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failing to build tiledb 2.9.0 heap_memory.cc #3191

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okanisis opened this issue May 19, 2022 · 5 comments
Closed

failing to build tiledb 2.9.0 heap_memory.cc #3191

okanisis opened this issue May 19, 2022 · 5 comments

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@okanisis
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Trying to build on Arch Linux.

cmake configuration:

   cmake -B build \
         -DCMAKE_BUILD_TYPE='Release' \
         -DCMAKE_INSTALL_PREFIX="/usr" \
         -DCMAKE_INSTALL_BINDIR='bin' \
         -DCMAKE_INSTALL_DOCDIR='doc' \
         -DTILEDB_TOOLS='ON' \
         -DTILEDB_S3='ON' \
         -DTILEDB_AZURE='OFF' \
         -DTILEDB_GCS='OFF' \
         -DTILEDB_SERIALIZATION='ON' \
         -DTILEDB_VERBOSE='ON' \
         -Wno-dev

Compilation Error:

[ 90%] Performing configure step for 'tiledb'
-- The C compiler identification is GNU 12.1.0
-- The CXX compiler identification is GNU 12.1.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Starting TileDB regular build.
-- The TileDB library is compiled with NEW thread pool (OFF).
-- Performing Test HAVE_AVX2
-- Performing Test HAVE_AVX2 - Success
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
-- searching for catch in /build/tiledb/src/tiledb-2.9.0/build/externals/src
-- Found Catch2: /usr/include/catch2  
-- searching for catch in /build/tiledb/src/tiledb-2.9.0/build/externals/src
-- searching for catch in /build/tiledb/src/tiledb-2.9.0/build/externals/src
-- searching for catch in /build/tiledb/src/tiledb-2.9.0/build/externals/src
-- searching for catch in /build/tiledb/src/tiledb-2.9.0/build/externals/src
-- searching for catch in /build/tiledb/src/tiledb-2.9.0/build/externals/src
-- searching for catch in /build/tiledb/src/tiledb-2.9.0/build/externals/src
-- Found Bzip2: /usr/lib/libbz2.so  
-- Found LZ4: /usr/lib/liblz4.so  
-- Found ZLIB: /usr/lib/libz.so (found version "1.2.12") 
-- Found Zlib, adding imported target: /usr/lib/libz.so
-- Found Zstd: /usr/lib/libzstd.so  
-- searching for catch in /build/tiledb/src/tiledb-2.9.0/build/externals/src
-- Found OpenSSL: /usr/lib/libcrypto.so (found suitable version "1.1.1o", minimum required is "1.1.0")  
-- Found OpenSSL: /usr/lib/libssl.so -- OpenSSL crypto: /usr/lib/libcrypto.so -- root: /build/tiledb/src/tiledb-2.9.0/build/externals/install;/usr/local/opt/openssl
-- searching for catch in /build/tiledb/src/tiledb-2.9.0/build/externals/src
-- searching for catch in /build/tiledb/src/tiledb-2.9.0/build/externals/src
-- searching for catch in /build/tiledb/src/tiledb-2.9.0/build/externals/src
-- Found OpenSSL: /usr/lib/libssl.so -- OpenSSL crypto: /usr/lib/libcrypto.so -- root: /build/tiledb/src/tiledb-2.9.0/build/externals/install;/usr/local/opt/openssl
-- Found libmagic: /build/tiledb/src/tiledb-2.9.0/build/externals/install/lib/liblibmagic.a  
-- searching for catch in /build/tiledb/src/tiledb-2.9.0/build/externals/src
-- The TileDB library is compiled with verbosity.
-- The TileDB library is compiled with stats enabled.
-- The TileDB library is compiled with query serialization enabled.
-- Found OpenSSL: /usr/lib/libssl.so -- OpenSSL crypto: /usr/lib/libcrypto.so -- root: /build/tiledb/src/tiledb-2.9.0/build/externals/install;/usr/local/opt/openssl
-- The TileDB library is compiled with S3 support.
-- Found AWS SDK for C++, Version: 1.9.241, Install Root:/usr, Platform Prefix:, Platform Dependent Libraries: pthread;crypto;ssl;z;curl
-- Found AWS lib: aws-cpp-sdk-s3 (/usr/lib/libaws-cpp-sdk-s3.so)
-- Found AWS lib: aws-cpp-sdk-core (/usr/lib/libaws-cpp-sdk-core.so)
-- Found AWS lib: aws-c-common (/usr/lib/libaws-c-common.so)
-- Found AWS lib: aws-c-event-stream (/usr/lib/libaws-c-event-stream.so)
-- Found AWS lib: aws-checksums (/usr/lib/libaws-checksums.so)
-- Found AWS lib: aws-cpp-sdk-sts (/usr/lib/libaws-cpp-sdk-sts.so)
-- Found AWS lib: aws-cpp-sdk-identity-management (/usr/lib/libaws-cpp-sdk-identity-management.so)
-- Found CURL: /usr/lib/libcurl.so (found version "7.83.1")  
-- Found CURL: '/usr/lib/libcurl.so' (found version "")
-- Found Zlib, adding imported target: /usr/lib/libz.so
-- Found CapnProto lib: capnp
-- Found CapnProto lib: kj
-- Found CapnProto lib: capnp-json
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success
-- searching for catch in /build/tiledb/src/tiledb-2.9.0/build/externals/src
-- searching for catch in /build/tiledb/src/tiledb-2.9.0/build/externals/src
-- searching for catch in /build/tiledb/src/tiledb-2.9.0/build/externals/src
CMake Warning (dev) at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:438 (message):
  The package name passed to `find_package_handle_standard_args` (Clipp) does
  not match the name of the calling package (Clipp_EP).  This can lead to
  problems in calling code that expects `find_package` result variables
  (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  cmake/Modules/FindClipp_EP.cmake:47 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
  tools/CMakeLists.txt:28 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found Clipp: /build/tiledb/src/tiledb-2.9.0/build/externals/install/include  
-- Configuring done
-- Generating done
-- Build files have been written to: /build/tiledb/src/tiledb-2.9.0/build/tiledb
[ 93%] Performing build step for 'tiledb'
make[3]: Entering directory '/build/tiledb/src/tiledb-2.9.0/build/tiledb'
make[4]: Entering directory '/build/tiledb/src/tiledb-2.9.0/build/tiledb'
make[5]: Entering directory '/build/tiledb/src/tiledb-2.9.0/build/tiledb'
make[5]: Leaving directory '/build/tiledb/src/tiledb-2.9.0/build/tiledb'
make[5]: Entering directory '/build/tiledb/src/tiledb-2.9.0/build/tiledb'
[  2%] Generating ../../../tiledb/sm/misc/magic_mgc_gzipped.bin
make[5]: Leaving directory '/build/tiledb/src/tiledb-2.9.0/build/tiledb'
[  2%] Built target gen_mgc_unarch
make[5]: Entering directory '/build/tiledb/src/tiledb-2.9.0/build/tiledb'
make[5]: Leaving directory '/build/tiledb/src/tiledb-2.9.0/build/tiledb'
make[5]: Entering directory '/build/tiledb/src/tiledb-2.9.0/build/tiledb'
[  2%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/common/heap_memory.cc.o
/build/tiledb/src/tiledb-2.9.0/tiledb/common/heap_memory.cc: In function ‘void* tiledb::common::tiledb_realloc(void*, std::size_t, const std::string&)’:
/build/tiledb/src/tiledb-2.9.0/tiledb/common/heap_memory.cc:93:31: error: pointer ‘p’ may be used after ‘void* realloc(void*, size_t)’ [-Werror=use-after-free]
   93 |   heap_profiler.record_dealloc(p);
      |   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/build/tiledb/src/tiledb-2.9.0/tiledb/common/heap_memory.cc:88:39: note: call to ‘void* realloc(void*, size_t)’ here
   88 |   void* const p_realloc = std::realloc(p, size);
      |                           ~~~~~~~~~~~~^~~~~~~~~
/build/tiledb/src/tiledb-2.9.0/tiledb/common/heap_memory.cc: In function ‘void tiledb::common::tiledb_free(void*)’:
/build/tiledb/src/tiledb-2.9.0/tiledb/common/heap_memory.cc:108:31: error: pointer ‘p’ used after ‘void free(void*)’ [-Werror=use-after-free]
  108 |   heap_profiler.record_dealloc(p);
      |   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/build/tiledb/src/tiledb-2.9.0/tiledb/common/heap_memory.cc:107:7: note: call to ‘void free(void*)’ here
  107 |   free(p);
      |   ~~~~^~~
cc1plus: all warnings being treated as errors
make[5]: *** [tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/build.make:76: tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/common/heap_memory.cc.o] Error 1
make[5]: Leaving directory '/build/tiledb/src/tiledb-2.9.0/build/tiledb'
make[4]: *** [CMakeFiles/Makefile2:983: tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/all] Error 2
make[4]: Leaving directory '/build/tiledb/src/tiledb-2.9.0/build/tiledb'
make[3]: *** [Makefile:146: all] Error 2
make[3]: Leaving directory '/build/tiledb/src/tiledb-2.9.0/build/tiledb'
make[2]: *** [CMakeFiles/tiledb.dir/build.make:86: tiledb-prefix/src/tiledb-stamp/tiledb-build] Error 2
make[2]: Leaving directory '/build/tiledb/src/tiledb-2.9.0/build'
make[1]: *** [CMakeFiles/Makefile2:175: CMakeFiles/tiledb.dir/all] Error 2
make[1]: Leaving directory '/build/tiledb/src/tiledb-2.9.0/build'
make: *** [Makefile:91: all] Error 2
make: Leaving directory '/build/tiledb/src/tiledb-2.9.0/build'
@okanisis
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Same error with 2.9.1

