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#1048 Memory leak in 3rd party library #1060

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merged 16 commits into from
Mar 14, 2023
Merged

#1048 Memory leak in 3rd party library #1060

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8b67405
stringpool fix
even1024 Mar 9, 2023
eb8d61d
stringpool fix
even1024 Mar 9, 2023
c1f781a
stringpool fix
even1024 Mar 9, 2023
9d5b6e9
stringpool fix
even1024 Mar 9, 2023
b0115c9
stringpool fix
even1024 Mar 9, 2023
6f5fecd
stringpool fix
even1024 Mar 9, 2023
b1f9c3f
stringpool fix
even1024 Mar 9, 2023
77ab33e
smart pointer fix
even1024 Mar 9, 2023
14a881f
leaks
even1024 Mar 10, 2023
890b935
ext
even1024 Mar 10, 2023
afc8d4d
clang issues
even1024 Mar 10, 2023
7508c13
lsan
even1024 Mar 10, 2023
7fe7252
lsan
even1024 Mar 10, 2023
33963ca
docker fixes
even1024 Mar 10, 2023
3a31906
docker fixes
even1024 Mar 10, 2023
4b20fd1
Merge branch 'master' into bugfix/1048-external-leaks
even1024 Mar 13, 2023
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3 changes: 3 additions & 0 deletions .ci/docker/buildpack-arm64/Dockerfile
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Expand Up @@ -31,6 +31,9 @@ RUN apt update && \
ENV CC=aarch64-linux-gnu-gcc-5
ENV CXX=aarch64-linux-gnu-g++-5
ENV INDIGO_QEMU_BINARY=qemu-aarch64-static
ENV ASAN_OPTIONS=alloc_dealloc_mismatch=0
RUN echo $'leak:libfontconfig\nleak:libc\n' >> /opt/external.supp
ENV LSAN_OPTIONS=suppressions=/opt/external.supp

RUN cmake --version && \
aarch64-linux-gnu-gcc-5 --version && \
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9 changes: 7 additions & 2 deletions .ci/docker/buildpack-centos7/Dockerfile
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Expand Up @@ -6,16 +6,21 @@ ARG GIT_VERSION=227
RUN yum install -y epel-release centos-release-scl
RUN rpm --import /etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-SIG-SCLo
RUN yum update -y
RUN yum install -y devtoolset-${DEVTOOLSET_VERSION}-gcc-c++ devtoolset-${DEVTOOLSET_VERSION}-libasan-devel freetype-devel fontconfig-devel make python3 rh-git${GIT_VERSION}
RUN yum install -y devtoolset-${DEVTOOLSET_VERSION}-gcc-c++ devtoolset-${DEVTOOLSET_VERSION}-libasan-devel devtoolset-${DEVTOOLSET_VERSION}-liblsan-devel freetype-devel fontconfig-devel make python3 rh-git${GIT_VERSION}
RUN yum clean -y all
RUN echo $'leak:libfontconfig\nleak:libc\n' >> /opt/external.supp

# Enable the SCL for all bash scripts.
ENV MANPATH=/opt/rh/rh-git${GIT_VERSION}/root/usr/share/man:/opt/rh/devtoolset-${DEVTOOLSET_VERSION}/root/usr/share/man \
X_SCLS="devtoolset-${DEVTOOLSET_VERSION} rh-git${GIT_VERSION}" \
PCP_DIR=/opt/rh/devtoolset-${DEVTOOLSET_VERSION}/root \
PATH=/opt/rh/rh-git${GIT_VERSION}/root/usr/bin:/opt/rh/devtoolset-${DEVTOOLSET_VERSION}/root/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin \
PKG_CONFIG_PATH=/opt/rh/devtoolset-${DEVTOOLSET_VERSION}/root/usr/lib64/pkgconfig \
LD_LIBRARY_PATH=/opt/rh/httpd24/root/usr/lib64:/opt/rh/devtoolset-${DEVTOOLSET_VERSION}/root/usr/lib64:/opt/rh/devtoolset-${DEVTOOLSET_VERSION}/root/usr/lib:/opt/rh/devtoolset-${DEVTOOLSET_VERSION}/root/usr/lib64/dyninst:/opt/rh/devtoolset-${DEVTOOLSET_VERSION}/root/usr/lib/dyninst:/opt/rh/devtoolset-${DEVTOOLSET_VERSION}/root/usr/lib64:/opt/rh/devtoolset-${DEVTOOLSET_VERSION}/root/usr/lib
LD_LIBRARY_PATH=/opt/rh/httpd24/root/usr/lib64:/opt/rh/devtoolset-${DEVTOOLSET_VERSION}/root/usr/lib64:/opt/rh/devtoolset-${DEVTOOLSET_VERSION}/root/usr/lib:/opt/rh/devtoolset-${DEVTOOLSET_VERSION}/root/usr/lib64/dyninst:/opt/rh/devtoolset-${DEVTOOLSET_VERSION}/root/usr/lib/dyninst:/opt/rh/devtoolset-${DEVTOOLSET_VERSION}/root/usr/lib64:/opt/rh/devtoolset-${DEVTOOLSET_VERSION}/root/usr/lib \
LSAN_OPTIONS=suppressions=/opt/external.supp \
ASAN_OPTIONS=alloc_dealloc_mismatch=0


