, experiment_id) # type: ignore
+  def get_task_status(self, experiment_id: str) -> tuple[str, JobState]:
+    job_details: dict[str, JobStatus] = self.api_server_client.get_job_statuses(self.airavata_token, experiment_id) # type: ignore
     job_id = job_state = None
-    # get the most recent job id and state
     for job_id, v in job_details.items():
-      if v.reason in states:
-        job_state = v.reason
-      else:
-        job_state = states[int(v.jobState)]
-    return job_id or "N/A", job_state # type: ignore
+      job_state = v.jobState
+    return job_id or "N/A", job_state or JobState.UNKNOWN
+  
+  JobState = JobState
 
diff --git a/dev-tools/airavata-python-sdk/airavata_experiments/base.py b/dev-tools/airavata-python-sdk/airavata_experiments/base.py
index e9ad36b68e..2ba99a3bcb 100644
--- a/dev-tools/airavata-python-sdk/airavata_experiments/base.py
+++ b/dev-tools/airavata-python-sdk/airavata_experiments/base.py
@@ -85,49 +85,64 @@ def with_resource(self, resource: Runtime) -> Experiment[T]:
     self.resource = resource
     return self
 
-  def create_task(self, *allowed_runtimes: Runtime, name: str | None = None) -> None:
+  def add_run(self, use: list[Runtime], cpus: int, nodes: int, walltime: int, name: str | None = None, **extra_params) -> None:
     """
     Create a task to run the experiment on a given runtime.
     """
-    runtime = random.choice(allowed_runtimes) if len(allowed_runtimes) > 0 else self.resource
+    runtime = random.choice(use) if len(use) > 0 else self.resource
     uuid_str = str(uuid.uuid4())[:4].upper()
-
+    # override runtime args with given values
+    runtime = runtime.model_copy()
+    runtime.args["cpu_count"] = cpus
+    runtime.args["node_count"] = nodes
+    runtime.args["walltime"] = walltime
+    # add extra inputs to task inputs
+    task_inputs = {**self.inputs, **extra_params}
+    # create a task with the given runtime and inputs
     self.tasks.append(
         Task(
-            name=name or f"{self.name}_{uuid_str}",
+            name=f"{name or self.name}_{uuid_str}",
             app_id=self.application.app_id,
-            inputs={**self.inputs},
+            inputs=task_inputs,
             runtime=runtime,
         )
     )
     print(f"Task created. ({len(self.tasks)} tasks in total)")
 
-  def add_sweep(self, *allowed_runtimes: Runtime, **space: list) -> None:
+  def add_sweep(self, use: list[Runtime], cpus: int, nodes: int, walltime: int, name: str | None = None, **space: list) -> None:
     """
     Add a sweep to the experiment.
 
     """
     for values in product(space.values()):
-      runtime = random.choice(allowed_runtimes) if len(allowed_runtimes) > 0 else self.resource
+      runtime = random.choice(use) if len(use) > 0 else self.resource
       uuid_str = str(uuid.uuid4())[:4].upper()
-
+      # override runtime args with given values
+      runtime = runtime.model_copy()
+      runtime.args["cpu_count"] = cpus
+      runtime.args["node_count"] = nodes
+      runtime.args["walltime"] = walltime
+      # add sweep params to task inputs
       task_specific_params = dict(zip(space.keys(), values))
       agg_inputs = {**self.inputs, **task_specific_params}
       task_inputs = {k: {"value": agg_inputs[v[0]], "type": v[1]} for k, v in self.input_mapping.items()}
-
+      # create a task with the given runtime and inputs
       self.tasks.append(Task(
-          name=f"{self.name}_{uuid_str}",
+          name=f"{name or self.name}_{uuid_str}",
           app_id=self.application.app_id,
           inputs=task_inputs,
           runtime=runtime or self.resource,
       ))
 
-  def plan(self, **kwargs) -> Plan:
-    if len(self.tasks) == 0:
-      self.create_task(self.resource)
+  def plan(self) -> Plan:
+    assert len(self.tasks) > 0, "add_run() must be called before plan() to define runtimes and resources."
     tasks = []
     for t in self.tasks:
       agg_inputs = {**self.inputs, **t.inputs}
       task_inputs = {k: {"value": agg_inputs[v[0]], "type": v[1]} for k, v in self.input_mapping.items()}
-      tasks.append(Task(name=t.name, app_id=self.application.app_id, inputs=task_inputs, runtime=t.runtime))
-    return Plan(tasks=tasks)
+      task = Task(name=t.name, app_id=self.application.app_id, inputs=task_inputs, runtime=t.runtime)
+      # task.freeze()  # TODO upload the task-related data and freeze the task
+      tasks.append(task)
+    plan = Plan(tasks=tasks)
+    plan.save()
+    return plan
diff --git a/dev-tools/airavata-python-sdk/airavata_experiments/plan.py b/dev-tools/airavata-python-sdk/airavata_experiments/plan.py
index f231e2583d..4f41135610 100644
--- a/dev-tools/airavata-python-sdk/airavata_experiments/plan.py
+++ b/dev-tools/airavata-python-sdk/airavata_experiments/plan.py
@@ -25,6 +25,7 @@
 from .runtime import is_terminal_state
 from .task import Task
 import uuid
+from airavata_auth.device_auth import AuthContext
 
 from .airavata import AiravataOperator
 
@@ -66,11 +67,13 @@ def __stage_status__(self) -> list:
       statuses.append(task.status())
     return statuses
 
-  def __stage_stop__(self) -> None:
-    print("Stopping task(s)...")
-    for task in self.tasks:
-      task.stop()
-    print("Task(s) stopped.")
+  def __stage_stop__(self, runs: list[int] = []) -> None:
+    runs = runs if len(runs) > 0 else list(range(len(self.tasks)))
+    print(f"Stopping task(s): {runs}")
+    for i, task in enumerate(self.tasks):
+      if i in runs:
+        task.stop()
+    print(f"Task(s) stopped: {runs}")
 
   def __stage_fetch__(self, local_dir: str) -> list[list[str]]:
     print("Fetching results...")
@@ -78,7 +81,7 @@ def __stage_fetch__(self, local_dir: str) -> list[list[str]]:
     for task in self.tasks:
       fps.append(task.download_all(local_dir))
     print("Results fetched.")
-    self.save_json(os.path.join(local_dir, "plan.json"))
+    self.export(os.path.join(local_dir, "plan.json"))
     return fps
 
   def launch(self, silent: bool = True) -> None:
@@ -119,17 +122,17 @@ def download(self, local_dir: str):
     assert os.path.isdir(local_dir)
     self.__stage_fetch__(local_dir)
 
-  def stop(self) -> None:
-    self.__stage_stop__()
+  def stop(self, runs: list[int] = []) -> None:
+    self.__stage_stop__(runs)
     self.save()
 
-  def save_json(self, filename: str) -> None:
+  def export(self, filename: str) -> None:
     with open(filename, "w") as f:
       json.dump(self.model_dump(), f, indent=2)
 
   def save(self) -> None:
     settings = Settings()
-    av = AiravataOperator(os.environ['CS_ACCESS_TOKEN'])
+    av = AiravataOperator(AuthContext.get_access_token())
     az = av.__airavata_token__(av.access_token, av.default_gateway_id())
     assert az.accessToken is not None
     assert az.claimsMap is not None
@@ -162,7 +165,7 @@ def load_json(filename: str) -> Plan:
 def load(id: str | None) -> Plan:
     settings = Settings()
     assert id is not None
-    av = AiravataOperator(os.environ['CS_ACCESS_TOKEN'])
+    av = AiravataOperator(AuthContext.get_access_token())
     az = av.__airavata_token__(av.access_token, av.default_gateway_id())
     assert az.accessToken is not None
     assert az.claimsMap is not None
@@ -183,7 +186,7 @@ def load(id: str | None) -> Plan:
     
 def query() -> list[Plan]:
     settings = Settings()
-    av = AiravataOperator(os.environ['CS_ACCESS_TOKEN'])
+    av = AiravataOperator(AuthContext.get_access_token())
     az = av.__airavata_token__(av.access_token, av.default_gateway_id())
     assert az.accessToken is not None
     assert az.claimsMap is not None
diff --git a/dev-tools/airavata-python-sdk/airavata_experiments/runtime.py b/dev-tools/airavata-python-sdk/airavata_experiments/runtime.py
index e843135843..f5c40e3c86 100644
--- a/dev-tools/airavata-python-sdk/airavata_experiments/runtime.py
+++ b/dev-tools/airavata-python-sdk/airavata_experiments/runtime.py
@@ -16,14 +16,37 @@
 
 from __future__ import annotations
 import abc
-from typing import Any
+from typing import Any, Literal
 from pathlib import Path
-import os
 
 import pydantic
 
+from airavata_auth.device_auth import AuthContext
+
 # from .task import Task
 Task = Any
+States = Literal[
+  # Experiment States
+  'CREATED',
+  'VALIDATED',
+  'SCHEDULED',
+  'LAUNCHED',
+  'EXECUTING',
+  'CANCELING',
+  'CANCELED',
+  'COMPLETED',
+  'FAILED',
+  # Job States
+  'SUBMITTED',
+  'QUEUED',
+  'ACTIVE',
+  'COMPLETE',
+  'CANCELED',
+  'FAILED',
+  'SUSPENDED',
+  'UNKNOWN',
+  'NON_CRITICAL_FAIL',
+]
 
 class Runtime(abc.ABC, pydantic.BaseModel):
 
@@ -36,6 +59,9 @@ def execute(self, task: Task) -> None: ...
   @abc.abstractmethod
   def execute_py(self, libraries: list[str], code: str, task: Task) -> None: ...
 
