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Valgrind finds Invalid read (means bad memory access) in BackwardSearchTest.NoVariants1 #28

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iqbal-lab opened this issue Jul 31, 2016 · 5 comments
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Valgrind finds Invalid read (means bad memory access) in BackwardSearchTest.NoVariants1 #28

iqbal-lab opened this issue Jul 31, 2016 · 5 comments
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@ffranr @iqbal-lab @sm0179

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iqbal-lab commented Jul 31, 2016 •
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At this commit:

[master a7c1d1e] Fixed bugs in references to data files, and fixed buggy mask input file.

I ran valgrind on the fast unit tests:

valgrind --leak-check=yes ./unittest_bidir_search_bwd_fwd

[==========] Running 9 tests from 1 test case.
[----------] Global test environment set-up.
[----------] 9 tests from BackwardSearchTest
[ RUN ] BackwardSearchTest.NoVariants1
==78121== Invalid read of size 1
==78121== at 0x43547E: bidir_search_fwd(sdsl::csa_wt<sdsl::wt_int<sdsl::int_vector<(unsigned char)1>, sdsl::rank_support_v5<(unsigned char)1, (unsigned char)1>, sdsl::select_support_mcl<(unsigned char)1, (unsigned char)1>, sdsl::select_support_mcl<(unsigned char)0, (unsigned char)1> >, 2u, 16777216u, sdsl::sa_order_sa_sampling<(unsigned char)0>, sdsl::isa_sampling<(unsigned char)0>, sdsl::int_alphabet<sdsl::sd_vector<sdsl::int_vector<(unsigned char)1>, sdsl::select_support_mcl<(unsigned char)1, (unsigned char)1>, sdsl::select_support_mcl<(unsigned char)0, (unsigned char)1> >, sdsl::rank_support_sd<(unsigned char)1, sdsl::int_vector<(unsigned char)1>, sdsl::select_support_mcl<(unsigned char)1, (unsigned char)1>, sdsl::select_support_mcl<(unsigned char)0, (unsigned char)1> >, sdsl::select_support_sd<(unsigned char)1, sdsl::int_vector<(unsigned char)1>, sdsl::select_support_mcl<(unsigned char)1, (unsigned char)1>, sdsl::select_support_mcl<(unsigned char)0, (unsigned char)1> >, sdsl::int_vector<(unsigned char)0> > >&, unsigned long, unsigned long, unsigned long, unsigned long, __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char, std::allocator > >, __gnu_cxx::_normal_iterator<unsigned char*, std::vector<unsigned char, std::allocator > >, std::list<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >&, std::list<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >&, std::list<std::vector<std::pair<unsigned int, std::vector<int, std::allocator > >, std::allocator<std::pair<unsigned int, std::vector<int, std::allocator > > > >, std::allocator<std::vector<std::pair<unsigned int, std::vector<int, std::allocator > >, std::allocator<std::pair<unsigned int, std::vector<int, std::allocator > > > > > >&, std::vector<int, std::allocator >&, unsigned long, bool&, bool) (bidir_search_fwd.cpp:134)
==78121== by 0x4360AE: BackwardSearchTest_NoVariants1_Test::TestBody() (unittest_bidir_search_bwd_fwd.cpp:78)
==78121== by 0x4815C7: void testing::internal::HandleSehExceptionsInMethodIfSupported<testing::Test, void>(testing::Test, void (testing::Test::)(), char const) (in /Net/fs1/home/zam/dev/git/gramtools/src/unittest_bidir_search_bwd_fwd)
==78121== by 0x47CA91: void testing::internal::HandleExceptionsInMethodIfSupported<testing::Test, void>(testing::Test_, void (testing::Test::)(), char const) (in /Net/fs1/home/zam/dev/git/gramtools/src/unittest_bidir_search_bwd_fwd)
==78121== by 0x464042: testing::Test::Run() (in /Net/fs1/home/zam/dev/git/gramtools/src/unittest_bidir_search_bwd_fwd)
==78121== by 0x46481F: testing::TestInfo::Run() (in /Net/fs1/home/zam/dev/git/gramtools/src/unittest_bidir_search_bwd_fwd)
==78121== by 0x464EB9: testing::TestCase::Run() (in /Net/fs1/home/zam/dev/git/gramtools/src/unittest_bidir_search_bwd_fwd)
==78121== by 0x46B67F: testing::internal::UnitTestImpl::RunAllTests() (in /Net/fs1/home/zam/dev/git/gramtools/src/unittest_bidir_search_bwd_fwd)
==78121== by 0x4828C7: bool testing::internal::HandleSehExceptionsInMethodIfSupported<testing::internal::UnitTestImpl, bool>(testing::internal::UnitTestImpl_, bool (testing::internal::UnitTestImpl::)(), char const) (in /Net/fs1/home/zam/dev/git/gramtools/src/unittest_bidir_search_bwd_fwd)
==78121== by 0x47D7C9: bool testing::internal::HandleExceptionsInMethodIfSupported<testing::internal::UnitTestImpl, bool>(testing::internal::UnitTestImpl_, bool (testing::internal::UnitTestImpl::)(), char const) (in /Net/fs1/home/zam/dev/git/gramtools/src/unittest_bidir_search_bwd_fwd)
==78121== by 0x46A2A5: testing::UnitTest::Run() (in /Net/fs1/home/zam/dev/git/gramtools/src/unittest_bidir_search_bwd_fwd)
==78121== by 0x43F343: RUN_ALL_TESTS() (gtest.h:2288)
==78121== Address 0x5341b61 is 0 bytes after a block of size 1 alloc'd
==78121== at 0x4A08EB6: operator new(unsigned long) (vg_replace_malloc.c:287)
==78121== by 0x42981B: gnu_cxx::new_allocator::allocate(unsigned long, void const) (new_allocator.h:94)
==78121== by 0x427BE2: std::Vector_base<unsigned char, std::allocator >::M_allocate(unsigned long) (in /Net/fs1/home/zam/dev/git/gramtools/src/unittest_bidir_search_bwd_fwd)
==78121== by 0x440955: void std::vector<unsigned char, std::allocator >::M_emplace_back_aux(unsigned char&&) (vector.tcc:402)
==78121== by 0x440186: void std::vector<unsigned char, std::allocator >::emplace_back(unsigned char&&) (vector.tcc:102)
==78121== by 0x43F95B: std::vector<unsigned char, std::allocator >::push_back(unsigned char&&) (stl_vector.h:900)
==78121== by 0x4359CB: BackwardSearchTest_NoVariants1_Test::TestBody() (unittest_bidir_search_bwd_fwd.cpp:59)
==78121== by 0x4815C7: void testing::internal::HandleSehExceptionsInMethodIfSupported<testing::Test, void>(testing::Test, void (testing::Test::)(), char const) (in /Net/fs1/home/zam/dev/git/gramtools/src/unittest_bidir_search_bwd_fwd)
==78121== by 0x47CA91: void testing::internal::HandleExceptionsInMethodIfSupported<testing::Test, void>(testing::Test, void (testing::Test::_)(), char const*) (in /Net/fs1/home/zam/dev/git/gramtools/src/unittest_bidir_search_bwd_fwd)
==78121== by 0x464042: testing::Test::Run() (in /Net/fs1/home/zam/dev/git/gramtools/src/unittest_bidir_search_bwd_fwd)
==78121== by 0x46481F: testing::TestInfo::Run() (in /Net/fs1/home/zam/dev/git/gramtools/src/unittest_bidir_search_bwd_fwd)
==78121== by 0x464EB9: testing::TestCase::Run() (in /Net/fs1/home/zam/dev/git/gramtools/src/unittest_bidir_search_bwd_fwd)
==78121==
[ OK ] BackwardSearchTest.NoVariants1 (64701 ms)
[ RUN ] BackwardSearchTest.OneSNP
[ OK ] BackwardSearchTest.OneSNP (34704 ms)
..etc