RUN PIP_ONLY_BINARY="cmake" python3 -m pip install cmake

RUN cmake --version && \
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10 changes: 5 additions & 5 deletions api/c/indigo-renderer/src/indigo_render2d.cpp
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Expand Up @@ -33,7 +33,7 @@
#include "indigo_renderer_internal.h"
#include "option_manager.h"

//#define INDIGO_DEBUG
// #define INDIGO_DEBUG

#ifdef INDIGO_DEBUG
#include <iostream>
Expand Down Expand Up @@ -488,18 +488,18 @@ CEXPORT int indigoRender(int object, int output)
if (IndigoBaseMolecule::is(obj))
{
if (obj.getBaseMolecule().isQueryMolecule())
rp.mol = std::make_unique<QueryMolecule>();
rp.mol.reset(new QueryMolecule());
else
rp.mol = std::make_unique<Molecule>();
rp.mol.reset(new Molecule());
rp.mol->clone_KeepIndices(self.getObject(object).getBaseMolecule());
rp.rmode = RENDER_MOL;
}
else if (IndigoBaseReaction::is(obj))
{
if (obj.getBaseReaction().isQueryReaction())
rp.rxn = std::make_unique<QueryReaction>();
rp.rxn.reset(new QueryReaction());
else
rp.rxn = std::make_unique<Reaction>();
rp.rxn.reset(new Reaction());
rp.rxn->clone(self.getObject(object).getBaseReaction(), 0, 0, 0);
rp.rmode = RENDER_RXN;
}
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9 changes: 4 additions & 5 deletions api/c/tests/unit/CMakeLists.txt
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Expand Up @@ -4,11 +4,10 @@ project(indigo-api-unit-tests LANGUAGES CXX)

if (ENABLE_TESTS)
if(UNIX AND NOT APPLE)
# commented out due to memory leaks
# set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address -fsanitize=leak -g")
# set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fsanitize=address -fsanitize=leak -g")
# set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -fsanitize=address -fsanitize=leak")
# set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} -fsanitize=address -fsanitize=leak")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address -fsanitize=leak -g")
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fsanitize=address -fsanitize=leak -g")
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -fsanitize=address -fsanitize=leak")
set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} -fsanitize=address -fsanitize=leak")
endif()
set(DATA_PATH ${CMAKE_SOURCE_DIR}/data)
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/common.h.in ${CMAKE_CURRENT_BINARY_DIR}/common.h)
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9 changes: 4 additions & 5 deletions api/cpp/tests/CMakeLists.txt
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Expand Up @@ -4,11 +4,10 @@ project(indigo-cpp-unit-tests LANGUAGES CXX)

if (ENABLE_TESTS)
if(UNIX AND NOT APPLE)
# set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address -fsanitize=leak -g")
# set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fsanitize=address -fsanitize=leak -g")
# set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -fsanitize=address -fsanitize=leak")
# set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} -fsanitize=address -fsanitize=leak")
# set(CMAKE_CXX_COMPILER_LAUNCHER ${CMAKE_COMMAND} -E env ASAN_OPTIONS=strict_string_checks=1:detect_stack_use_after_return=1:check_initialization_order=1:strict_init_order=1)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address -fsanitize=leak -g")
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fsanitize=address -fsanitize=leak -g")
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -fsanitize=address -fsanitize=leak")
set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} -fsanitize=address -fsanitize=leak")
endif()
set(DATA_PATH ${CMAKE_SOURCE_DIR}/data)
file(GLOB_RECURSE ${PROJECT_NAME}_SOURCES CONFIGURE_DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/**/*.cpp)
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8 changes: 3 additions & 5 deletions core/indigo-core/common/base_cpp/string_pool.cpp
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Expand Up @@ -41,14 +41,12 @@ int StringPool::_add(const char* str, int size)

if (idx >= _storage.size())
_storage.resize(idx + 1);
if (_storage.at(idx) == 0)
_storage.set(idx, new Array<char>());
if (size == -1 && str == 0)
throw Error("Internal error: size == -1 && str == 0");

if (size == -1)
size = strlen(str);
_storage.at(idx)->resize(size + 1);
_storage.at(idx).resize(size + 1);
if (str != 0 && size != 0)
memcpy(at(idx), str, size);
at(idx)[size] = 0;
Expand Down Expand Up @@ -77,12 +75,12 @@ void StringPool::remove(int idx)

char* StringPool::at(int idx)
{
return _storage[_pool[idx]]->ptr();
return _storage[_pool[idx]].ptr();
}

const char* StringPool::at(int idx) const
{
return _storage[_pool[idx]]->ptr();
return _storage[_pool[idx]].ptr();
}

int StringPool::size() const
Expand Down
4 changes: 2 additions & 2 deletions core/indigo-core/common/base_cpp/string_pool.h
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Expand Up @@ -20,8 +20,8 @@
#define __string_pool_h__

