[gmx-users] Illegal instruction flag raised in GMX 5.0.4

Carsten Kutzner ckutzne at gwdg.de
Tue Dec 23 09:26:20 CET 2014

Hi there,

On 23 Dec 2014, at 08:59, Harry Mark Greenblatt <harry.greenblatt at weizmann.ac.il> wrote:

> BS"D
> Gromacs is telling you that the -h option you supplied is not valid for this command.
No, that is not true, the -h option works for all Gromacs commands. 
It is exactly this option that lists the valid command line arguments :)

One reason why you could get an illegal instruction at that point is
that your executable was compiled with an instruction set that the CPU you
are running on is not supporting.

E.g. if you run Gromacs cmake on an Intel Ivy Bridge it will compile
in AVX_256 vector instructions. Running mdrun -h on a machine that
has only SSE4.1 will then result in an illegal instruction.

In that case, either compile on the machine you are running on, or use
-DGMX_SIMD=SSE2 for the tools for maximum compatibility.


>  You can see all the valid arguments for each
> command here
> http://manual.gromacs.org/online.html
> Harry M. Greenblatt
> Associate Staff Scientist
> Dept of Structural Biology           harry.greenblatt at weizmann.ac.il
> Weizmann Institute of Science        Phone:  972-8-934-3625
> 234 Herzl St.                        Facsimile:   972-8-934-4159
> Rehovot, 76100
> Israel
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Jayant James [jayant.james at gmail.com]
> Sent: Tuesday, December 23, 2014 9:42 AM
> To: Discussion list for GROMACS users
> Subject: [gmx-users] Illegal instruction flag raised in GMX 5.0.4
> Hi!
> In the process of trying to simulate phosphorylated serines I installed
> gromacs 5.0.4 because I was running into problems with pdb2gmx command not
> able to merge files. After installation I ran a test command and got the
> error below.  I am kinda lost as to what could be happening!!
> I would appreciate any suggestions
> Thank you
> Jayant James
> --------------------------
> GROMACS:      gmx editconf, VERSION 5.0.4
> Executable:   /share/apps/gromacs/5.0.4/bin/gmx
> Library dir:  /share/apps/gromacs/5.0.4/share/gromacs/top
> Command line:
>  editconf -h
> Illegal instruction
> -- 
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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