+  @abc.abstractmethod
+  def execute_cmd(self, cmd: str, task: Task) -> bytes: ...
+
   @abc.abstractmethod
   def status(self, task: Task) -> tuple[str, str]: ...
 
@@ -87,6 +113,9 @@ def execute(self, task: Task) -> None:
     task.agent_ref = str(uuid.uuid4())
     task.ref = str(uuid.uuid4())
 
+  def execute_cmd(self, cmd: str, task: Task) -> bytes:
+    return b""
+
   def execute_py(self, libraries: list[str], code: str, task: Task) -> None:
     pass
 
@@ -135,7 +164,7 @@ def execute(self, task: Task) -> None:
     print(f"[Remote] Creating Experiment: name={task.name}")
 
     from .airavata import AiravataOperator
-    av = AiravataOperator(os.environ['CS_ACCESS_TOKEN'])
+    av = AiravataOperator(AuthContext.get_access_token())
     try:
       launch_state = av.launch_experiment(
           experiment_name=task.name,
@@ -158,6 +187,23 @@ def execute(self, task: Task) -> None:
     except Exception as e:
       print(f"[Remote] Failed to launch experiment: {repr(e)}")
       raise e
+    
+  def execute_cmd(self, cmd: str, task: Task) -> bytes:
+    assert task.ref is not None
+    assert task.agent_ref is not None
+    assert task.pid is not None
+    assert task.sr_host is not None
+    assert task.workdir is not None
+
+    from .airavata import AiravataOperator
+    av = AiravataOperator(AuthContext.get_access_token())
+    try:
+      result = av.execute_cmd(task.agent_ref, cmd)
+      return result
+    except Exception as e:
+      print(f"[Remote] Failed to execute command: {repr(e)}")
+      return b""
+
 
   def execute_py(self, libraries: list[str], code: str, task: Task) -> None:
     assert task.ref is not None
@@ -165,29 +211,29 @@ def execute_py(self, libraries: list[str], code: str, task: Task) -> None:
     assert task.pid is not None
 
     from .airavata import AiravataOperator
-    av = AiravataOperator(os.environ['CS_ACCESS_TOKEN'])
+    av = AiravataOperator(AuthContext.get_access_token())
     result = av.execute_py(task.project, libraries, code, task.agent_ref, task.pid, task.runtime.args)
     print(result)
 
-  def status(self, task: Task) -> tuple[str, str]:
+  def status(self, task: Task) -> tuple[str, States]:
     assert task.ref is not None
     assert task.agent_ref is not None
 
     from .airavata import AiravataOperator
-    av = AiravataOperator(os.environ['CS_ACCESS_TOKEN'])
+    av = AiravataOperator(AuthContext.get_access_token())
     # prioritize job state, fallback to experiment state
     job_id, job_state = av.get_task_status(task.ref)
-    if not job_state or job_state == "UN_SUBMITTED":
-      return job_id, av.get_experiment_status(task.ref)
+    if job_state in [AiravataOperator.JobState.UNKNOWN, AiravataOperator.JobState.NON_CRITICAL_FAIL]:
+      return job_id, av.get_experiment_status(task.ref).name
     else:
-      return job_id, job_state
+      return job_id, job_state.name
 
   def signal(self, signal: str, task: Task) -> None:
     assert task.ref is not None
     assert task.agent_ref is not None
     
     from .airavata import AiravataOperator
-    av = AiravataOperator(os.environ['CS_ACCESS_TOKEN'])
+    av = AiravataOperator(AuthContext.get_access_token())
     av.stop_experiment(task.ref)
 
   def ls(self, task: Task) -> list[str]:
@@ -198,7 +244,7 @@ def ls(self, task: Task) -> list[str]:
     assert task.workdir is not None
 
     from .airavata import AiravataOperator
-    av = AiravataOperator(os.environ['CS_ACCESS_TOKEN'])
+    av = AiravataOperator(AuthContext.get_access_token())
     files = av.list_files(task.pid, task.agent_ref, task.sr_host, task.workdir)
     return files
 
@@ -210,7 +256,7 @@ def upload(self, file: Path, task: Task) -> str:
     assert task.workdir is not None
 
     from .airavata import AiravataOperator
-    av = AiravataOperator(os.environ['CS_ACCESS_TOKEN'])
+    av = AiravataOperator(AuthContext.get_access_token())
     result = av.upload_files(task.pid, task.agent_ref, task.sr_host, [file], task.workdir).pop()
     return result
 
@@ -222,7 +268,7 @@ def download(self, file: str, local_dir: str, task: Task) -> str:
     assert task.workdir is not None
 
     from .airavata import AiravataOperator
-    av = AiravataOperator(os.environ['CS_ACCESS_TOKEN'])
+    av = AiravataOperator(AuthContext.get_access_token())
     result = av.download_file(task.pid, task.agent_ref, task.sr_host, file, task.workdir, local_dir)
     return result
 
@@ -234,30 +280,44 @@ def cat(self, file: str, task: Task) -> bytes:
     assert task.workdir is not None
 
     from .airavata import AiravataOperator
-    av = AiravataOperator(os.environ['CS_ACCESS_TOKEN'])
+    av = AiravataOperator(AuthContext.get_access_token())
     content = av.cat_file(task.pid, task.agent_ref, task.sr_host, file, task.workdir)
     return content
 
 
-def list_runtimes(
+def find_runtimes(
     cluster: str | None = None,
     category: str | None = None,
-    group: str | None = None,
     node_count: int | None = None,
     cpu_count: int | None = None,
-    walltime: int | None = None,
+    group: str | None = None,
 ) -> list[Runtime]:
   from .airavata import AiravataOperator
-  av = AiravataOperator(os.environ['CS_ACCESS_TOKEN'])
-  all_runtimes = av.get_available_runtimes()
-  out_runtimes = []
-  for r in all_runtimes:
-    if (cluster in [None, r.args["cluster"]]) and (category in [None, r.args["category"]]) and (group in [None, r.args["group"]]):
-      r.args["node_count"] = node_count or r.args["node_count"]
-      r.args["cpu_count"] = cpu_count or r.args["cpu_count"]
-      r.args["walltime"] = walltime or r.args["walltime"]
-      out_runtimes.append(r)
-  return out_runtimes
-
-def is_terminal_state(x):
-  return x in ["CANCELED", "COMPLETED", "FAILED"]
\ No newline at end of file
+  av = AiravataOperator(AuthContext.get_access_token())
+  grps = av.get_available_groups()
+  grp_names = [str(x.groupResourceProfileName) for x in grps]
+  if group is not None:
+    assert group in grp_names, f"Group {group} was not found. Available groups: {repr(grp_names)}"
+    groups = [g for g in grps if str(g.groupResourceProfileName) == group]
+  else:
+    groups = grps
+  runtimes = []
+  for g in groups:
+    matched_runtimes = []
+    assert g.groupResourceProfileName is not None, f"Group {g} has no name"
+    r: Runtime
+    for r in av.get_available_runtimes(group=g.groupResourceProfileName):
+      if (node_count or 1) > int(r.args["node_count"]):
+        continue
+      if (cpu_count or 1) > int(r.args["cpu_count"]):
+        continue
+      if (cluster or r.args["cluster"]) != r.args["cluster"]:
+        continue
+      if (category or r.args["category"]) != r.args["category"]:
+        continue
+      matched_runtimes.append(r)
+    runtimes.extend(matched_runtimes)
+  return runtimes
+
+def is_terminal_state(x: States) -> bool:
+  return x in ["CANCELED", "COMPLETE", "COMPLETED", "FAILED"]
\ No newline at end of file
diff --git a/dev-tools/airavata-python-sdk/airavata_experiments/task.py b/dev-tools/airavata-python-sdk/airavata_experiments/task.py
index bcda796518..fea221b1cf 100644
--- a/dev-tools/airavata-python-sdk/airavata_experiments/task.py
+++ b/dev-tools/airavata-python-sdk/airavata_experiments/task.py
@@ -72,7 +72,13 @@ def download(self, file: str, local_dir: str) -> str:
     assert self.ref is not None
     from pathlib import Path
     Path(local_dir).mkdir(parents=True, exist_ok=True)
-    return self.runtime.download(file, local_dir, self)
+    try:
+      saved_path = self.runtime.download(file, local_dir, self)
+      print(f"[Remote] Downloaded {file} -> {saved_path}")
+      return saved_path
+    except Exception as e:
+      print(f"[Remote] Failed to download file: {repr(e)}")
+      return ""
   
