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qsimulate-open / bagel

Brilliantly Advanced General Electronic-structure Library
GNU General Public License v3.0
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Installation error #216

Closed wubaihua closed 3 years ago

wubaihua commented 3 years ago

Dear all: I am trying to install BAGEL on supercomputer. However, the following error will occurred while I run make：

libtool: compile: mpicxx -DHAVE_CONFIG_H -I. -I../../../src/pt2 -I../.. -I/public1/soft/boost/1_57_0-gcc485//include -I../../.. -DNDEBUG -O3 -mavx -std=c++11 -MT nevpt2/nevpt2.lo -MD -MP -MF nevpt2/.deps/nevpt2.Tpo -c ../../../src/pt2/nevpt2/nevpt2.cc -fPIC -DPIC -o nevpt2/.libs/nevpt2.o init2.c:52: MPFR assertion failed: p >= 2 && p <= ((mpfr_prec_t)((mpfr_uprec_t)(~(mpfr_uprec_t)0)>>1)) ../../../src/pt2/nevpt2/nevpt2.cc: In member function ‘void bagel::NEVPT2::compute() [with DataType = std::complex]’: ../../../src/pt2/nevpt2/nevpt2.cc:928:46: internal compiler error: Aborted template class bagel::NEVPT2<complex>; ^ Please submit a full bug report, with preprocessed source if appropriate. See http://bugzilla.redhat.com/bugzilla for instructions. Preprocessed source stored into /tmp/cc6Tr1r4.out file, please attach this to your bugreport. make[3]: [nevpt2/nevpt2.lo] Error 1 make[3]: Leaving directory `/public3/home/sc31119/local/bagel_old/obj/src/pt2' make[2]: [all-recursive] Error 1 make[2]: Leaving directory /public3/home/sc31119/local/bagel_old/obj/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory/public3/home/sc31119/local/bagel_old/obj' make: *** [all] Error 2

How can I solve this problem？Thanks a lot.

shiozaki commented 3 years ago

This is an error in the compilers you are using. Use a different version. Later gcc is more stable, I suppose.

