[gmx-users] Error: illegal instruction (core dumped)

Ly Minh Nhat ganuongphap at gmail.com
Fri Mar 21 08:46:39 CET 2014

Hi all,

When I was following the protein - ligand complex tutorial
I met an error while running pdb2gmx. The error is: *illegal instruction
(core dumped)*.

According to this <http://redmine.gromacs.org/issues/1123>, this error is
unavoidable if I "tell the compiler it can optimize for AVX". After
googling around, I get that AVX is a structure (or something) of Intel's
chip came from early 2011. My computer was bought before that so absolutely
it doesn't support. How can I tell the compiler not to optimize for AVX? My
machine is Intel Pentium P6200 (2.13 GHz, 3 MB L3 cache).

According to this<http://gromacs.5086.x6.nabble.com/pdb2gmx-illegal-instruction-core-dumped-td4411430.html>,
and this<http://gromacs.5086.x6.nabble.com/Compiling-GROMACS-on-IBM-AIX-power4-td4398786.html>the
problem is that I have optimized for a Power4 note but run it on a
Power2 note structure because of the FFTW library's default compilation. I
have tried to remove and install the newest GROMACS (5.0 beta 2) with
either FFTW or MKL (both are the newests). Nevertheless, if I follow the
Installation Instructions or use any modified cmake command, the result
after make command is always like this:

*CMake Error at fftwBuild-stamp/extract-fftwBuild.cmake:11 (message):
error: file to extract does not exist: *
(like this question). I don't know how to link those libraries to GROMACS.
What should I do?

I know my machine can do it because it used to work.

Thank you so much.

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