@eddelbuettel
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Did you see #3189 about adding --disable-werror ?

@okanisis
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okanisis commented Jun 2, 2022

Did you see #3189 about adding --disable-werror ?

I tried adding -Wdisable-werror and -Wno-error to the cmake configuration but I see in the output the build fails with cc1plus: all warnings being treated as errors still. So tells me it's not being applied by cmake.

@eddelbuettel
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See the script bootstrap, the invocation you need (if done directly to cmake) is likely something like

 cmake -B build \
         -DCMAKE_BUILD_TYPE='Release' \
         -DCMAKE_INSTALL_PREFIX="/usr" \
         -DCMAKE_INSTALL_BINDIR='bin' \
         -DCMAKE_INSTALL_DOCDIR='doc' \
         -DTILEDB_TOOLS='ON' \
         -DTILEDB_S3='ON' \
         -DTILEDB_AZURE='OFF' \
         -DTILEDB_GCS='OFF' \
         -DTILEDB_SERIALIZATION='ON' \
         -DTILEDB_VERBOSE='ON' \
         -Wno-dev \
         -DTILEDB_WERROR='OFF'

and note the last line I added.

@okanisis
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okanisis commented Jun 2, 2022

Duplicate of #3189

@okanisis okanisis closed this as completed Jun 2, 2022
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@eddelbuettel @okanisis