[Pw_forum] Segmentation Fault (11)

[Paolo Giannozzi]

Please see here:
http://www.quantum-espresso.org/faq/frequent-errors-during-execution/#5.2
Since zdotc is the function that segfaults, this (from the user guide)
could be relevant:

2.7.6.3 Linux PCs with gfortran

"There is a known incompatibility problem between the calling convention
for Fortran functions that return complex values: there is the convention
used by g77/f2c, where in practice the compiler converts such functions to
subroutines with a further parameter for the return value; gfortran instead
produces a normal function returning a complex value. If your system
libraries were compiled using g77 (which may happen for system-provided
libraries in not-too-recent Linux distributions), and you instead use
gfortran to compile QUANTUM ESPRESSO, your code may crash or produce random
results. This typically happens during calls to zdotc, which is one the
most commonly used complex-returning functions of BLAS+LAPACK.

For further details see for instance this link:
http://www.macresearch.org/lapackblas-fortran-106#comment-17071
or read the man page of gfortran under the flag -ff2c.

If your code crashes during a call to zdotc, try to recompile QUANTUM ESPRESSO
using the internal BLAS and LAPACK routines (using the -with-internal-blas
and -with-internal-lapack parameters of the configure script) to see if the
problem disappears; or, add the -ff2c flag" (info by Giovanni Pizzi, Jan.
2013).

Note that a similar problem with complex functions exists with MKL
libraries as well: if you compile with gfortran, link -lmkl_gf_lp64, not
-lmkl_intel_lp64, and the like for other architectures. Since v.5.1, you
may use the following workaround: add preprocessing option
-Dzdotc=zdotc_wrapper to DFLAGS.


On Tue, Oct 27, 2015 at 10:27 PM, Pulkit Garg <pgarg8 at asu.edu> wrote:

> [sparky-32:92490] *** Process received signal ***
> [sparky-32:92490] Signal: Segmentation fault (11)
> [sparky-32:92490] Signal code:  (128)
> [sparky-32:92490] Failing at address: (nil)
> [sparky-32:92490] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0)
> [0x2ac8b2aa7cb0]
> [sparky-32:92490] [ 1]
> /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_avx.so(mkl_blas_avx_zdotc+0xe0)
> [0x2ac8c4de7da0]
> [sparky-32:92490] [ 2]
> /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_gf_lp64.so(zdotc_gf+0x2e)
> [0x2ac8b007a56e]
> [sparky-32:92490] [ 3]
> /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_gf_lp64.so(zdotc+0x26)
> [0x2ac8b007a87e]
> [sparky-32:92490] *** End of error message ***
> --------------------------------------------------------------------------
> mpirun noticed that process rank 12 with PID 92490 on node sparky-32
> exited on signal 11 (Segmentation fault).
>
> I am able to run QE for my structure with 4 atoms and also when my
> structure has 50 atoms. But when I run QE for bigger structure (108 atoms)
> I am getting the above error. People have posted similar errors but I am
> not sure what to do to fix this.
>
> Pulkit Garg
>
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-- 
Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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