   def download_all(self, local_dir: str) -> list[str]:
     assert self.ref is not None
@@ -92,6 +98,10 @@ def download_all(self, local_dir: str) -> list[str]:
   def cat(self, file: str) -> bytes:
     assert self.ref is not None
     return self.runtime.cat(file, self)
+  
+  def exec(self, cmd: str) -> bytes:
+    assert self.ref is not None
+    return self.runtime.execute_cmd(cmd, self)
 
   def stop(self) -> None:
     assert self.ref is not None
diff --git a/dev-tools/airavata-python-sdk/airavata_jupyter_magic/__init__.py b/dev-tools/airavata-python-sdk/airavata_jupyter_magic/__init__.py
index 1528304462..c445e654b2 100644
--- a/dev-tools/airavata-python-sdk/airavata_jupyter_magic/__init__.py
+++ b/dev-tools/airavata-python-sdk/airavata_jupyter_magic/__init__.py
@@ -43,6 +43,7 @@
 from jupyter_client.blocking.client import BlockingKernelClient
 
 from airavata_auth.device_auth import AuthContext
+from airavata_experiments.plan import Plan
 from airavata_sdk import Settings
 
 # ========================================================================
@@ -62,6 +63,7 @@ class RequestedRuntime:
     group: str
     file: str | None
     use: str | None
+    plan: str | None
 
 
 class ProcessState(IntEnum):
@@ -101,6 +103,7 @@ class ProcessState(IntEnum):
     ('envName', str),
     ('pids', list[int]),
     ('tunnels', dict[str, tuple[str, int]]),
+    ('links', dict[str, str]),
 ])
 
 PENDING_STATES = [
@@ -139,23 +142,6 @@ class State:
 # HELPER FUNCTIONS
 
 
-def get_access_token(envar_name: str = "CS_ACCESS_TOKEN", state_path: str = "/tmp/av.json") -> str | None:
-    """
-    Get access token from environment or file
-
-    @param None:
-    @returns: access token if present, None otherwise
-
-    """
-    token = os.getenv(envar_name)
-    if not token:
-        try:
-            token = json.load(Path(state_path).open("r")).get("access_token")
-        except (FileNotFoundError, json.JSONDecodeError):
-            pass
-    return token
-
-
 def is_runtime_ready(access_token: str, rt: RuntimeInfo, rt_name: str):
     """
     Check if the runtime (i.e., agent job) is ready to receive requests
@@ -470,7 +456,8 @@ def submit_agent_job(
     memory: int | None = None,
     gpus: int | None = None,
     gpu_memory: int | None = None,
-    file: str | None = None,
+    spec_file: str | None = None,
+    plan_file: str | None = None,
 ) -> None:
     """
     Submit an agent job to the given runtime
@@ -487,7 +474,8 @@ def submit_agent_job(
     @param memory: the memory for cpu (MB)
     @param gpus: the number of gpus (int)
     @param gpu_memory: the memory for gpu (MB)
-    @param file: environment file (path)
+    @param spec_file: environment file (path)
+    @param plan_file: experiment plan file (path)
     @returns: None
 
     """
@@ -506,14 +494,14 @@ def submit_agent_job(
     pip: list[str] = []
 
     # if file is provided, validate it and use the given values as defaults
-    if file is not None:
-        fp = Path(file)
+    if spec_file is not None:
+        fp = Path(spec_file)
         # validation
-        assert fp.exists(), f"File {file} does not exist"
+        assert fp.exists(), f"File {spec_file} does not exist"
         with open(fp, "r") as f:
-            content = yaml.safe_load(f)
+            spec = yaml.safe_load(f)
         # validation: /workspace
-        assert (workspace := content.get("workspace", None)) is not None, "missing section: /workspace"
+        assert (workspace := spec.get("workspace", None)) is not None, "missing section: /workspace"
         assert (resources := workspace.get("resources", None)) is not None, "missing section: /workspace/resources"
         assert (min_cpu := resources.get("min_cpu", None)) is not None, "missing section: /workspace/resources/min_cpu"
         assert (min_mem := resources.get("min_mem", None)) is not None, "missing section: /workspace/resources/min_mem"
@@ -523,12 +511,29 @@ def submit_agent_job(
         assert (datasets := workspace.get("data_collection", None)) is not None, "missing section: /workspace/data_collection"
         collection = models + datasets
         # validation: /additional_dependencies
-        assert (additional_dependencies := content.get("additional_dependencies", None)) is not None, "missing section: /additional_dependencies"
+        assert (additional_dependencies := spec.get("additional_dependencies", None)) is not None, "missing section: /additional_dependencies"
         assert (modules := additional_dependencies.get("modules", None)) is not None, "missing /additional_dependencies/modules section"
         assert (conda := additional_dependencies.get("conda", None)) is not None, "missing /additional_dependencies/conda section"
         assert (pip := additional_dependencies.get("pip", None)) is not None, "missing /additional_dependencies/pip section"
         mounts = [f"{i['identifier']}:{i['mount_point']}" for i in collection]
 
+    # if plan file is provided, link its runs into the workspace
+    links = {}
+    if plan_file is not None:
+        assert Path(plan_file).exists(), f"Plan {plan_file} does not exist"
+        assert Path(plan_file).is_file(), f"Plan {plan_file} is not a file"
+        with open(Path(plan_file), "r") as f:
+            from airavata_experiments.base import Plan
+            plan = Plan(**json.load(f))
+        for task in plan.tasks:
+            plan_cluster = str(task.runtime.args.get("cluster", "N/A"))
+            if plan_cluster == "N/A":
+                print(f"[av] skipping plan task {task.name}: cluster not specified in the plan")
+                continue
+            assert plan_cluster == cluster, f"[av] cluster mismatched: {plan_cluster} in plan, {cluster} in request"
+            assert task.pid is not None, f"[av] plan task {task.name} has no pid"
+            links[task.pid] = task.name
+
     # payload
     data = {
         'experimentName': app_name,
@@ -554,6 +559,7 @@ def submit_agent_job(
     print(f"* libraries={data['libraries']}", flush=True)
     print(f"* pip={data['pip']}", flush=True)
     print(f"* mounts={data['mounts']}", flush=True)
+    print(f"* links={links}", flush=True)
 
     # Send the POST request
     headers = generate_headers(access_token, gateway_id)
@@ -584,6 +590,7 @@ def submit_agent_job(
             envName=obj['envName'],
             pids=[],
             tunnels={},
+            links=links,
         )
         state.all_runtimes[rt_name] = rt
         print(f'Requested runtime={rt_name}', flush=True)
@@ -1114,7 +1121,7 @@ def request_runtime(line: str):
     Request a runtime with given capabilities
 
     """
-    access_token = get_access_token()
+    access_token = AuthContext.get_access_token()
     assert access_token is not None
 
     [rt_name, *cmd_args] = line.strip().split()
@@ -1151,12 +1158,32 @@ def request_runtime(line: str):
     p.add_argument("--group", type=str, help="resource group", required=False, default="Default")
     p.add_argument("--file", type=str, help="yml file", required=False)
     p.add_argument("--use", type=str, help="allowed resources", required=False)
+    p.add_argument("--plan", type=str, help="experiment plan file", required=False)
 
     args = p.parse_args(cmd_args, namespace=RequestedRuntime())
 
     if args.file is not None:
-        assert args.use is not None
-        cluster, queue  = meta_scheduler(args.use.split(","))
+        assert (args.use or args.plan) is not None
+        if args.use:
+          cluster, queue  = meta_scheduler(args.use.split(","))
+        else:
+          assert args.plan is not None, "--plan is required when --use is not provided"
+          assert os.path.exists(args.plan), f"--plan={args.plan} file does not exist"
+          assert os.path.isfile(args.plan), f"--plan={args.plan} is not a file"
+          with open(args.plan, "r") as f:
+            plan: Plan = Plan(**json.load(f))
+            clusters = []
+            queues = []
+            for task in plan.tasks:
+              c, q = task.runtime.args.get("cluster"), task.runtime.args.get("queue_name")
+              clusters.append(c)
+              queues.append(q)
+            assert len(set(clusters)) == 1, "all tasks must be on the same cluster"
+            assert len(set(queues)) == 1, "all tasks must be on the same queue"
+            cluster, queue = clusters[0], queues[0]
+            assert cluster is not None, "cluster is required"
+            assert queue is not None, "queue is required"
+
         submit_agent_job(
             rt_name=rt_name,
             access_token=access_token,
@@ -1166,7 +1193,8 @@ def request_runtime(line: str):
             cluster=cluster,
             queue=queue,
             group=args.group,
-            file=args.file,
+            spec_file=args.file,
+            plan_file=args.plan,
         )
     else:
         assert args.cluster is not None
@@ -1194,7 +1222,7 @@ def stat_runtime(line: str):
     Show the status of the runtime
 
