Thanks, Geoff! It is definitely time to update our cluster OS. Our old Rocks clusters is still on gcc4.
Off-topic: Computational chemists around: any tips on Linux distros for clusters that are still under active development? All the best, Alessandro Em qui, 8 de jun de 2023 15:32, Geoffrey Hutchison < geoff.hutchi...@gmail.com> escreveu: > GCC 4.8.2 is known to be problematic with C++ and is also an ancient > compiler. > https://www.gnu.org/software/gcc/gcc-4.8/ > > The original release was in 2013 (10 years ago). > > Please install a more recent version of GCC / G++ > > Best regards, > -Geoff > > On Jun 8, 2023 at 1:34:12 PM, Alessandro S. Nascimento via > OpenBabel-discuss <openbabel-discuss@lists.sourceforge.net> wrote: > >> Dear all, >> >> I've been facing some issues when trying to compile OB 3.1.1 on my linux >> cluster (rocks clusters, gcc 4.8.2). >> >> Cmake goes well with: >> >> $ cmake -DCMAKE_INSTALL_PREFIX=/home/cjoliveira/tools/openbabel3 >> -DEIGEN3_INCLUDE_DIR=/share/apps/eigen3 /share/apps/openbabel-3.1.1/ >> >> Compilation starts fine, as copied below. I get a warning about >> std::binder1st, but the problems show up during the linking. The message >> seems to be similar to some functions not being included in the Makefile to >> generate the shared library libopenbabel.so. >> >> For the sake of comparison, I tested compiling OB 3.0.0 using the same >> flags and everything went fine. Any ideas about what may be going on? >> >> Thanks in advance, >> >> Alessandro >> >> ... >> [ 4%] Built target coordgen >> [ 4%] Linking CXX shared library ../../../lib/libmaeparser.so >> [ 4%] Built target maeparser >> ... >> [ 17%] Building CXX object src/CMakeFiles/openbabel.dir/patty.cpp.o >> [ 17%] Linking C shared library ../../../lib/libinchi.so >> [ 17%] Built target inchi >> [ 17%] Building CXX object src/CMakeFiles/openbabel.dir/phmodel.cpp.o >> ... >> [ 23%] Building CXX object >> src/CMakeFiles/openbabel.dir/stereo/facade.cpp.o >> [ 24%] Building CXX object >> src/CMakeFiles/openbabel.dir/stereo/gen3dstereohelper.cpp.o >> /share/apps/iMcLiBELa/src/openbabel-3.1.1/src/stereo/perception.cpp: In >> function 'void OpenBabel::ImplicitRefToStereo(OpenBabel::OBMol&, >> OpenBabel::OBStereo::Ref, OpenBabel::OBStereo::Ref)': >> /share/apps/iMcLiBELa/src/openbabel-3.1.1/src/stereo/perception.cpp:3005:57: >> warning: 'binder1st' is deprecated (declared at >> /share/apps/gcc/4.8.2/include/c++/4.8.2/backward/binders.h:104) >> [-Wdeprecated-declarations] >> const std::binder1st<std::equal_to<OBStereo::Ref> > >> equal_to_implicitRef = std::bind1st (equal_to<OBStereo::Ref>(), >> (OBStereo::Ref) OBStereo::ImplicitRef); >> ^ >> [ 24%] Linking CXX shared library ../lib/libopenbabel.so >> CMakeFiles/openbabel.dir/mol.cpp.o: In function >> `OpenBabel::OBMol::CorrectForPH(double)': >> mol.cpp:(.text+0x1e8c): undefined reference to `_ZTHN9OpenBabel7phmodelE' >> CMakeFiles/openbabel.dir/mol.cpp.o: In function >> `OpenBabel::OBMol::PerceiveBondOrders()': >> mol.cpp:(.text+0x11956): undefined reference to >> `_ZTHN9OpenBabel9bondtyperE' >> CMakeFiles/openbabel.dir/atom.cpp.o: In function >> `OpenBabel::OBAtom::GetType()': >> atom.cpp:(.text+0x5f1): undefined reference to >> `_ZTHN9OpenBabel9atomtyperE' >> CMakeFiles/openbabel.dir/atom.cpp.o: In function >> `OpenBabel::OBAtom::GetHyb() const': >> atom.cpp:(.text+0x6b9): undefined reference to >> `_ZTHN9OpenBabel9atomtyperE' >> CMakeFiles/openbabel.dir/atom.cpp.o: In function >> `OpenBabel::OBAtom::GetPartialCharge()': >> atom.cpp:(.text+0x75d): undefined reference to `_ZTHN9OpenBabel7phmodelE' >> collect2: error: ld returned 1 exit status >> >> -- >> ***************************************************************** >> * Alessandro S. Nascimento * >> * Associate Professor - Sao Carlos Institute of Physics * >> * University of São Paulo (IFSC/USP) * >> * Phone: +55-16-3364-8075 * >> * E-mail: asnascime...@ifsc.usp.br * >> ***************************************************************** >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> >
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