"(...) points to uninitialised byte(s) (...) " under valgrind

[dvalenzu]

Runing the code under valgrind, store_to_file(...) may lead to a:

"Syscall param writev(vector[...]) points to uninitialised byte(s) (...) "

The code that can trigger the problem is: //

include <sdsl/suffix_trees.hpp>

include

using namespace sdsl; using namespace std;

int main() { csa_wt<wt_huff<rrr_vector<127> >, 512, 1024> index; string index_filename = "tmp_file"; construct(index, "problem_input", 1); std::cout << "Index constructed" << std::endl; store_to_file(index, index_filename); std::cout << "Done." << std::endl; } //

And an input that triggers it is here: https://www.cs.helsinki.fi/u/dvalenzu/tmp/bug/problem_input I run into this on release 2.0.3, but I have just verified that the behavior is the same in the latest release.

If you cannot reproduce it I'll be happy to provide more details,

Best, Daniel

[simongog]

Hi Daniel, thanks for letting me know. Best, Simon

[mpetri]

If I run this code:

#include "sdsl/suffix_arrays.hpp"

using namespace sdsl;
using namespace std;

int main()
{
        csa_wt<> index;
        string index_filename = "tmp_file";
        construct(index, "problem_input", 1);
        std::cout << "Index constructed" << std::endl;
        store_to_file(index, index_filename);
        std::cout << "Done." << std::endl;
}

I don't get any leaks:

[mpetri@haathee ../examples]$ valgrind ./test.x
==24059== Memcheck, a memory error detector
==24059== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al.
==24059== Using Valgrind-3.11.0 and LibVEX; rerun with -h for copyright info
==24059== Command: ./test.x
==24059==
Index constructed
Done.
==24059==
==24059== HEAP SUMMARY:
==24059==     in use at exit: 72,704 bytes in 1 blocks
==24059==   total heap usage: 1,452 allocs, 1,451 frees, 6,882,262 bytes allocated
==24059==
==24059== LEAK SUMMARY:
==24059==    definitely lost: 0 bytes in 0 blocks
==24059==    indirectly lost: 0 bytes in 0 blocks
==24059==      possibly lost: 0 bytes in 0 blocks
==24059==    still reachable: 72,704 bytes in 1 blocks
==24059==         suppressed: 0 bytes in 0 blocks
==24059== Rerun with --leak-check=full to see details of leaked memory
==24059==
==24059== For counts of detected and suppressed errors, rerun with: -v
==24059== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)

[dvalenzu]

Hi, I'm sory that my code was posted without proper formatting, the actual code is here https://www.cs.helsinki.fi/u/dvalenzu/tmp/bug/construct-in-memory.cpp It is slightly different than yours (using a specific csa / wt_huff / rrr / 127, 512, 1024 .... (in the process of realizing why your code didn't throw the error I made another setup to reproduce it in a CI enviroment here: https://gitlab.com/dvalenzu/sdsl_border_case/builds/2364218 ) Best, Daniel

[mpetri]

with this new example, I get the following valgrind output:

