51 lines
1.9 KiB
Bash
Executable file
51 lines
1.9 KiB
Bash
Executable file
#!/usr/bin/env bash
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#SBATCH --time=4:00:00
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#SBATCH --mem=4G
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# Batch script to run on sc.uni-leipzig.de cluster, i used
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# > sbatch -a "1-$(cat acyclic.list | wc -l)" ./scripts/sc-batch.sh
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# or
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# > sbatch -a "1-14999" --mail-type BEGIN,END,FAIL --output 'slurms/slurm-%A_%a.out' --job-name "ABA2SAT-$(date)" ./scripts/sc-batch.sh
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# > sbatch -a "15000-22680" --mail-type BEGIN,END,FAIL --output 'slurms/slurm-%A_%a.out' --job-name "ABA2SAT-$(date)" ./scripts/sc-batch.sh
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# for when there's more than 15k files..
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# Somehow all paths used in spawned processes need to be absolute,
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# there's probably a good explanation, but I don't have it
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FILE_LIST=acyclic.list
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# Calculate the task index based on the SLURM array task ID and an optional offset.
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# The OFFSET variable is set to 0 if it is not already defined.
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NR="$(("${OFFSET:=0}" + "$SLURM_ARRAY_TASK_ID"))"
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# Pick line `$SLURM_ARRAY_TASK_ID` from the FILE_LIST
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# This will probably cause issues if more processes are allocated
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# than lines in the FILE_LIST, but who knows
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file="$(awk "NR == $NR" "$FILE_LIST")"
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basefile="$(basename "$file")"
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# Read the extra argument
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arg=$(cat "$(pwd)/$file.asm")
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# Make sure we get all the data in one central place
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OUTPUT_DIR="output"
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# Number of loops to look for
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MAX_LOOPS=18446744073709551615
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# Run singularity, this is basically docker
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# We mount /in and /out inside the container and use that to read and write
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# validate.sif is a converted format, easily done with
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# > singularity build validate.sif docker-archive://<your-docker-image.tar.gz>
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# The docker image was build using
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# > nix bundle .#validate --bundler github:NixOS/bundlers#toDockerImage
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# on my local machine to create an agnostic package that could run on the cluster
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mkdir -p "$(pwd)/$OUTPUT_DIR"
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singularity run \
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--env OUTPUT_DIR=/out \
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--bind "$(pwd)/acyclic:/in:ro" \
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--bind "$(pwd)/$OUTPUT_DIR:/out" \
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validate.sif \
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validate --file "/in/$basefile" --arg "$arg" --time --problem dc-co --max-loops "$MAX_LOOPS"
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