[QE-users] Error compiling qe5.1 linked to libbeef-v0.1.1, “Nonexistent include directory .. [-Wmissing-include-dirs]”

[Delgado DelgadoJorge]

Dear Paolo,


Once again, thank you very much for the quick reply. I considered your last suggestion, but before of doing so, I tried to compile qe using intel compilers and (to my surprise) it finally succeeded!.

Since the procedure that worked for me include details not described so far in the web, here I try to share a detailed explanation for the compilation of qe5.1-lbeef (libbeef) that worked for me, in case somebody else face similar issues in the future:



OS: Ubuntu v.18.04.1 (64bit Virtual machine guest on Windows 10 host – VirtualBox6.0)

icc : Intel® Parallel Studio XE 2019 Update 4 Cluster Eddition for Linux



1. (after installing intel compilers) Initialize the intel compiler:

Initiallize the icc, ifortran in the working terminal. Stepped at e.g. "/intel/bin", type

              source compilervars.sh intel64

              source iccvars.sh intel64

              source ifortvars.sh intel64



2. lbeef configuration-installation:

Check the icc compiler is active in the working terminal (should be icc..)

              icc --version



Configuration of lbeef 0.1.1.

Installation/compilation of lbeef

             ./configure CC=icc --prefix=/home/jorge/aist-qe-installations/37/libbeef-0.1.1

              make

              make install



3. Compilation of qe5.1-patched/lbeef

Configuration (A detailed tutorial about the compilation of qe using intel compilers can be find in:  https://www.youtube.com/watch?v=doudMLEaq3w)

              ./configure MPIF90=mpiifort CC=mpiicc F90=ifort F77=mpiifort -enable-parallel BEEF_LIBS="-L/home/jorge/aist-qe-installations/37/libbeef-0.1.1/lib -lbeef"



Edit the make.sys file generated after the configuration with the corresponding Intel MKL libraries:

BLAS_LIBS      =   -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread -lm -ldl

LAPACK_LIBS    = -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread -lm -ldl

SCALAPACK_LIBS = -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread -lm -ldl

FFT_LIBS       = -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread -lm -ldl

MPI_LIBS       = -L/home/intel/impi/2019.4.243/intel64/lib/ -lmpi

MASS_LIBS      = -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread -lm -ldl

Note:  the Intel Math Kernel Libraries are specific for the system used (version if icc, OS, etc), please see to the following video for a detailed explanation of this step:  https://www.youtube.com/watch?v=doudMLEaq3w); remember to save the file!





compilation of qe:

              make pw



generation of kernel tables

             bin/generate_rVV10_kernel_table.x

              bin/generate_vdW_kernel_table.x



4. Running a calculation

Note: The generated "generate_vdW_kernel_table", table (located also in the qe folder) must be copied into the folder containig the input file to be run

Note: Remember to have intialized icc/intel compiler and libraries in the working terminal



check the intel mpirun, must be icc …

              which mpirun



run (synthax)

              mpirun '/home/jorge/aist-qe-installations/37/espresso.5.1.r11289.pybeef/espresso/bin/pw.x' -in test20.in> test20.out




Regards,

Jorge

-----
Jorge A. Delgado, Ph.D.
Research Scientist - Catalysis and Nanomaterials
Flow Chemistry Team, Catalytic Chemistry Research Center (IRC3)
National Institute of Advanced Industrial Science and Technology (AIST)
Central 5-2, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
Phone: +81 80-2151-8731
Email:  delgadodelgado.jorge at aist.go.jp<mailto:ayada at sbchem.kyoto-u.ac.jp>


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