Molcas Forum

Rafael

Member

Registered: 2016-11-16

Posts: 12

[SOLVED] Compiling WFA module

Hi,

I have been trying to compile OpenMolcas on the RACKHAM cluster (Uppsala, Sweden), with the WFA module, but I keep getting some error.

This is my cmake:

CC=icc FC=ifort cmake -DWFA=ON -DARMADILLO_INC=/sw/libs/Armadillo/7.900.0/rackham/include -DLINALG=MKL -DCMAKE_INSTALL_PREFIX=/home/rccouto/omolcas ../

My loaded module list:

Currently Loaded Modules:
  1) uppmax                          8) ifort/2018.3.222-GCC-7.3.0-2.30                     15) cURL/7.60.0-GCCcore-7.3.0
  2) Armadillo/7.900.0               9) iccifort/2018.3.222-GCC-7.3.0-2.30                  16) netCDF/4.6.1-intel-2018b
  3) python/2.7.15                  10) impi/2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30  17) YAXT/0.6.0-intel-2018b
  4) python3/3.7.2                  11) iimpi/2018b                                         18) JasPer/2.0.14-GCCcore-7.3.0
  5) GCCcore/7.3.0                  12) imkl/2018.3.222-iimpi-2018b                         19) ecCodes/2.9.2-intel-2018b
  6) binutils/2.30-GCCcore-7.3.0    13) intel/2018b                                         20) CDO/1.9.5-intel-2018b
  7) icc/2018.3.222-GCC-7.3.0-2.30  14) Szip/2.1.1-GCCcore-7.3.0

And this is the error I'm getting:

Linking Fortran executable bin/wfa.exe
ifort: command line remark #10148: option '-i_dynamic' not supported
lib/libwfa_molcas.a(molcas_wf_analysis_data.C.o): In function `libwfa::molcas_wf_analysis_data::molcas_wf_analysis_data(char*)':
molcas_wf_analysis_data.C:(.text+0x10a): undefined reference to `H5::H5File::H5File(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, H5::FileCreatPropList const&, H5::FileAccPropList const&)'
lib/libwfa_molcas.a(molcas_wf_analysis_data.C.o): In function `libwfa::molcas_wf_analysis_data::orbital_printer(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
molcas_wf_analysis_data.C:(.text+0x29a5): undefined reference to `libwfa::orbital_printer_molden::orbital_printer_molden(libwfa::export_molden_i&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::bitset<5ul> const&)'
lib/libwfa_molcas.a(molcas_wf_analysis_data.C.o): In function `libwfa::molcas_wf_analysis_data::read_vec_h5(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
molcas_wf_analysis_data.C:(.text+0x5e36): undefined reference to `H5::CommonFG::openDataSet(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
lib/libwfa_molcas.a(molcas_wf_analysis_data.C.o): In function `libwfa::molcas_wf_analysis_data::read_cube_h5(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
molcas_wf_analysis_data.C:(.text+0x6269): undefined reference to `H5::CommonFG::openDataSet(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
lib/libwfa_molcas.a(molcas_wf_analysis_data.C.o): In function `libwfa::molcas_wf_analysis_data::molcas_wf_analysis_data(char*)':
molcas_wf_analysis_data.C:(.text+0x819a): undefined reference to `H5::H5File::H5File(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, H5::FileCreatPropList const&, H5::FileAccPropList const&)'
lib/libwfa_molcas.a(molcas_wf_analysis_data.C.o): In function `libwfa::molcas_wf_analysis_data::read_mltpl_mat(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long, unsigned long)':
molcas_wf_analysis_data.C:(.text+0x8c99): undefined reference to `H5::CommonFG::openDataSet(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
lib/libwfa_molcas.a(molcas_wf_analysis_data.C.o): In function `libwfa::molcas_wf_analysis_data::get_mo_types(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
molcas_wf_analysis_data.C:(.text+0x9d2c): undefined reference to `H5::CommonFG::openDataSet(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
lib/libwfa_molcas.a(molcas_wf_analysis_data.C.o): In function `libwfa::molcas_wf_analysis_data::get_mo_vectors(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
molcas_wf_analysis_data.C:(.text+0x9f23): undefined reference to `H5::CommonFG::openDataSet(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
lib/libwfa_molcas.a(molcas_wf_analysis_data.C.o): In function `libwfa::molcas_wf_analysis_data::initialize()':
molcas_wf_analysis_data.C:(.text+0xab07): undefined reference to `H5::Attribute::read(H5::DataType const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&) const'
molcas_wf_analysis_data.C:(.text+0xabb7): undefined reference to `H5::CommonFG::openDataSet(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
molcas_wf_analysis_data.C:(.text+0xae70): undefined reference to `H5::CommonFG::openDataSet(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
molcas_wf_analysis_data.C:(.text+0xb12e): undefined reference to `H5::CommonFG::openDataSet(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
molcas_wf_analysis_data.C:(.text+0xb2d6): undefined reference to `H5::CommonFG::openDataSet(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
molcas_wf_analysis_data.C:(.text+0xb4eb): undefined reference to `H5::CommonFG::openDataSet(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
lib/libwfa_molcas.a(molcas_export_h5orbs.C.o): In function `libwfa::molcas_export_h5orbs::h5_vec(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, arma::Col<double>)':
molcas_export_h5orbs.C:(.text+0x25c9): undefined reference to `H5::CommonFG::createDataSet(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, H5::DataType const&, H5::DataSpace const&, H5::DSetCreatPropList const&) const'
molcas_export_h5orbs.C:(.text+0x2677): undefined reference to `H5::Attribute::write(H5::DataType const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
molcas_export_h5orbs.C:(.text+0x2764): undefined reference to `H5::CommonFG::openDataSet(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
lib/libwfa_molcas.a(molcas_export_h5orbs.C.o): In function `libwfa::molcas_export_h5orbs::setup(H5::H5File&)':
molcas_export_h5orbs.C:(.text+0x3139): undefined reference to `H5::Attribute::write(H5::DataType const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
make[2]: *** [bin/wfa.exe] Error 1
make[1]: *** [CMakeFiles/wfa.exe.dir/all] Error 2
make: *** [all] Error 2

Can anyone help me with this?

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,012

Re: [SOLVED] Compiling WFA module

This works for me:

$ module purge
$ module load uppmax intel cmake python3 Armadillo
$ module list
Currently Loaded Modules:
  1) uppmax   2) intel/19.5   3) cmake/3.13.2   4) python3/3.7.2   5) Armadillo/7.900.0

$ FC=ifort CC=icc CXX=icpc cmake -D LINALG=MKL -D BUILD_SHARED_LIBS=ON -D OPENMP=ON -D WFA=ON -D TOOLS=ON ..

Rafael

Member

Registered: 2016-11-16

Posts: 12

Re: [SOLVED] Compiling WFA module

It worked now.
Thank you Ignacio