parsing a very big file into mysql - php

Question

i have a task where i need to parse an extremely big file and write the results into a mysql database. "extremely big" means we are talking about 1.4GB of sort-of-CSV data, totalling in approx 10 million lines of text.
Thing is not "HOW" to do it, but how to do it FAST. my first approach was to just do it in php without any speed optimization and then let it run for a few days until it's done. unfortunately, it's been running for 48 hours straight right now and has processed only 2% of the total file. therefore, that's not an option.
the file format is as follows:
A:1,2
where the amount of comma separated numbers following the ":" can be 0-1000. the example dataset has to go into a table as follows:
| A | 1 |
| A | 2 |
so right now, i did it like this:
$fh = fopen("file.txt", "r");
$line = ""; // buffer for the data
$i = 0; // line counter
$start = time(); // benchmark
while($line = fgets($fh))
{
$i++;
echo "line " . $i . ": ";
//echo $i . ": " . $line . "<br>\n";
$line = explode(":", $line);
if(count($line) != 2 || !is_numeric(trim($line[0])))
{
echo "error: source id [" . trim($line[0]) . "]<br>\n";
continue;
}
$targets = explode(",", $line[1]);
echo "node " . $line[0] . " has " . count($targets) . " links<br>\n";
// insert links in link table
foreach($targets as $target)
{
if(!is_numeric(trim($target)))
{
echo "line " . $i . " has malformed target [" . trim($target) . "]<br>\n";
continue;
}
$sql = "INSERT INTO link (source_id, target_id) VALUES ('" . trim($line[0]) . "', '" . trim($target) . "')";
mysql_query($sql) or die("insert failed for SQL: ". mysql_error());
}
}
echo "<br>\n--<br>\n<br>\nseconds wasted: " . (time() - $start);
this is obviously not optimized for speed in ANY way. any hints for a fresh start? should i switch to another language?

Answer 1

The first optimization would be to insert with a transaction - each 100 or 1000 lines commit and begin a new transaction. Obviously you'd have to use a storage engine that supports transactions.
Then observe the CPU usage with the top command - if you have multiple cores, the mysql process does not do much and the PHP process does much of the work, rewrite the script to accept a parameter that skips n lines from the beginning and only import 10000 lines or so. Then start multiple instances of the script, each with a different starting point.
Third solution would be to convert the file into a CSV with PHP (no INSERT at all, just writing to a file) and the using LOAD DATA INFILE as m4t1t0 suggested.

Answer 2

as promised, attached you'll find the solution i went for in this post. i benchmarked it and it turned out, that it is 40 times (!) faster than the old one :)
sure - there's still much room for optimization, but it's fast enough for me right now :)
$db = mysqli_connect(/*...*/) or die("could not connect to database");
$fh = fopen("data", "r");
$line = ""; // buffer for the data
$i = 0; // line counter
$start = time(); // benchmark timer
$node_ids = array(); // all (source) node ids
mysqli_autocommit($db, false);
while($line = fgets($fh))
{
$i++;
echo "line " . $i . ": ";
$line = explode(":", $line);
$line[0] = trim($line[0]);
if(count($line) != 2 || !is_numeric($line[0]))
{
echo "error: source node id [" . $line[0] . "] - skipping...\n";
continue;
}
else
{
$node_ids[] = $line[0];
}
$targets = explode(",", $line[1]);
echo "node " . $line[0] . " has " . count($targets) . " links\n";
// insert links in link table
foreach($targets as $target)
{
if(!is_numeric($target))
{
echo "line " . $i . " has malformed target [" . trim($target) . "]\n";
continue;
}
$sql = "INSERT INTO link (source_id, target_id) VALUES ('" . $line[0] . "', '" . trim($target) . "')";
mysqli_query($db, $sql) or die("insert failed for SQL: ". $db::error);
}
if($i%1000 == 0)
{
$node_ids = array_unique($node_ids);
foreach($node_ids as $node)
{
$sql = "INSERT INTO node (node_id) VALUES ('" . $node . "')";
mysqli_query($db, $sql);
}
$node_ids = array();
mysqli_commit($db);
mysqli_autocommit($db, false);
echo "committed to database\n\n";
}
}
echo "<br>\n--<br>\n<br>\nseconds wasted: " . (time() - $start);

Answer 3

I find your description rather confusing - and it doesn't match up with the code you've provided.
if(count($line) != 2 || !is_numeric(trim($line[0])))
the trim here is redundant - whitespace doesn't change the behaviour of is_numberic. But you've said aleswhere that the start of the line is a letter - therefore this will always fail.
If you want to speed it up then switch to using stream processing of the input rather than message processing (PHP arrays can be very slow) or use a different language and aggregate the insert statements into multi-line inserts.

Answer 4

I would first just use the script to create a SQL file. Then lock the table using this http://dev.mysql.com/doc/refman/5.0/en/lock-tables.html by placing the appropriate commands at the start/end of the SQL file (could get you script to do this).
Then just use the command tool to inject the SQL into the database (preferably on the machine where the database resides).