     """
-    access_token = get_access_token()
+    access_token = AuthContext.get_access_token()
     assert access_token is not None
 
     rt_name = line.strip()
@@ -1226,7 +1254,7 @@ def wait_for_runtime(line: str):
         rt_name, render_live_logs = parts[0], True
     else:
         raise ValueError("Usage: %wait_for_runtime <rt> [--live]")
-    access_token = get_access_token()
+    access_token = AuthContext.get_access_token()
     assert access_token is not None
 
     rt = state.all_runtimes.get(rt_name, None)
@@ -1238,8 +1266,14 @@ def wait_for_runtime(line: str):
         random_port = random.randint(2000, 6000) * 5
         launch_remote_kernel(rt_name, random_port, hostname="127.0.0.1")
         print(f"Remote Jupyter kernel launched and connected for runtime={rt_name}.")
-    return
-
+    
+    # create symlinks
+    for pid, name in rt.links.items():
+        try:
+            state.kernel_clients[rt_name].execute(f"!ln -s ../{pid} {name}", silent=True, store_history=False)
+            print(f"[av] linked ../{pid} -> {name}")
+        except Exception as e:
+            print(f"[av] failed to link ../{pid} -> {name}: {e}")
 
 @register_line_magic
 def run_subprocess(line: str):
@@ -1247,7 +1281,7 @@ def run_subprocess(line: str):
     Run a subprocess asynchronously
 
     """
-    access_token = get_access_token()
+    access_token = AuthContext.get_access_token()
     assert access_token is not None
 
     rt_name = state.current_runtime
@@ -1279,7 +1313,7 @@ def kill_subprocess(line: str):
     Kill a running subprocess asynchronously
 
     """
-    access_token = get_access_token()
+    access_token = AuthContext.get_access_token()
     assert access_token is not None
 
     rt_name = state.current_runtime
@@ -1308,7 +1342,7 @@ def open_tunnels(line: str):
     Open tunnels to the runtime
 
     """
-    access_token = get_access_token()
+    access_token = AuthContext.get_access_token()
     assert access_token is not None
 
     rt_name = state.current_runtime
@@ -1348,7 +1382,7 @@ def close_tunnels(line: str):
     Close tunnels to the runtime
 
     """
-    access_token = get_access_token()
+    access_token = AuthContext.get_access_token()
     assert access_token is not None
 
     rt_name = state.current_runtime
@@ -1374,7 +1408,7 @@ def restart_runtime(rt_name: str):
     Restart the runtime
 
     """
-    access_token = get_access_token()
+    access_token = AuthContext.get_access_token()
     assert access_token is not None
 
     rt = state.all_runtimes.get(rt_name, None)
@@ -1389,7 +1423,7 @@ def stop_runtime(rt_name: str):
     Stop the runtime
 
     """
-    access_token = get_access_token()
+    access_token = AuthContext.get_access_token()
     assert access_token is not None
 
     rt = state.all_runtimes.get(rt_name, None)
@@ -1457,7 +1491,7 @@ def launch_remote_kernel(rt_name: str, base_port: int, hostname: str):
     Launch a remote Jupyter kernel, open tunnels, and connect a local Jupyter client.
     """
     assert ipython is not None
-    access_token = get_access_token()
+    access_token = AuthContext.get_access_token()
     assert access_token is not None
 
     # launch kernel and tunnel ports
@@ -1535,7 +1569,7 @@ def open_web_terminal(line: str):
     cmd = f"ttyd -p {random_port} -i 0.0.0.0 --writable bash"
 
     # Get access token
-    access_token = get_access_token()
+    access_token = AuthContext.get_access_token()
     if access_token is None:
         print("Not authenticated. Please run %authenticate first.")
         return
@@ -1667,7 +1701,7 @@ async def run_cell_async(
         return await orig_run_code(raw_cell, store_history, silent, shell_futures, transformed_cell=transformed_cell, preprocessing_exc_tuple=preprocessing_exc_tuple, cell_id=cell_id)
     else:
         # Validation: check runtime is ready and kernel is started
-        access_token = get_access_token()
+        access_token = AuthContext.get_access_token()
         assert access_token is not None
         rt_info = state.all_runtimes.get(rt, None)
         if rt_info is None:
diff --git a/dev-tools/airavata-python-sdk/airavata_sdk/__init__.py b/dev-tools/airavata-python-sdk/airavata_sdk/__init__.py
index 546c3bcd67..0a559918e8 100644
--- a/dev-tools/airavata-python-sdk/airavata_sdk/__init__.py
+++ b/dev-tools/airavata-python-sdk/airavata_sdk/__init__.py
@@ -164,7 +164,7 @@ def GATEWAY_DATA_STORE_DIR(self):
 
     @property
     def STORAGE_RESOURCE_HOST(self):
-        return str(os.getenv("STORAGE_RESOURCE_HOST", "cybershuttle.org"))
+        return str(os.getenv("STORAGE_RESOURCE_HOST", "gateway.cybershuttle.org"))
 