BidhanChandra commented 3 years ago

While installing I am getting this kind of error

make all-recursive make[1]: Entering directory '/home/titan/bagel-1.1.1/obj' Making all in src make[2]: Entering directory '/home/titan/bagel-1.1.1/obj/src' Making all in util make[3]: Entering directory '/home/titan/bagel-1.1.1/obj/src/util' Making all in parallel make[4]: Entering directory '/home/titan/bagel-1.1.1/obj/src/util/parallel' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/util/parallel' Making all in io make[4]: Entering directory '/home/titan/bagel-1.1.1/obj/src/util/io' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/util/io' Making all in input make[4]: Entering directory '/home/titan/bagel-1.1.1/obj/src/util/input' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/util/input' Making all in math make[4]: Entering directory '/home/titan/bagel-1.1.1/obj/src/util/math' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/util/math' make[4]: Entering directory '/home/titan/bagel-1.1.1/obj/src/util' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/util' make[3]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/util' Making all in molecule make[3]: Entering directory '/home/titan/bagel-1.1.1/obj/src/molecule' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/molecule' Making all in integral make[3]: Entering directory '/home/titan/bagel-1.1.1/obj/src/integral' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/integral' Making all in df make[3]: Entering directory '/home/titan/bagel-1.1.1/obj/src/df' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/df' Making all in opt make[3]: Entering directory '/home/titan/bagel-1.1.1/obj/src/opt' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/opt' Making all in grad make[3]: Entering directory '/home/titan/bagel-1.1.1/obj/src/grad' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/grad' Making all in pt2 make[3]: Entering directory '/home/titan/bagel-1.1.1/obj/src/pt2' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/pt2' Making all in wfn make[3]: Entering directory '/home/titan/bagel-1.1.1/obj/src/wfn' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/wfn' Making all in scf make[3]: Entering directory '/home/titan/bagel-1.1.1/obj/src/scf' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/scf' Making all in multi make[3]: Entering directory '/home/titan/bagel-1.1.1/obj/src/multi' Making all in casscf make[4]: Entering directory '/home/titan/bagel-1.1.1/obj/src/multi/casscf' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/multi/casscf' Making all in zcasscf make[4]: Entering directory '/home/titan/bagel-1.1.1/obj/src/multi/zcasscf' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/multi/zcasscf' make[4]: Entering directory '/home/titan/bagel-1.1.1/obj/src/multi' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/multi' make[3]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/multi' Making all in smith make[3]: Entering directory '/home/titan/bagel-1.1.1/obj/src/smith' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/smith' Making all in prop make[3]: Entering directory '/home/titan/bagel-1.1.1/obj/src/prop' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/prop' Making all in ci make[3]: Entering directory '/home/titan/bagel-1.1.1/obj/src/ci' Making all in ciutil make[4]: Entering directory '/home/titan/bagel-1.1.1/obj/src/ci/ciutil' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/ci/ciutil' Making all in fci make[4]: Entering directory '/home/titan/bagel-1.1.1/obj/src/ci/fci' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/ci/fci' Making all in ras make[4]: Entering directory '/home/titan/bagel-1.1.1/obj/src/ci/ras' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/ci/ras' Making all in zfci make[4]: Entering directory '/home/titan/bagel-1.1.1/obj/src/ci/zfci' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/ci/zfci' make[4]: Entering directory '/home/titan/bagel-1.1.1/obj/src/ci' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/ci' make[3]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/ci' Making all in