lundi 20 avril 2015

PostgreSQL/JooQ bulk insertion performance issues when loading from CSV; how do I improve the process?

For this project, I intend to make a web version and am right now working on making a PostgreSQL (9.x) backend from which the webapp will query.

Right now, what happens is that the tracer generates a zip file with two CSVs in it, load it into an H2 database at runtime whose schema is this (and yes, I'm aware that the SQL could be written a little better):

create table matchers (
    id integer not null,
    class_name varchar(255) not null,
    matcher_type varchar(30) not null,
    name varchar(1024) not null
);

alter table matchers add primary key(id);

create table nodes (
    id integer not null,
    parent_id integer not null,
    level integer not null,
    success integer not null,
    matcher_id integer not null,
    start_index integer not null,
    end_index integer not null,
    time bigint not null
);

alter table nodes add primary key(id);
alter table nodes add foreign key (matcher_id) references matchers(id);
create index nodes_parent_id on nodes(parent_id);
create index nodes_indices on nodes(start_index, end_index);

Now, since the PostgreSQL database will be able to handle more than one trace, I had to add a further table; the schema on the PostgreSQL backend looks like this (less than average SQL alert as well; also, in the parse_info table, the content column contains the full text of the file parsed, in the zip file it is stored separately):

create table parse_info (
    id uuid primary key,
    date timestamp not null,
    content text not null
);

create table matchers (
    parse_info_id uuid references parse_info(id),
    id integer not null,
    class_name varchar(255) not null,
    matcher_type varchar(30) not null,
    name varchar(1024) not null,
    unique (parse_info_id, id)
);

create table nodes (
    parse_info_id uuid references parse_info(id),
    id integer not null,
    parent_id integer not null,
    level integer not null,
    success integer not null,
    matcher_id integer not null,
    start_index integer not null,
    end_index integer not null,
    time bigint not null,
    unique (parse_info_id, id)
);

alter table nodes add foreign key (parse_info_id, matcher_id)
    references matchers(parse_info_id, id);
create index nodes_parent_id on nodes(parent_id);
create index nodes_indices on nodes(start_index, end_index);

Now, what I am currently doing is taking existing zip files and inserting them into a postgresql database; I'm using JooQ and its CSV loading API.

The process is a little complicated... Here are the current steps:

  • a UUID is generated;
  • I read the necessary info from the zip (parse date, input text) and write the record in the parse_info table;
  • I create temporary copies of the CSV in order for the JooQ loading API to be able to use it (see after the code extract as to why);
  • I insert all matchers, then all nodes.

Here is the code:

public final class Zip2Db2
{
    private static final Pattern SEMICOLON = Pattern.compile(";");
    private static final Function<String, String> CSV_ESCAPE
        = TraceCsvEscaper.ESCAPER::apply;

    // Paths in the zip to the different components
    private static final String INFO_PATH = "/info.csv";
    private static final String INPUT_PATH = "/input.txt";
    private static final String MATCHERS_PATH = "/matchers.csv";
    private static final String NODES_PATH = "/nodes.csv";

    // Fields to use for matchers zip insertion
    private static final List<Field<?>> MATCHERS_FIELDS = Arrays.asList(
        MATCHERS.PARSE_INFO_ID, MATCHERS.ID, MATCHERS.CLASS_NAME,
        MATCHERS.MATCHER_TYPE, MATCHERS.NAME
    );

    // Fields to use for nodes zip insertion
    private static final List<Field<?>> NODES_FIELDS = Arrays.asList(
        NODES.PARSE_INFO_ID, NODES.PARENT_ID, NODES.ID, NODES.LEVEL,
        NODES.SUCCESS, NODES.MATCHER_ID, NODES.START_INDEX, NODES.END_INDEX,
        NODES.TIME
    );

    private final FileSystem fs;
    private final DSLContext jooq;
    private final UUID uuid;

    private final Path tmpdir;

    public Zip2Db2(final FileSystem fs, final DSLContext jooq, final UUID uuid)
        throws IOException
    {
        this.fs = fs;
        this.jooq = jooq;
        this.uuid = uuid;

        tmpdir = Files.createTempDirectory("zip2db");
    }

    public void removeTmpdir()
        throws IOException
    {
        // From java7-fs-more (http://ift.tt/1GcqTYT)
        MoreFiles.deleteRecursive(tmpdir, RecursionMode.KEEP_GOING);
    }

    public void run()
    {
        time(this::generateMatchersCsv, "Generate matchers CSV");
        time(this::generateNodesCsv, "Generate nodes CSV");
        time(this::writeInfo, "Write info record");
        time(this::writeMatchers, "Write matchers");
        time(this::writeNodes, "Write nodes");
    }

    private void generateMatchersCsv()
        throws IOException
    {
        final Path src = fs.getPath(MATCHERS_PATH);
        final Path dst = tmpdir.resolve("matchers.csv");

        try (
            final Stream<String> lines = Files.lines(src);
            final BufferedWriter writer = Files.newBufferedWriter(dst,
                StandardOpenOption.CREATE_NEW);
        ) {
            // Throwing below is from throwing-lambdas
            // (http://ift.tt/1wjtgOE)
            lines.map(this::toMatchersLine)
                .forEach(Throwing.consumer(writer::write));
        }
    }

    private String toMatchersLine(final String input)
    {
        final List<String> parts = new ArrayList<>();
        parts.add('"' + uuid.toString() + '"');
        Arrays.stream(SEMICOLON.split(input, 4))
            .map(s -> '"' + CSV_ESCAPE.apply(s) + '"')
            .forEach(parts::add);
        return String.join(";", parts) + '\n';
    }

    private void generateNodesCsv()
        throws IOException
    {
        final Path src = fs.getPath(NODES_PATH);
        final Path dst = tmpdir.resolve("nodes.csv");