     @property
     def SFTP_PORT(self):
diff --git a/dev-tools/airavata-python-sdk/pyproject.toml b/dev-tools/airavata-python-sdk/pyproject.toml
index d6fa91b41e..d995930f1b 100644
--- a/dev-tools/airavata-python-sdk/pyproject.toml
+++ b/dev-tools/airavata-python-sdk/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "airavata-python-sdk"
-version = "2.1.7"
+version = "2.2.3"
 description = "Apache Airavata Python SDK"
 readme = "README.md"
 license = "Apache-2.0"
diff --git a/modules/agent-framework/airavata-agent/application/README.md b/modules/agent-framework/airavata-agent/application/README.md
new file mode 100644
index 0000000000..f57bb9b204
--- /dev/null
+++ b/modules/agent-framework/airavata-agent/application/README.md
@@ -0,0 +1,19 @@
+# Applications Scripts - Agent
+
+## NAMD
+
+### Expanse
+```sh
+NAMD_CPU_MODULES="cpu/0.17.3b gcc/10.2.0 openmpi/4.1.1"
+NAMD_CPU_PATH=/home/scigap/applications/NAMD_3.1alpha2_Linux-x86_64-multicore
+NAMD_GPU_MODULES="gpu/0.17.3b"
+NAMD_GPU_PATH=/home/scigap/applications/NAMD_3.0.1_Linux-x86_64-multicore-CUDA
+```
+
+### Delta
+```sh
+NAMD_CPU_MODULES="openmpi/4.1.6 fftw/3.3.10"
+NAMD_CPU_PATH=/sw/namd/NAMD_3.0b3_Linux-x86_64-multicore
+NAMD_GPU_MODULES="namd3/2024.02.mulitcore_cuda.s11"
+NAMD_GPU_PATH=/sw/namd/NAMD_3.0b3_Linux-x86_64-multicore-CUDA
+```
diff --git a/modules/agent-framework/airavata-agent/application/alphafold2.sh b/modules/agent-framework/airavata-agent/application/alphafold2.sh
new file mode 100644
index 0000000000..2d1318ffe0
--- /dev/null
+++ b/modules/agent-framework/airavata-agent/application/alphafold2.sh
@@ -0,0 +1,91 @@
+#!/bin/bash -x
+set -euo pipefail
+
+while getopts t:p:m: option
+ do
+  case $option in
+    t ) MaxDate=$OPTARG ;;
+    p ) MODEL_PRESET=$OPTARG ;;
+    m ) Num_Multi=$OPTARG ;;
+     \? ) cat << ENDCAT1
+>! Usage: $0  [-t Maximum Template Date ]    !<
+>!            [-p  Model Preset ]      !<
+>!            [-m  Number of Multimers per Model ]      !<
+ENDCAT1
+#   exit 1 ;;
+  esac
+done
+
+if [ $Num_Multi = "" ]; then
+  export Num_Multi=1
+fi
+#set the environment PATH
+export PYTHONNOUSERSITE=True
+module reset
+module load singularitypro
+ALPHAFOLD_HOME=/expanse/projects/qstore/data/alphafold-v2.3.2
+ALPHAFOLD_MODELS=$ALPHAFOLD_HOME/params
+
+pdb70=""
+uniprot=""
+pdbseqres=""
+nummulti=""
+
+# check_flags
+  if [ "monomer" = "${MODEL_PRESET%_*}" ];then
+     export pdb70="--pdb70_database_path=/data/pdb70/pdb70"
+  else
+     export uniprot="--uniprot_database_path=/data/uniprot/uniprot.fasta"
+     export pdbseqres="--pdb_seqres_database_path=/data/pdb_seqres/pdb_seqres.txt"
+     export nummulti="--num_multimer_predictions_per_model=$Num_Multi"
+  fi
+
+## Copy input to node local scratch
+cp input.fasta /scratch/$USER/job_$SLURM_JOBID
+#cp -r /expanse/projects/qstore/data/alphafold/uniclust30/uniclust30_2018_08 /scratch/$USER/job_$SLURM_JOBID/
+cd /scratch/$USER/job_$SLURM_JOBID
+ln -s /expanse/projects/qstore/data/alphafold/uniclust30/uniclust30_2018_08
+mkdir bfd
+cp /expanse/projects/qstore/data/alphafold/bfd/*index bfd/
+#cp /expanse/projects/qstore/data/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffdata bfd/
+#cp /expanse/projects/qstore/data/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffdata bfd/
+cd bfd
+ln -s  /expanse/projects/qstore/data/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffdata
+ln -s /expanse/projects/qstore/data/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffdata
+ln -s /expanse/projects/qstore/data/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffdata
+cd ../
+mkdir alphafold_output
+# Create soft links ro rundir form submitdir
+
+ln -s /scratch/$USER/job_$SLURM_JOBID $SLURM_SUBMIT_DIR/rundir
+
+#Run the command
+singularity run --nv \
+ -B /expanse/lustre \
+ -B /expanse/projects \
+ -B /scratch \
+ -B $ALPHAFOLD_HOME:/data \
+ -B $ALPHAFOLD_MODELS \
+ /cm/shared/apps/containers/singularity/alphafold/alphafold_aria2_v2.3.2.simg \
+ --fasta_paths=/scratch/$USER/job_$SLURM_JOBID/input.fasta \
+ --uniref90_database_path=/data/uniref90/uniref90.fasta \
+ --data_dir=/data \
+ --mgnify_database_path=/data/mgnify/mgy_clusters_2022_05.fa \
+ --bfd_database_path=/scratch/$USER/job_$SLURM_JOBID/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
+ --uniref30_database_path=/data/uniref30/UniRef30_2021_03 \
+ $pdbseqres \
+ $pdb70 \
+ $uniprot \
+ --template_mmcif_dir=/data/pdb_mmcif/mmcif_files \
+ --obsolete_pdbs_path=/data/pdb_mmcif/obsolete.dat \
+ --output_dir=/scratch/$USER/job_$SLURM_JOBID/alphafold_output \
+ --max_template_date=$MaxDate \
+ --model_preset=$MODEL_PRESET \
+ --use_gpu_relax=true \
+ --models_to_relax=best \
+ $nummulti
+
+unlink $SLURM_SUBMIT_DIR/rundir
+
+### Copy back results
+tar -cvf $SLURM_SUBMIT_DIR/alphafold_output.tar alphafold_output
diff --git a/modules/agent-framework/airavata-agent/application/gaussian16.sh b/modules/agent-framework/airavata-agent/application/gaussian16.sh
new file mode 100644
index 0000000000..f4089d116a
--- /dev/null
+++ b/modules/agent-framework/airavata-agent/application/gaussian16.sh
@@ -0,0 +1,256 @@
+#!/bin/sh -x
+# $Id: run_g09_chk_recovery.sh,v 1.0 2017/04/22 14:15:00 Sudhakar Exp $
+
+if [ $# -lt 1 -o $# -gt 3 ]; then
+    echo 1>&2 "Usage: $0 gaussian_input_gjf [SEAGrid_UserName] [GPU] "
+    #echo 1>&2 "Usage: $0 subdir gaussian_input_gjf clobber [gcvars]"
+    exit 127
+fi
+
+# subdir depends on whether we're doing freq, water or PES. For freq and water,
+# it should be hardcoded in the Xbaya workflow. For PES, it should be an
+# additional array generated by the frontend. The contents of this array are
+# trivial, but creating an extra Xbaya service to generate it would add
+# unnecessary extra complexity. Besides, the frontend cannot avoid having to
+# pass at least one array: the array with gjf files.
+#subdir=$1
+subdir="$PWD"
+#export GAUSS_SCRDIR=/oasis/scratch/comet/$USER/temp_project/$SLURM_JOBID
+#export GAUSS_SCRDIR=/expanse/lustre/scratch/$USER/temp_project/$SLURM_JOBID
+scratch_subid=$(id -u $user | tail -c2)
+scrdir="/storage/scratch1/$scratch_subid/$USER"
+export GAUSS_SCRDIR=$scrdir/$SLURM_JOBID
+mkdir -p $GAUSS_SCRDIR
+gaussian_input_full=$1
+if [ $AIRAVATA_USERNAME ]; then
+  echo " The Airavata Gateway User is $AIRAVATA_USERNAME"
+  SG_UserName="$AIRAVATA_USERNAME"
+#elif [ $2 ]; then
+#  SG_UserName=$2
+else
+  echo " The Airavata Gateway User is missing "
+exit
+fi
+
+        #export PATH="/storage/home/hcoda1/7/spamidig6/ideas_storage/apps/g16:$PATH"
+        #export GAUSS_EXEDIR="/storage/home/hcoda1/7/spamidig6/ideas_storage/apps/g16"
+        #. ~/.bash_profile
+#if [ "$2" = "GPU" ]; then
+	echo "Using GPU version of Gaussian 16"
+	#module reset; module load  gpu/0.15.4  gaussian/16.C.01-cuda
+	#module load gaussian/16.C.02
+        #export PATH="/storage/home/hcoda1/7/spamidig6/ideas_storage/apps/g16:$PATH"
+        #export GAUSS_EXEDIR="/storage/home/hcoda1/7/spamidig6/ideas_storage/apps/g16"
+        #. ~/.bash_profile
+#fi
+
+if [ $AIRAVATA_ExptDataDir ]; then
