Postgres cartridge build fails under Ubuntu

[SPKorhonen]

Describe the bug

I have trouble building Postgres cartridge under Linux. All other parts of RDKit compile and pass tests (with -DRDK_BUILD_PGSQL=OFF, Windows compilation of cartridge also works)

The problem is that cartridge build fails due to invalid link command: /BUILD/boost/lib/libboost_iostreams-mt-d-x64.so -loptimized_static /BUILD/boost/lib/libboost_regex-mt-x64.so -ldebug_static /BUILD/boost/lib/libboost_regex-mt-d-x64.so ../../GraphMol/MolAlign/libRDKitMolAlign_static.a

It seems that whatever code automatically adds boost libraries is somehow mangling in configuration information. I also get both debug and release versions of boost libraries in link command ../../Catalogs/libRDKitCatalogs_static.a /BUILD/boost/lib/libboost_serialization-mt-x64.so /BUILD/boost/lib/libboost_serialization-mt-d-x64.so /usr/lib/x86_64-linux-gnu/libfreetype.so though I'm not sure if this is an issue also.

To Reproduce

I'm building RDKit from source using boost 1.76 built locally. Postgres 12 is installed from PostgreSQL Apt Repository. Cmake 3.21.3 is installed from KitWare apt repository.

Run cmake referencing custom boost:

cmake -DBOOST_ROOT:PATHNAME=$BOOST_BASE_PATH -DBoost_LIBRARY_DIRS=$BOOST_LIBRARYDIR -DBoost_NO_SYSTEM_PATHS=ON -DBoost_NO_BOOST_CMAKE=TRUE -DBoost_ARCHITECTURE=-x64 -DRDK_BUILD_PYTHON_WRAPPERS=ON -DPYTHON_EXECUTABLE:FILEPATH=$PYTHONBIN_DIR -DPYTHON_LIBRARY=$PYTHON_LIBRARY -DPYTHON_INCLUDE_DIR=$PYTHON_INCLUDE_DIR -DPYTHON_NUMPY_INCLUDE_PATH=$PYTHON_NUMPY_INCLUDE_PATH -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_FREESASA_SUPPORT=ON -DRDK_BUILD_YAEHMOP_SUPPORT=ON -DRDK_BUILD_MOLINTERCHANGE_SUPPORT=ON -DRDK_BUILD_PGSQL=ON -DPostgreSQL_CONFIG=$POSTGRES_CONFIG ..

Run make

Expected behavior

Cartridge is built successfully.

Configuration (please complete the following information):

• RDKit version: 2021.09.2
• OS: Ubuntu 20.04
• Python version : Python 3.8
• Building rdkit from source

Additional context

Link.txt generated by CMake:

