Error while compiling Abinit 9.4.2

Building Abinit
1

Hai all,
I got the below error message while compiling abinit 9.4.2.

/home52_fft_mpi_noabirule//iyaddfti_fftrisc.finc/software:/431abinit:- 9.4.2undefined/ srcreference/ 52_fft_mpi_noabiruleto/ dfti_fftrisc.finc`:dfti_free_descriptor_external_479':
undefined reference to `dfti_free_descriptor_external_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:423: undefined reference to `MKL_free'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:424: undefined reference to `MKL_free'
/home/collect2: error: ld returned 1 exit status
iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:429: undefined reference to `dfti_free_descriptor_external_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:430: undefined reference to `dfti_free_descriptor_external_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:431: undefined reference to `dfti_free_descriptor_external_'

../../src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a(m_dfti.o): In function `__m_dfti_MOD_dfti_fftrisc_sp':

/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:632: undefined reference to `dfti_create_descriptor_1d_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:633: undefined reference to `dfti_set_value_intval_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:634: undefined reference to `dfti_set_value_intvec_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:635: undefined reference to `dfti_set_value_intval_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:636: undefined reference to `dfti_set_value_intval_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:639: undefined reference to `dfti_commit_descriptor_external_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:642: undefined reference to `dfti_compute_backward_c_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:644: undefined reference to `dfti_free_descriptor_external_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:672: undefined reference to `dfti_create_descriptor_1d_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:675: undefined reference to `dfti_set_value_intval_'
/home/iyad/softwareMakefile:4333: recipe for target 'abinit' failed
/abinitmake[3]: *** [abinit] Error 1
-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:676: undefined reference to `dfti_set_value_intval_'

I am not sure of what is wrong. Are any packages missing? Can someone help me by giving some comments.

Thanks in advance
Seba

2

Hi,

we need you configuration file to understand what’s happening.

3

Hai,
Thank you for the reply. The steps followed are as follows:

  1. ./configure –prefix=/home/iyad/Abinit

  2. Got error and solution provided by abinit to run fallbacks

  3. After running fallbacks –

  4. ./configure --prefix=/home/iyad/software/abinit942 with_libxc=/home/iyad/software/abinit-9.4.2/fallbacks/install_fb/gnu/7.5/libxc/4.3.4 with_netcdf=/home/iyad/software/netcdf with_hdf5=/home/iyad/software/hdf512 with_netcdf_fortran==/home/iyad/software/netcdf

  5. This was successful

  6. Make

7.During make – I got undefined ref. errors.

PATHs Exported-

export PATH=/home/iyad/software/fftw339/bin:$PATH

export LD_LIBRARY_PATH=/home/iyad/software/fftw339/lib:$LD_LIBRARY_PATH

export PATH=/home/iyad/software/hdf512/bin:$PATH

export LD_LIBRARY_PATH=/home/iyad/software/hdf512/lib:$LD_LIBRARY_PATH

Can you please give any suggestions based on the above. Also let me know if you require more information.

Thanks in advance,
Seba

4

Hi Seba,

7.During make – I got undefined ref. errors.

Can you provide :

  • some undef refs ?
  • the “Final remark” at the end of output of ./configure

jmb

5

We also need the config.log file.
It seems that the build system is activating HAVE_DFTI

6

Hai,

Thank you for the reply.

The Steps Followed and errors are as follows:


./configure --prefix=/home/iyad/software/abinit942 \
with_libxc=/home/iyad/software/abinit-9.4.2/fallbacks/install_fb/gnu/7.5/libxc/4.3.4 \ with_netcdf=/home/iyad/software/netcdf \
with_hdf5=/home/iyad/software/hdf512 \ 
with_netcdf_fortran==/home/iyad/software/netcdf

Outcome of ./configure –

==============================================================================

=== Final remarks                                                          ===

==============================================================================

Core build parameters

---------------------

   * C compiler        : gnu version 7.5
  * Fortran compiler  : gnu version 7.5
  * architecture      : intel xeon (64 bits)
  * debugging         : basic
  * optimizations     : standard

  * OpenMP enabled    : no (collapse: ignored)
  * MPI    enabled    : yes (flavor: none)
  * MPI    in-place   : no
  * MPI-IO enabled    : yes
  * GPU    enabled    : no (flavor: none)

  * LibXML2 enabled   : no
  * LibPSML enabled   : no
  * XMLF90  enabled   : no
  * HDF5 enabled      : yes (MPI support: yes)
  * NetCDF enabled    : yes (MPI support: yes)
  * NetCDF-F enabled  : yes (MPI support: yes)

  * FFT flavor        : dfti (libs: auto-detected)
  * LINALG flavor     : mkl+openblas (libs: auto-detected)
  * SCALAPACK enabled : no
  * ELPA enabled      : unknown

  * FCFLAGS           : -g -ffree-line-length-none     -I/home/iyad/software/netcdf/include  -I=/home/iyad/software/netcdf/include

  * CPATH             : /opt/intel/oneapi/vpl/2021.2.2/include:/opt/intel/oneapi/tbb/2021.2.0/env/../include:/opt/intel/oneapi/mpi/2021.2.0//include:/opt/intel/oneapi/mkl/latest/include:/opt/intel/oneapi/ipp/2021.2.0/include:/opt/intel/oneapi/ippcp/2021.2.0/include:/opt/intel/oneapi/ipp/2021.2.0/include:/opt/intel/oneapi/dpl/2021.2.0/linux/include:/opt/intel/oneapi/dpcpp-ct/2021.2.0/include:/opt/intel/oneapi/dnnl/2021.2.0/cpu_dpcpp_gpu_dpcpp/lib:/opt/intel/oneapi/dev-utilities/2021.2.0/include:/opt/intel/oneapi/dal/2021.2.0/include:/opt/intel/oneapi/compiler/2021.2.0/linux/include:/opt/intel/oneapi/ccl/2021.2.0/include/cpu_gpu_dpcpp

  * Build workflow    : monolith

0 deprecated options have been used:.