+    echo "The Airavata Storage Directory for this job is $AIRAVATA_ExptDataDir"
+    echo "Preparing Cron to push log data to storage periodically"
+    # Get Slurm total time
+#        flds=`squeue -j $SLURM_JOBID -l | awk 'END { print $7}' | awk -F: '{print NF}'`
+#        flds=`squeue -j $SLURM_JOBID -l | awk 'END { print $7}' | awk -F- '{print NF}'` + $flds
+#        # if flds 3 $1 is hrs $2 is min and $3 is sec
+#        if [ $flds = 4 ]; then
+#          jdys=`squeue -j $SLURM_JOBID -l | awk 'END { print $7}' |awk -F- '{print $1}'`
+#          hrmnse=`squeue -j $SLURM_JOBID -l | awk 'END { print $7}' |awk -F- '{print $2}'`
+#          jhrs=`echo $hrmnse | awk -F: '{print $1}'`+24*$jdys
+#	  jmin=`echo $hrmnse | awk -F: '{print $2}'`+60*$jhrs
+#        elif [ $flds = 3 ]; then
+#          jhrs=`squeue -j $SLURM_JOBID -l | awk 'END { print $7}' |awk -F: '{print $1}'`
+#	  jmin=`squeue -j $SLURM_JOBID -l | awk 'END { print $7}' |awk -F: '{print $2}'`+60*$jhrs
+#        elif [ $flds = 2 ]; then
+#          jmin=`squeue -j $SLURM_JOBID -l | awk 'END { print $7}' |awk -F: '{print $1}'`
+#        fi
+#        if [ $jhrs .gt. 5 ]; then
+#          upd=30
+#        else
+#          upd=$jmin/10
+#        fi
+    # For 5hrs and above uperiod is 30 min and for less than 5 hrs it is 10% of total time
+    # compute uperiod
+    # preapre or use prepared updateatorage script
+    # i(crontab -l 2>/dev/null; echo "*/$uperiod * * * * /path/to/job -with args") | crontab - */30 * * * * /path/to/command
+    # Use crontab -r to remove it after the job is finished or ended ( under trap)
+#      mycron=jcron$$
+#      #write out current crontab
+#      crontab -l > $mycron
+#      #echo new cron into cron file
+#      #echo "*/$upd * * * * /home/gridchem/bin/joblogscp.sh >/dev/null 2>&1" >> $mycron
+#      echo "*/$upd * * * *  scp *.log  pga@gf4.ucs.indiana.edu:$AIRAVATA_ExptDataDir >/dev/null 2>&1" >> $mycron
+#      #echo "* * * * * sleep 20; /Users/spamidig1/bin/testscp.sh >/dev/null 2>&1" >> $mycron
+##install new cron file
+#      crontab $mycron
+#      crontab -l
+#      # delete this entry at the end of the job or trap...
+fi
+inputs=`echo $AIRAVATA_INPUTS | sed 's/[//'`
+inputs=`echo $inputs | sed 's/]//'`
+echo "Airavata Inputs: $inputs"
+cd $subdir
+dos2unix -k $gaussian_input_full
+gaussian_input=${gaussian_input_full##*/}
+gaussian_output=${gaussian_input%.*}.log
+clobber="$3" # set to "" for rerun or debug; otherwise set to 1
+gcvars=$4
+null=""
+
+# Next line will ususally return "cp: `GCVARS' and `GCVARS' are the same file"
+#if [ "$gcvars" ] ; then cp -p $gcvars GCVARS 2>/dev/null ; fi
+
+#if [ ! "$LOCAL_LOCATION" ] ; then
+#  if [ -s ~/.paramchemlocation ] ; then
+#    read LOCAL_LOCATION < ~/.paramchemlocation
+#    . $LOCAL_LOCATION/environment
+#   fi
+# fi
+#if [ ! -d "$LOCAL_LOCATION" ] ; then
+#  echo "Warning: no valid LOCAL_LOCATION found" >&2
+#gauss_mem=56GB
+#gauss_nproc=24
+## Escaping spaces rather than quoting because quoting prevents tilde expansion
+##charmm_location=~gridchem/workflow_script/sys_exec/local/c36a6-132-serial\ -chsize\ 25140
+#SCRIPT_LOCATION=~gridchem/workflow_script/sys_exec/tools
+#LOCAL_LOCATION=~gridchem/workflow_script/sys_exec/local-comet
+#export CONPATH=$SCRIPT_LOCATION
+localarc="$HOME/scratch"
+##globalarc="ccguser@gridchem.uits.iu.edu:/home/ccguser/mss/internal/$SGUserName"
+##  exit 1
+# fi
+#. $LOCAL_LOCATION/environment
+
+#read GC_UserName GC_ProjectName GC_WorkflowName TIMESTAMP < GCVARS
+usrchkdir=$localarc/${SG_UserName}/
+echo " The Airavata Gateway User Directory is $usrchkdir"
+copysubdir="./"
+mkdir -p $usrchkdir
+#copysubdir=$localarc/${GC_UserName}/${GC_ProjectName}/${GC_WorkflowName}/$subdir
+# The way a "false" boolean variable is passed seems to be unstable; it's
+# been "", "0" and "false", so we try to cover all reasonable possibilities.
+if [ ! "$clobber" ] ; then
+  clobber=0
+ fi
+if [ "$clobber" = "0" -o "$clobber" = "false" -o "$clobber" = "no" ] ; then
+  if [ -s $copysubdir/$gaussian_output ] ; then
+    echo gaussian_output_log=$copysubdir/$gaussian_output
+    exit 0
+   fi
+  gaussian_output_full=${gaussian_input_full%.*}.log
+  if [ -s $gaussian_output_full ] ; then
+    #mkdir -p $copysubdir
+    rm -f $copysubdir/$gaussian_output # clean up symlink if something went wrong earlier
+    if [ $gaussian_input_full -nt $copysubdir/$gaussian_input ] ; then sed 's/\r$//' $gaussian_input_full > $copysubdir/$gaussian_input ; fi
+    cp -up $gaussian_output_full $copysubdir
+    echo gaussian_output_log=$gaussian_output_full
+    exit 0
+   fi
+ fi
+
+#Process inputfile for run files and other job requirements
+  # PROCESS CHECKPOINT FILE
+  # Check to see if the checkpoint file is given a name in input deck
+  # Input file to look into
+  dummy="$gaussian_input_full"
+  #dummy="$Diskinputdir/$Diskinputfile"
+  checkpt="no"
+  junk=`/usr/bin/head -5 $dummy | /bin/grep -i "%chk"`
+  if [ "$junk" !=  "" ]; then
+    junk=`echo $junk | /bin/sed 's/=/@/'`
+    junk=`echo $junk | /bin/sed 's/ //'`
+    #
+    # Be careful: Don't lose the subdirectory information for CHKPT file
+    # Also, add .chk if there is no extension to the Checkpoint file
+    #
+    Chkfile=`expr $junk : '.*@\(.*\)'`
+    Chkdir="$Diskinputdir"
+    Chkfile=`/bin/basename $Chkfile`
+    dummy=`expr $Chkfile : '.*\(\..*\)'`
+    Chkfile=`/bin/basename $Chkfile $dummy`
+    ChkfileWNE="$Chkfile"
+    Chkfile="$Chkfile${dummy:-.chk}"
+//"`Chkfile=`echo $Chkfile | sed "s/
+    # 2005/12/08 create name for $formated_chkfile
+    formated_chkfile="$ChkfileWNE.fchk"
+    Chkfile_with_arch="${Chkfile}_$architecture"
+    echo "DEBUG: checkfile = $Chkfile and formated_chkfile = $formated_chkfile ";
+    checkpt="yes"
+#Retrieve the checkpoint file from the user archive directory
+     if [ -f "$usrchkdir/$Chkfile" ]; then
+        cp $usrchkdir/$Chkfile .
+     fi
+//"`     export PJobID=`grep -i localjobid $gaussian_input_full | awk -F= '{print $2}' | sed "s/
+#     /bin/cat >> $qsubin << HERE2
+    #export PJobID=`grep -i localjobid $Diskinputfile | awk -F= '{print $2}' | sed "s/^M//"`
+    #cd /oasis/scratch/comet/gridchem/temp_project/$PJobID
+    #cd \$SCRATCH_BATCH
+    ##if [ ${PJobID:-null} != "$null" ]; then
+    if [ "${PJobID}" != "" ]; then
+      #cp -r /work/ccguser/batch_scratch/$PJobID*/* .
+      #cp -r /oasis/scratch/comet/gridchem/temp_project/$PJobID*/* .
+      cp -r $HOME/scratch/$PJobID*/* .
+      ls -l
+    fi
+   else
+    echo "******** NO CHECKPOINT FILE IDENTIFIED ******** "
+  fi
+
+mkdir -p $copysubdir
+mkdir -p $subdir
+cd $subdir
+cwd=`pwd`
+if [ $gaussian_input_full -nt $copysubdir/$gaussian_input ] ; then sed 's/\r$//' $gaussian_input_full > $copysubdir/$gaussian_input ; fi
+cd $copysubdir
+rm -f $gaussian_output
+if [ "$cwd" != "$subdir" ]; then
+   ln -s $cwd/$gaussian_output $subdir/$gaussian_output
+fi
+cd $cwd
+if [ $gaussian_input_full -nt $gaussian_input ] ; then sed 's/\r$//' $gaussian_input_full > $gaussian_input ; fi
+signals_to_trap="XCPU INT TERM CHLD"
