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Hanjun-Dai / pytorch_structure2vec

pytorch implementation of structure2vec (https://arxiv.org/abs/1603.05629)
MIT License
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error message when running make -j4 #8

Closed xuzhang5788 closed 5 years ago

xuzhang5788 commented 6 years ago

After I ran these cd harvard_cep make -j4 I received

g++ -Wall -O3 -std=c++11 -I./include -I/home/xuzhang/anaconda3/envs/rdkit/Code -Wno-unused-local-typedef -fPIC -MMD -c -o build/lib/mol_utils.o src/lib/mol_utils.cpp In file included from src/lib/mol_utils.cpp:1:0: ./include/mol_utils.h:5:31: fatal error: GraphMol/RingInfo.h: No such file or directory compilation terminated. Makefile:41: recipe for target 'build/lib/mol_utils.o' failed make: *** [build/lib/mol_utils.o] Error 1

Your help is highly appreciated

Hanjun-Dai commented 6 years ago

It requires the c++ header. I'm not sure whether you have downloaded the rdkit source. It seems the anaconda build is not enough

ManSoSec commented 6 years ago

I installed rdkit by "https://github.com/rdkit/homebrew-rdkit" on Mac, but got the same error. I solved it by cloning the rdkit source code, compiling it, and passing its path to RDBASE instead of the installed path.

xuzhang5788 commented 6 years ago

Thank you @ManSoSec & @Hanjun-Dai

I am using Ubuntu and I installed rdkit by anaconda. If I reinstall rdkit through source code, I don't know if my other codes using rdkit will not work. By the way, I don't understand what I should do when you say compiling it @ManSoSec

ManSoSec commented 6 years ago

@xuzhang5788 Download rdkit source code: https://github.com/rdkit/rdkit unzip rdkit-master.zip cd rdkit-master cmake . make -j4 Then use 'rdkit-master' path for RDBASE.

xuzhang5788 commented 6 years ago

Thank you @ManSoSec very much.

I followed your instruction, but after I run make -j4, I got

[ 80%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors_static.dir/WHIM.cpp.o [ 80%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so [ 80%] Built target Descriptors [ 80%] Linking CXX static library libRDKitDescriptors_static.a [ 80%] Built target Descriptors_static Makefile:160: recipe for target 'all' failed make: *** [all] Error 2

If I ignore those things and directly run python main.py -gm loopy_bp -saved_model saved/loopy_bp.model -phase test

I got Traceback (most recent call last): File "main.py", line 3, in from mol_lib import MOLLIB, MolGraph File "/media/projects/pytorch_structure2vec/harvard_cep/mol_lib.py", line 115, in MOLLIB = _mol_lib() File "/media/projects/pytorch_structure2vec/harvard_cep/mol_lib.py", line 12, in init self.lib = ctypes.CDLL('%s/build/dll/libmol.so' % dir_path) File "/home/xuzhang/anaconda3/lib/python3.5/ctypes/init.py", line 351, in init self._handle = _dlopen(self._name, mode) OSError: /media/projects/pytorch_structure2vec/harvard_cep/build/dll/libmol.so: undefined symbol: _ZN5RDKit17SmilesMolSupplierC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_iibb

Any ideas? Many thanks

Hanjun-Dai commented 6 years ago

can you provide more information about the compilation error?

xuzhang5788 commented 6 years ago

@Hanjun-Dai I follow @ManSoSec 's procedure like this Download rdkit source code: https://github.com/rdkit/rdkit unzip rdkit-master.zip cd rdkit-master cmake . make -j4

