Fail to install anphon

[LePingKYXK]

Dear Dr. Tadano,

I am trying to install alamode through the native environment in the high-performance cluster (HPC) following the instruction in the high-performance cluster (HPC). However, an error

The Boost C++ was downloaded via boost.org with the version of 1.82.0, while the Eigen3 library was downloaded via libeigen Gitlab with the version of 3.4.
The spglib was downloaded from spglib Github with the version of 2.1.

The compilers I used were Intel OneAPI compiler 2022.2, cmake 3.20.1

(base) [clxy_wh@login anphon]$ module list
Currently Loaded Modulefiles:
  1) compiler/gcc/9.5.0               2) compiler/oneapi/2022.2.0         3) mpi/oneapi/2021.6.0              4) compiler/cmake-compiler/3.20.1

I extracted the Boost C++ and Eigen3 libraries into the /public/home/clxy_wh/myapps/ect directory and then set the symbolic link in the /public/home/clxy_wh/myapps/include directory. The spglib was installed in the /public/home/clxy_wh/myapps/spglib directory.

Before compiling alamode, I set export SPGLIB_ROOT=/public/home/clxy_wh/myapps/spglib.

The alamode was put in the /public/home/clxy_wh/myapps/alamode directory.
In the alm directory, I copied the Makefile.linux to Makefile and modified the following lines,

CXX = icpc
CXXFLAGS = -O2 -xHOST -qopenmp -std=c++11
INCLUDE = -I../include -I$(HOME)/myapps/include -I$(SPGLIB_ROOT)/include

CXXL = ${CXX}
LDFLAGS = -qmkl -L$(SPGLIB_ROOT)/lib64 -lsymspg

Here, I specified the -I$(HOME)/myapps/include, and set LDFLAGS =-qmkl since I used the MKL of Intel OneAPI. It worked well and got the binary file alm.

In the anphon directory, I performed similarly as the previous step, modifying the Makefile as

MPICXX = mpiicpc

CXXFLAGS = -O3 -xHOST -qopenmp -std=c++11

INCLUDE = -I../include -I$(HOME)/myapps/include -I$(MKLROOT)/include/fftw

LINKER = ${MPICXX}
LDFLAGS = -qmkl

When I run make -j, however, it reported an error, shown below

(base) [clxy_wh@login anphon]$ make -j
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c kpoint.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c dielec.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c gruneisen.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c phonons.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c isotope.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c thermodynamics.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c write_phonons.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c symmetry_core.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c ewald.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c fcs_phonon.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c timer.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c mode_analysis.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c anharmonic_core.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c conductivity.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c system.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c selfenergy.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c phonon_velocity.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c integration.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c dynamical.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c phonon_dos.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c mpi_common.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c main.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c scph.cpp
mpiicpc  -O3 -xHOST -qopenmp -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -I/public/software/compiler/intel-compiler/2022.2.0/mkl/2022.1.0/include/fftw -c parsephon.cpp
In file included from /public/home/clxy_wh/myapps/include/boost/math/special_functions/detail/round_fwd.hpp(11),
                 from /public/home/clxy_wh/myapps/include/boost/math/special_functions/math_fwd.hpp(29),
                 from /public/home/clxy_wh/myapps/include/boost/math/special_functions/erf.hpp(13),
                 from ewald.cpp(27):
/public/home/clxy_wh/myapps/include/boost/math/tools/config.hpp(23): warning #1224: #warning directive: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
  #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
       ^