+#trap "| grep -v $AIRAVATA_ExptDataDir | crontab -; rm -rf $mycron; cp -p $gaussian_output $copysubdir; cp -p $Chkfile $copysubdir; exit 99" $signals_to_trap
+#trap "crontab -l | grep -v $AIRAVATA_ExptDataDir | crontab -; rm -rf $mycron; cp -p $gaussian_output $copysubdir; cp -p $Chkfile $copysubdir; exit 99" $signals_to_trap
+cd $HOME/scratch
+ln -s $subdir $SLURM_JOBID
+ls -l $SLURM_JOBID/
+cd $cwd
+#$LOCAL_LOCATION/run_gaussian_local.sh $gaussian_input $gaussian_output
+which g16
+g16 $gaussian_input $gaussian_output
+#BEGIN{while(getline < infile) if ($0 ~ "^ *--[lL][iI][nN][kK]1--") nlink++}
+
+#if awk -v infile=$gaussian_input '
+#    BEGIN{while(getline < infile) if ($0 ~ "^ *[lL][iI][nN][kK]1") nlink++}
+#    /^ *Normal termination of Gaussian/{nnormal++}
+#    END{if (nnormal == nlink+1) exit 1}' $gaussian_output ; then
+#  echo "Gaussian terminated abnormally." >&2
+#  exit 1
+#fi
+# Remove the cron entry to periodically stage the data to storage
+#crontab -l | grep -v "$AIRAVATA_ExptDataDir"" | crontab -
+#crontab -l
+#rm $mycron
+
+#rm $copysubdir/$gaussian_output
+cp -p $gaussian_output $copysubdir
+ if [ -f "$Chkfile" ]; then
+    cp -p $Chkfile $copysubdir
+ fi
+ if [ -f "$GAUSS_SCRDIR/$Chkfile" ]; then
+    cp -p $GAUSS_SCRDIR/$Chkfile .
+ fi
+  # Save  checkpoint file to usrchkdir
+  #mkdir -p $usrchkdir
+  if [ -f "$Chkfile" ]; then
+        formchk $Chkfile
+  	cp -f $Chkfile $usrchkdir
+        cp -f *.fchk $usrchkdir
+        cp -f *.fchk $copysubdir
+  fi
+#remove rwf files
+rm *.rwf*
+cd $HOME/scratch
+#ln -s $subdir $PBS_JOBID
+ls -l $SLURM_JOBID
+rm $SLURM_JOBID/*.rwf*
+echo gaussian_output_log=$cwd/$gaussian_output
+cat: S: No such file or directory
diff --git a/modules/agent-framework/airavata-agent/application/gromacs.sh b/modules/agent-framework/airavata-agent/application/gromacs.sh
new file mode 100644
index 0000000000..dacb52f24e
--- /dev/null
+++ b/modules/agent-framework/airavata-agent/application/gromacs.sh
@@ -0,0 +1,165 @@
+#!/bin/sh -x
+# $Id: run_Gromacs_data_recovery.sh,v 1.0 2017/11/23 12:15:00 Sudhakar Exp $
+
+if [ $# -lt 1 -o $# -gt 11 ]; then
+    echo 1>&2 "Usage: $0 -c coord_file -s tpr_file -g log_file -e ener_file [SEAGrid_UserName] [Gromacs_restart_input] "
+    #echo 1>&2 "Usage: $0 subdir Gromacs_restart_input"
+    exit 127
+fi
+
+# subdir depends on whether we're doing freq, water or PES. For freq and water,
+# it should be hardcoded in the Xbaya workflow. For PES, it should be an
+# additional array generated by the frontend. The contents of this array are
+# trivial, but creating an extra Xbaya service to generate it would add
+# unnecessary extra complexity. Besides, the frontend cannot avoid having to
+# pass at least one array: the array with gjf files.
+#subdir=$1
+subdir="$PWD"
+#Gromacs_res_input_full=$1
+Coord_file=$2
+Tpr_file=$4
+Log_file=$6
+Ener_file=$8
+Rest_file=$10
+if [ $AIRAVATA_USERNAME ]; then
+  echo " The Airavata Gateway User is $AIRAVATA_USERNAME"
+  SG_UserName="$AIRAVATA_USERNAME"
+elif [ $9 ]; then
+  SG_UserName=$9
+else
+  echo " The Airavata Gateway User is missing "
+exit
+fi
+dos2unix -k $Gromacs_res_input_full
+Gromacs_input=${Gromacs_res_input_full##*/}
+Gromacs_output=${Gromacs_input%.*}.log
+#clobber="$3" # set to "" for rerun or debug; otherwise set to 1
+clobber="1" # set to "" for rerun or debug; otherwise set to 1
+#gcvars=$4
+gcvars="GCVARS"
+null=""
+localarc="$HOME/scratch"
+# Next line will ususally return "cp: `GCVARS' and `GCVARS' are the same file"
+if [ "$gcvars" ] ; then cp -p $gcvars GCVARS 2>/dev/null ; fi
+##
+#if [ ! "$LOCAL_LOCATION" ] ; then
+#  if [ -s ~/.paramchemlocation ] ; then
+#    read LOCAL_LOCATION < ~/.paramchemlocation
+#   fi
+# fi
+#if [ ! -d "$LOCAL_LOCATION" ] ; then
+#  echo "Error: no valid LOCAL_LOCATION found" >&2
+#  exit 1
+# fi
+#. $LOCAL_LOCATION/environment
+
+#read GC_UserName GC_ProjectName GC_WorkflowName TIMESTAMP < GCVARS
+usrchkdir=$localarc/${SG_UserName}/
+echo " The Airavata Gateway User Directory is $usrchkdir"
+copysubdir="./"
+#copysubdir=$localarc/${GC_UserName}/${GC_ProjectName}/${GC_WorkflowName}/$subdir
+# The way a "false" boolean variable is passed seems to be unstable; it's
+# been "", "0" and "false", so we try to cover all reasonable possibilities.
+if [ ! "$clobber" ] ; then
+  clobber=0
+ fi
+if [ "$clobber" = "0" -o "$clobber" = "false" -o "$clobber" = "no" ] ; then
+  if [ -s $copysubdir/$Gromacs_output ] ; then
+    echo Gromacs_output_log=$copysubdir/$Gromacs_output
+    exit 0
+   fi
+  Gromacs_output_full=${Gromacs_input_full%.*}.log
+  if [ -s $Gromacs_output_full ] ; then
+    mkdir -p $copysubdir
+    rm -f $copysubdir/$Gromacs_output # clean up symlink if something went wrong earlier
+    if [ $Gromacs_input_full -nt $copysubdir/$Gromacs_input ] ; then sed 's/\r$//' $Gromacs_input_full > $copysubdir/$Gromacs_input ; fi
+    cp -up $Gromacs_output_full $copysubdir
+    echo Gromacs_output_log=$Gromacs_output_full
+    exit 0
+   fi
+ fi
+
+#Process inputfile for run files and other job requirements
+//"`export PJobID=`grep -i localjobid restart.txt| awk -F= '{print $2}' | sed "s/
+    if [ ${PJobID:-null} != "$null" ]; then
+    cp -r /home/scigap/scratch/${SG_UserName}/$PJobID*/* .
+    fi
+#  # PROCESS CHECKPOINT FILE
+#  # Check to see if the checkpoint file is given a name in input deck
+#  # Input file to look into
+#  dummy="$Gromacs_input_full"
+#  #dummy="$Diskinputdir/$Diskinputfile"
+#  checkpt="no"
+#  junk=`/usr/bin/head -5 $dummy | /bin/grep -i "%chk"`
+#  if [ "$junk" !=  "" ]; then
+#    junk=`echo $junk | /bin/sed 's/=/@/'`
+#    junk=`echo $junk | /bin/sed 's/ //'`
+#    #
+#    # Be careful: Don't lose the subdirectory information for CHKPT file
+#    # Also, add .chk if there is no extension to the Checkpoint file
+#    #
+#    Chkfile=`expr $junk : '.*@\(.*\)'`
+#    Chkdir="$Diskinputdir"
+#    Chkfile=`/bin/basename $Chkfile`
+#    dummy=`expr $Chkfile : '.*\(\..*\)'`
+#    Chkfile=`/bin/basename $Chkfile $dummy`
+#    ChkfileWNE="$Chkfile"
+#    Chkfile="$Chkfile${dummy:-.chk}"
+//"` Chkfile=`echo $Chkfile | sed "s/
+#    # 2005/12/08 create name for $formated_chkfile
+#    formated_chkfile="$ChkfileWNE.fchk"
+#    Chkfile_with_arch="${Chkfile}_$architecture"
+#    echo "DEBUG: checkfile = $Chkfile and formated_chkfile = $formated_chkfile ";
+#    checkpt="yes"
+##Retrieve the checkpoint file from the user archive directory
+#     if [ -f "$usrchkdir/$Chkfile" ]; then
+#        cp $usrchkdir/$Chkfile .
+#     fi
+#   else
+#    echo "******** NO CHECKPOINT FILE IDENTIFIED ******** "
+#  fi
+
+mkdir -p $copysubdir
+mkdir -p $subdir
+cd $subdir
+cwd=`pwd`
+if [ $Gromacs_input_full -nt $copysubdir/$Gromacs_input ] ; then sed 's/\r$//' $Gromacs_input_full > $copysubdir/$Gromacs_input ; fi
+cd $copysubdir
+rm -f $Gromacs_output
+if [ "$cwd" != "$subdir" ]; then
+   ln -s $cwd/$Gromacs_output $subdir/$Gromacs_output
+fi
+cd $cwd
+if [ $Gromacs_input_full -nt $Gromacs_input ] ; then sed 's/\r$//' $Gromacs_input_full > $Gromacs_input ; fi