/usr/bin/c++ -fPIC -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O3 -DNDEBUG -shared -Wl,-soname,librdkit.so -o librdkit.so CMakeFiles/rdkit.dir/adapter.cpp.o CMakeFiles/rdkit.dir/bfp_op.c.o CMakeFiles/rdkit.dir/cache.c.o CMakeFiles/rdkit.dir/guc.c.o CMakeFiles/rdkit.dir/low_gist.c.o CMakeFiles/rdkit.dir/mol_op.c.o CMakeFiles/rdkit.dir/rdkit_gist.c.o CMakeFiles/rdkit.dir/bfp_gist.c.o CMakeFiles/rdkit.dir/bfp_gin.c.o CMakeFiles/rdkit.dir/bitstring.c.o CMakeFiles/rdkit.dir/rdkit_io.c.o CMakeFiles/rdkit.dir/rxn_op.c.o CMakeFiles/rdkit.dir/sfp_op.c.o -L/BUILD/rdkit/lib -Wl,-rpath,/BUILD/rdkit/lib:/BUILD/boost/lib /usr/lib/x86_64-linux-gnu/libpq.so ../../../External/AvalonTools/libRDKitAvalonLib_static.a ../../../External/AvalonTools/libRDKitavalon_clib_static.a ../../../External/INCHI-API/libRDKitRDInchiLib_static.a ../../../External/INCHI-API/libRDKitInchi_static.a ../../GraphMol/MolInterchange/libRDKitMolInterchange_static.a ../../GraphMol/MolDraw2D/libRDKitMolDraw2D_static.a ../../GraphMol/MolTransforms/libRDKitMolTransforms_static.a ../../GraphMol/MolHash/libRDKitMolHash_static.a ../../GraphMol/FMCS/libRDKitFMCS_static.a ../../GraphMol/ChemReactions/libRDKitChemReactions_static.a ../../GraphMol/ChemTransforms/libRDKitChemTransforms_static.a ../../GraphMol/FileParsers/libRDKitFileParsers_static.a ../../GraphMol/SmilesParse/libRDKitSmilesParse_static.a ../../GraphMol/Fingerprints/libRDKitFingerprints_static.a ../../GraphMol/Subgraphs/libRDKitSubgraphs_static.a ../../GraphMol/Descriptors/libRDKitDescriptors_static.a ../../GraphMol/PartialCharges/libRDKitPartialCharges_static.a ../../GraphMol/Substruct/libRDKitSubstructMatch_static.a ../../GraphMol/libRDKitGraphMol_static.a ../../Numerics/EigenSolvers/libRDKitEigenSolvers_static.a ../../DataStructs/libRDKitDataStructs_static.a ../../GraphMol/Depictor/libRDKitDepictor_static.a ../../Geometry/libRDKitRDGeometryLib_static.a ../../RDGeneral/libRDKitRDGeneral_static.a ../../../External/RingFamilies/libRDKitRingDecomposerLib_static.a ../../GraphMol/FilterCatalog/libRDKitFilterCatalog_static.a ../../Catalogs/libRDKitCatalogs_static.a /BUILD/boost/lib/libboost_serialization-mt-x64.so /BUILD/boost/lib/libboost_serialization-mt-d-x64.so /usr/lib/x86_64-linux-gnu/libfreetype.so ../../GraphMol/Subgraphs/libRDKitSubgraphs_static.a ../../GraphMol/FileParsers/libRDKitFileParsers_static.a /usr/lib/x86_64-linux-gnu/libz.so ../../GraphMol/SmilesParse/libRDKitSmilesParse_static.a ../../GraphMol/Depictor/libRDKitDepictor_static.a ../../../External/CoordGen/libRDKitmaeparser_static.a /BUILD/boost/lib/libboost_system-mt-x64.so /BUILD/boost/lib/libboost_system-mt-d-x64.so /BUILD/boost/lib/libboost_iostreams-mt-x64.so /BUILD/boost/lib/libboost_iostreams-mt-d-x64.so -loptimized_static /BUILD/boost/lib/libboost_regex-mt-x64.so -ldebug_static /BUILD/boost/lib/libboost_regex-mt-d-x64.so ../../GraphMol/MolAlign/libRDKitMolAlign_static.a ../../GraphMol/MolTransforms/libRDKitMolTransforms_static.a ../../Numerics/EigenSolvers/libRDKitEigenSolvers_static.a ../../GraphMol/Substruct/libRDKitSubstructMatch_static.a ../../GraphMol/libRDKitGraphMol_static.a ../../Numerics/Alignment/libRDKitAlignment_static.a ../../Geometry/libRDKitRDGeometryLib_static.a ../../DataStructs/libRDKitDataStructs_static.a ../../RDGeneral/libRDKitRDGeneral_static.a ../../../External/CoordGen/libRDKitcoordgen_static.a -lpthread

[ptosco]

@SPKorhonen Thanks for providing details regarding your installation. I'll try to reproduce this over the next few days. Could you please also share your boost build script (you mentioned that you have built this locally) and any relevant configuration file?

[SPKorhonen]

Here is the relevant portion of our build script:

#BOOST
cd boost

tee user-config_gcc93_PY38-64.jam <<EOF
import toolset : using ;  
using gcc : 9.3 ;  
using python  
     : 3.8  
     : "/usr/bin/python3"
     : "/usr/include/python3.8"
     : "/usr/lib/x86_64-linux-gnu"
     ;
EOF

wget https://github.com/unicode-org/icu/releases/download/release-69-1/icu4c-69_1-src.tgz
rm -rf icu
tar xvf icu4c-68_2-src.tgz
cd icu/source
CXXFLAGS=-std=c++11 ./runConfigureICU Linux/gcc
make
make install
cd $NMRS_DEV_BUILDBOOST

wget https://boostorg.jfrog.io/artifactory/main/release/1.76.0/source/boost_1_76_0.tar.bz2
tar -xvf boost_1_76_0.tar.bz2
mv boost_1_76_0 1_76_0_BUILD
cp -Rf ./1_76_0_BUILD/boost .
cp -f user-config_gcc93_PY38-64.jam $HOME/user-config.jam
cd 1_76_0_BUILD
./bootstrap.sh gcc --with-python=/usr/bin/python3 --with-python-version=3.8 --with-python-root=/usr/lib/x86_64-linux-gnu
rm -rf bin.v2
rm -rf stage
./b2 variant=debug,release runtime-link=shared threading=multi address-model=64 architecture=x86 -j12 --without-mpi --build-type=complete --layout=tagged --toolset=gcc
cp -rf ./stage/lib ../lib
cd $NMRS_BUILDBASE

[ptosco]

@SPKorhonen Thanks!