response make[3]: Entering directory '/home/titan/bagel-1.1.1/obj/src/response' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/response' Making all in asd make[3]: Entering directory '/home/titan/bagel-1.1.1/obj/src/asd' Making all in dmrg make[4]: Entering directory '/home/titan/bagel-1.1.1/obj/src/asd/dmrg' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/asd/dmrg' Making all in dimer make[4]: Entering directory '/home/titan/bagel-1.1.1/obj/src/asd/dimer' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/asd/dimer' Making all in multisite make[4]: Entering directory '/home/titan/bagel-1.1.1/obj/src/asd/multisite' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/asd/multisite' Making all in orbital make[4]: Entering directory '/home/titan/bagel-1.1.1/obj/src/asd/orbital' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/asd/orbital' make[4]: Entering directory '/home/titan/bagel-1.1.1/obj/src/asd' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/asd' make[3]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/asd' Making all in mat1e make[3]: Entering directory '/home/titan/bagel-1.1.1/obj/src/mat1e' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/mat1e' Making all in basis make[3]: Entering directory '/home/titan/bagel-1.1.1/obj/src/basis' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/basis' Making all in periodic make[3]: Entering directory '/home/titan/bagel-1.1.1/obj/src/periodic' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/titan/bagel-1.1.1/obj/src/periodic' make[3]: Entering directory '/home/titan/bagel-1.1.1/obj/src' /bin/bash ../libtool --tag=CXX --mode=link mpicxx -I../.. -g -O2 -o BAGEL main.o libbagel.la opt/libbagel_opt.la multi/zcasscf/libbagel_zcasscf.la ci/zfci/libbagel_zfci.la ci/fci/libbagel_fci.la ci/ras/libbagel_ras.la response/libbagel_response.la scf/libbagel_scf.la multi/casscf/libbagel_casscf.la pt2/libbagel_pt2.la grad/libbagel_grad.la wfn/libbagel_wfn.la df/libbagel_df.la smith/libbagel_smith.la prop/libbagel_prop.la asd/libbagel_asd.la asd/dmrg/libbagel_asd_dmrg.la asd/orbital/libbagel_asd_orbital.la asd/dimer/libbagel_dimer.la asd/multisite/libbagel_multisite.la ci/ciutil/libbagel_ciutil.la mat1e/libbagel_mat1e.la periodic/libbagel_periodic.la integral/libbagel_integral.la molecule/libbagel_molecule.la util/io/libbagel_io.la util/libbagel_util.la util/parallel/libbagel_parallel.la util/math/libbagel_math.la util/input/libbagel_input.la -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -lboost_unit_test_framework -lboost_regex -lboost_serialization
libtool: link: mpicxx -I../.. -g -O2 -o .libs/BAGEL main.o ./.libs/libbagel.so opt/.libs/libbagel_opt.so multi/zcasscf/.libs/libbagel_zcasscf.so ci/zfci/.libs/libbagel_zfci.so ci/fci/.libs/libbagel_fci.so ci/ras/.libs/libbagel_ras.so response/.libs/libbagel_response.so scf/.libs/libbagel_scf.so multi/casscf/.libs/libbagel_casscf.so pt2/.libs/libbagel_pt2.so grad/.libs/libbagel_grad.so wfn/.libs/libbagel_wfn.so df/.libs/libbagel_df.so smith/.libs/libbagel_smith.so prop/.libs/libbagel_prop.so asd/.libs/libbagel_asd.so asd/dmrg/.libs/libbagel_asd_dmrg.so asd/orbital/.libs/libbagel_asd_orbital.so asd/dimer/.libs/libbagel_dimer.so asd/multisite/.libs/libbagel_multisite.so ci/ciutil/.libs/libbagel_ciutil.so mat1e/.libs/libbagel_mat1e.so periodic/.libs/libbagel_periodic.so integral/.libs/libbagel_integral.so molecule/.libs/libbagel_molecule.so util/io/.libs/libbagel_io.so util/.libs/libbagel_util.so util/parallel/.libs/libbagel_parallel.so util/math/.libs/libbagel_math.so util/input/.libs/libbagel_input.so -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -lboost_unit_test_framework -lboost_regex -lboost_serialization -Wl,-rpath -Wl,/usr/local/bagel/lib main.o: In function boost::archive::detail::common_iarchive<boost::archive::binary_iarchive>::vload(boost::archive::class_name_type&)': main.cc:(.text._ZN5boost7archive6detail15common_iarchiveINS0_15binary_iarchiveEE5vloadERNS0_15class_name_typeE[_ZN5boost7archive6detail15common_iarchiveINS0_15binary_iarchiveEE5vloadERNS0_15class_name_typeE]+0x1): undefined reference