Use std::vector for varying sized buffers

[leekillough]

While investigating Valgrind errors, I noticed this code which is much simpler and less error-prone if std::vector<char> is used to manage a varying-size buffer.

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[leekillough]

There are valgrind uninitialized memory errors which are not fixed by this change which was motivated by analyzing these valgrind errors, but the change is wanted nonetheless, since it makes the code simpler.

==213066== Syscall param writev(vector[1]) points to uninitialised byte(s)
==213066==    at 0x5408034: writev (writev.c:26)
==213066==    by 0x513EC71: std::__basic_file<char>::xsputn_2(char const*, long, char const*, long) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.32)
==213066==    by 0x518332B: std::basic_filebuf<char, std::char_traits<char> >::xsputn(char const*, long) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.32)
==213066==    by 0x51AC9A5: std::ostream::write(char const*, long) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.32)
==213066==    by 0x319D5A: SST::Simulation_impl::checkpoint(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) (simulation.cc:1729)
==213066==    by 0x270EEB: SST::CheckpointAction::createCheckpoint(SST::Simulation_impl*) (checkpointAction.cc:130)
==213066==    by 0x271A1C: SST::CheckpointAction::execute() (checkpointAction.cc:79)
==213066==    by 0x317187: SST::Simulation_impl::run() (simulation.cc:877)
==213066==    by 0x236C60: start_simulation(unsigned int, SimThreadInfo_t&, SST::Core::ThreadSafe::Barrier&) (main.cc:601)
==213066==    by 0x217F73: main (main.cc:1109)
==213066==  Address 0x6c97042 is 98 bytes inside a block of size 16,912 alloc'd
==213066==    at 0x4859047: operator new(unsigned long) (vg_replace_malloc.c:472)
==213066==    by 0x31DA4B: allocate (new_allocator.h:137)
==213066==    by 0x31DA4B: allocate (alloc_traits.h:464)
==213066==    by 0x31DA4B: _M_allocate (stl_vector.h:378)
==213066==    by 0x31DA4B: std::vector<char, std::allocator<char> >::_M_default_append(unsigned long) (vector.tcc:657)
==213066==    by 0x319E80: resize (stl_vector.h:1011)
==213066==    by 0x319E80: SST::Simulation_impl::checkpoint(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) (simulation.cc:1722)
==213066==    by 0x270EEB: SST::CheckpointAction::createCheckpoint(SST::Simulation_impl*) (checkpointAction.cc:130)
==213066==    by 0x271A1C: SST::CheckpointAction::execute() (checkpointAction.cc:79)
==213066==    by 0x317187: SST::Simulation_impl::run() (simulation.cc:877)
==213066==    by 0x236C60: start_simulation(unsigned int, SimThreadInfo_t&, SST::Core::ThreadSafe::Barrier&) (main.cc:601)
==213066==    by 0x217F73: main (main.cc:1109)
==213066==  Uninitialised value was created by a heap allocation
==213066==    at 0x4859047: operator new(unsigned long) (vg_replace_malloc.c:472)
==213066==    by 0x2966DE: SST::ConfigGraph::addComponent(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&) (configGraph.cc:784)
==213066==    by 0x3DD16E: addComponent (pymodel.h:94)
==213066==    by 0x3DD16E: compInit(ComponentPy_t*, _object*, _object*) (pymodel_comp.cc:95)
==213066==    by 0x4A7E431: ??? (in /usr/lib/x86_64-linux-gnu/libpython3.11.so.1.0)
==213066==    by 0x4A186C0: _PyObject_MakeTpCall (in /usr/lib/x86_64-linux-gnu/libpython3.11.so.1.0)
==213066==    by 0x49ABBB6: _PyEval_EvalFrameDefault (in /usr/lib/x86_64-linux-gnu/libpython3.11.so.1.0)
==213066==    by 0x4C6E13B: ??? (in /usr/lib/x86_64-linux-gnu/libpython3.11.so.1.0)
==213066==    by 0x4B069F4: PyEval_EvalCode (in /usr/lib/x86_64-linux-gnu/libpython3.11.so.1.0)
==213066==    by 0x4B55E28: ??? (in /usr/lib/x86_64-linux-gnu/libpython3.11.so.1.0)
==213066==    by 0x4B567E5: _PyRun_SimpleFileObject (in /usr/lib/x86_64-linux-gnu/libpython3.11.so.1.0)
==213066==    by 0x4B56DBF: _PyRun_AnyFileObject (in /usr/lib/x86_64-linux-gnu/libpython3.11.so.1.0)
==213066==    by 0x4B56E7C: PyRun_AnyFileExFlags (in /usr/lib/x86_64-linux-gnu/libpython3.11.so.1.0)
==213066==

With this PR's changes, the use of std::vector instead of new char[] makes the memory initialized to 0 upon creation and resizing (the same effect could have been done by adding {} to the end of new char[]), but it does not remove the uninitialized memory error, which seems to mean that the uninitialized data is copied from somewhere else to buffer or size is wrong. valgrind flags the uninitialized memory read as occurring in:

        fs.write(&buffer[0], size);

in the part of the loop:

    // Serialize component blobs individually
    for ( auto comp = compInfoMap.begin(); comp != compInfoMap.end(); comp++ ) {
        ser.start_sizing();
        ComponentInfo* compinfo = *comp;
        ser&           compinfo;
        size = ser.size();
        buffer.resize(size);

        ser.start_packing(&buffer[0], size);
        ser& compinfo;

        component_blob_offsets_.emplace_back(compinfo->id_, offset);
        fs.write(reinterpret_cast<const char*>(&size), sizeof(size));
        fs.write(&buffer[0], size);
        offset += (sizeof(size) + size);
    }

The buffer.resize(size) call should initialize all new elements to 0 if size increases, but the ser& compinfo should initialize all size elements, if the size reported by the ser.start_sizing() ... size = ser.size() sequence is working correctly (which it might not be).

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Pull Request Author: leekillough

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