why the HDF5 and libxc is enable but not work？  [SOLVED]

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jianzhifu
Posts: 21
Joined: Tue Oct 29, 2013 9:20 am

why the HDF5 and libxc is enable but not work？

Post by jianzhifu » Sat Oct 24, 2020 12:07 pm

Dear all,
When I compile the libxc, and then compile the abinit,
The libxc and HDF5 is enabled but can not work.

I use centos 8.2, intel compilers_and_libraries_2020.2.254 && parallel_studio_xe_2020.2.108

The configure error is:

Code: Select all

Abinit feature triggers status
==============================

The following summary table indicates the status of the feature triggers,
whether they are available and working, how they have been initialized
and whether there are fallbacks to substitute broken ones.

  +----------------+--------+--------+--------+--------+
  |Feature         |Enabled |Init    |Working |Fallback|
  +----------------+--------+--------+--------+--------+
  |abinit_common   |no      |def     |unknown |no      |
  |bigdft          |no      |def     |unknown |disabled|
  |fft             |yes     |kwd     |yes     |no      |
  |fftw3           |no      |def     |unknown |no      |
  |gpu             |no      |def     |no      |no      |
  |hdf5            |yes     |dir     |no      |disabled|
  |levmar          |no      |def     |unknown |no      |
  |libpaw          |no      |def     |unknown |no      |
  |libpsml         |no      |def     |unknown |disabled|
  |libxc           |yes     |dir     |no      |disabled|
  |libxml2         |no      |def     |unknown |no      |
  |linalg          |yes     |env     |no      |disabled|
  |mpi             |yes     |yon     |yes     |no      |
  |netcdf          |yes     |dir     |no      |disabled|
  |netcdf_fortran  |yes     |dir     |no      |disabled|
  |papi            |no      |def     |unknown |no      |
  |pfft            |no      |def     |unknown |no      |
  |triqs           |no      |def     |unknown |no      |
  |wannier90       |no      |def     |unknown |disabled|
  |xmlf90          |no      |def     |unknown |disabled|
  +----------------+--------+--------+--------+--------+


  +------------------------------------------------------------------+
  | WARNING : HDF5 is not WORKING !                                      |
  +------------------------------------------------------------------+
  |                                                                  |
  | Please point the configuration to a working HDF5 installation    |
  |                                                                  |
  | Note: NetCDF and NetCDFF depend of HDF5. So we cannot test         |
  | whether NetCDF and NetCDFF are properly installed.               |
  +------------------------------------------------------------------+


  +------------------------------------------------------------------+
  | WARNING : LibXC is not WORKING !                                     |
  +------------------------------------------------------------------+
  | Please point the configuration to a working libXC installation   |
  +------------------------------------------------------------------+


  +------------------------------------------------------------------+
  | Problems must be solved before continuing                          |
  +------------------------------------------------------------------+

checking that generated files are newer than configure... done
The config.ac9 is:

Code: Select all

# MPI settings
FC="mpiifort"
CC="mpiicc"
CXX="mpiicpc"
with_mpi="yes"
enable_mpi_io="yes"

# linear algebra settings
with_linalg_flavor="mkl"
LINALG_CPPFLAGS="-I${MKLROOT}/include"
LINALG_FCFLAGS="-I${MKLROOT}/include"
LINALG_LIBS="-L${MKLROOT}/lib/intel64 -lmkl_intel_ilp64 -lmkl_core -lmkl_intel_thread -lmkl_scalapack_ilp64 -lmkl_blacs_intelmpi_ilp64 -lpthread -lm"

