dftfedevelopers/dftfe

DFT-FE: Real-space DFT calculations using Finite Elements

dftfe's Issues

Trying to build dft-fe with PetSC on CPU's (intel/2023.1 + gcc/9.2.0)

Attempting to build separate real and complex versions - and everything is working up to the final linking. Both the real and complex versions fail with similar linking errors.

I am using

dftfe - release1.0
dealiiCustomizedCUDARelease
petsc/3.17.5
intel/2023.1 (with gcc/9.2.0)
mpiicc and mpiicpc compilers

I noticed (after getting this far) in the user guide it mentions that intel compilers are not supported - and I'm wondering if this is the issue? Or is there something about using the dealiiCustomizedCUDARelease branch but building without cuda support?

$ make VERBOSE=1
/cm/shared/software/cmake/3.20.0/bin/cmake -S/cm/shared/software/dft-fe/1.0.2/b1/src/dftfe -B/cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real --check-build-system CMakeFiles/Makefile.cmake 0
/cm/shared/software/cmake/3.20.0/bin/cmake -E cmake_progress_start /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real/CMakeFiles /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real' make -f CMakeFiles/dftfem.dir/build.make CMakeFiles/dftfem.dir/depend make[2]: Entering directory /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real'
cd /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real && /cm/shared/software/cmake/3.20.0/bin/cmake -E cmake_depends "Unix Makefiles" /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real/CMakeFiles/
dftfem.dir/DependInfo.cmake --color=
make[2]: Leaving directory /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real' make -f CMakeFiles/dftfem.dir/build.make CMakeFiles/dftfem.dir/build make[2]: Entering directory /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real'
make[2]: Nothing to be done for CMakeFiles/dftfem.dir/build'. make[2]: Leaving directory /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real'
[ 95%] Built target dftfem
make -f CMakeFiles/dftfe.dir/build.make CMakeFiles/dftfe.dir/depend
make[2]: Entering directory /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real' cd /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real && /cm/shared/software/cmake/3.20.0/bin/cmake -E cmake_depends "Unix Makefiles" /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real/CMakeFiles/ dftfe.dir/DependInfo.cmake --color= make[2]: Leaving directory /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real'
make -f CMakeFiles/dftfe.dir/build.make CMakeFiles/dftfe.dir/build
make[2]: Entering directory /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real' [ 97%] Linking CXX executable dftfe /cm/shared/software/cmake/3.20.0/bin/cmake -E cmake_link_script CMakeFiles/dftfe.dir/link.txt --verbose=1 /cm/shared/software/intel/2023.1/mpi/2021.9.0/bin/mpiicpc -O2 -fPIC -fopenmp -shared-intel -qopenmp -rdynamic CMakeFiles/dftfe.dir/src/main.cc.o -o dftfe -Wl,-rpath,/cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real:/cm/shared/software/dealii/20230907/b3/lib:/cm/shared/software/slepc/3.17.2/b1/src/slepc-v3.17.2/arch-ci-linux-intel-mkl-single/lib:/cm/shared/software/petsc/3.17.5/b1/src/petsc-3.17.5/arch-ci-linux-intel-mkl-sing le/lib:/cm/shared/software/lle/petsc-hash-pkgs/b3d0e4/lib: libdftfem.so /cm/shared/software/dealii/20230907/b3/lib/libdeal_II.so.9.3.0-pre /usr/lib64/libz.so -lrt /cm/shared/software/p4est/2.2/b1/lib/libp4est.so /cm/shared/software/p4est/2.2/b1/lib/libsc.so -qmkl-ilp64=parallel -lmkl_scalapack_ilp64 -lmkl_blacs_intelmpi_ilp64 -L/cm/shared/software/intel/2023.1/mkl/2023.1.0/lib/intel64 -Wl,--no-as-needed -lmkl_intel_lp64 -lmkl_gnu_thread -lmk l_core -lgomp -lpthread -lm -ldl /cm/shared/software/slepc/3.17.2/b1/src/slepc-v3.17.2/arch-ci-linux-intel-mkl-single/lib/libslepc.so /cm/shared/software/petsc/3.17.5/b1/src/petsc-3.17.5/arch-ci-linux-intel-mkl-single/lib/libpetsc.so /cm/shared/software/intel/2023.1/mkl/2023.1.0/lib/intel64/libmkl_scalapack_lp64.so /cm/shared/software/intel/2023.1/mkl/2023.1.0/lib/intel64/libmkl_blacs_intelmpi_lp64.so /cm/shared/software/intel/2023.1/mkl/2023 .1.0/lib/intel64/libmkl_intel_lp64.so /cm/shared/software/intel/2023.1/mkl/2023.1.0/lib/intel64/libmkl_core.so /cm/shared/software/intel/2023.1/mkl/2023.1.0/lib/intel64/libmkl_sequential.so /cm/shared/software/lle/petsc-hash-pkgs/b3d0e4/lib/libparmetis.so /cm/shared/software/lle/petsc-hash-pkgs/b3d0e4/lib/libmetis.so /usr/lib64/libX11.so -lifport /cm/shared/software/intel/2023.1/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libifcoremt_pic .a /cm/shared/software/intel/2023.1/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libimf.so /cm/shared/software/intel/2023.1/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libsvml.so -lm /cm/shared/software/intel/2023.1/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libipgo.a /cm/shared/software/intel/2023.1/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libirc.so /cm/shared/software/intel/2023.1/compiler/2023.1.0/linux/compiler/lib/ intel64_lin/libirc_s.a -lquadmath -ldl -lAlglib /cm/shared/software/libxc/6.2.2/b1/lib/libxc.a /usr/lib64/libxml2.so /cm/shared/software/spglib/2.1.0/b1/lib64/libsymspg.so /cm/shared/software/elpa/2021.05.002/b1/lib/libelpa_openmp.so icpc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated and will be removed from product release in the second half of 2023. The Intel(R) oneAPI DPC++/C++ Compiler (ICX) is the recommended compiler moving forward. Please transition to use this compiler. Use '-diag-disable=10441' to disable this message. libdftfem.so: undefined reference to void dealii::LinearAlgebra::distributed::Vector<std::complex, dealii::MemorySpace::Host>::reinit<std::complex >(dealii::LinearAlgebra::distributed::Vector<std::complex, dealii::MemorySpace::Host> const&, bool)'
libdftfem.so: undefined reference to dealii::LinearAlgebra::distributed::Vector<std::complex<double>, dealii::MemorySpace::Host>::compress_finish(dealii::VectorOperation::values)' libdftfem.so: undefined reference to dealii::LinearAlgebra::distributed::Vector<std::complex, dealii::MemorySpace::Host>::Vector()'
libdftfem.so: undefined reference to dealii::LinearAlgebra::distributed::Vector<std::complex<double>, dealii::MemorySpace::Host>::zero_out_ghosts() const' libdftfem.so: undefined reference to void dealii::LinearAlgebra::distributed::Vector<std::complex, dealii::MemorySpace::Host>::reinit<std::complex >(dealii::LinearAlgebra::distributed::Vector<std::complex, dealii::MemorySpace::Host> const&, bool)'
libdftfem.so: undefined reference to dealii::LinearAlgebra::distributed::Vector<std::complex<float>, dealii::MemorySpace::Host>::swap(dealii::LinearAlgebra::distributed::Vector<std::complex<float>, dealii::MemorySpace::Host>&)' libdftfem.so: undefined reference to dealii::LinearAlgebra::distributed::Vector<std::complex, dealii::MemorySpace::Host>::Vector()'
libdftfem.so: undefined reference to dealii::LinearAlgebra::distributed::Vector<std::complex<float>, dealii::MemorySpace::Host>::reinit(dealii::IndexSet const&, dealii::IndexSet const&, int const&)' libdftfem.so: undefined reference to dealii::LinearAlgebra::distributed::Vector<std::complex, dealii::MemorySpace::Host>::zero_out_ghosts() const'
libdftfem.so: undefined reference to dealii::LinearAlgebra::distributed::Vector<std::complex<double>, dealii::MemorySpace::Host>::update_ghost_values() const' libdftfem.so: undefined reference to dealii::LinearAlgebra::distributed::Vector<std::complex, dealii::MemorySpace::Host>::compress_start(unsigned int, dealii::VectorOperation::values)'
libdftfem.so: undefined reference to dealii::LinearAlgebra::distributed::Vector<std::complex<float>, dealii::MemorySpace::Host>::update_ghost_values_finish() const' libdftfem.so: undefined reference to dealii::LinearAlgebra::distributed::Vector<std::complex, dealii::MemorySpace::Host>::update_ghost_values() const'
libdftfem.so: undefined reference to dealii::LinearAlgebra::distributed::Vector<std::complex<double>, dealii::MemorySpace::Host>::update_ghost_values_start(unsigned int) const' libdftfem.so: undefined reference to dealii::LinearAlgebra::distributed::Vector<std::complex, dealii::MemorySpace::Host>::swap(dealii::LinearAlgebra::distributed::Vector<std::complex, dealii::MemorySpace::Host>&)'
libdftfem.so: undefined reference to dealii::LinearAlgebra::distributed::Vector<std::complex<double>, dealii::MemorySpace::Host>::update_ghost_values_finish() const' libdftfem.so: undefined reference to dealii::LinearAlgebra::distributed::Vector<std::complex, dealii::MemorySpace::Host>::reinit(dealii::IndexSet const&, dealii::IndexSet const&, int const&)'
libdftfem.so: undefined reference to dealii::LinearAlgebra::distributed::Vector<std::complex<float>, dealii::MemorySpace::Host>::update_ghost_values_start(unsigned int) const' libdftfem.so: undefined reference to dealii::LinearAlgebra::distributed::Vector<std::complex, dealii::MemorySpace::Host>::compress_finish(dealii::VectorOperation::values)'
libdftfem.so: undefined reference to dealii::LinearAlgebra::distributed::Vector<std::complex<double>, dealii::MemorySpace::Host>::compress_start(unsigned int, dealii::VectorOperation::values)' make[2]: *** [dftfe] Error 1 make[2]: Leaving directory /cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real'
make[1]: *** [CMakeFiles/dftfe.dir/all] Error 2
make[1]: Leaving directory `/cm/shared/software/dft-fe/1.0.2/b1/src/dftfe/build/release/real'
make: *** [all] Error 2

