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

[Mark Abraham]

On Mar 21, 2014 8:52 AM, "Ly Minh Nhat" <ganuongphap at gmail.com> wrote:
>
>
http://gromacs.5086.x6.nabble.com/Guidance-on-how-to-install-Gromacs-5-0-beta2-td5014681.html
> Hi all,
>
> When I was following the protein - ligand complex tutorial
> (link<
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html
>),
> 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).

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<
http://gromacs.5086.x6.nabble.com/pdb2gmx-illegal-instruction-core-dumped-td4411430.html
>,
> this<
http://gromacs.5086.x6.nabble.com/Parallel-gromacs-job-unknown-error-td4398749.html#a4398751
>,
> 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?

Delete the build directory and start again clean.

Mark

> I know my machine can do it because it used to work.
>
> Thank you so much.
> Nhat
> --
> Gromacs Users mailing list
>
> * Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-request at gromacs.org.