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Fix memory leak from CompressZFP. #1977

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merged 4 commits into from
Feb 21, 2020
Merged

Fix memory leak from CompressZFP. #1977

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a82cccd
Fix memory leak from CompressZFP.
NAThompson Feb 20, 2020
fa189ed
Free the bitstream pointer with the correct ZFP call.
NAThompson Feb 21, 2020
d698fc6
Fix ZFP bistream leak through SST.
NAThompson Feb 21, 2020
41ec6fa
CI: Add ZFP to the AddressSanitizer build
Feb 21, 2020
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12 changes: 5 additions & 7 deletions scripts/ci/cmake/ci-fedora-asan.cmake
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Original file line number Diff line number Diff line change
@@ -1,20 +1,18 @@
# Client maintainer: chuck.atkins@kitware.com

set(ENV{CC} gcc)
set(ENV{CXX} g++)
set(ENV{FC} gfortran)
set(ASAN_FLAGS "-fsanitize=address -pthread")
set(ENV{CC} clang)
set(ENV{CXX} clang++)
set(ASAN_FLAGS "-fsanitize=address -fno-omit-frame-pointer -pthread")
set(ENV{CFLAGS} "${ASAN_FLAGS}")
set(ENV{CXXFLAGS} "${ASAN_FLAGS}")
set(ENV{FFLAGS} "${ASAN_FLAGS}")

set(dashboard_cache "
ADIOS2_USE_Fortran:STRING=OFF
ADIOS2_USE_HDF5:STRING=ON
ADIOS2_USE_MPI:STRING=OFF
ADIOS2_USE_Python:STRING=OFF

HDF5_C_COMPILER_EXECUTABLE:FILEPATH=/usr/bin/h5cc
HDF5_DIFF_EXECUTABLE:FILEPATH=/usr/bin/h5diff
ADIOS2_USE_ZFP:STRING=ON
")

set(dashboard_track "Analysis")
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13 changes: 13 additions & 0 deletions scripts/ci/images/fedora-asan/Dockerfile
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Expand Up @@ -3,6 +3,19 @@ FROM ornladios/adios2:fedora-sanitizers-base
# Install core dev packages
RUN dnf -y install libasan python3-devel python3-numpy hdf5-devel

# Install ZFP
WORKDIR /opt/zfp
RUN curl -L https://github.com/LLNL/zfp/releases/download/0.5.5/zfp-0.5.5.tar.gz | tar -xvz && \
mkdir build && \
cd build && \
cmake -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/opt/zfp/0.5.5 ../zfp-0.5.5 && \
make -j$(grep -c '^processor' /proc/cpuinfo) install && \
cd .. && \
rm -rf zfp-0.5.5 build
ENV PATH=/opt/zfp/0.5.5/bin:${PATH} \
LD_LIBRARY_PATH=/opt/zfp/0.5.5/lib64:${LD_LIBRARY_PATH} \
CMAKE_PREFIX_PATH=/opt/zfp/0.5.5:${CMAKE_PREFIX_PATH}

# Misc cleanup
RUN dnf clean all && \
rm -rfv /tmp/* /var/cache/dnf
1 change: 1 addition & 0 deletions source/adios2/operator/compress/CompressZFP.cpp
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Expand Up @@ -63,6 +63,7 @@ size_t CompressZFP::Compress(const void *dataIn, const Dims &dimensions,

zfp_field_free(field);
zfp_stream_close(stream);
stream_close(bitstream);
return sizeOut;
}

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1 change: 1 addition & 0 deletions source/adios2/toolkit/sst/cp/ffs_zfp.c
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Expand Up @@ -153,6 +153,7 @@ extern char *FFS_ZFPCompress(SstStream Stream, const size_t DimCount,
size_t sizeOut = zfp_compress(stream, field);
zfp_field_free(field);
zfp_stream_close(stream);
stream_close(bitstream);
*ByteCountP = sizeOut;
return bufferOut;
}
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