Build issue involving conversion to std::function<...>

I was trying to build DFT-FE according to the build manula. However, I get many errors related to std::function<...>

In file included from /home/davidkleiven/Documents/dftfe/src/triangulation/triangulationManager/triangulationManager.cc:32:
/home/davidkleiven/Documents/dftfe/src/triangulation/triangulationManager/restartUtils.cc: In member function ‘void dftfe::triangulationManager::saveTriangulationsCellQuadData(const std::vector<const std::map<dealii::CellId, std::vector<double> >*>&, const MPI_Comm&, const MPI_Comm&)’:
/home/davidkleiven/Documents/dftfe/src/triangulation/triangulationManager/restartUtils.cc:270:90: error: cannot convert ‘const unsigned int’ to ‘const std::function<std::vector<char>(const dealii::TriaIterator<dealii::CellAccessor<3, 3> >&, dealii::Triangulation<3, 3>::CellStatus)>&’
  270 |          const unsigned int offset = d_parallelTriangulationUnmoved.register_data_attach(dataSizeInBytes,
      |                                                                                          ^~~~~~~~~~~~~~~
      |                                                                                          |
      |                                                                                          const unsigned int

there are many similar errors where std::function is involved. Any ideas on what causes this error?

Here is the full output from running setup.sh
setup_output.txt

A GUI for DFT-FE

I have recently installed DFT-FE and started running a few test calculations. I couldn't find a way to easily convert my existing input files or CIFs to the DFT-FE format.

Therefore, to streamline the process of setting up calculations and facilitate the creation of the input files, I have created a web app (https://dft-fe.streamlit.app/) that can serve as a GUI for DFT-FE.

It creates input files such as coordinates.inp, domainVectors.inp, pseudo.inp, and parameters.prm. It also automatically fetches the SG15 pseudopotentials.

Currently, it allows one to create input files for a given material in the materialsproject.org database, or a molecule in PubChem database. It also allows to create input files form Quantum ESPRESSO input, CIFs, POSCARs, extended XYZs, etc.

Hope the developers and users of DFT-FE will find it useful and can test it out. Essentially, I created the web app by modifying an existing app (https://ripertools.turbomole.org/), that I created for TURBOMOLE (https://www.turbomole.org/).

question about dealii::DoFTools::make_hanging_node_constraints_from_serial

HI All,

I'm helping some users with getting going with DFT FE version 1.0.2. I'm noticing an issue with DEALII's DoFTtools, in particular DFT FE is using a make_hanging_node_constraints_from_serial method which is not defined in any of the branches of DEALII that are on the public github repo - [email protected]:dealii/dealii.git - that i've checked so far.

Does one need to use a special version of DEALII to build DFT FE 1.0.2?

Thanks,

Howard

Print out citation information from libxc

Hi,

DFT-FE appears to use libxc exclusively to evaluate density functionals, but doesn't seem to be printing out any information about it. I would kindly ask to include the following information in the DFT-FE output:

• the version of libxc used (produced by xc_version_string())
• the citation for the used version of libxc (journal reference produced by xc_reference() and doi by xc_reference_doi())

In addition to Libxc, users should also cite the employed density functionals. This information is conveniently stored inside Libxc in the func->info->refs field, which should be likewise printed out by DFT-FE.