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Add 2 scripts to run eagle more conveniently #196

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f5a16c2
add run scripts
weihuang-jedi Jun 10, 2026
a8c689a
add run scripts
weihuang-jedi Jun 11, 2026
8eb1a8e
sync
weihuang-jedi Jun 24, 2026
f0cf942
adding two run scripts
weihuang-jedi Jun 24, 2026
92f4cfc
adding two run scripts
weihuang-jedi Jun 24, 2026
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332 changes: 332 additions & 0 deletions runeagle.sh
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Original file line number Diff line number Diff line change
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#!/usr/bin/env bash

# default setting
EAGLEhome=`pwd`
MACHINE_ID=ursa
#expname=default
expname="eagle_case"
verbose="NO"
step="training"

function _usage() {
cat << EOF
Run EAGLE on head node (ursa).

Usage: ${BASH_SOURCE[0]} [-h][-v] -n name_of_experiment -s [env devenv config data training inference verification visualization] -m machine_id
-h:
Print this help message and exit
-v:
Verbose mode
-n:
Name of the experiment
-s:
Steps of EAGLE
-m:
Machine ID (default: ursa)

Input arguments are the step(s) to run.
Valid options are
env devenv config data training inference verification visualization
(default is "training")
EOF
exit 0
}

#set +u

# FIXED: Added colons after n, s, and m so they handle trailing arguments properly!
while getopts ":hn:s:m:v" option; do
case "${option}" in
h) _usage ;;
n) expname=${OPTARG} ;; # Changed from e to n to match documentation
s) step=${OPTARG} ;;
m) MACHINE_ID=${OPTARG} ;;
v) verbose="YES" ;;
*)
echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
_usage
;;
esac
done

if [[ "${verbose}" == "YES" ]]; then
set -x
fi

source ${EAGLEhome}/conda/etc/profile.d/conda.sh

# Ensure EAGLEhome is expanded cleanly
conda_bin_path="${EAGLEhome}/conda/bin"

if [[ ":$PATH:" =~ ":${conda_bin_path}:" ]]; then
if [[ "${verbose}" == "YES" ]]; then
echo "Success: ${conda_bin_path} is already in your PATH."
fi
else
# echo "Warning: ${conda_bin_path} is missing from your PATH. Adding it now..."
export PATH="${conda_bin_path}:$PATH"
fi

eval "$(mamba shell hook --shell bash)"

wait_for_file() {
local file_path="$1"
local timeout=1800 # 30 minutes in seconds (30 * 60)
local interval=10 # Check every 10 seconds

# Initail check to see if the file exists
if [ -f "$file_path" ]; then
return 0
fi

echo "Checking for file: $file_path..."

# Initialize Bash's builtin SECONDS counter
SECONDS=0

# Loop until the file exists or the 30-minute timeout is reached
until [ -f "$file_path" ] || (( SECONDS >= timeout )); do
sleep "$interval"
echo "Still waiting... ($((SECONDS))s elapsed)"
done

# Final check to see if the file exists or if we timed out
if [ -f "$file_path" ]; then
echo "Success! File '$file_path' is ready."
return 0
else
echo "Error: File '$file_path' was not produced within 30 minutes."
return 1
fi
}

# Example of how to use it:
# wait_for_file "/path/to/your/file.txt"

case "${step}" in
env|devenv)
if [[ -f "${EAGLEhome}/conda/bin/mamba" ]]; then
echo "Conda env already install....."
# Prompt the user (-n 1 limits input to exactly 1 character, -r prevents backslash escapes)
read -n 1 -r -p "Do you want to overwrite? (y/n): " response
echo "" # Prints a clean newline after the user keypress

case "${response}" in
[Yy])
echo "Proceeding to overwrite..."
;;
[Nn]|*)
echo "Stop signal received. Exiting script."
exit 11
;;
esac
fi

mamba activate /scratch5/purged/Wei.Huang/src/EAGLE/conda/envs/anemoi
make env cudascript=${MACHINE_ID}
;;
config)
mamba activate /scratch5/purged/Wei.Huang/src/EAGLE/conda/envs/anemoi
make config compose=base:nested:${MACHINE_ID} > eagle.yaml
sed -i "s?/path/to/eagle?${EAGLEhome}?g" eagle.yaml
sed -i "s|experiment_name: default|experiment_name: \'${expname}\'|g" eagle.yaml
sed -i "s?/path/to/checkpoint?'{{ app.rundir }}/checkpoint'?g" eagle.yaml
;;
data)
mamba activate ${EAGLEhome}/conda/envs/data
make data config=eagle.yaml
;;
training)
# Check if training data are ready:
if [[ ! -f "${EAGLEhome}/run/${expname}/data/runscript.zarr-gfs.done" ]] || \
[[ ! -f "${EAGLEhome}/run/${expname}/data/runscript.zarr-hrrr.done" ]]; then
echo "Training data are not ready, need to run ${BASH_SOURCE[0]} -n ${expname} -s data"
echo "Then wait and check data are available."
exit 14
fi
mamba activate ${EAGLEhome}/conda/envs/anemoi
make training config=eagle.yaml
;;
inference)
# Check if training is done:
if [[ ! -f "${EAGLEhome}/run/${expname}/training/runscript.training.done" ]]; then
echo "Training is not done, need to run ${BASH_SOURCE[0]} -n ${expname} -s training"
echo "Then wait and re-run when training is done."
squeue -u $USER
exit 15
fi
mamba activate ${EAGLEhome}/conda/envs/anemoi
make inference config=eagle.yaml
;;
veri*)
# Check if inference is done:
if [[ ! -f "${EAGLEhome}/run/${expname}/inference/runscript.inference.done" ]]; then
echo "Inference is not done, need to run ${BASH_SOURCE[0]} -n ${expname} -s inference"
echo "Then wait and re-run when inference is done."
squeue -u $USER
exit 16
fi
mamba activate ${EAGLEhome}/conda/envs/wxvx
for kind in grid obs
do
for region in global lam
do
make vx-${kind}-${region} config=eagle.yaml &
done
done
wait
mamba deactivate
;;
visu*)
# re-check if verifications are done:
mamba activate ${EAGLEhome}/conda/envs/wxvx
for kind in grid obs
do
for region in global lam
do
script="${EAGLEhome}/run/${expname}/vx/grid2${kind}/${region}/runscript.wxvx-grid2${kind}-${region}"
done_file="${script}.done"
if [[ -f "${script}" ]] && [[ ! -f "${done_file}" ]]; then
sbatch ${script}
wait_for_file "${done_file}" &
fi
done
done
wait
mamba deactivate

