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Last Commit
Apr. 21, 2017
Created
Mar. 25, 2015

nvParse

Parsing CSV files with GPU

Parsing delimiter-separated files is a common task in data processing. The regular way of extracting the columns from a text file is to use strtok function :

char * p = strtok(line, "|");
while (p != NULL)
{
    printf ("%s\n",p);
    p = strtok (NULL, "|");
}

However this method of parsing is CPU bound because

  • it doesn't take advantage of multiple cores of modern CPUs.

  • memory bandwidth limitations

This is how the same task can be done using a GPU :

auto break_cnt = thrust::count(d_readbuff.begin(), d_readbuff.end(), '\n');
thrust::device_vector<int> dev_pos(break_cnt);
thrust::copy_if(thrust::make_counting_iterator(0),
                thrust::make_counting_iterator(bytes_read-1),
                d_readbuff.begin(), dev_pos.begin(), _1 == '\n');

The first line counts the number of lines in a buffer (assuming that file is read into memory and copied to gpu buffer d_readbuff). The second line creates a vector in gpu memory that will hold the positions of new line characters. The last line compares the characters in a buffer to new line character and, if a match is found, copies the position of the character to dev_pos vector.

Now that we know the starting positions of every line in a buffer, we can launch a gpu procedure that will parse the lines using several thousands gpu cores :

thrust::counting_iterator<unsigned int> begin(0);
parse_functor ff(...); // examples of call's parameters are in test.cu file
thrust::for_each(begin, begin + break_cnt, ff);

As a result we get the needed columns in separate arrays in gpu memory and can copy them to host memory. Or convert them to binary values using relevant gpu procedures :

gpu_atoll atoll_ff(...);
thrust::for_each(begin, begin + break_cnt, atoll_ff);

Benchmarks !

Hardware : PC with one Intel i3-4130, 16GB of RAM, one 2TB hard drive and GTX Titan

File : 750MB lineitem.tbl text file (6001215 lines)

Parsing 1 field using CPU :

$ time cut -d "|" -f 6 lineitem.tbl > /dev/null

real 0m28.764s

Parsing 11 fields using hand-written program with strtok : (no threads, no memory-mapped file)

14.5s

Parsing 11 fields using GPU :

$ time ./test

0.77s

And the actual gpu parsing part is done in just 0.25 seconds.

P.S. Thanks to Nicolas Guillemot for suggestion on memory-mapping files.