Memory leaks in BP5Deserializer::InstallMetaData

[dqwu]

This issue is reproducible with latest ADIOS2 2.9.0 and a simple C example of SCORPIO.

Steps to reproduce on a Linux workstation with GCC compiler and its LeakSanitizer:

git clone https://github.com/E3SM-Project/scorpio.git
cd scorpio

mkdir build
cd build

CFLAGS="-fsanitize=leak -fno-omit-frame-pointer -g" \
ADIOS2_DIR=/path/to/adios2/installation \
CC=mpicc CXX=mpicxx FC=mpifort cmake -Wno-dev \
-DWITH_ADIOS2=ON \
-DADIOS_BP2NC_TEST=ON \
-DWITH_NETCDF=OFF \
-DPnetCDF_PATH=/path/to/pnetcdf/installation \
-DPIO_USE_MALLOC=ON \
-DPIO_ENABLE_EXAMPLES=ON \
..

make

cd examples/c
mpiexec -n 2 ./example1

Example output on a Linux workstation of ANL:

=================================================================
==2414827==ERROR: LeakSanitizer: detected memory leaks

Direct leak of 72 byte(s) in 3 object(s) allocated from:
    #0 0x7f80f14a7ac4 in operator new(unsigned long) /nfs/gce/software/tmp/svcbuilder/spack-stage-gcc-11.1.0-qsjmpcgt7go2ourefdh2i5z2g5u7bxmk/spack-src/libsanitizer/lsan/lsan_interceptors.cpp:238
    #1 0x864501 in adios2::format::BP5Deserializer::InstallMetaData(void*, unsigned long, unsigned long, unsigned long) ADIOS2-2.9.0/source/adios2/toolkit/format/bp5/BP5Deserializer.cpp:717
    #2 0x83825e in adios2::core::engine::BP5Reader::InstallMetadataForTimestep(unsigned long) ADIOS2-2.9.0/source/adios2/engine/bp5/BP5Reader.cpp:81

Valgrind also reports similar memory leaks:

==2420468== 40 (24 direct, 16 indirect) bytes in 1 blocks are definitely lost in loss record 5 of 10
==2420468==    at 0x483BE63: operator new(unsigned long) (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so)
==2420468==    by 0x864501: adios2::format::BP5Deserializer::InstallMetaData(void*, unsigned long, unsigned long, unsigned long) (in scorpio/build/examples/c/example1)
==2420468==    by 0x83825E: adios2::core::engine::BP5Reader::InstallMetadataForTimestep(unsigned long) (in scorpio/build/examples/c/example1)
==2420468==    by 0x83C265: adios2::core::engine::BP5Reader::BeginStep(adios2::StepMode, float) (in scorpio/build/examples/c/example1)
==2420468==    by 0xA055FC: ConvertBPFile(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int) (in scorpio/build/examples/c/example1)
==2420468==    by 0xA073B1: ConvertBPToNC(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int) (in scorpio/build/examples/c/example1)
==2420468==    by 0xA07DBD: C_API_ConvertBPToNC (in scorpio/build/examples/c/example1)
==2420468==    by 0x45D598: PIOc_closefile (in scorpio/build/examples/c/example1)
==2420468==    by 0x45B579: main (in scorpio/build/examples/c/example1)

Additional information:

• Reproducible with ADIOS2 2.9.0 (released on Mar 30 2023) and latest master branch
• Not reproducible with ADIOS2 built with master branch on Nov 30 2022
• A similar issue has been fixed for ADIOS2 2.9.0, see Memory Leak in BP5Deserializer #3443

[dqwu]

@eisenhauer
Could you please take a look? Thanks.

[eisenhauer]

On it...

[dqwu]

@eisenhauer
FYI, the same memory leaks issue is also mentioned in #3580

[eisenhauer]

Found the issue and will have a PR in momentarily...

[vicentebolea]

This was resolved at #3619