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Fix ADIOS1 String Attributes #269

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merged 2 commits into from
Jun 18, 2018
Merged

Fix ADIOS1 String Attributes #269

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caba260
Travis: ADIOS1 on OSX
ax3l Jun 16, 2018
a8b0fb6
Fix String Attribute Writes
ax3l Jun 16, 2018
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2 changes: 1 addition & 1 deletion .travis.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -116,7 +116,7 @@ jobs:
os: osx
language: generic
env:
- USE_MPI=OFF USE_PYTHON=ON USE_HDF5=ON USE_ADIOS1=OFF USE_ADIOS2=OFF USE_SAMPLES=ON
- USE_MPI=OFF USE_PYTHON=ON USE_HDF5=ON USE_ADIOS1=ON USE_ADIOS2=OFF USE_SAMPLES=ON
compiler: clang
before_install:
- COMPILERSPEC="%[email protected]"
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1 change: 1 addition & 0 deletions CHANGELOG.rst
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Expand Up @@ -37,6 +37,7 @@ Bug Fixes
- recursive directory creation with existing base #261
- ``FindADIOS.cmake``: reset on multiple calls #263
- ``SerialIOTest``: remove variable shadowing #262
- ADIOS1: memory violation in string attribute writes #269

Other
"""""
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16 changes: 8 additions & 8 deletions src/IO/ADIOS/ADIOS1IOHandler.cpp
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Expand Up @@ -718,7 +718,7 @@ ADIOS1IOHandlerImpl::writeAttribute(Writable* writable,

Attribute att = Attribute(parameters.resource);

int nelems;
int nelems = 0;
switch( parameters.dtype )
{
using DT = Datatype;
Expand Down Expand Up @@ -840,9 +840,9 @@ ADIOS1IOHandlerImpl::writeAttribute(Writable* writable,
}
case DT::STRING:
{
using uptr = std::unique_ptr< void, std::function< void(void*) > >;
values = uptr(const_cast< char* >(att.get< std::string >().c_str()),
[](void*){ });
auto const & v = att.get< std::string >();
values = auxiliary::allocatePtr(Datatype::CHAR, v.length() + 1u);
strcpy((char*)values.get(), v.c_str());
break;
}
case DT::VEC_CHAR:
Expand Down Expand Up @@ -977,7 +977,7 @@ ADIOS1IOHandlerImpl::writeAttribute(Writable* writable,
"",
getBP1DataType(parameters.dtype),
nelems,
values.get());
values.get()); // Invalid read of size 1 (could be in ADIOS itself?)
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in strlen() in adios_get_type_size (adios_bp_v1.c:2415) in adios_common_define_attribute_byvalue (adios_internals.c:1109) in adios_define_attribute_byvalue (adios.c:442) in openPMD::ADIOS1IOHandlerImpl::writeAttribute on string value: serial_fileBased_write%T

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we already pass the invalid c-string.

strlen((const char*)values.get()) is an invalid read of size 1

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Very likely because of #269 (comment).

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ah dang, just found it as well :)
yes, we can not defer/forward the pointer we get there :)

VERIFY(status == err_no_error, "Internal error: Failed to define ADIOS attribute by value");

if( parameters.dtype == Datatype::VEC_STRING )
Expand Down Expand Up @@ -1053,9 +1053,9 @@ ADIOS1IOHandlerImpl::readAttribute(Writable* writable,
attrname += "/";
attrname += parameters.name;

ADIOS_DATATYPES datatype;
int size;
void* data;
ADIOS_DATATYPES datatype = adios_unknown;
int size = 0;
void* data = nullptr;

int status;
status = adios_get_attr(f,
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