Problem compiling

I’m trying to compile on Ubuntu 16.04. I used:

cmake -H. -Bobj

to configure. I’m using cmake version 3.6 and gcc version 5.4.

When I compile it gets all the way up to 100% and then fails with the following error message:

[100%] Linking CXX shared library core.so
cd /home/avcopan/Documents/code/github/psi4/obj/psi4_core-prefix/src/psi4_core-build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/core.dir/link.txt --verbose=1
/usr/bin/c++  -fPIC  -march=native -fopenmp -O3 -DNDEBUG  -shared -Wl,-soname,core.so -o core.so CMakeFiles/core.dir/export_psio.cc.o CMakeFiles/core.dir/export_mints.cc.o CMakeFiles/core.dir/export_fock.cc.o CMakeFiles/core.dir/export_functional.cc.o CMakeFiles/core.dir/export_oeprop.cc.o CMakeFiles/core.dir/export_plugins.cc.o CMakeFiles/core.dir/export_blas_lapack.cc.o CMakeFiles/core.dir/export_benchmarks.cc.o CMakeFiles/core.dir/export_efp.cc.o CMakeFiles/core.dir/export_cubeprop.cc.o CMakeFiles/core.dir/export_misc.cc.o CMakeFiles/core.dir/create_new_plugin.cc.o CMakeFiles/core.dir/read_options.cc.o CMakeFiles/versioned_code.dir/core.cc.o psi4/adc/libadc.a psi4/ccdensity/libccdensity.a psi4/ccenergy/libccenergy.a psi4/cceom/libcceom.a psi4/cchbar/libcchbar.a psi4/cclambda/libcclambda.a psi4/ccresponse/libccresponse.a psi4/ccsort/libccsort.a psi4/cctransort/libcctransort.a psi4/cctriples/libcctriples.a psi4/dcft/libdcft.a psi4/detci/libdetci.a psi4/dfmp2/libdfmp2.a psi4/dfocc/libdfocc.a psi4/efp_interface/libefp_interface.a psi4/findif/libfindif.a psi4/fisapt/libfisapt.a psi4/fnocc/libfnocc.a psi4/mcscf/libmcscf.a psi4/mrcc/libmrcc.a psi4/occ/libocc.a psi4/optking/liboptking.a psi4/psimrcc/libpsimrcc.a psi4/sapt/libsapt.a psi4/scfgrad/libscfgrad.a psi4/thermo/libthermo.a psi4/transqt2/libtransqt2.a psi4/gdma_interface/libgdma_interface.a psi4/dmrg/libdmrg.a -lpython2.7 psi4/libthce/libthce.a psi4/libcubeprop/libcubeprop.a psi4/libmoinfo/libmoinfo.a psi4/libsapt_solver/libsapt_solver.a psi4/libscf_solver/libscf_solver.a psi4/libdiis/libdiis.a psi4/libdpd/libdpd.a psi4/lib3index/lib3index.a psi4/libfock/libfock.a psi4/lib3index/lib3index.a psi4/libfock/libfock.a psi4/libfunctional/libfunctional.a psi4/libdisp/libdisp.a psi4/libplugin/libplugin.a -ldl psi4/libmints/libmints.a psi4/libtrans/libtrans.a psi4/libqt/libqt.a psi4/libefp_solver/libefp_solver.a psi4/libmints/libmints.a psi4/libtrans/libtrans.a psi4/libqt/libqt.a psi4/libefp_solver/libefp_solver.a psi4/libiwl/libiwl.a psi4/libpsi4util/libpsi4util.a /home/avcopan/Documents/code/github/psi4/obj/stage/usr/local/external/lib/libderiv.a /home/avcopan/Documents/code/github/psi4/obj/stage/usr/local/external/lib/libint.a psi4/libpsio/libpsio.a psi4/libciomr/libciomr.a psi4/libparallel/libparallel.a psi4/liboptions/liboptions.a psi4/libfilesystem/libfilesystem.a /home/avcopan/Documents/code/github/psi4/obj/stage/usr/local/external/lib/libefp.a -lopenblas -Wl,--start-group/usr/lib/liblapack.so -lblas -Wl,--end-group -Wl,-rpath,/usr/local/lib:/home/avcopan/Documents/code/github/psi4/obj/stage//usr/local/lib:/usr/lib/x86_64-linux-gnu 
/usr/bin/ld: unrecognized option '--start-group/usr/lib/liblapack.so'
/usr/bin/ld: use the --help option for usage information
collect2: error: ld returned 1 exit status
src/CMakeFiles/core.dir/build.make:473: recipe for target 'src/core.so' failed
make[5]: *** [src/core.so] Error 1
make[5]: Leaving directory '/home/avcopan/Documents/code/github/psi4/obj/psi4_core-prefix/src/psi4_core-build'
CMakeFiles/Makefile2:248: recipe for target 'src/CMakeFiles/core.dir/all' failed
make[4]: *** [src/CMakeFiles/core.dir/all] Error 2
make[4]: Leaving directory '/home/avcopan/Documents/code/github/psi4/obj/psi4_core-prefix/src/psi4_core-build'
Makefile:127: recipe for target 'all' failed
make[3]: *** [all] Error 2
make[3]: Leaving directory '/home/avcopan/Documents/code/github/psi4/obj/psi4_core-prefix/src/psi4_core-build'
CMakeFiles/psi4_core.dir/build.make:111: recipe for target 'psi4_core-prefix/src/psi4_core-stamp/psi4_core-build' failed
make[2]: *** [psi4_core-prefix/src/psi4_core-stamp/psi4_core-build] Error 2
make[2]: Leaving directory '/home/avcopan/Documents/code/github/psi4/obj'
CMakeFiles/Makefile2:357: recipe for target 'CMakeFiles/psi4_core.dir/all' failed
make[1]: *** [CMakeFiles/psi4_core.dir/all] Error 2
make[1]: Leaving directory '/home/avcopan/Documents/code/github/psi4/obj'
Makefile:138: recipe for target 'all' failed
make: *** [all] Error 2

