diff --git a/examples/mlperf/flux1/megatron/run_and_time.sh b/examples/mlperf/flux1/megatron/run_and_time.sh
index ad0e1c0b0..90d0e43c4 100755
--- a/examples/mlperf/flux1/megatron/run_and_time.sh
+++ b/examples/mlperf/flux1/megatron/run_and_time.sh
@@ -51,6 +51,12 @@ export RESULTS_DIR RUN_INDEX PRIMUS_SEED MLLOG_OUTPUT_FILE
 
 mkdir -p "${RESULTS_DIR}"
 
+# The MLLOG logger opens this append-only, so a relaunch under the same
+# RUN_INDEX concatenates two runs into one file and the compliance checker
+# reports every once-per-run key twice. One file is one run.
+mkdir -p "$(dirname "${MLLOG_OUTPUT_FILE}")"
+: > "${MLLOG_OUTPUT_FILE}"
+
 # --- Cold start -------------------------------------------------------------
 # cache_clear is a claim about the machine, so drop the caches here and report
 # what actually happened rather than what was requested. Dropping caches needs