toboost::archive::basic_binary_iarchive::load_override(boost::archive::class_name_type&)' main.o: In function void boost::serialization::throw_exception<boost::archive::archive_exception>(boost::archive::archive_exception const&)': main.cc:(.text._ZN5boost13serialization15throw_exceptionINS_7archive17archive_exceptionEEEvRKT_[_ZN5boost13serialization15throw_exceptionINS_7archive17archive_exceptionEEEvRKT_]+0x1d): undefined reference toboost::archive::archive_exception::archive_exception(boost::archive::archive_exception const&)' wfn/.libs/libbagel_wfn.so: undefined reference to bagel::RelFCI::RelFCI(std::shared_ptr<bagel::PTree const>, std::shared_ptr<bagel::Geometry const>, std::shared_ptr<bagel::Reference const>, int, int, std::shared_ptr<bagel::ZCoeff_Block const>, bool, bool)' asd/.libs/libbagel_asd.so: undefined reference tovtable for bagel::RASCivector_impl' smith/.libs/libbagel_smith.so: undefined reference to bagel::ZHarrison::read_external_rdm3(int, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool) const' wfn/.libs/libbagel_wfn.so: undefined reference tobagel::ZHarrison::rdm3(int, int) const' asd/dmrg/.libs/libbagel_asd_dmrg.so: undefined reference to bagel::ApplyOperator::operator()(double, bagel::RASBlockVectors const&, bagel::RASBlockVectors&, std::vector<bagel::GammaSQ, std::allocator<bagel::GammaSQ> > const&, std::vector<int, std::allocator<int> > const&) const' pt2/.libs/libbagel_pt2.so: undefined reference tobagel::ZCASSecond::ZCASSecond(std::shared_ptr, std::shared_ptr, std::shared_ptr)' wfn/.libs/libbagel_wfn.so: undefined reference to bagel::ZCASNoopt::ZCASNoopt(std::shared_ptr<bagel::PTree const>, std::shared_ptr<bagel::Geometry const>, std::shared_ptr<bagel::Reference const>)' asd/.libs/libbagel_asd.so: undefined reference tobagel::RASDeterminants::RASDeterminants(int, int, int, int, int, int, int, bool)' asd/dmrg/.libs/libbagel_asddmrg.so: undefined reference to `bagel::RASCivecView::RASCivecView_(std::shared_ptr, double*)' asd/.libs/libbagel_asd.so: undefined reference to vtable for bagel::RASCivector<double>' asd/.libs/libbagel_asd.so: undefined reference tobagel::FormSigmaRAS::operator()(std::shared_ptr<bagel::Dvector_base<bagel::RASCivector > const>, std::shared_ptr, std::vector<int, std::allocator > const&) const' wfn/.libs/libbagel_wfn.so: undefined reference to vtable for bagel::ZHarrison' wfn/.libs/libbagel_wfn.so: undefined reference tobagel::CIS::CIS(std::shared_ptr, std::shared_ptr, std::shared_ptr)' asd/.libs/libbagel_asd.so: undefined reference to bagel::RASCivector<double>::spin() const' asd/dmrg/.libs/libbagel_asd_dmrg.so: undefined reference tobagel::RAS::spin_raiseimpl(bagel::RASCivecView, bagel::RASCivecView_)' wfn/.libs/libbagel_wfn.so: undefined reference to typeinfo for bagel::ZHarrison' wfn/.libs/libbagel_wfn.so: undefined reference tobagel::RelDvector<std::complex >::extract_state(std::vector<int, std::allocator >) const' wfn/.libs/libbagel_wfn.so: undefined reference to bagel::RASCI::RASCI(std::shared_ptr<bagel::PTree const>, std::shared_ptr<bagel::Geometry const>, std::shared_ptr<bagel::Reference const>)' pt2/.libs/libbagel_pt2.so: undefined reference tobagel::RelJop::compute_half[abi:cxx11](std::shared_ptr, std::shared_ptr, bool, bool)' smith/.libs/libbagel_smith.so: undefined reference to bagel::ZHarrison::read_external_rdm2(int, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' smith/.libs/libbagel_smith.so: undefined reference tobagel::RelDvector<std::complex >::clone() const' pt2/.libs/libbagel_pt2.so: undefined reference to bagel::ZCASSCF::conv_to_ref_(bool) const' asd/dmrg/.libs/libbagel_asd_dmrg.so: undefined reference tobagel::RASCivector_impl::normalize()' asd/dmrg/.libs/libbagel_asd_dmrg.so: undefined reference to bagel::Sparse_IJ::Sparse_IJ(std::shared_ptr<bagel::CIStringSet<bagel::RASString, void> const>, std::shared_ptr<bagel::CIStringSet<bagel::RASString, void> const>)' asd/dmrg/.libs/libbagel_asd_dmrg.so: undefined reference tobagel::RAS::DenomTask::compute()' wfn/.libs/libbagel_wfn.so: undefined reference to bagel::ZCASNoopt_London::ZCASNoopt_London(std::shared_ptr<bagel::PTree