Add exact duplicates checking scripts

Author: ZJaume

scripts/check-duplicates.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+set -euo pipefail
+source .env
+source .checks
+
+L=$1
+dir=$2
+
+INDEX=1-$(ls -1 $WORKSPACE/$dir/$L/${L}_*.zst | sed -E 's#.*/\w{2,3}_([0-9]+)\.jsonl\.zst#\1#' | sort -n | tail -1)
+sbatch -J $L-findups-$dir --array=$INDEX scripts/check-duplicates.slurm $L $dir

scripts/check-duplicates.slurm

@@ -0,0 +1,19 @@
+#!/bin/bash
+#SBATCH --job-name=findups-fix
+#SBATCH --partition="small"
+#SBATCH --time=72:00:00
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=8
+#SBATCH --mem-per-cpu=1750
+#SBATCH --output=logs/%x.out
+module load cray-python/3.9.12.1
+source .env
+set -euo pipefail
+module load parallel
+
+L=$1
+dir=$2
+
+zstdcat $WORKSPACE/$dir/$L/${L}_$SLURM_ARRAY_TASK_ID.jsonl.zst \
+| parallel --pipe -j4 jq ".text" \
+| python scripts/exactdups.py

scripts/exactdups.py

@@ -0,0 +1,14 @@
+from xxhash import xxh64_intdigest
+import sys
+
+hashtable = set()
+for line in sys.stdin:
+    digest = xxh64_intdigest(line.rstrip())
+
+    if digest in hashtable:
+        sys.stderr.write("Found duplicate!\n")
+        sys.exit(1)
+
+    hashtable.add(digest)
+
+sys.stderr.write("No duplicates found\n")