# mandatory libraries
with_hdf5="yes"
with_netcdf="yes"
with_netcdf_fortran="yes"
with_libxc="yes"

# FFT flavor
with_fft_flavor="dfti"
FFT_FCFLAGS="-I${MKLROOT}/include"

# Enable Netcdf mode in Abinit (use netcdf as default I/O library)
enable_netcdf_default="yes"

with_libxc=/home/sunlight/work/abinit/abinit-9.2.1/buildfallbacks/install/libxc-5.0.0
with_hdf5=/home/sunlight/work/5208abinit/abinit-9.2.1/build/fallbacks/install_fb/intel/19.1/hdf5/1.10.6
H5CC="/home/sunlight/work/abinit/abinit-9.2.1/build/fallbacks/install_fb/intel/19.1/hdf5/bin"
HDF5_CPPFLAGS="-I/home/sunlight/work/abinit/abinit-9.2.1/build/fallbacks/install_fb/intel/19.1/hdf5/1.10.6/include"
HDF5_FCFLAGS="-I/home/sunlight/work/abinit/abinit-9.2.1/build/fallbacks/install_fb/intel/19.1/hdf5/1.10.6/include"
HDF5_LIBS="-L/home/sunlight/work/abinit/abinit-9.2.1/build/fallbacks/install_fb/intel/19.1/hdf5/1.10.6/lib -lhdf5 -lhdf5_hl"
with_netcdf=/home/sunlight/work/abinit/abinit-9.2.1/build/fallbacks/install_fb/intel/19.1/netcdf4/4.6.3
with_netcdf_fortran=/home/sunlight/work/abinit/abinit-9.2.1/build/fallbacks/install_fb/intel/19.1/netcdf4_fortran/4.5.2
Could you give me some advice?
Thanks!
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jbeuken
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Re: why the HDF5 and libxc is enable but not work？

Post by jbeuken » Mon Oct 26, 2020 8:37 pm

Hi,

in your ac file, there are a few unnecessary "extra" lines that may have produced the problem :

Code: Select all

# MPI settings
FC="mpiifort"
CC="mpiicc"
CXX="mpiicpc"
with_mpi="yes"
enable_mpi_io="yes"

# linear algebra settings
with_linalg_flavor="mkl"
LINALG_CPPFLAGS="-I${MKLROOT}/include"
LINALG_FCFLAGS="-I${MKLROOT}/include"
LINALG_LIBS="-L${MKLROOT}/lib/intel64 -lmkl_intel_ilp64 -lmkl_core -lmkl_intel_thread -lmkl_scalapack_ilp64 -lmkl_blacs_intelmpi_ilp64 -lpthread -lm"

# FFT flavor
with_fft_flavor="dfti"
FFT_FCFLAGS="-I${MKLROOT}/include"

# Enable Netcdf mode in Abinit (use netcdf as default I/O library)
enable_netcdf_default="yes"

with_libxc=/home/sunlight/work/abinit/abinit-9.2.1/buildfallbacks/install/libxc-5.0.0
with_hdf5=/home/sunlight/work/5208abinit/abinit-9.2.1/build/fallbacks/install_fb/intel/19.1/hdf5/1.10.6
with_netcdf=/home/sunlight/work/abinit/abinit-9.2.1/build/fallbacks/install_fb/intel/19.1/netcdf4/4.6.3
with_netcdf_fortran=/home/sunlight/work/abinit/abinit-9.2.1/build/fallbacks/install_fb/intel/19.1/netcdf4_fortran/4.5.2
------
Jean-Michel Beuken
Computer Scientist
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jianzhifu
Posts: 21
Joined: Tue Oct 29, 2013 9:20 am

Re: why the HDF5 and libxc is enable but not work？

Post by jianzhifu » Wed Oct 28, 2020 7:46 am

Dear Jean-Michel Beuken,
As you suggested, the config.ac9 is modified, but the problem still exists,
the config.log is shown in the attachment.

Could you give me some advice?

