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Issue 70: 832 HPC Recon Bug Fixes #72

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Merged
dylanmcreynolds merged 2 commits into from
Apr 9, 2025
Merged

Issue 70: 832 HPC Recon Bug Fixes #72

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61f84ad
Updating alcf flow to read the Prefect JSON block alcf-allocation-roo…
davramov Apr 8, 2025
8fbaa65
adding prefect block alcf-allocation-root-path to test_globus_flow.py…
davramov Apr 8, 2025
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4 changes: 2 additions & 2 deletions config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -27,13 +27,13 @@ globus:
alcf832_raw:
root_path: /data/raw
uri: alcf.anl.gov
uuid: a89365da-e614-48fe-9ee5-f5e1698a68c8 # 55c3adf6-31f1-4647-9a38-52591642f7e7
uuid: 2f9e7035-f4d8-4aa3-a911-d110bc2c8110
name: alcf_raw

alcf832_scratch:
root_path: /data/scratch
uri: alcf.anl.gov
uuid: a89365da-e614-48fe-9ee5-f5e1698a68c8 # 55c3adf6-31f1-4647-9a38-52591642f7e7
uuid: 2f9e7035-f4d8-4aa3-a911-d110bc2c8110
name: alcf_scratch

alcf_eagle832:
Expand Down
6 changes: 5 additions & 1 deletion orchestration/_tests/test_globus_flow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,10 +37,14 @@ def prefect_test_fixture():

decision_settings = JSON(value={
"alcf_recon_flow/alcf_recon_flow": True,
"nersc_recon/nersc_recon": False, # This is a placeholder for the NERSC reconstruction flow
"nersc_recon_flow/nersc_recon_flow": False,
"new_832_file_flow/new_file_832": False
})
decision_settings.save(name="decision-settings")

alcf_allocation_root = JSON(value={"alcf-allocation-root-path": "/eagle/IRIProd/ALS"})
alcf_allocation_root.save(name="alcf-allocation-root-path")

yield


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29 changes: 18 additions & 11 deletions orchestration/flows/bl832/alcf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,13 @@ def __init__(
config: Config832
) -> None:
super().__init__(config)
# Load allocation root from the Prefect JSON block
# The block must be registered with the name "alcf-allocation-root-path"
allocation_data = JSON.load("alcf-allocation-root-path").value
self.allocation_root = allocation_data.get("alcf-allocation-root-path")
if not self.allocation_root:
raise ValueError("Allocation root not found in JSON block 'alcf-allocation-root-path'")
logger.info(f"Allocation root loaded: {self.allocation_root}")

def reconstruct(
self,
Expand All @@ -51,8 +58,8 @@ def reconstruct(
file_name = Path(file_path).stem + ".h5"
folder_name = Path(file_path).parent.name

iri_als_bl832_rundir = "/eagle/IRI-ALS-832/data/raw"
iri_als_bl832_recon_script = "/eagle/IRI-ALS-832/scripts/globus_reconstruction.py"
iri_als_bl832_rundir = f"{self.allocation_root}/data/raw"
iri_als_bl832_recon_script = f"{self.allocation_root}/scripts/globus_reconstruction.py"

gcc = Client(code_serialization_strategy=CombinedCode())

Expand All @@ -70,8 +77,8 @@ def reconstruct(

@staticmethod
def _reconstruct_wrapper(
rundir: str = "/eagle/IRI-ALS-832/data/raw",
script_path: str = "/eagle/IRI-ALS-832/scripts/globus_reconstruction.py",
rundir: str = "/eagle/IRIProd/ALS/data/raw",
script_path: str = "/eagle/IRIProd/ALS/scripts/globus_reconstruction.py",
h5_file_name: str = None,
folder_path: str = None
) -> str:
Expand Down Expand Up @@ -125,11 +132,11 @@ def build_multi_resolution(
file_name = Path(file_path).stem
folder_name = Path(file_path).parent.name