[mpetri@umelb-168-918 ../examples]$ valgrind ./construct-in-memory.x 
==2224== Memcheck, a memory error detector
==2224== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al.
==2224== Using Valgrind-3.11.0 and LibVEX; rerun with -h for copyright info
==2224== Command: ./construct-in-memory.x
==2224== 
==2224== Conditional jump or move depends on uninitialised value(s)
==2224==    at 0x41470E: bool sdsl::load_vector_from_file<sdsl::int_vector<(unsigned char)8> >(sdsl::int_vector<(unsigned char)8>&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned char, unsigned char) (in /home/mpetri/data/dev/sdsl-lite/examples/construct-in-memory.x)
==2224==    by 0x4193BF: void sdsl::construct<sdsl::csa_wt<sdsl::wt_pc<sdsl::huff_shape, sdsl::rrr_vector<(unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::rank_support_rrr<(unsigned char)1, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::select_support_rrr<(unsigned char)1, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::select_support_rrr<(unsigned char)0, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::byte_tree<false> >, 512u, 1024u, sdsl::sa_order_sa_sampling<(unsigned char)0>, sdsl::isa_sampling<(unsigned char)0>, sdsl::byte_alphabet> >(sdsl::csa_wt<sdsl::wt_pc<sdsl::huff_shape, sdsl::rrr_vector<(unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::rank_support_rrr<(unsigned char)1, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::select_support_rrr<(unsigned char)1, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::select_support_rrr<(unsigned char)0, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::byte_tree<false> >, 512u, 1024u, sdsl::sa_order_sa_sampling<(unsigned char)0>, sdsl::isa_sampling<(unsigned char)0>, sdsl::byte_alphabet>&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, sdsl::cache_config&, unsigned char, sdsl::csa_tag) (in /home/mpetri/data/dev/sdsl-lite/examples/construct-in-memory.x)
==2224==    by 0x41A128: void sdsl::construct<sdsl::csa_wt<sdsl::wt_pc<sdsl::huff_shape, sdsl::rrr_vector<(unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::rank_support_rrr<(unsigned char)1, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::select_support_rrr<(unsigned char)1, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::select_support_rrr<(unsigned char)0, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::byte_tree<false> >, 512u, 1024u, sdsl::sa_order_sa_sampling<(unsigned char)0>, sdsl::isa_sampling<(unsigned char)0>, sdsl::byte_alphabet> >(sdsl::csa_wt<sdsl::wt_pc<sdsl::huff_shape, sdsl::rrr_vector<(unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::rank_support_rrr<(unsigned char)1, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::select_support_rrr<(unsigned char)1, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::select_support_rrr<(unsigned char)0, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::byte_tree<false> >, 512u, 1024u, sdsl::sa_order_sa_sampling<(unsigned char)0>, sdsl::isa_sampling<(unsigned char)0>, sdsl::byte_alphabet>&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned char) (in /home/mpetri/data/dev/sdsl-lite/examples/construct-in-memory.x)
==2224==    by 0x404756: main (in /home/mpetri/data/dev/sdsl-lite/examples/construct-in-memory.x)
==2224== 
==2224== Conditional jump or move depends on uninitialised value(s)
==2224==    at 0x414725: bool sdsl::load_vector_from_file<sdsl::int_vector<(unsigned char)8> >(sdsl::int_vector<(unsigned char)8>&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned char, unsigned char) (in /home/mpetri/data/dev/sdsl-lite/examples/construct-in-memory.x)
==2224==    by 0x4193BF: void sdsl::construct<sdsl::csa_wt<sdsl::wt_pc<sdsl::huff_shape, sdsl::rrr_vector<(unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::rank_support_rrr<(unsigned char)1, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::select_support_rrr<(unsigned char)1, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::select_support_rrr<(unsigned char)0, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::byte_tree<false> >, 512u, 1024u, sdsl::sa_order_sa_sampling<(unsigned char)0>, sdsl::isa_sampling<(unsigned char)0>, sdsl::byte_alphabet> >(sdsl::csa_wt<sdsl::wt_pc<sdsl::huff_shape, sdsl::rrr_vector<(unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::rank_support_rrr<(unsigned char)1, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::select_support_rrr<(unsigned char)1, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::select_support_rrr<(unsigned char)0, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::byte_tree<false> >, 512u, 1024u, sdsl::sa_order_sa_sampling<(unsigned char)0>, sdsl::isa_sampling<(unsigned char)0>, sdsl::byte_alphabet>&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, sdsl::cache_config&, unsigned char, sdsl::csa_tag) (in /home/mpetri/data/dev/sdsl-lite/examples/construct-in-memory.x)
==2224==    by 0x41A128: void sdsl::construct<sdsl::csa_wt<sdsl::wt_pc<sdsl::huff_shape, sdsl::rrr_vector<(unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::rank_support_rrr<(unsigned char)1, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::select_support_rrr<(unsigned char)1, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::select_support_rrr<(unsigned char)0, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::byte_tree<false> >, 512u, 1024u, sdsl::sa_order_sa_sampling<(unsigned char)0>, sdsl::isa_sampling<(unsigned char)0>, sdsl::byte_alphabet> >(sdsl::csa_wt<sdsl::wt_pc<sdsl::huff_shape, sdsl::rrr_vector<(unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::rank_support_rrr<(unsigned char)1, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::select_support_rrr<(unsigned char)1, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::select_support_rrr<(unsigned char)0, (unsigned short)127, sdsl::int_vector<(unsigned char)0>, (unsigned short)32>, sdsl::byte_tree<false> >, 512u, 1024u, sdsl::sa_order_sa_sampling<(unsigned char)0>, sdsl::isa_sampling<(unsigned char)0>, sdsl::byte_alphabet>&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned char) (in /home/mpetri/data/dev/sdsl-lite/examples/construct-in-memory.x)
==2224==    by 0x404756: main (in /home/mpetri/data/dev/sdsl-lite/examples/construct-in-memory.x)
==2224== 
Index construced
Done.
==2224== 
==2224== HEAP SUMMARY:
==2224==     in use at exit: 72,704 bytes in 1 blocks
==2224==   total heap usage: 441 allocs, 440 frees, 6,497,337 bytes allocated
==2224== 
==2224== LEAK SUMMARY:
==2224==    definitely lost: 0 bytes in 0 blocks
==2224==    indirectly lost: 0 bytes in 0 blocks
==2224==      possibly lost: 0 bytes in 0 blocks
==2224==    still reachable: 72,704 bytes in 1 blocks
==2224==         suppressed: 0 bytes in 0 blocks
==2224== Rerun with --leak-check=full to see details of leaked memory
==2224== 
==2224== For counts of detected and suppressed errors, rerun with: -v
==2224== Use --track-origins=yes to see where uninitialised values come from
==2224== ERROR SUMMARY: 2 errors from 2 contexts (suppressed: 0 from 0)