DininduSenanayake
commented
2 months ago I think the standard out coming out of #35 can be used to trap the progress . Perhaps we can use tput command to create a basic progress bar ?
#!/bin/bash
#SBATCH --job-name=apsim_models
#SBATCH --output=slurmlogs/%j.out
#SBATCH --cpus-per-task=4
#SBATCH --mem=8G
#SBATCH --time=16:00:00
module load Apptainer
export APPTAINER_BIND="/agr/scratch,/agr/persist"
export APPTAINER_CMD="apptainer exec /agr/persist/projects/2024_apsim_improvements/apsim-simulations/container/apsim-2024.09.7579.0.aimg"
# Create FAILED directory if it doesn't exist
mkdir -p FAILED
consecutive_failures=0
max_consecutive_failures=10
# Count total number of .txt files (excluding ExampleConfig.txt)
total_files=$(find . -maxdepth 1 -name "*.txt" ! -name "ExampleConfig.txt" | wc -l)
processed_files=0
# Function to update progress bar
update_progress() {
local progress=$((processed_files * 100 / total_files))
local completed=$((progress / 2))
local remaining=$((50 - completed))
printf "\rProgress: [%-${completed}s%-${remaining}s] %d%%" "$(printf '#%.0s' $(seq 1 $completed))" "$(printf ' %.0s' $(seq 1 $remaining))" "$progress"
}
# Function to process a file
process_file() {
local file="$1"
if ${APPTAINER_CMD} Models --cpu-count ${SLURM_CPUS_PER_TASK} --apply "$file"; then
echo "Successfully processed $file"
return 0
else
echo "Failed to process $file"
return 1
fi
}
# Run command for all .txt files, excluding ExampleConfig.txt
for file in *.txt; do
if [ -f "$file" ] && [ "$file" != "ExampleConfig.txt" ]; then
if process_file "$file"; then
consecutive_failures=0
else
mv "$file" FAILED/
((consecutive_failures++))
if [ $consecutive_failures -ge $max_consecutive_failures ]; then
echo "Error: $max_consecutive_failures consecutive failures reached. Terminating job." >&2
exit 1
fi
fi
((processed_files++))
update_progress
fi
done
echo -e "\nProcessing completed."
-
At the beginning of the script, It counts the total number of .txt files (excluding ExampleConfig.txt) in the current directory:
total_files=$(find . -maxdepth 1 -name "*.txt" ! -name "ExampleConfig.txt" | wc -l) processed_files=0 -
function
update_progress()calculates and displays the progress bar:update_progress() { local progress=$((processed_files * 100 / total_files)) local completed=$((progress / 2)) local remaining=$((50 - completed)) printf "\rProgress: [%-${completed}s%-${remaining}s] %d%%" "$(printf '#%.0s' $(seq 1 $completed))" "$(printf ' %.0s' $(seq 1 $remaining))" "$progress" }This function creates a 50-character wide progress bar and displays the percentage of completion.
-
In the main loop, we increment the
processed_filescounter and callupdate_progressafter each file is processed:((processed_files++)) update_progress -
At the end of the script, we add a newline character to ensure the final output is on a new line:
echo -e "\nProcessing completed."
This progress bar will update in real-time as each file is processed, A few notes about this implementation:
-
The progress bar updates on the same line using the
\r(carriage return) character, which works well in most terminal environments. -
This implementation assumes that processing each file takes roughly the same amount of time. If processing times vary significantly between files, the progress bar might not accurately represent the time remaining.
At the moment, standard out coming out from https://github.com/DininduSenanayake/APSIM-eri-mahuika/blob/main/4-create-apsimx-files/create_apsimx.sl doesn't have any verbose levels which means it is rather difficult to keep track of the progress. Particularly when it is being done for thousands of files. Therefore, it will be ideal to have an ASCII level progress bar