MIT-LCP
Troubleshooting Slow MIMIC-III gz Data Import into PostgreSQL Database
I imported the mimic3 data into the database using postpreSQL and 7zip commands:
DROP DATABASE IF EXISTS mimic;
CREATE DATABASE mimic OWNER postgres;
\c mimic;
CREATE SCHEMA mimiciii;
set search_path to mimiciii;
\i D:/postgraduate/doctor/second/mimic3/postgres_create_tables.sql
\set ON_ERROR_STOP 1
\set mimic_data_dir 'D:/postgraduate/doctor/second/mimic3'
\i D:/postgraduate/doctor/second/mimic3/postgres_load_data_7zip.sql
After using these commands, my program stopped updating and got stuck importing the chartevent table for a long time:
mimic=# \i D:/postgraduate/doctor/second/mimic3/postgres_load_data_7zip.sql
COPY 58976
COPY 34499
COPY 7567
My machine hardware is win10, 16GB memory, no GPU, the hard disk storing the csv.gz data has 50GB free space. Is this normal? Are there ways to see the progress or diagnose if it's working correctly?
Hi! I think this is normal. This exact behaviour is described here: https://github.com/MIT-LCP/mimic-code/tree/main/mimic-iii/buildmimic/postgres
Chartevents is a large table and it will take a while to load the data
I have run it sucessfully. However, the chartevent seems to copy 0.
I used the solution in this https://github.com/MIT-LCP/mimic-code/issues/182 issue to count items in chartevents.
SELECT COUNT(*) FROM chartevents;
However, it run a long time and got stuck.
I have run it sucessfully. However, the chartevent seems to copy 0.
It looks to me like the table built successfully. As I remember, postgres reports zero rows due to the partitioning.
Side note, but I'd recommend working with the data on Google BigQuery rather than building the database locally: https://mimic.mit.edu/docs/gettingstarted/cloud/bigquery/