I just redo it and I got the followings: [ 0%] Built target coordgen_support [ 0%] Built target inchi_support [ 1%] Built target maeparser_static [ 1%] Built target maeparser [ 2%] Built target RDGeneral [ 3%] Built target RDGeneral_static [ 3%] Built target hc [ 4%] Built target hc_static [ 5%] Built target coordgenlib [ 7%] Built target coordgenlib_static [ 7%] Built target EigenSolvers [ 7%] Built target RDBoost [ 8%] Built target DataStructs [ 8%] Built target testDict [ 8%] Built target testRDValue [ 9%] Built target testFPB [ 10%] Built target RDBoost_static [ 10%] Built target testMultiFPB [ 11%] Built target testDataStructs [ 11%] Built target testMatrices [ 11%] Built target rdBase [ 12%] Built target DataStructs_static [ 13%] Built target cDataStructs [ 13%] Built target EigenSolvers_static [ 13%] Built target testQuery [ 13%] Built target testMatCalc [ 14%] Built target Catalogs_static [ 14%] Built target Catalogs [ 14%] Built target SimDivPickers [ 15%] Built target rdMetricMatrixCalc [ 15%] Built target SimDivPickers_static [ 15%] Built target Clustering [ 15%] Built target InfoTheory_static [ 15%] Built target testSimDivPickers [ 15%] Built target RDGeometryLib [ 15%] Built target rdSimDivPickers [ 16%] Built target RDGeometryLib_static [ 16%] Built target Alignment [ 17%] Built target testGrid [ 17%] Built target InfoTheory [ 18%] Built target testTransforms [ 18%] Built target Alignment_static [ 18%] Built target testAlignment [ 18%] Built target rdAlignment [ 18%] Built target rdInfoTheory [ 19%] Built target cQuantize [ 19%] Built target ChemicalFeatures [ 20%] Built target ChemicalFeatures_static [ 20%] Built target testChemicalFeatures [ 21%] Built target rdGeometry [ 25%] Built target GraphMol_static [ 28%] Built target GraphMol [ 28%] Built target Trajectory_static [ 28%] Built target SubstructMatch_static [ 29%] Built target Subgraphs [ 29%] Built target Subgraphs_static [ 30%] Built target SmilesParse_static [ 30%] Built target MolTransforms_static [ 30%] Built target MolCatalog_static [ 30%] Built target PartialCharges [ 30%] Built target PartialCharges_static [ 31%] Built target MolCatalog [ 31%] Built target ReducedGraphs_static [ 32%] Built target SLNParse_static [ 32%] Built target MolInterchange_static [ 32%] Built target MolInterchange [ 32%] Built target SLNParse [ 33%] Built target rdChemicalFeatures [ 33%] Built target rdqueries [ 34%] Built target MolTransforms [ 35%] Built target SubstructMatch [ 35%] Built target Trajectory [ 36%] Built target Optimizer_static [ 38%] Built target SmilesParse [ 38%] Built target ChemTransforms_static [ 39%] Built target testPartialCharges [ 40%] Built target Fingerprints_static [ 41%] Built target FilterCatalog_static [ 41%] Built target rdPartialCharges [ 42%] Built target FragCatalog_static [ 43%] Built target rdMolTransforms [ 43%] Built target ShapeHelpers [ 43%] Built target MolChemicalFeatures [ 44%] Built target MolChemicalFeatures_static [ 45%] Built target ShapeHelpers_static [ 45%] Built target rdMolInterchange [ 46%] Built target ReducedGraphs [ 46%] Built target SubstructLibrary_static [ 47%] Built target rdSLNParse [ 48%] Built target testSLNParse [ 48%] Built target Optimizer [ 48%] Built target rdtrajectory [ 48%] Built target graphmoltestCanon [ 48%] Built target graphmolIterTest [ 48%] Built target graphmolqueryTest [ 49%] Built target test-valgrind [ 50%] Built target graphmolcpTest [ 50%] Built target graphmolMemTest1 [ 50%] Built target smaTest1 [ 51%] Built target ChemTransforms [ 52%] Built target FilterCatalog [ 53%] Built target testSubgraphs1 [ 53%] Built target testSubgraphs2 [ 53%] Built target Fingerprints [ 56%] Built target ForceField_static [ 56%] Built target rdShapeHelpers [ 56%] Built target rdReducedGraphs [ 56%] Built target SubstructLibrary [ 57%] Built target rdMolChemicalFeatures [ 57%] Built target testReducedGraphs [ 57%] Built target FragCatalog [ 57%] Built target testOptimizer [ 58%] Built target ForceFieldHelpers_static [ 59%] Built target rdchem [ 59%] Built target MolAlign_static [ 62%] Built target ForceField [ 63%] Built target DistGeometry_static [ 63%] Built target ForceFieldHelpers [ 63%] Built target Depictor_static [ 64%] Built target DistGeomHelpers_static [ 64%] Built target rdForceField [ 65%] Built target MolAlign [ 65%] Built target DistGeometry [ 65%] Built target rdForceFieldHelpers [ 65%] Built target rdCoordGen [ 66%] Built target Depictor [ 66%] Built target testDistGeom [ 66%] Built target DistGeomHelpers [ 66%] Built target DistGeom [ 68%] Built target FileParsers_static Scanning dependencies of target FMCS_static Scanning dependencies of target MMPA_static [ 70%] Built target FileParsers [ 70%] Built target testCoordGen [ 70%] Built target testUFFForceField [ 70%] Built target testMMFFForceField [ 73%] Built target Descriptors_static [ 73%] Built target graphmoltestChirality [ 73%] Built target molBundleTest [ 74%] Built target graphmoltestPickler [ 74%] Built target graphmolMolOpsTest [ 74%] Built target hanoiTest [ 74%] Built target graphmoltestPicklerGlobalSetting [ 75%] Built target resMolSupplierTest [ 75%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA_static.dir/MMPA.cpp.o [ 75%] Built target graphmolTest1 [ 75%] Built target testDepictor [ 75%] Built target rdDepictor [ 75%] Built target cxsmilesTest [ 75%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS_static.dir/FMCS.cpp.o [ 75%] Built target smiTest1 [ 75%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS_static.dir/Seed.cpp.o [ 75%] Built target fileParsersTest1 [ 75%] Built target testTplParser [ 75%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS_static.dir/MaximumCommonSubgraph.cpp.o [ 75%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS_static.dir/SubstructMatchCustom.cpp.o [ 75%] Linking CXX static library libRDKitMMPA_static.a [ 75%] Built target MMPA_static [ 75%] Built target testMol2ToMol [ 76%] Built target testMolWriter [ 76%] Built target testMolSupplier [ 76%] Built target testSequence [ 76%] Built target testSubstructMatch Scanning dependencies of target ChemReactions_static [ 78%] Built target Descriptors [ 79%] Built target testChemTransforms [ 80%] Linking CXX executable filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1dev1: undefined reference to boost::archive::text_iarchive_impl<boost::archive::text_iarchive>::load(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)' ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1dev1: undefined reference toboost::archive::text_oarchive_impl::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)' collect2: error: ld returned 1 exit status Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make:116: recipe for target 'Code/GraphMol/FilterCatalog/filterCatalogTest' failed make[2]: [Code/GraphMol/FilterCatalog/filterCatalogTest] Error 1 CMakeFiles/Makefile2:5415: recipe for target 'Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/all' failed make[1]: [Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/all] Error 2 make[1]: Waiting for unfinished jobs.... [ 80%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions_static.dir/Reaction.cpp.o [ 80%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions_static.dir/MDLParser.cpp.o [ 80%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions_static.dir/DaylightParser.cpp.o [ 80%] Linking CXX static library libRDKitFMCS_static.a [ 80%] Built target FMCS_static [ 80%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions_static.dir/ReactionPickler.cpp.o [ 80%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions_static.dir/ReactionWriter.cpp.o [ 80%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions_static.dir/ReactionDepict.cpp.o [ 80%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions_static.dir/ReactionFingerprints.cpp.o [ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions_static.dir/ReactionUtils.cpp.o [ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions_static.dir/MoleculeParser.cpp.o [ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions_static.dir/ReactionRunner.cpp.o [ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions_static.dir/PreprocessRxn.cpp.o [ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions_static.dir/SanitizeRxn.cpp.o [ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions_static.dir/Enumerate/Enumerate.cpp.o [ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions_static.dir/Enumerate/EnumerationPickler.cpp.o [ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions_static.dir/Enumerate/EvenSamplePairs.cpp.o [ 81%] Linking CXX static library libRDKitChemReactions_static.a [ 81%] Built target ChemReactions_static Makefile:160: recipe for target 'all' failed make: [all] Error 2

Hanjun-Dai commented 6 years ago

It seems you didn't have boost c++ installed?

xuzhang5788 commented 6 years ago

@Hanjun-Dai When I reinstall boost using $ sudo apt-get install libboost-all-dev, I got

Reading package lists... Done Building dependency tree
Reading state information... Done libboost-all-dev is already the newest version (1.58.0.1ubuntu1). The following packages were automatically installed and are no longer required: linux-headers-4.13.0-38 linux-headers-4.13.0-38-generic linux-headers-4.13.0-39 linux-headers-4.13.0-39-generic linux-headers-4.13.0-41 linux-headers-4.13.0-41-generic linux-image-4.13.0-38-generic linux-image-4.13.0-39-generic linux-image-4.13.0-41-generic linux-image-extra-4.13.0-38-generic linux-image-extra-4.13.0-39-generic linux-image-extra-4.13.0-41-generic Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.

Hanjun-Dai commented 5 years ago

probably you may want to install boost C++ from source