Custom HPC software & tools from Wirawan. Primarily tailored toward ODU HPC sytems.
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#!/bin/bash
#
# GAUSSIAN09 SUBMISSION SCRIPT
#
# Author: ODU Research Computing Services
#
# Usage: g09slurm INPUT_FILE.com [OUTPUT_FILE.out] [START_TIME]
set -e
usage () {
echo "Usage: g09slurm INPUT_FILE.com [OUTPUT_FILE.out] [START_TIME]"
echo "Please refer to https://wiki.hpc.odu.edu/Software/Gaussian for more information"
}
if [ "$1" == --help ]; then
echo "g09slurm - Gaussian09 submission script"
usage
exit 0
fi
if [ $# -lt 1 ]; then
echo "Error: Missing Gaussian G09 input file"
usage >&2
exit 1
fi
input_file=$1
output_file=$2
begin_date=$3
if [ ! -r $1 ]; then
echo "Error: Unable to open Gaussian G09 input file"
usage >&2
exit 2
fi
if [ -z "$output_file" ]; then
output_file=${input_file%.[Cc][Oo][Mm]}.out
fi
# Detect & support multicore Gaussian calculations
ncpus=$(grep -E '^ *%' "$1" | grep -i -w nprocshared | awk '{ L = tolower($0); print gensub("%nprocshared=","","G", L)}')
if [ -z "$ncpus" ]; then
ncpus=$(grep -E '^ *%' "$1" | grep -i -w 'nprocs?' | awk '{ L = tolower($0); print gensub("%nprocs?=","","G", L)}')
fi
if [ -z "$ncpus" ]; then
ncpus=1
fi
# Detect & support custom directories
collect_scratch_objects () {
# Usage: cat $FILE | collect_scratch_objects LINK0_KEYWORD
# Parses line like this:
# %RWF=/dalton/s0/
# %RWF=/dalton/s0/,4GB,/scratch/,3GB,/temp/s0/my_job,-1
# and prints the scratch dirs/files found to the standard output
#
# The first argument is the keyword to look for, and it must
# be must be in lowercase
local KWD="$1"
awk 'tolower($0) ~ /^ *% *'$KWD' *=/ {
A = $0
# Erase keyword
sub(/^[^=]*= */, "", A)
# Erase comment, if any
sub(/ *\!.*$/, "", A)
Args_count = split(A, Args, ",")
# print out the directory/file parts
for (i = 1; i <= Args_count; ++i)
print(Args[i])
}'
}
create_scratch_dirs () {
# Usage: create_scratch_dir "$scratch_dir_lines" LINK0_KEYWORD
local SCR_DIRS="$1"
local KWD="$2"
if [ -n "$SCR_DIRS" ]; then
echo "Found scratch dirs for $KWD:"
local IFS=$'\n'
for D in $SCR_DIRS; do
echo " $D"
case "$D" in
*/)
mkdir -p -v "$D"
;;
*)
mkdir -p -v "$(dirname "$D")"
;;
esac
done
fi
}
rwf_scratch_dirs=$(cat "$input_file" | collect_scratch_objects rwf)
create_scratch_dirs "$rwf_scratch_dirs" "RWF files"
int_scratch_dirs=$(cat "$input_file" | collect_scratch_objects int)
create_scratch_dirs "$int_scratch_dirs" "INT files"
d2e_scratch_dirs=$(cat "$input_file" | collect_scratch_objects d2e)
create_scratch_dirs "$d2e_scratch_dirs" "D2E files"
# Allow delayed start
if [ -z "$begin_date" ]; then
begin_date=now
fi
if [ -f "$output_file" ]; then
read -p "Output file $output_file already exists, do you want overwrite? [N/y]" confirm
if [ "$confirm" = "y" ]; then
> "$output_file"
else
echo "Cancelling job submission" >&2
exit 1
fi
fi
CLUSTER=$(cat /etc/cluster)
case "$CLUSTER" in
wahab)
SBATCH=/shared/apps/common/slurm/current/bin/sbatch
;;
turing)
SBATCH=/cm/shared/applications/slurm/current/bin/sbatch
;;
*)
echo "Error: unsupported cluster. Please contact itshelp@odu.edu for assistance." >&2
exit 2
;;
esac
GAUSSIAN_SCRIPT=/cm/shared/apps/gaussian/g09revD.01/script/g09/script/g09.slurm
"$SBATCH" \
--job-name="G09-$input_file" \
--ntasks=1 \
--cpus-per-task=$ncpus \
--output="$output_file" \
--begin=$begin_date \
"$GAUSSIAN_SCRIPT" "$input_file"