Configuration complete.

You may now type "make" to build Abinit.

(or "make -j<n>", where <n> is the number of available processors)

  1.   Make –j8

Outcome of Make

/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:253: undefined reference to `dfti_set_value_intval_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:255: undefined reference to `dfti_commit_descriptor_external_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:423: undefined reference to `MKL_free'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:424: undefined reference to `MKL_free'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:429: undefined reference to `dfti_free_descriptor_external_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:430: undefined reference to `dfti_free_descriptor_external_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:431: undefined reference to `dfti_free_descriptor_external_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:434: undefined reference to `dfti_free_descriptor_external_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:435: undefined reference to `dfti_free_descriptor_external_'
../../src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a(m_dfti.o):/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:436: more undefined references to `dfti_free_descriptor_external_' follow
../../src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a(m_dfti.o): In function `__m_dfti_MOD_dfti_fftrisc_sp':
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:443: undefined reference to `dfti_create_descriptor_1d_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:446: undefined reference to `dfti_set_value_intval_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:447: undefined reference to `dfti_set_value_intvec_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:448: undefined reference to `dfti_set_value_intval_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:449: undefined reference to `dfti_set_value_intval_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:450: undefined reference to `dfti_set_value_dblval_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:452: undefined reference to `dfti_commit_descriptor_external_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:455: undefined reference to `dfti_compute_forward_c_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:479: undefined reference to `dfti_free_descriptor_external_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:423: undefined reference to `MKL_free'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:424: undefined reference to `MKL_free'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:429: undefined reference to `dfti_free_descriptor_external_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:430: undefined reference to `dfti_free_descriptor_external_'
/home/iyad/software/abinit-9.4.2/src/52_fft_mpi_noabirule/dfti_fftrisc.finc:431: undefined reference to `dfti_free_descriptor_external_'
collect2: error: ld returned 1 exit status
Makefile:4333: recipe for target 'abinit' failed
make[3]: *** [abinit] Error 1
make[3]: Leaving directory '/home/iyad/software/abinit-9.4.2/src/98_main'
Makefile:1232: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/home/iyad/software/abinit-9.4.2/src'
Makefile:1448: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/iyad/software/abinit-9.4.2'
Makefile:1372: recipe for target 'all' failed
make: *** [all] Error 2

I have also attached the config.log along with this for your reference. config.log (209.1 KB)

Hope you could help me with the above information.

Thanks in advance,
Seba

7

Hi Seba,

There are some problems:

1) you don’t take advantage of the Intel compiler

mpif90 -show
gfortran -I"/home/softs/intel/oneapi/mpi/2021.2.0/include/gfortran/7.5.0"

use mpiifort :

mpiifort -show
ifort -I"/home/softs/intel/oneapi/mpi/2021.2.0//include" …

2) “bad” detection of linalg

LINALG flavor : mkl+openblas !

fix choice of linalg with :

with_linalg_flavor="mkl"
LINALG_CPPFLAGS="-I${MKLROOT}/include"
LINALG_FCFLAGS="-I${MKLROOT}/include"
LINALG_LIBS=" -L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl"

3) mix fallbacks is not recommended : libxc from internal FB and “your” netcdf :

with_libxc=/home/iyad/software/abinit-9.4.2/fallbacks/install_fb/gnu/7.5/libxc/4.3.4
with_netcdf=/home/iyad/software/netcdf

At first, it is better to compile all internal FBs with build-abinit-fallbacks.sh script…

Then, create a file “config.ac9” with :

enable_avx_safe_mode="no"
CPP="icc -E"
CC="mpiicc"
CXX="mpiicpc"
FC="mpiifort"
with_mpi="yes"
enable_mpi_io="yes"

with_linalg_flavor="mkl"
LINALG_CPPFLAGS="-I${MKLROOT}/include"
LINALG_FCFLAGS="-I${MKLROOT}/include"
LINALG_LIBS=" -L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl"

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

with_libxc="/home/iyad/software/abinit-9.4.2/fallbacks/install_fb/.../libxc/4.3.4 "
with_hdf5="/home/iyad/software/abinit-9.4.2/fallbacks/install_fb/.../hdf5/1.10.6"
with_netcdf="/home/iyad/software/abinit-9.4.2/fallbacks/install_fb/.../netcdf4/4.6.3"
with_netcdf_fortran="/home/iyad/software/abinit-9.4.2/fallbacks/install_fb/.../netcdf4_fortran/4.5.2"

enable_netcdf_default="yes"
enable_python_invocation="no"
enable_gw_dpc="yes"

and run :

./configure --with-config-file='config.ac9'

Caution : the four links to the internal fallbacks in config.ac9 are not “complete” : replace them with the links generated by build-abinit-fallbacks.sh

jmb