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java – Xodus producing a huge file when passing from key-value (Environment) to relational (Entity)-Exceptionshub

Posted by: admin February 25, 2020 Leave a comment

Questions:

I originally created a key-value database with Xodus Entity that created a small, 2GB database:

public static void main(String[] args) throws Exception{

        if (args.length != 2){
            throw new Exception("Argument missing. Current number of arguments: " + args.length); 
        }

        long offset = Long.parseLong(args[0]);
        long chunksize = Long.parseLong(args[1]);

        Path pathBabelNet = Paths.get("/mypath/BabelNet-API-3.7/config");
        BabelNetLexicalizationDataSource dataSource = new BabelNetLexicalizationDataSource(pathBabelNet);
        Map<String, List<String>> data = new HashMap<String, List<String>>();
        data = dataSource.getDataChunk(offset, chunksize);

        jetbrains.exodus.env.Environment env = Environments.newInstance(".myAppData");
        final Transaction txn = env.beginTransaction();
        Store store = env.openStore("xodus-lexicalizations", StoreConfig.WITHOUT_DUPLICATES, txn);

        for (Map.Entry<String, List<String>> entry : data.entrySet()) {
            String key = entry.getKey();
            String value = entry.getValue().get(0);

            store.put(txn, StringBinding.stringToEntry(key), StringBinding.stringToEntry(value));
        }

        txn.commit();
        env.close();

    }

I used a batch script to do this in chunks:

#!/bin/bash

START_TIME=$SECONDS

chunksize=50000

for ((offset=0; offset<165622128;))
do
    echo $offset;
    java -Xmx10g -jar /path/to/jar.jar $offset $chunksize
    offset=$((offset+(chunksize*12)))
done

ELAPSED_TIME=$(($SECONDS - $START_TIME))

echo $ELAPSED_TIME;

Now I changed it so it is relational:

public static void main(String[] args) throws Exception{

        if (args.length != 2){
            throw new Exception("Argument missing. Current number of arguments: " + args.length); 
        }

        long offset = Long.parseLong(args[0]);
        long chunksize = Long.parseLong(args[1]);

        Path pathBabelNet = Paths.get("/mypath/BabelNet-API-3.7/config");
        BabelNetLexicalizationDataSource dataSource = new BabelNetLexicalizationDataSource(pathBabelNet);
        Map<String, List<String>> data = new HashMap<String, List<String>>();
        data = dataSource.getDataChunk(offset, chunksize);

        PersistentEntityStore store = PersistentEntityStores.newInstance("lexicalizations-test");
        final StoreTransaction txn = store.beginTransaction(); 

        Entity synsetID;
        Entity lexicalization;
        String id;

        for (Map.Entry<String, List<String>> entry : data.entrySet()) {
            String key = entry.getKey();
            String value = entry.getValue().get(0);

            synsetID = txn.newEntity("SynsetID");
            synsetID.setProperty("synsetID", key);

            lexicalization = txn.newEntity("Lexicalization");
            lexicalization.setProperty("lexicalization", value);

            lexicalization.addLink("synsetID", synsetID);
            synsetID.addLink("lexicalization", lexicalization);

            txn.flush();
        }

        txn.commit();
    }

And this created a file over 17GB and it only stopped because I ran out of memory. I understand that it will be larger because it has to store the links, among other things, but ten times bigger? What am I doing wrong?

How to&Answers:

For some reason removing the txn.flush() fixes everything. Now it’s just 5.5GB.