Looks like a missing space --start-group /usr/lib/liblapack.so. I’ll try to locate it and fix.

1 Like

Hi there,

I’m having the exact same issue on Ubuntu 16.10 using Intel compilers and MKL, is there a known fix to this?

   [ 99%] Linking CXX shared library core.so
   CMakeFiles/core.dir/export_mints.cc.o: file not recognized: File truncated
    src/CMakeFiles/core.dir/build.make:555: recipe for target 'src/core.so' failed
    make[5]: *** [src/core.so] Error 1
    CMakeFiles/Makefile2:170: recipe for target 'src/CMakeFiles/core.dir/all' failed
    make[4]: *** [src/CMakeFiles/core.dir/all] Error 2
    Makefile:127: recipe for target 'all' failed
    make[3]: *** [all] Error 2
    CMakeFiles/psi4-core.dir/build.make:111: recipe for target 'psi4-core-prefix/src/psi4-core-stamp/psi4-core-build' failed
    make[2]: *** [psi4-core-prefix/src/psi4-core-stamp/psi4-core-build] Error 2
    CMakeFiles/Makefile2:643: recipe for target 'CMakeFiles/psi4-core.dir/all' failed
    make[1]: *** [CMakeFiles/psi4-core.dir/all] Error 2
    Makefile:138: recipe for target 'all' failed
    make: *** [all] Error 2

Sure you’re using a current version of the code? Build system has changed a lot in past year, and I’d be surprised if --start-group is getting invoked for a normal build.

I am using the master build, so that’s the newest version….

What’s your cmake command and cmake config output? And git log --oneline?

Hi, turns out the error is not really the same I jumped to conclusions by skimming over the error, my compilation fails at 99% with
> CMakeFiles/core.dir/export_mints.cc.o: file not recognized: File truncated

    src/CMakeFiles/core.dir/build.make:555: recipe for target 'src/core.so' failed

as shown above.

This is my cmake command

cmake -H. -Bbuild -DMAX_AM_ERI=6 -DENABLE_gdma=ON -DBUILD_SHARED_LIBS=ON -DCMAKE_Fortran_COMPILER=ifort -DENABLE_dkh=ON -DENABLE_dftd3=ON -DENABLE_cfour=ON -DENABLE_PCMSolver=ON -DENABLE_erd=ON -DENABLE_simint=ON -DENABLE_mrcc=ON -DENABLE_gcp=ON -DENABLE_PLUGIN_TESTING=ON -DCMAKE_CXX_COMPILER=icpc -DCMAKE_C_COMPILER=icc -DCMAKE_BLAS_TYPE=MKL

and the cmake config output and some more files:
CMakeOutput.log.txt (97.6 KB)

gitlog.txt (684.5 KB)

CMakeCache.txt (30.1 KB)
Makefile.txt (25.3 KB)

The thing I’d most like to see is the screen result of your cmake -H. -Bbuild -D... command. You can just issue it again with a -Bbuild2 or something. I’m afraid your error doesn’t make much sense. Did you try multiple cmake commands w/o deleting build/ in between? That could cause problems. Also, dftd3, cfour, mrcc, and gcp are option runtime dependencies, so enabling them won’t do anything. Add the executables to your path to activate test cases.