const>, std::shared_ptr<bagel::Geometry const>, std::shared_ptr<bagel::Reference const>)' asd/dmrg/.libs/libbagel_asd_dmrg.so: undefined reference tobagel::RAS::spin_lowerimpl(bagel::RASCivecView, bagel::RASCivecView_)' wfn/.libs/libbagel_wfn.so: undefined reference to bagel::ZHarrison::rdm1(int, int) const' asd/.libs/libbagel_asd.so: undefined reference tobagel::RASCivector::spin_lower(std::shared_ptr) const' wfn/.libs/libbagel_wfn.so: undefined reference to bagel::FCI_London::FCI_London(std::shared_ptr<bagel::PTree const>, std::shared_ptr<bagel::Geometry const>, std::shared_ptr<bagel::Reference const>, int, int, std::shared_ptr<bagel::ZCoeff_Block const>)' wfn/.libs/libbagel_wfn.so: undefined reference tobagel::ZHarrison::rdm4(int, int) const' asd/dmrg/.libs/libbagel_asddmrg.so: undefined reference to `bagel::ApplyOperator::operator()(double, bagel::RASCivecView, bagel::RASCivecView_, std::vector<bagel::GammaSQ, std::allocator > const&, std::vector<int, std::allocator > const&) const' asd/dmrg/.libs/libbagel_asd_dmrg.so: undefined reference to bagel::RASCivector_impl<double>::print(double) const' pt2/.libs/libbagel_pt2.so: undefined reference tobagel::RelJop::compute_full(std::shared_ptr, std::cxx11::list<std::shared_ptr, std::allocator<std::shared_ptr > >, bool)' wfn/.libs/libbagel_wfn.so: undefined reference to bagel::ZFCI_bare::ZFCI_bare(std::shared_ptr<bagel::CIWfn_<bagel::RelDvector<std::complex<double> >, std::pair<std::shared_ptr<bagel::RelSpace const>, std::shared_ptr<bagel::RelSpace const> > > const>)' asd/dmrg/.libs/libbagel_asd_dmrg.so: undefined reference tobagel::RAS::spinimpl(bagel::RASCivecView, bagel::RASCivecView_)' wfn/.libs/libbagel_wfn.so: undefined reference to bagel::ZCASNoopt_base::compute()' asd/dmrg/.libs/libbagel_asd_dmrg.so: undefined reference tobagel::RASCivecView_::data()' asd/.libs/libbagel_asd.so: undefined reference to bagel::RASCivector<double>::RASCivector(std::shared_ptr<bagel::RASDeterminants const>)' smith/.libs/libbagel_smith.so: undefined reference tobagel::ZHarrison::read_external_rdm1(int, int, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' smith/.libs/libbagel_smith.so: undefined reference to bagel::ZHarrison::read_external_rdm4(int, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' asd/.libs/libbagel_asd.so: undefined reference tobagel::FormSigmaRAS::operator()(std::shared_ptr<bagel::Dvector_base<bagel::RASCivector > const>, std::shared_ptr, std::shared_ptr, std::vector<int, std::allocator > const&) const' wfn/.libs/libbagel_wfn.so: undefined reference to bagel::ZHarrison::rdm2(int, int) const' asd/.libs/libbagel_asd.so: undefined reference tobagel::RASCivector::spin_raise(std::shared_ptr) const' wfn/.libs/libbagel_wfn.so: undefined reference to bagel::ZCASSecond_London::ZCASSecond_London(std::shared_ptr<bagel::PTree const>, std::shared_ptr<bagel::Geometry const>, std::shared_ptr<bagel::Reference const>)' asd/.libs/libbagel_asd.so: undefined reference tobagel::RASCivector::RASCivector(bagel::RASCivector const&)' asd/.libs/libbagel_asd.so: undefined reference to bagel::RASCivector_impl<double>::synchronize(int)' smith/.libs/libbagel_smith.so: undefined reference tobagel::ZHarrison::rdm34f(int, int, std::shared_ptr) const' collect2: error: ld returned 1 exit status Makefile:533: recipe for target 'BAGEL' failed make[3]: [BAGEL] Error 1 make[3]: Leaving directory '/home/titan/bagel-1.1.1/obj/src' Makefile:584: recipe for target 'all-recursive' failed make[2]: [all-recursive] Error 1 make[2]: Leaving directory '/home/titan/bagel-1.1.1/obj/src' Makefile:416: recipe for target 'all-recursive' failed make[1]: [all-recursive] Error 1 make[1]: Leaving directory '/home/titan/bagel-1.1.1/obj' Makefile:348: recipe for target 'all' failed make: [all] Error 2

can you please help?

shiozaki commented 3 years ago

Without seeing all of the configure options I cannot tell, but there are two things to try: (1) add "--enable-static --disable-shared" (2) add "-Wl,--copy-dt-needed-entries -Wl,--no-as-needed" to CXXFLAGS

shiozaki commented 3 years ago

Please reopen if you have further question.