+module unload intel; module load gromacs
+if [ ${PJobID:-null} != "$null" ]; then
+    cp -r /home/scigap/scratch/${SG_UserName}/$PJobID*/* .
+    #mpiexec -genv I_MPI_FABRICS shm:ofa gmx_mpi mdrun -s $Tpr_file -cpi state.cpt
+    mpirun -np $SLURM_NTASKS  -genv I_MPI_FABRICS shm:ofa gmx_mpi mdrun -v -deffnm em -s $Tpr_file -cpi state.cpt
+else
+    mpirun -np $SLURM_NTASKS  -genv I_MPI_FABRICS shm:ofa  gmx_mpi mdrun -v -deffnm em -s $Tpr_file -c $Coord_file -g $Log_file -e $Ener_file
+fi
+
+mpiexec gmx_mpi mdrun -s $Tpr_file -cpi state.cpt
+##$LOCAL_LOCATION/run_Gromacs_local.sh $Gromacs_input $Gromacs_output
+##$LOCAL_LOCATION/run_Gromacs_local.sh $Gromacs_input $Gromacs_output
+#BEGIN{while(getline < infile) if ($0 ~ "^ *--[lL][iI][nN][kK]1--") nlink++}
+
+#if awk -v infile=$Gromacs_input '
+#    BEGIN{while(getline < infile) if ($0 ~ "^ *[lL][iI][nN][kK]1") nlink++}
+#    /^ *Normal termination of Gaussian/{nnormal++}
+#    END{if (nnormal == nlink+1) exit 1}' $Gromacs_output ; then
+#  echo "Gaussian terminated abnormally." >&2
+#  exit 1
+#fi
+#rm $copysubdir/$Gromacs_output
+cp -p $Gromacs_output $copysubdir
+  # Save  checkpoint file to usrchkdir
+#  mkdir -p $usrchkdir
+#  if [ -f "$Chkfile" ]; then
+#  	cp -f $Chkfile $usrchkdir
+#  fi
+#  # Create a link directory for this job with jobID in user scratch
+  ln -s $PWD ~/scratch/${SG_USERNAME}/$PBS_JOBID
+echo Gromacs_output_log=$cwd/$Gromacs_output
+#rm *.wfc*
diff --git a/modules/agent-framework/airavata-agent/application/namd.sh b/modules/agent-framework/airavata-agent/application/namd.sh
new file mode 100644
index 0000000000..240cc2ad10
--- /dev/null
+++ b/modules/agent-framework/airavata-agent/application/namd.sh
@@ -0,0 +1,130 @@
+#!/bin/bash -x
+set -euo pipefail
+
+# ----------------------------------------------------------------------
+# SETUP
+# ----------------------------------------------------------------------
+export PATH=$PWD:$PATH
+export WORKDIR=$PWD
+export CS_HOME=$HOME/cybershuttle
+export MAMBA_ROOT_PREFIX=$CS_HOME/scratch
+export TMPDIR=$CS_HOME/scratch/tmp
+
+# initialize scratch/tmp and scratch/envs (node-local)
+CS_TEMP=$(readlink $CS_HOME/scratch/tmp)
+CS_ENVS=$(readlink $CS_HOME/scratch/envs)
+[ -n "$CS_TEMP" ] && mkdir -p $CS_TEMP
+[ -n "$CS_ENVS" ] && mkdir -p $CS_ENVS
+NAMD_EXTRA_ARGS=()
+FIFO=$(mktemp -u)
+mkfifo $FIFO
+
+# ----------------------------------------------------------------------
+# PARSE COMMAND LINE ARGUMENTS
+# ----------------------------------------------------------------------
+
+required_vars=("NAMD_CPU_PATH" "NAMD_GPU_PATH" "NAMD_CPU_MODULES" "NAMD_GPU_MODULES")
+for var in "${required_vars[@]}"; do
+  if [ -z "${!var}" ]; then
+    echo "$var is not set"
+    exit 2
+  fi
+done
+
+while getopts t:n:i:a:s: option; do
+  case $option in
+    t) 
+      if [[ "$OPTARG" != "CPU" && "$OPTARG" != "GPU" ]]; then
+        echo "invalid argument -t $OPTARG: must be CPU|GPU."
+        exit 2
+      fi
+      EXECUTION_TYPE=$OPTARG
+      echo "EXECUTION_TYPE=$EXECUTION_TYPE"
+      module reset
+      if [ $EXECUTION_TYPE = "CPU" ]; then
+        # one replica at a time
+        echo 0 > $FIFO &
+        NAMD_PATH=$NAMD_CPU_PATH
+        module load $NAMD_CPU_MODULES
+      elif [ $EXECUTION_TYPE = "GPU" ]; then
+        # one replica per GPU
+        for ((i=0; i<${SLURM_GPUS_ON_NODE:-0}; i++)); do echo "$i" > $FIFO & done
+        NAMD_PATH=$NAMD_GPU_PATH
+        NAMD_EXTRA_ARGS+=("--CUDASOAintegrate" "on")
+        module load $NAMD_GPU_MODULES
+      fi
+      module list
+      ;;
+    n) 
+      NUM_REPLICAS=$OPTARG
+      echo "NUM_REPLICAS=$NUM_REPLICAS"
+      ;;
+    i) 
+      NAMD_INPUT_FILES=$(find $WORKDIR -maxdepth 1 -type f ! -name "*slurm*" ! -name "*.stdout" ! -name "*.stderr")
+      NAMD_CONF_FILE=$OPTARG
+      echo "NAMD_INPUT_FILES=$NAMD_INPUT_FILES"
+      echo "NAMD_CONF_FILE=$NAMD_CONF_FILE"
+      ;;
+    a) 
+      AGENT_ID=$OPTARG
+      echo "AGENT_ID=$AGENT_ID"
+      ;;
+    s) 
+      AGENT_SERVER=$OPTARG
+      echo "AGENT_SERVER=$AGENT_SERVER"
+      ;;
+    \?) 
+      echo 1>&2 "Usage: $0"
+      echo 1>&2 "  -t [CPU|GPU]"
+      echo 1>&2 "  -n [NUM_REPLICAS]"
+      echo 1>&2 "  -i [NAMD_CONF_FILE]"
+      echo 1>&2 "  -a [AGENT_ID]"
+      echo 1>&2 "  -s [AGENT_SERVER]"
+      exit 2
+      ;;
+  esac
+done
+shift $((OPTIND - 1))
+
+# ----------------------------------------------------------------------
+# RUN AGENT
+# ----------------------------------------------------------------------
+
+wget -q https://github.com/cyber-shuttle/binaries/releases/download/1.0.1/airavata-agent-linux-amd64 -O $WORKDIR/airavata-agent
+wget -q https://github.com/cyber-shuttle/binaries/releases/download/1.0.1/kernel.py -O $WORKDIR/kernel.py
+wget -q https://github.com/mamba-org/micromamba-releases/releases/download/2.3.0-1/micromamba-linux-64 -O $WORKDIR/micromamba
+chmod +x $WORKDIR/airavata-agent $WORKDIR/micromamba
+$WORKDIR/airavata-agent --server "$AGENT_SERVER:19900" --agent "$AGENT_ID" --environ "$AGENT_ID" --lib "" --pip "" &
+AGENT_PID=$!
+trap 'kill -TERM $AGENT_PID' EXIT
+echo "Agent started with PID $AGENT_PID"
+
+
+# ----------------------------------------------------------------------
+# RUN NAMD3
+# ----------------------------------------------------------------------
+PIDS=()
+for REPLICA_ID in $(seq 1 $NUM_REPLICAS); do
+  (
+  read TOKEN <$FIFO
+
+  REPLICA_DIR=$WORKDIR/$REPLICA_ID
+  mkdir $REPLICA_DIR
+  cp $NAMD_INPUT_FILES $REPLICA_DIR/
+
+  [[ $EXECUTION_TYPE == "GPU" ]] && export CUDA_VISIBLE_DEVICES=$TOKEN
+  $NAMD_PATH/namd3 +setcpuaffinity +p $SLURM_CPUS_ON_NODE --cwd $REPLICA_DIR "${NAMD_EXTRA_ARGS[@]}" \
+  $REPLICA_DIR/$NAMD_CONF_FILE >$REPLICA_DIR/$NAMD_CONF_FILE.out 2>$REPLICA_DIR/$NAMD_CONF_FILE.err
+  [[ $EXECUTION_TYPE == "GPU" ]] && unset CUDA_VISIBLE_DEVICES
+  
+  echo $TOKEN > $FIFO &
+
+  for FILE in $(ls $REPLICA_DIR/*.*); do
+    mv $FILE $REPLICA_ID"_"$(basename $FILE)
+  done
+  rm -rf $REPLICA_DIR/
+
+  ) &
+  PIDS+=($!)
+done
+wait "${PIDS[@]}"
diff --git a/modules/agent-framework/airavata-agent/application/pmemd_cuda.sh b/modules/agent-framework/airavata-agent/application/pmemd_cuda.sh
new file mode 100644
index 0000000000..59378da8bb
--- /dev/null
+++ b/modules/agent-framework/airavata-agent/application/pmemd_cuda.sh
@@ -0,0 +1,4 @@
+#!/bin/bash -x
+set -euo pipefail
+
+srun pmemd.cuda "$@"
diff --git a/modules/agent-framework/airavata-agent/application/pmemd_mpi.sh b/modules/agent-framework/airavata-agent/application/pmemd_mpi.sh
new file mode 100644
index 0000000000..b00bd75162
--- /dev/null
+++ b/modules/agent-framework/airavata-agent/application/pmemd_mpi.sh
@@ -0,0 +1,4 @@
+#!/bin/bash -x
+set -euo pipefail
+
+srun pmemd.MPI "$@"
diff --git a/modules/agent-framework/airavata-agent/application/psi4.sh b/modules/agent-framework/airavata-agent/application/psi4.sh
new file mode 100644
index 0000000000..404c713d33
--- /dev/null
+++ b/modules/agent-framework/airavata-agent/application/psi4.sh
@@ -0,0 +1,4 @@
+#!/bin/bash -x
+set -euo pipefail
+
+psi4 "$@"