mamba activate ${EAGLEhome}/conda/envs/visualization
for kind in grid obs
do
for region in global lam
do
make vis-${kind}-${region} config=eagle.yaml &
done
done
wait
mamba deactivate
;;
all)
# 1. setup env
if [[ -f "${EAGLEhome}/conda/bin/mamba" ]]; then
echo "Conda env already install....."
# Prompt the user (-n 1 limits input to exactly 1 character, -r prevents backslash escapes)
read -n 1 -r -p "Do you want to overwrite? (y/n): " response
echo "" # Prints a clean newline after the user keypress

case "${response}" in
[Yy])
echo "Proceeding to overwrite..."
mamba activate /scratch5/purged/Wei.Huang/src/EAGLE/conda/envs/anemoi
make env cudascript=${MACHINE_ID}
mamba deactivate
;;
[Nn]|*)
echo "Continue to config..."
;;
esac
else
mamba activate /scratch5/purged/Wei.Huang/src/EAGLE/conda/envs/anemoi
make env cudascript=${MACHINE_ID}
mamba deactivate
fi

# 2. config
mamba activate /scratch5/purged/Wei.Huang/src/EAGLE/conda/envs/anemoi
make config compose=base:nested:${MACHINE_ID} > eagle.yaml
sed -i "s?/path/to/eagle/src?${EAGLEhome}?g" eagle.yaml
sed -i "s|experiment_name: default|experiment_name: \'${expname}\'|g" eagle.yaml
sed -i "s?/path/to/checkpoint?'{{ app.rundir }}/checkpoint'?g" eagle.yaml
mamba deactivate

# 3. prepare data
mamba activate ${EAGLEhome}/conda/envs/data
make data config=eagle.yaml
mamba deactivate

# 4. training
nwait=0
while [[ ! -f "${EAGLEhome}/run/${expname}/data/runscript.zarr-gfs.done" ]] || \
[[ ! -f "${EAGLEhome}/run/${expname}/data/runscript.zarr-hrrr.done" ]]; do
echo "Training data are not ready, waiting..."
sleep 30
nwait=$(( nwait+1 ))
if [[ "${nwait}" -ge 60 ]]; then
echo "Waited to long for training data. quit..."
exit 22
fi
done
mamba activate ${EAGLEhome}/conda/envs/anemoi
make training config=eagle.yaml
mamba deactivate

# 5. inference
nwait=0
while [[ ! -f "${EAGLEhome}/run/${expname}/training/runscript.training.done" ]]; do
echo "Waiting for training..."
sleep 30
nwait=$(( nwait+1 ))
if [[ "${nwait}" -ge 60 ]]; then
echo "Waited to long for training. quit..."
exit 23
fi
done
mamba activate ${EAGLEhome}/conda/envs/anemoi
make inference config=eagle.yaml
mamba deactivate

# 6. Verification
nwait=0
while [[ ! -f "${EAGLEhome}/run/${expname}/inference/runscript.inference.done" ]]; do
echo "Waiting for inference..."
sleep 30
nwait=$(( nwait+1 ))
if [[ "${nwait}" -ge 60 ]]; then
echo "Waited to long for inference. quit..."
exit 24
fi
done
mamba activate ${EAGLEhome}/conda/envs/wxvx
for kind in grid obs
do
for region in global lam
do
make vx-${kind}-${region} config=eagle.yaml &
done
done
wait
# re-check verification
for kind in grid obs
do
for region in global lam
do
script="${EAGLEhome}/run/${expname}/vx/grid2${kind}/${region}/runscript.wxvx-grid2${kind}-${region}"
done_file="${script}.done"
if [[ -f "${script}" ]] && [[ ! -f "${done_file}" ]]; then
sbatch ${script}
wait_for_file "${done_file}" &
fi
done
done
wait
mamba deactivate

# 7. visualization
mamba activate ${EAGLEhome}/conda/envs/visualization
for kind in grid obs
do
for region in global lam
do
make vis-${kind}-${region} config=eagle.yaml &
done
done
wait
mamba deactivate
;;
*)
echo "Unrecognized step: ${step}"
;;
esac

exit 0

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