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add log file submited jobs #504

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add log file submited jobs #504

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9108185
add log file submited jobs
tayllatheodoro Feb 18, 2025
4875a9e
using unique_id
tayllatheodoro Feb 18, 2025
5ee2d90
using unique_id
tayllatheodoro Feb 18, 2025
01ebd9d
correcting code
tayllatheodoro Feb 18, 2025
84c0b5b
correcting code
tayllatheodoro Feb 18, 2025
d68a2b7
working reconstruction
tayllatheodoro Apr 29, 2025
6b77313
check for nans or zeros before phase recon
ieivanov Apr 29, 2025
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14 changes: 12 additions & 2 deletions recOrder/cli/apply_inverse_transfer_function.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@
transfer_function_dirpath,
ram_multiplier,
unique_id,
verbose
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@talonchandler talonchandler Feb 18, 2025

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I'm guessing you forgot to add parsing.py to the commit? The test show this import is failing.

)
from recOrder.cli.printing import echo_headline, echo_settings
from recOrder.cli.settings import ReconstructionSettings
Expand Down Expand Up @@ -349,6 +350,7 @@ def apply_inverse_transfer_function_cli(
executor = submitit.AutoExecutor(folder=Path(executor_folder))

executor.update_parameters(
slurm_job_name = "reconstruct",
slurm_array_parallelism=np.min([50, num_jobs]),
slurm_mem_per_cpu=f"{gb_ram_request}G",
slurm_cpus_per_task=cpu_request,
Expand All @@ -374,9 +376,10 @@ def apply_inverse_transfer_function_cli(
echo_headline(
f"{num_jobs} job{'s' if num_jobs > 1 else ''} submitted {'locally' if executor.cluster == 'local' else 'via ' + executor.cluster}."
)



doPrint = True # CLI prints Job status when used as cmd line
if unique_id != "": # no unique_id means no job submission info being listened to
if unique_id != "" and unique_id !="-1": # no unique_id means no job submission info being listened to
JM.start_client()
i=0
for j in jobs:
Expand All @@ -388,6 +391,13 @@ def apply_inverse_transfer_function_cli(
JM.send_data_thread()
JM.set_shorter_timeout()
doPrint = False # CLI printing disabled when using GUI
elif unique_id==-1: # CLI used to run automatic pipeline
doPrint = False
job_ids = [job.job_id for job in jobs] # Access job IDs after batch submission

log_path = Path(executor_folder/"submitit_jobs_ids.log")
with log_path.open("w") as log_file:
log_file.write("\n".join(job_ids))

monitor_jobs(jobs, input_position_dirpaths, doPrint)

Expand Down
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