/public/home/clxy_wh/myapps/include/Eigen/src/Core/products/GeneralMatrixMatrix.h(104): warning #2196: routine is both "inline" and "noinline"
        pack_rhs(blockB, rhs.getSubMapper(k,0), actual_kc, nc);
                                                              ^
          detected during:
            instantiation of "void Eigen::internal::general_matrix_matrix_product<Index, LhsScalar, LhsStorageOrder, ConjugateLhs, RhsScalar, RhsStorageOrder, ConjugateRhs, 0, ResInnerStride>::run(Index, Index, Index, const LhsScalar *, Index, const RhsScalar *, Index, Eigen::internal::general_matrix_matrix_product<Index, LhsScalar, LhsStorageOrder, ConjugateLhs, RhsScalar, RhsStorageOrder, ConjugateRhs, 0, ResInnerStride>::ResScalar *, Index, Index,
                      Eigen::internal::general_matrix_matrix_product<Index, LhsScalar, LhsStorageOrder, ConjugateLhs, RhsScalar, RhsStorageOrder, ConjugateRhs, 0, ResInnerStride>::ResScalar, Eigen::internal::level3_blocking<LhsScalar, RhsScalar> &, Eigen::internal::GemmParallelInfo<Index> *) [with Index=Eigen::Index={std::ptrdiff_t={long}}, LhsScalar=std::complex<double>, LhsStorageOrder=0, ConjugateLhs=true, RhsScalar=std::complex<double>, RhsStorageOrder=1, ConjugateRhs=false,
                      ResInnerStride=1]" at line 40
            instantiation of "void Eigen::internal::general_matrix_matrix_product<Index, LhsScalar, LhsStorageOrder, ConjugateLhs, RhsScalar, RhsStorageOrder, ConjugateRhs, 1, ResInnerStride>::run(Index, Index, Index, const LhsScalar *, Index, const RhsScalar *, Index, Eigen::internal::general_matrix_matrix_product<Index, LhsScalar, LhsStorageOrder, ConjugateLhs, RhsScalar, RhsStorageOrder, ConjugateRhs, 1, ResInnerStride>::ResScalar *, Index, Index,
                      Eigen::internal::general_matrix_matrix_product<Index, LhsScalar, LhsStorageOrder, ConjugateLhs, RhsScalar, RhsStorageOrder, ConjugateRhs, 1, ResInnerStride>::ResScalar, Eigen::internal::level3_blocking<RhsScalar, LhsScalar> &, Eigen::internal::GemmParallelInfo<Index> *) [with Index=Eigen::Index={std::ptrdiff_t={long}}, LhsScalar=std::complex<double>, LhsStorageOrder=0, ConjugateLhs=false, RhsScalar=std::complex<double>, RhsStorageOrder=1, ConjugateRhs=true,
                      ResInnerStride=1]" at line 230
            instantiation of "void Eigen::internal::gemm_functor<Scalar, Index, Gemm, Lhs, Rhs, Dest, BlockingType>::operator()(Index, Index, Index, Index, Eigen::internal::GemmParallelInfo<Index> *) const [with Scalar=std::complex<double>, Index=Eigen::Index={std::ptrdiff_t={long}}, Gemm=Eigen::internal::general_matrix_matrix_product<Eigen::Index={std::ptrdiff_t={long}}, std::complex<double>, 0, false, std::complex<double>, 1, true, 1, 1>, Lhs=Eigen::Matrix<std::complex<double>, -1, -1, 0, -1,
                      -1>, Rhs=Eigen::Transpose<const Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>>, Dest=Eigen::Matrix<std::complex<double>, -1, -1, 1, -1, -1>, BlockingType=Eigen::internal::gemm_blocking_space<1, std::complex<double>, std::complex<double>, -1, -1, -1, 1, false>]" at line 141 of "/public/home/clxy_wh/myapps/include/Eigen/src/Core/products/Parallelizer.h"
            instantiation of "void Eigen::internal::parallelize_gemm<Condition,Functor,Index>(const Functor &, Index, Index, Index, bool) [with Condition=true, Functor=Eigen::internal::gemm_functor<std::complex<double>, Eigen::Index={std::ptrdiff_t={long}}, Eigen::internal::general_matrix_matrix_product<Eigen::Index={std::ptrdiff_t={long}}, std::complex<double>, 0, false, std::complex<double>, 1, true, 1, 1>, Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>, Eigen::Transpose<const
                      Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>>, Eigen::Matrix<std::complex<double>, -1, -1, 1, -1, -1>, Eigen::internal::gemm_blocking_space<1, std::complex<double>, std::complex<double>, -1, -1, -1, 1, false>>, Index=Eigen::Index={std::ptrdiff_t={long}}]" at line 509
            instantiation of "void Eigen::internal::generic_product_impl<Lhs, Rhs, Eigen::DenseShape, Eigen::DenseShape, 8>::scaleAndAddTo(Dest &, const Lhs &, const Rhs &, const Eigen::internal::generic_product_impl<Lhs, Rhs, Eigen::DenseShape, Eigen::DenseShape, 8>::Scalar &) [with Lhs=Eigen::Product<Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>, Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>, 0>,
                      Rhs=Eigen::CwiseUnaryOp<Eigen::internal::scalar_conjugate_op<std::complex<double>>, const Eigen::Transpose<const Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>>>, Dest=Eigen::Matrix<std::complex<double>, -1, -1, 1, -1, -1>]" at line 445
            [ 5 instantiation contexts not shown ]
            instantiation of "Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const T &) [with _Scalar=std::complex<double>, _Rows=-1, _Cols=-1, _Options=1, _MaxRows=-1, _MaxCols=-1, T=Eigen::Product<Eigen::Product<Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>, Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>, 0>, Eigen::CwiseUnaryOp<Eigen::internal::scalar_conjugate_op<std::complex<double>>, const Eigen::Transpose<const
                      Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>>>, 0>]" at line 850 of "/public/home/clxy_wh/myapps/include/Eigen/src/Core/AssignEvaluator.h"
            instantiation of "void Eigen::internal::call_assignment(Dst &, const Src &, const Func &, Eigen::internal::enable_if<Eigen::internal::evaluator_assume_aliasing<Src, Eigen::internal::evaluator_traits<Src>::Shape>::value, void *>::type) [with Dst=Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>, Src=Eigen::Product<Eigen::Product<Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>, Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>, 0>,
                      Eigen::CwiseUnaryOp<Eigen::internal::scalar_conjugate_op<std::complex<double>>, const Eigen::Transpose<const Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>>>, 0>, Func=Eigen::internal::assign_op<std::complex<double>, std::complex<double>>]" at line 836 of "/public/home/clxy_wh/myapps/include/Eigen/src/Core/AssignEvaluator.h"
            instantiation of "void Eigen::internal::call_assignment(Dst &, const Src &) [with Dst=Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>, Src=Eigen::Product<Eigen::Product<Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>, Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>, 0>, Eigen::CwiseUnaryOp<Eigen::internal::scalar_conjugate_op<std::complex<double>>, const Eigen::Transpose<const Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>>>, 0>]" at line 779 of
                      "/public/home/clxy_wh/myapps/include/Eigen/src/Core/PlainObjectBase.h"
            instantiation of "Derived &Eigen::PlainObjectBase<Derived>::_set(const Eigen::DenseBase<OtherDerived> &) [with Derived=Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>, OtherDerived=Eigen::Product<Eigen::Product<Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>, Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>, 0>, Eigen::CwiseUnaryOp<Eigen::internal::scalar_conjugate_op<std::complex<double>>, const Eigen::Transpose<const Eigen::Matrix<std::complex<double>, -1, -1,
                      0, -1, -1>>>, 0>]" at line 225 of "/public/home/clxy_wh/myapps/include/Eigen/src/Core/Matrix.h"
            instantiation of "Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols> &Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::operator=(const Eigen::DenseBase<OtherDerived> &) [with _Scalar=std::complex<double>, _Rows=-1, _Cols=-1, _Options=0, _MaxRows=-1, _MaxCols=-1, OtherDerived=Eigen::Product<Eigen::Product<Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>, Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>, 0>,
                      Eigen::CwiseUnaryOp<Eigen::internal::scalar_conjugate_op<std::complex<double>>, const Eigen::Transpose<const Eigen::Matrix<std::complex<double>, -1, -1, 0, -1, -1>>>, 0>]" at line 6565 of "scph.cpp"