Thanks!

zj.
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jbeuken
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Re: why the HDF5 and libxc is enable but not work？

Post by jbeuken » Mon Nov 02, 2020 2:41 pm

Hi,

something strange...
in your first post ( 24 Oct ), You used abinit 9.2.1
with_libxc=/home/sunlight/work/abinit/abinit-9.2.1/buildfallbacks/install/libxc-5.0.0
PS : We do not support libXC 5.0.0 yet. !
in your lst post, you used abinit 9.0.4
/home/sunlight/work/abinit/abinit-9.0.4/build/fallbacks/install_fb/intel/19.1/libxc/4.2.3/lib
did you mixed two versions of fallbacks ?

can you retry with the last version : https://www.abinit.org/package/9.2.1
and sent to me config.log, ac file and output of .configure ?

A+
jmb
------
Jean-Michel Beuken
Computer Scientist
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jianzhifu
Posts: 21
Joined: Tue Oct 29, 2013 9:20 am

Re: why the HDF5 and libxc is enable but not work？

Post by jianzhifu » Wed Dec 02, 2020 10:01 am

Dear Jean-Michel Beuken,
when I compile abinit 9.2.1，the fallback could not be compiled rightly，so the fallback of abinit 9.0.4 is used for installing
abinit 9.2.1.

When I replace by abinit 9.2.2，the problem is solved。

But when I make the makefile of 9.2.2， there are many “undefined reference”，

Code: Select all

../../src/28_numeric_noabirule/lib28_numeric_noabirule.a(m_hide_lapack.o)：infunction‘zginv’：
/home/sunlight/work/abinit/abinit-9.2.2/build/shared/common/src/28_numeric_noabirule/../../../../../shared/common/src/28_numeric_noabirule/m_hide_lapack.F90:2921：Undefined reference to‘
zgetrf_’ 
/home/sunlight/work/abinit/abinit-9.2.2/build/shared/common/src/28_numeric_noabirule/../../../../../shared/common/src/28_numeric_noabirule/m_hide_lapack.F90:2941：Undefined reference to‘
zgetri_’ 
../../src/28_numeric_noabirule/lib28_numeric_noabirule.a(m_hide_lapack.o)：infunction‘m_hide_lapack_mp_matrginv_’：
/home/sunlight/work/abinit/abinit-9.2.2/build/shared/common/src/28_numeric_noabirule/../../../../../shared/common/src/28_numeric_noabirule/m_hide_lapack.F90:3304：Undefined reference to‘
dgetrf_’ 
/home/sunlight/work/abinit/abinit-9.2.2/build/shared/common/src/28_numeric_noabirule/../../../../../shared/common/src/28_numeric_noabirule/m_hide_lapack.F90:3314：Undefined reference to‘
dgetri_’ 
../../src/28_numeric_noabirule/lib28_numeric_noabirule.a(m_hide_lapack.o)：infunction‘m_hide_lapack_mp_matr3eigval_’：
/home/sunlight/work/abinit/abinit-9.2.2/build/shared/common/src/28_numeric_noabirule/../../../../../shared/common/src/28_numeric_noabirule/m_hide_lapack.F90:3376：Undefined reference to‘
zhpev_’
../../src/28_numeric_noabirule/lib28_numeric_noabirule.a(m_numeric_tools.o)：infunction‘m_numeric_tools_mp_llsfit_svd_’：
/home/sunlight/work/abinit/abinit-9.2.2/build/shared/common/src/28_numeric_noabirule/../../../../../shared/common/src/28_numeric_noabirule/m_numeric_tools.F90:2246：Undefined reference t
o‘dgesvd_’ 
make[3]: *** [Makefile:4238：abinit] error 1
make[2]: *** [Makefile:1232：all-recursive] error 1
make[1]: *** [Makefile:1448：all-recursive] error 1
make: *** [Makefile:1372：all] error 2
could you give me some advice？
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jianzhifu
Posts: 21
Joined: Tue Oct 29, 2013 9:20 am

Re: why the HDF5 and libxc is enable but not work？  [SOLVED]

Post by jianzhifu » Tue Dec 08, 2020 4:10 am

Code: Select all

LINALG_LIBS="-L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread -lm -ldl"
the above setting in the file configure.ac9 could solve the "undefined reference to" error
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