#include "base_cpp/auto_iter.h"
#include "base_cpp/obj_array.h"
#include "base_cpp/pool.h"
#include "base_cpp/ptr_array.h"

#ifdef _WIN32
#pragma warning(push)
Expand Down Expand Up @@ -96,7 +96,7 @@ namespace indigo
int _add(const char* str, int size);

Pool<int> _pool;
PtrArray<Array<char>> _storage;
ObjArray<Array<char>> _storage;

private:
StringPool(const StringPool&); // no implicit copy
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2 changes: 0 additions & 2 deletions core/indigo-core/molecule/molecule.h
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Expand Up @@ -33,8 +33,6 @@ namespace indigo
{
public:
Molecule();
~Molecule() override;

Molecule& asMolecule() override;

void clear() override;
Expand Down
4 changes: 0 additions & 4 deletions core/indigo-core/molecule/src/molecule.cpp
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Expand Up @@ -33,10 +33,6 @@ Molecule::Molecule()
_ignore_bad_valence = false;
}

Molecule::~Molecule()
{
}

Molecule& Molecule::asMolecule()
{
return *this;
Expand Down
1 change: 0 additions & 1 deletion core/indigo-core/tests/CMakeLists.txt
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Expand Up @@ -8,7 +8,6 @@ if (ENABLE_TESTS)
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fsanitize=address -fsanitize=leak -g")
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -fsanitize=address -fsanitize=leak")
set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} -fsanitize=address -fsanitize=leak")
set(CMAKE_CXX_COMPILER_LAUNCHER ${CMAKE_COMMAND} -E env ASAN_OPTIONS=strict_string_checks=1:detect_stack_use_after_return=1:check_initialization_order=1:strict_init_order=1)
endif()
set(DATA_PATH ${CMAKE_SOURCE_DIR}/data)
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/common.h.in ${CMAKE_CURRENT_BINARY_DIR}/common.h)
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15 changes: 3 additions & 12 deletions core/render2d/src/render_cdxml.cpp
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Expand Up @@ -149,20 +149,11 @@ void RenderParamCdxmlInterface::render(RenderParams& params)
void RenderParamCdxmlInterface::_renderRxns(RenderParams& params)
{
ReactionCdxmlSaver saver(*params.rOpt.output);

Array<BaseReaction*> rxns;

if (params.rxns.size() != 0)
for (int i = 0; i < params.rxns.size(); ++i)
rxns.push(params.rxns[i]);
else if (params.rxn.get() != 0)
rxns.push(params.rxn.get());

for (int rxn_ind = 0; rxn_ind < rxns.size(); rxn_ind++)
{
BaseReaction& rxn = (BaseReaction&)*rxns[rxn_ind];
saver.saveReaction(rxn);
}
saver.saveReaction(*params.rxns[i]);
else if (params.rxn)
saver.saveReaction(*params.rxn);
}

void RenderParamCdxmlInterface::_renderMols(RenderParams& params)
Expand Down
2 changes: 0 additions & 2 deletions core/render2d/src/render_params.cpp
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Expand Up @@ -69,8 +69,6 @@ void RenderParams::clear()
relativeThickness = 1.0f;
bondLineWidthFactor = 1.0f;
rmode = RENDER_NONE;
mol.reset(nullptr);
rxn.reset(nullptr);
rOpt.clear();
cnvOpt.clear();
clearArrays();
Expand Down
9 changes: 2 additions & 7 deletions third_party/inchi/INCHI_BASE/src/runichi4.c
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Expand Up @@ -1324,21 +1324,16 @@ void FreeAllINChIArrays( PINChI2 *pINChI[INCHI_NUM],
int k;
for (k = 0; k < INCHI_NUM; k++)
{
int nk = num_components[k];

FreeINChIArrays( pINChI[k], pINChI_Aux[k], num_components[k] );

num_components[k] = 0;

if (nk && /* added check for nk: 2013-12-15 IPl */
pINChI[k])
if ( pINChI[k] )
{
inchi_free( pINChI[k] );
pINChI[k] = NULL;
}

if (nk && /* added check for nk: 2013-12-15 IPl */
pINChI_Aux[k])
if ( pINChI_Aux[k] )
{
inchi_free( pINChI_Aux[k] );
pINChI_Aux[k] = NULL;
Expand Down