The bad access happens here

`
while (it!=sa_intervals.end() && it_rev!=sa_intervals_rev.end() && it_s!=sites.end()) {

                    //calculate sum to return- can do this in top fcns                                                                         

                    if (bidir_search(csa_rev,(*it).first,(*it).second,(*it_rev).first,(*it_rev).second,c)>0) {

                            ++it;

                            ++it_rev;

                            ++it_s;
                    }
                    else {
                            if (it==sa_intervals.begin()) first_del=true;
                            //might need to see first_del from top fcns to check if there are matches in the reference                         
                            it=sa_intervals.erase(it);
                            it_rev=sa_intervals_rev.erase(it_rev);
                            it_s=sites.erase(it_s);
                    }
            }
            ++pat_it;  
            c=*pat_it;   <<<<<<<<<<<< HERE!!

`
@iqbal-lab
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Note, this is in bidir_search_FORWARD

@iqbal-lab
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I think this is because there is just one byte here, and incrementing the iterator goes off the end somehow

iqbal-lab pushed a commit that referenced this issue Jul 31, 2016
@zamiqbal
Fix one definite bug and one maybe.
b899b8c 
1. Was reading an empty string and treating it as the prg
2. csa_constr has an argument asking for largest alphabet number, and in no variation case
   that should be 4, but we were entering 5.

THis bug is still open #28
@iqbal-lab
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Reproduced on latest commit: 45ab6dc

@iqbal-lab
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I know @rffrancon has set up valgrind - is this bug still there?

@iqbal-lab
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Robyn says fixed

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