tiff_scratch_path = f"/eagle/IRI-ALS-832/data/scratch/{folder_name}/rec{file_name}/"
raw_path = f"/eagle/IRI-ALS-832/data/raw/{folder_name}/{file_name}.h5"
tiff_scratch_path = f"{self.allocation_root}/data/scratch/{folder_name}/rec{file_name}/"
raw_path = f"{self.allocation_root}/raw/{folder_name}/{file_name}.h5"

iri_als_bl832_rundir = "/eagle/IRI-ALS-832/data/raw"
iri_als_bl832_conversion_script = "/eagle/IRI-ALS-832/scripts/tiff_to_zarr.py"
iri_als_bl832_rundir = f"{self.allocation_root}/data/raw"
iri_als_bl832_conversion_script = f"{self.allocation_root}/scripts/tiff_to_zarr.py"

gcc = Client(code_serialization_strategy=CombinedCode())

Expand All @@ -147,8 +154,8 @@ def build_multi_resolution(

@staticmethod
def _build_multi_resolution_wrapper(
rundir: str = "/eagle/IRI-ALS-832/data/raw",
script_path: str = "/eagle/IRI-ALS-832/scripts/tiff_to_zarr.py",
rundir: str = "/eagle/IRIProd/ALS/data/raw",
script_path: str = "/eagle/IRIProd/ALS/scripts/tiff_to_zarr.py",
recon_path: str = None,
raw_path: str = None
) -> str:
Expand Down Expand Up @@ -461,7 +468,7 @@ def alcf_recon_flow(

if __name__ == "__main__":
folder_name = 'dabramov'
file_name = '20240425_104614_nist-sand-30-100_27keV_z8mm_n2625'
file_name = '20230606_151124_jong-seto_fungal-mycelia_roll-AQ_fungi1_fast'
flow_success = alcf_recon_flow(
file_path=f"/{folder_name}/{file_name}.h5",
config=Config832()
Expand Down
12 changes: 6 additions & 6 deletions orchestration/flows/bl832/dispatcher.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,8 @@ class FlowParameterMapper:
"file_path",
"is_export_control",
"config"],
# Placeholder parameters for NERSC reconstruction
"nersc_recon/nersc_recon": [
# From nersc.py
"nersc_recon_flow/nersc_recon_flow": [
"file_path",
"is_export_control",
"config"] # Placeholder parameters for NERSC reconstruction
Expand Down Expand Up @@ -71,7 +71,7 @@ def setup_decision_settings(alcf_recon: bool, nersc_recon: bool, new_file_832: b
# Define which flows to run based on the input settings
settings = {
"alcf_recon_flow/alcf_recon_flow": alcf_recon,
"nersc_recon/nersc_recon": nersc_recon, # This is a placeholder for the NERSC reconstruction flow
"nersc_recon_flow/nersc_recon_flow": nersc_recon,
"new_832_file_flow/new_file_832": new_file_832
}
# Save the settings in a JSON block for later retrieval by other flows
Expand Down Expand Up @@ -143,9 +143,9 @@ async def dispatcher(
alcf_params = FlowParameterMapper.get_flow_parameters("alcf_recon_flow/alcf_recon_flow", available_params)
tasks.append(run_specific_flow("alcf_recon_flow/alcf_recon_flow", alcf_params))

if decision_settings.value.get("nersc_recon/nersc_recon"):
nersc_params = FlowParameterMapper.get_flow_parameters("nersc_recon/nersc_recon", available_params)
tasks.append(run_specific_flow("nersc_recon/nersc_recon", nersc_params))
if decision_settings.value.get("nersc_recon_flow/nersc_recon_flow"):
nersc_params = FlowParameterMapper.get_flow_parameters("nersc_recon_flow/nersc_recon_flow", available_params)
tasks.append(run_specific_flow("nersc_recon_flow/nersc_recon_flow", nersc_params))

# Run ALCF and NERSC flows in parallel, if any
if tasks:
Expand Down