mpiicpc  -qmkl  -o anphon kpoint.o dielec.o gruneisen.o phonons.o isotope.o thermodynamics.o write_phonons.o symmetry_core.o ewald.o fcs_phonon.o timer.o mode_analysis.o anharmonic_core.o conductivity.o system.o selfenergy.o phonon_velocity.o integration.o dynamical.o phonon_dos.o mpi_common.o main.o scph.o parsephon.o 
kpoint.o: In function `niggli_reduction(Eigen::Matrix<double, 3, 3, 0, 3, 3> const&, Eigen::Matrix<double, 3, 3, 0, 3, 3>&, Eigen::Matrix<double, 3, 3, 0, 3, 3>&, double)':
kpoint.cpp:(.text._Z16niggli_reductionRKN5Eigen6MatrixIdLi3ELi3ELi0ELi3ELi3EEERS1_S4_d[_Z16niggli_reductionRKN5Eigen6MatrixIdLi3ELi3ELi0ELi3ELi3EEERS1_S4_d]+0x79): undefined reference to `niggli_reduce'
make: *** [anphon] Error 1

For tools, I modified Makefile as

#Intel compiler
CXX = icpc

CXXFLAGS = -O2 -std=c++11

# Add the directory containing boost header files here
INCLUDE = -I../include -I$(HOME)/myapps/include

Then, I run make -j in the tools directory

(base) [clxy_wh@login tools]$ make  -j
icpc -O2 -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -c analyze_phonons.cpp
icpc -O2 -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -c qe2alm.cpp
icpc -O2 -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -c dfc2.cpp
icpc -O2 -std=c++11 -I../include -I/public/home/clxy_wh/myapps/include -c fc_virtual.cpp
analyze_phonons.cpp(609): warning #3180: unrecognized OpenMP #pragma
  #pragma omp parallel
  ^

analyze_phonons.cpp(618): warning #3180: unrecognized OpenMP #pragma
  #pragma omp for private(nsame, tau_tmp, c_tmp, vel_tmp, mfp_tmp, is, i, j, k)
  ^

analyze_phonons.cpp(650): warning #3180: unrecognized OpenMP #pragma
  #pragma omp critical
  ^

analyze_phonons.cpp(752): warning #3180: unrecognized OpenMP #pragma
  #pragma omp parallel
  ^

analyze_phonons.cpp(763): warning #3180: unrecognized OpenMP #pragma
  #pragma omp for private(nsame, tau_tmp, c_tmp, mfp_tmp, is_longer_than_L, is, i, j, k)
  ^

analyze_phonons.cpp(800): warning #3180: unrecognized OpenMP #pragma
  #pragma omp critical
  ^

icpc -O2 -std=c++11 -o analyze_phonons analyze_phonons.o
icpc -O2 -std=c++11 -o qe2alm qe2alm.o
icpc -O2 -std=c++11 -o fc_virtual fc_virtual.o
icpc -O2 -std=c++11 -o dfc2 dfc2.o
(base) [clxy_wh@login tools]$

It reported some warnings, but four binary files were obtained, i.e., analyze_phonons, dfc2, fc_virtual, and qe2alm. I am not sure is that correct for tools.

It would be greatly appreciated if you could provide any suggestions to solve the error in anphon.
Thank you very much.
Best regards,
Huan

[ttadano]

Can you recompile anphon without the -xHOST option? (or replace it with an older SIMD option, such as -xCORE-AVX2)