        try (
            final Stream<String> lines = Files.lines(src);
            final BufferedWriter writer = Files.newBufferedWriter(dst,
                StandardOpenOption.CREATE_NEW);
        ) {
            lines.map(this::toNodesLine)
                .forEach(Throwing.consumer(writer::write));
        }
    }

    private String toNodesLine(final String input)
    {
        final List<String> parts = new ArrayList<>();
        parts.add('"' + uuid.toString() + '"');
        SEMICOLON.splitAsStream(input)
            .map(s -> '"' + CSV_ESCAPE.apply(s) + '"')
            .forEach(parts::add);
        return String.join(";", parts) + '\n';
    }

    private void writeInfo()
        throws IOException
    {
        final Path path = fs.getPath(INFO_PATH);

        try (
            final BufferedReader reader = Files.newBufferedReader(path);
        ) {
            final String[] elements = SEMICOLON.split(reader.readLine());

            final long epoch = Long.parseLong(elements[0]);
            final Instant instant = Instant.ofEpochMilli(epoch);
            final ZoneId zone = ZoneId.systemDefault();
            final LocalDateTime time = LocalDateTime.ofInstant(instant, zone);

            final ParseInfoRecord record = jooq.newRecord(PARSE_INFO);

            record.setId(uuid);
            record.setContent(loadText());
            record.setDate(Timestamp.valueOf(time));

            record.insert();
        }
    }

    private String loadText()
        throws IOException
    {
        final Path path = fs.getPath(INPUT_PATH);

        try (
            final BufferedReader reader = Files.newBufferedReader(path);
        ) {
            return CharStreams.toString(reader);
        }
    }

    private void writeMatchers()
        throws IOException
    {
        final Path path = tmpdir.resolve("matchers.csv");

        try (
            final BufferedReader reader = Files.newBufferedReader(path);
        ) {
            jooq.loadInto(MATCHERS)
                .onErrorAbort()
                .loadCSV(reader)
                .fields(MATCHERS_FIELDS)
                .separator(';')
                .execute();
        }
    }

    private void writeNodes()
        throws IOException
    {
        final Path path = tmpdir.resolve("nodes.csv");

        try (
            final BufferedReader reader = Files.newBufferedReader(path);
        ) {
            jooq.loadInto(NODES)
                .onErrorAbort()
                .loadCSV(reader)
                .fields(NODES_FIELDS)
                .separator(';')
                .execute();
        }
    }

    private void time(final ThrowingRunnable runnable, final String description)
    {
        System.out.println(description + ": start");
        final Stopwatch stopwatch = Stopwatch.createStarted();
        runnable.run();
        System.out.println(description + ": done (" + stopwatch.stop() + ')');
    }

    public static void main(final String... args)
        throws IOException
    {
        if (args.length != 1) {
            System.err.println("missing zip argument");
            System.exit(2);
        }

        final Path zip = Paths.get(args[0]).toRealPath();

        final UUID uuid = UUID.randomUUID();
        final DSLContext jooq = PostgresqlTraceDbFactory.defaultFactory()
            .getJooq();

        try (
            final FileSystem fs = MoreFileSystems.openZip(zip, true);
        ) {
            final Zip2Db2 zip2Db = new Zip2Db2(fs, jooq, uuid);
            try {
                zip2Db.run();
            } finally {
                zip2Db.removeTmpdir();
            }
        }
    }
}

Now, here is my first problem... It is much slower than loading into H2. Here is a timing for a CSV containing 620 matchers and 45746 nodes:

Generate matchers CSV: start
Generate matchers CSV: done (45.26 ms)
Generate nodes CSV: start
Generate nodes CSV: done (573.2 ms)
Write info record: start
Write info record: done (311.1 ms)
Write matchers: start
Write matchers: done (4.192 s)
Write nodes: start
Write nodes: done (22.64 s)

Give or take, and forgetting the part about writing specialized CSVs (see below), that is 25 seconds. Loading this into an on-the-fly, disk-based H2 database takes less than 5 seconds!

The other problem I have is that I have to write dedicated CSVs; it appears that the CSV loading API is not really flexible in what it accepts, and I have, for instance, to turn this line:

328;SequenceMatcher;COMPOSITE;token

into this:

"some-randome-uuid-here";"328";"SequenceMatcher";"COMPOSITE";"token"

But my biggest problem is in fact that this zip is pretty small. For instance, I have a zip with not 620, but 1532 matchers, and not 45746 nodes, but more than 34 million nodes; even if we dismiss the CSV generation time (the original nodes CSV is 1.2 GiB), since it takes 20 minutes for H2 injection, multiplying this by 5 gives a time some point south of 1h30mn, which is a lot!

All in all, the process is quite inefficient at the moment...


Now, in the defence of PostgreSQL:

  • constraints on the PostgreSQL instance are much higher than those on the H2 instance: I don't need a UUID in generated zip files;
  • H2 is tuned "insecurely" for writes: jdbc:h2:/path/to/db;LOG=0;LOCK_MODE=0;UNDO_LOG=0;CACHE_SIZE=131072.

Still, this difference in insertion times seems a little excessive, and I am quite sure that it can be better. But I don't know where to start.

Also, I am aware that PostgreSQL has a dedicated mechanism to load from CSVs, but here the CSVs are in a zip file to start with, and I'd really like to avoid having to create a dedicated CSV as I am currently doing... Ideally I'd like to read line by line from the zip directly (which is what I do for H2 injection), transform the line and write into the PostgreSQL schema.

Finally, I am also aware that I currently do not disable constraints on the PostgreSQL schema before insertion; I have yet to try this (will it make a difference?).

So, what do you suggest I do to improve the performance?

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