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[Backfill corrections] Allocate enough shared memory for parallel prediction generation #1827

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Merged
merged 5 commits into from
Apr 12, 2023
Merged

[Backfill corrections] Allocate enough shared memory for parallel prediction generation #1827

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510a11e
log when geo-splitting is over
nmdefries Apr 11, 2023
02c8c40
remove everything in output dir
nmdefries Apr 11, 2023
dd671bf
increase shared memory size to support parallel prediction generation
nmdefries Apr 11, 2023
8875b40
check logs for lack of shared memory error
nmdefries Apr 11, 2023
b55abe8
lower shared memory allocation
nmdefries Apr 11, 2023
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5 changes: 4 additions & 1 deletion backfill_corrections/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,8 @@ run-local: setup-dirs
grep "backfill correction completed successfully" $(LOG_FILE)
grep "scheduled core" $(LOG_FILE) ; \
[ "$$?" -eq 1 ]
grep "SIGBUS" $(LOG_FILE) ; \
[ "$$?" -eq 1 ]

gurobi.lic:
@echo WLSACCESSID=$(GRB_WLSACCESSID) >> $(GRB_LICENSE_FILE)
Expand All @@ -81,6 +83,7 @@ run:
-v "`realpath $(USR_CACHE_DIR)`:/backfill_corrections/${CACHE_DIR}" \
-v "${PWD}"/params.json:/backfill_corrections/params.host.json \
--env GRB_LICENSE_FILE=$(GRB_LICENSE_FILE) \
--shm-size=2gb \
-it "${DOCKER_IMAGE}:${DOCKER_TAG}" \
/bin/bash -c "cp params.host.json params.json && make gurobi.lic && make standardize-dirs && make run-local OPTIONS=\"${OPTIONS}\" LOG_FILE=${LOG_FILE}"

Expand Down Expand Up @@ -124,7 +127,7 @@ standardize-dirs:
$(PYTHON) -m delphi_utils set export_dir $(EXPORT_DIR)

clean:
rm -f $(USR_EXPORT_DIR)/*.csv.gz
rm -rf $(USR_EXPORT_DIR)/*

coverage:
Rscript -e 'covr::package_coverage("delphiBackfillCorrection")'
Expand Down
1 change: 1 addition & 0 deletions backfill_corrections/delphiBackfillCorrection/R/main.R
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Expand Up @@ -60,6 +60,7 @@ run_backfill <- function(df, params,
msg_ts("Splitting data into geo groups")
group_dfs <- group_split(df, geo_value)

msg_ts("Beginning training and/or testing...")
# Build model for each location
apply_fn <- ifelse(params$parallel, mclapply, lapply)
result <- apply_fn(group_dfs, function(subdf) {
Expand Down