internal compiler error: Segmentation fault during make  [SOLVED]

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internal compiler error: Segmentation fault during make

Postby shiva » Wed Jul 11, 2018 8:57 am

config.log
config log file
(92.02 KiB) Downloaded 63 times
config.log
config log file
(92.02 KiB) Downloaded 63 times
Dear Moderators and users,

I am new user of abinit and compiling abinit-8.8.3 on a cluster. I prepared a hostname.ac file and run the configure in the build directory with .ac file as config file. After configuration with no error or warning, I issued make. In this step I am getting "../../../src/41_xc_lowlevel/drivexc.F90:894: internal compiler error: Segmentation fault" error.

I am giving the system information and configure details below:

OS : CentOS 6.7
uname -a
Linux 2.6.32-504.23.4.el6.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux

ifort (icc) -V : Intel(R) 64, Version 13.0.1.117 Build 20121010

My hostname.ac file:
Code: Select all
FC="gfortran"
CC="gcc"
enable_mpi="yes"
enable_mpi_io="yes"
with_mpi_prefix="/opt/soft/share/openmpigcc"
with_tardir="/home/shiva/.abinit/tarballs"
with_trio_flavor="netcdf"
with_fft_flavor="fftw3"
with_fft_libs="-L/opt/soft/share/intel/composer_xe_2013.1.117/mkl/lib/intel64 -Wl,--start-group  -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group"
with_linalg_flavor="mkl"
with_linalg_libs="-L/opt/soft/share/intel/composer_xe_2013.1.117/mkl/lib/intel64 -Wl,--start-group  -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group"
with_dft_flavor="atompaw+bigdft+libxc+wannier90"
enable_gw_dpc="yes"


Code: Select all
 ==============================================================================
 === Final remarks                                                          ===
 ==============================================================================


Summary of important options:

  * C compiler      : gnu version 4.4
  * Fortran compiler: gnu version 4.4
  * architecture    : intel xeon (64 bits)

  * debugging       : basic
  * optimizations   : standard

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

  * TRIO   flavor = netcdf-fallback
  * TIMER  flavor = abinit (libs: ignored)
  * LINALG flavor = mkl (libs: user-defined)
  * ALGO   flavor = none (libs: ignored)
  * FFT    flavor = fftw3 (libs: user-defined)
  * MATH   flavor = none (libs: ignored)
  * DFT    flavor = libxc-fallback+atompaw-fallback+bigdft-fallback+wannier90-fallback



I have tried configuring with icc and ifort(also with mpif90 and mpicc) in hostname.ac but abinit configure was automatically taking gcc and gfortran 4.4.
I have also tried basic abinit compilation with_dft_flavor="none and got the same error.

I have attached config.log.

Thank you
Shivaprasad
IIT Mandi,
shiva
 
Posts: 2
Joined: Wed Jul 11, 2018 7:09 am

Re: internal compiler error: Segmentation fault during make  [SOLVED]

Postby shiva » Fri Jul 13, 2018 6:40 pm

The error is solved.

The error was due to very old gfortran version 4.4.7 in the cluster. Used gfortran-4.8.2 (still it is older) and with abinit lapack + blas libraries was able to compile successfully with suboptimal configuration. Passed all the tests.

gfortran-4.8.2 + intel mkl for linear algebra was also successfully compiled in the previous try, in the cluster but all the tests were not passed.
shiva
 
Posts: 2
Joined: Wed Jul 11, 2018 7:09 am


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