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

Mark Abraham mark.j.abraham at gmail.com
Fri Mar 21 09:06:50 CET 2014

On Mar 21, 2014 8:52 AM, "Ly Minh Nhat" <ganuongphap at gmail.com> wrote:
> Hi all,
> When I was following the protein - ligand complex tutorial
> (link<
> 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
> it doesn't support. How can I tell the compiler not to optimize for AVX?
> machine is Intel Pentium P6200 (2.13 GHz, 3 MB L3 cache).

cmake will do the right thing automatically if you run it on the same
machine you plan to run GROMACS. There are other ways, but this is simplest.

> According to this<
> this<
> and this<
> 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?

Delete the build directory and start again clean.


> I know my machine can do it because it used to work.
> Thank you so much.
> Nhat
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